- A - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- a - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- A - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- aaBondInfo() - Static method in class org.openscience.cdk.templates.AminoAcids
-
Creates matrix with info about the bonds in the amino acids.
- ABINITFormat - Class in org.openscience.cdk.io.formats
-
- abortOnErrors - Variable in class org.openscience.cdk.io.cml.CMLErrorHandler
-
- AbstractAtomicDescriptor - Class in org.openscience.cdk.qsar
-
Abstract atomic descriptor class with helper functions for descriptors
that require the whole molecule to calculate the descriptor values,
which in turn need to be cached for all atoms, so that they can be
retrieved one by one.
- AbstractAtomicDescriptor() - Constructor for class org.openscience.cdk.qsar.AbstractAtomicDescriptor
-
- AbstractAWTDrawVisitor - Class in org.openscience.cdk.renderer.visitor
-
Partial implementation of the
IDrawVisitor
interface for the AWT
widget toolkit, allowing molecules to be rendered with toolkits based on
AWT, like the Java reference graphics platform Swing.
- AbstractAWTDrawVisitor() - Constructor for class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
-
- AbstractBondDescriptor - Class in org.openscience.cdk.qsar
-
Abstract bond descriptor class with helper functions for descriptors
that require the whole molecule to calculate the descriptor values,
which in turn need to be cached for all bonds, so that they can be
retrieved one by one.
- AbstractBondDescriptor() - Constructor for class org.openscience.cdk.qsar.AbstractBondDescriptor
-
- AbstractDifference - Class in org.openscience.cdk.tools.diff.tree
-
Difference between two IChemObjects.
- AbstractDifferenceList - Class in org.openscience.cdk.tools.diff.tree
-
Diff between two IChemObjects.
- AbstractFontManager - Class in org.openscience.cdk.renderer.font
-
- AbstractFontManager() - Constructor for class org.openscience.cdk.renderer.font.AbstractFontManager
-
Call this in subclasses with the super() constructor.
- AbstractGeneratorParameter<T> - Class in org.openscience.cdk.renderer.generators.parameter
-
- AbstractGeneratorParameter() - Constructor for class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
-
- AbstractMCS - Class in org.openscience.cdk.smsd.interfaces
-
Interface for all MCS algorithms.
- AbstractMCS() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
- AbstractMCSAlgorithm - Class in org.openscience.cdk.smsd.interfaces
-
Interface for MCS search algorithm.
- AbstractMCSAlgorithm() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
-
- AbstractReactionLabeller - Class in org.openscience.cdk.smsd.labelling
-
- AbstractReactionLabeller() - Constructor for class org.openscience.cdk.smsd.labelling.AbstractReactionLabeller
-
- AbstractRenderer<T extends IChemObject> - Class in org.openscience.cdk.renderer
-
The base class for all renderers, handling the core aspects of rendering
such as the location of the model in 'model space' and the location on
the screen to draw the model.
- AbstractRenderer(RendererModel) - Constructor for class org.openscience.cdk.renderer.AbstractRenderer
-
- AbstractSelection - Class in org.openscience.cdk.renderer.selection
-
- AbstractSelection() - Constructor for class org.openscience.cdk.renderer.selection.AbstractSelection
-
- AbstractSubGraph - Class in org.openscience.cdk.smsd.interfaces
-
Interface class for reporting only substructure searches.
- AbstractSubGraph() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractSubGraph
-
- AbstractValidator - Class in org.openscience.cdk.validate
-
Abstract validator that does nothing but provide all the methods that the
ValidatorInterface requires.
- AbstractValidator() - Constructor for class org.openscience.cdk.validate.AbstractValidator
-
- AC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.ArrowElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.AtomSymbolElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.ElementGroup
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.GeneralPath
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in interface org.openscience.cdk.renderer.elements.IRenderingElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.LineElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.OvalElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.PathElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.RectangleElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.RingElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.TextElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement
-
Converts this
TextElement
into widget specific objects.
- accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.WedgeLineElement
-
Converts this
TextElement
into widget specific objects.
- accepts(Class) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.CIFReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.CMLReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.CMLWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.CrystClustReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.CrystClustWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.CTXReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.GamessReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- accepts(Class) - Method in class org.openscience.cdk.io.Gaussian98Reader
-
- accepts(Class) - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.HINReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.HINWriter
-
- accepts(Class<? extends IChemObject>) - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Returns whether the given
IChemObject
can be read or written.
- accepts(Class) - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.INChIReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.MDLReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.MDLRXNReader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- accepts(Class) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- accepts(Class) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- accepts(Class) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- accepts(Class) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- accepts(Class) - Method in class org.openscience.cdk.io.Mol2Reader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.Mol2Reader
-
- accepts(Class) - Method in class org.openscience.cdk.io.Mol2Writer
-
- accepts(Class) - Method in class org.openscience.cdk.io.MoSSOutputReader
-
Returns whether the given
IChemObject
can be read or written.
- accepts(Class) - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PDBReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.PDBWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PMPReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
Returns whether the given
IChemObject
can be read or written.
- accepts(Class) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Returns whether the given
IChemObject
can be read or written.
- accepts(Class) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Returns true for accepted input types.
- accepts(Class) - Method in class org.openscience.cdk.io.RssWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.SDFWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.ShelXReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.ShelXWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.SMILESReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.SMILESWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.VASPReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.XYZReader
-
- accepts(Class) - Method in class org.openscience.cdk.io.XYZWriter
-
- accepts(Class) - Method in class org.openscience.cdk.io.ZMatrixReader
-
- acceptStructure() - Method in class org.openscience.cdk.structgen.RandomGenerator
-
Tell the RandomGenerator to accept the last structure that had been proposed.
- Aces2Format - Class in org.openscience.cdk.io.formats
-
- AcidicGroupCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Returns the number of acidic groups.
- AcidicGroupCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
- ACTINIUM - Static variable in class org.openscience.cdk.config.Elements
-
- ACTINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- actionPerformed(ActionEvent) - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Dummy method.
- actionSuffix - Static variable in class org.openscience.cdk.renderer.JCPAction2D
-
Description of the Field
- add(IAtomContainer) - Method in class org.openscience.cdk.AtomContainer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IAtomContainerSet) - Method in class org.openscience.cdk.AtomContainerSet
-
Adds all atomContainers in the AtomContainerSet to this container.
- add(IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
-
Add a conformer to the end of the list.
- add(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
-
- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- add(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- add(IMoleculeSet) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- add(IReactionScheme) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing
-
- add(IRingSet) - Method in class org.openscience.cdk.debug.DebugRingSet
-
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand
-
- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.AdductFormula
-
Adds all molecularFormulas in the AdductFormula to this chemObject.
- add(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Adds an molecularFormula to this MolecularFormula.
- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
- add(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Addition from two matrices.
- add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Adds all atomContainers in the AtomContainerSet to this container.
- add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Adds the atoms in the AtomContainer as cell content.
- add(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Adds an molecularFormula to this MolecularFormula.
- add(IMolecularFormulaSet) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
- add(IMoleculeSet) - Method in interface org.openscience.cdk.interfaces.IMoleculeSet
-
Adds all molecules in the MoleculeSet to this container.
- add(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme
-
Add a scheme of reactions.
- add(IRingSet) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
Adds all rings of another RingSet if they are not allready part of this ring set.
- add(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- add(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
- add(Complex) - Method in class org.openscience.cdk.math.Complex
-
Add a complex value
- add(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Addition from two matrices
- add(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Addition from two matrices
- add(IVector) - Method in class org.openscience.cdk.math.IVector
-
Addition from two vectors
- add(IVector, IVector) - Method in class org.openscience.cdk.math.IVector
-
Addition from two vectors
- add(Matrix) - Method in class org.openscience.cdk.math.Matrix
-
Adds two matrices.
- add(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
-
- add(Vector) - Method in class org.openscience.cdk.math.Vector
-
Addition from two vectors
- add(IMoleculeSet) - Method in class org.openscience.cdk.MoleculeSet
-
Adds all molecules in the MoleculeSet to this container.
- add(double) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
-
- add(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
-
- add(IReactionScheme) - Method in class org.openscience.cdk.ReactionScheme
-
Add a Scheme of Reactions.
- add(IRenderingElement) - Method in class org.openscience.cdk.renderer.elements.ElementGroup
-
Add a new element to the group.
- add(IRingSet) - Method in class org.openscience.cdk.RingSet
-
Adds all rings of another RingSet if they are not already part of this ring set.
- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.AdductFormula
-
Adds all molecularFormulas in the AdductFormula to this chemObject.
- add(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IAtomContainerSet) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Adds all atomContainers in the AtomContainerSet to this container.
- add(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Adds an molecularFormula to this MolecularFormula.
- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
- add(IMoleculeSet) - Method in class org.openscience.cdk.silent.MoleculeSet
-
Adds all molecules in the MoleculeSet to this container.
- add(IReactionScheme) - Method in class org.openscience.cdk.silent.ReactionScheme
-
Add a Scheme of Reactions.
- add(IRingSet) - Method in class org.openscience.cdk.silent.RingSet
-
Adds all rings of another RingSet if they are not already part of this ring set.
- add(Map<Integer, Integer>) - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Adds mapping to the mapping list
- add(Map<Integer, Integer>) - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Adds mapping to the mapping list
- add3DCoordinates1(AtomContainer) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Generate coordinates for all atoms which are singly bonded and have
no coordinates.
- add3DCoordinatesForSinglyBondedLigands(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Generate coordinates for all atoms which are singly bonded and have no
coordinates.
- addAcidicOxygen(IAminoAcid) - Static method in class org.openscience.cdk.tools.manipulator.AminoAcidManipulator
-
Adds the singly bonded oxygen from the acid group of the AminoAcid.
- addAgent(IMolecule) - Method in class org.openscience.cdk.debug.DebugReaction
-
- addAgent(IMolecule) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds an agent to this reaction.
- addAgent(IMolecule) - Method in class org.openscience.cdk.Reaction
-
Adds an agent to this reaction.
- addAgent(IMolecule) - Method in class org.openscience.cdk.silent.Reaction
-
Adds an agent to this reaction.
- addAll(Collection<? extends IAtomContainer>) - Method in class org.openscience.cdk.ConformerContainer
-
- addAll(int, Collection<? extends IAtomContainer>) - Method in class org.openscience.cdk.ConformerContainer
-
- addAminoAcidAtCTerminus(BioPolymer, AminoAcid, Strand, AminoAcid) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool
-
Builds a protein by connecting a new amino acid at the C-terminus of the
given strand.
- addAminoAcidAtNTerminus(BioPolymer, AminoAcid, Strand, AminoAcid) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool
-
Builds a protein by connecting a new amino acid at the N-terminus of the
given strand.
- addAtom(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Adds an atom to this container.
- addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.BioPolymer
-
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
- addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.BioPolymer
-
Adds the atom to a specified Strand and a specified Monomer.
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds an atom to this container.
- addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Adds the atom oAtom without specifying a Monomer or a Strand.
- addAtom(IAtom, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
- addAtom(IAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Adds the atom to a specified Strand and a specified Monomer.
- addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Adds the atom to the crystal.
- addAtom(IPDBAtom) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
-
Adds the atom oAtom without specifying a Monomer or a Strand.
- addAtom(IPDBAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
-
Adds the atom to a specified Strand and a specified Monomer.
- addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Adds the atom oAtom without specifying a Monomer.
- addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IStrand
-
Adds the atom oAtom without specifying a Monomer or a Strand.
- addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IStrand
-
Adds the atom oAtom to a specific Monomer.
- addAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Polymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IPDBAtom) - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
Adds the atom oAtom without specifying a
IMonomer
or a Strand.
- addAtom(IPDBAtom, IMonomer) - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.protein.data.PDBStrand
-
Adds the atom oAtom to a specified Monomer.
- addAtom(int) - Method in class org.openscience.cdk.signature.Orbit
-
Adds an atom index to the orbit.
- addAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds an atom to this container.
- addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer
-
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
- addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer
-
Adds the atom to a specified Strand and a specified Monomer.
- addAtom(IPDBAtom) - Method in class org.openscience.cdk.silent.PDBPolymer
-
Adds the atom oAtom without specifying a
IMonomer
or a Strand.
- addAtom(IPDBAtom, IMonomer) - Method in class org.openscience.cdk.silent.PDBPolymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.PDBPolymer
-
Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Polymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IAtom) - Method in class org.openscience.cdk.silent.Strand
-
Adds the atom oAtom without specifying a Monomer or a Strand.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Strand
-
Adds the atom oAtom to a specific Monomer.
- addAtom(IAtom) - Method in class org.openscience.cdk.Strand
-
Adds the atom oAtom without specifying a Monomer or a Strand.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Strand
-
Adds the atom oAtom to a specific Monomer.
- addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet
-
Adds an atomContainer to this container.
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.AtomContainerSet
-
Adds an atomContainer to this container with the given
multiplier.
- addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- addAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Adds an atomContainer to this container.
- addAtomContainer(IAtomContainer, double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Adds an atomContainer to this container with the given
multiplier.
- addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.MoleculeSet
-
Adds an atomContainer to this container.
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.MoleculeSet
-
Adds an atomContainer to this container with the given
multiplier.
- addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Adds an atomContainer to this container.
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Adds an atomContainer to this container with the given
multiplier.
- addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.silent.MoleculeSet
-
Adds an atomContainer to this container.
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.silent.MoleculeSet
-
Adds an atomContainer to this container with the given
multiplier.
- addAtomVector(double[]) - Method in class org.openscience.cdk.Vibration
-
Adds a atom vector to the vibration.
- addBond(IBond) - Method in class org.openscience.cdk.AtomContainer
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.AtomContainer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.AtomContainer
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugRing
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugRing
-
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
- addBond(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a bond to this container.
- addCDKChangeListener(ICDKChangeListener) - Method in class org.openscience.cdk.renderer.RendererModel
-
Adds a change listener to the list of listeners
- addCDKError(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport
-
Adds a CDK problem.
- addChargeGroup(ChargeGroup) - Method in class org.openscience.cdk.libio.md.MDMolecule
-
Add a ChargeGroup to the MDMolecule if not already present
- addChemModel(IChemModel) - Method in class org.openscience.cdk.ChemSequence
-
Adds an chemModel to this container.
- addChemModel(IChemModel) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- addChemModel(IChemModel) - Method in interface org.openscience.cdk.interfaces.IChemSequence
-
Adds an chemModel to this container.
- addChemModel(IChemModel) - Method in class org.openscience.cdk.silent.ChemSequence
-
Adds an chemModel to this container.
- addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
-
- addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.DefaultChemObjectWriter
-
- addChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO
-
- addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
-
- addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
-
- addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
-
- addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- addChemSequence(IChemSequence) - Method in class org.openscience.cdk.ChemFile
-
Adds a ChemSequence to this container.
- addChemSequence(IChemSequence) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- addChemSequence(IChemSequence) - Method in interface org.openscience.cdk.interfaces.IChemFile
-
- addChemSequence(IChemSequence) - Method in class org.openscience.cdk.silent.ChemFile
-
Adds a ChemSequence to this container.
- addChild(String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement
-
Add a child text element.
- addChild(String, String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement
-
Add a child text element with a subscript.
- addChild(IDifference) - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
-
- addChild(IDifference) - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
-
- addChildren(List<IDifference>) - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
-
- addChildren(List<IDifference>) - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
-
- addCTerminus(IAtom) - Method in class org.openscience.cdk.AminoAcid
-
Add an Atom and makes it the C-terminus atom.
- addCTerminus(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addCTerminus(IAtom) - Method in interface org.openscience.cdk.interfaces.IAminoAcid
-
Add an Atom and makes it the C-terminus atom.
- addCTerminus(IAtom) - Method in class org.openscience.cdk.silent.AminoAcid
-
Add an Atom and makes it the C-terminus atom.
- addEdge(EdgeBuilder) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Adds edge to the edge list.
- addEdge(EdgeBuilder) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Adds edge to the edge list.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing
-
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a ElectronContainer to this AtomContainer.
- addEntry(Entry) - Method in class org.openscience.cdk.dict.Dictionary
-
- addError(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport
-
Adds a validation test which gives serious errors.
- addExampleReaction(String) - Method in class org.openscience.cdk.dict.EntryReact
-
add a example for this reaction.
- addFunction(IFunction) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Add a function to the set of functions
- addFunction(IFunction, Color) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Add a function to the set of functions
- addImplicitHydrogens(IAtomContainer) - Method in class org.openscience.cdk.tools.CDKHydrogenAdder
-
Sets implicit hydrogen counts for all atoms in the given IAtomContainer.
- addImplicitHydrogens(IAtomContainer, IAtom) - Method in class org.openscience.cdk.tools.CDKHydrogenAdder
-
Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.
- addIsotope(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- addIsotope(IIsotope, int) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- addIsotope(IsotopeContainer) - Method in class org.openscience.cdk.formula.IsotopePattern
-
Add an isotope object.
- addIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Adds an Isotope to this MolecularFormula one time.
- addIsotope(IIsotope, int) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Adds an Isotope to this MolecularFormula in a number of occurrences.
- addIsotope(IIsotope, int, int) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Adds an Isotope to this MolecularFormulaExpand in a number of
maximum and minimum occurrences allowed.
- addIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Adds an Isotope to this MolecularFormula one time.
- addIsotope(IIsotope, int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Adds an Isotope to this MolecularFormula in a number of occurrences.
- addIsotope(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Adds an Isotope to this MolecularFormula one time.
- addIsotope(IIsotope, int) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Adds an Isotope to this MolecularFormula in a number of occurrences.
- addLabel(String) - Method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Add label if its not present
- addLine(int, int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the resulting matrix of an elementary linear operation that consists of adding one line,
multiplied by some constant factor, to another line.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.ChemObject
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtom
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBond
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElement
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMapping
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReaction
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugRing
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addListener(IChemObjectListener) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAminoAcid
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAtom
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAtomContainer
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAtomContainerSet
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAtomType
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNBioPolymer
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNBond
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNChemFile
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNChemModel
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNChemObject
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNChemSequence
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNCrystal
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNElectronContainer
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNElement
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNFragmentAtom
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNIsotope
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNLonePair
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNMapping
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNMolecule
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNMoleculeSet
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNMonomer
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPDBAtom
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPDBMonomer
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPDBPolymer
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPDBStructure
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPolymer
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPseudoAtom
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNReaction
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNReactionScheme
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNReactionSet
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNRing
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNRingSet
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNSingleElectron
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNStrand
-
Deprecated.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.silent.ChemObject
-
Use this to add yourself to this IChemObject as a listener.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.AtomContainer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.AtomContainer
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing
-
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addLonePair(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a LonePair to this Atom.
- addMapping(IMapping) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a mapping between the reactant and product side to this
Reaction.
- addMapping(IMapping) - Method in class org.openscience.cdk.Reaction
-
Adds a mapping between the reactant and product side to this
Reaction.
- addMapping(IMapping) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a mapping between the reactant and product side to this
Reaction.
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula
-
Adds an molecularFormula to this chemObject.
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Adds an molecularFormula to this chemObject.
- addMolecularFormula(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
Adds an IMolecularFormula to this chemObject.
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula
-
Adds an molecularFormula to this chemObject.
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Adds an molecularFormula to this chemObject.
- addMolecule(IMolecule) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- addMolecule(IMolecule) - Method in interface org.openscience.cdk.interfaces.IMoleculeSet
-
Adds an IMolecule to this container.
- addMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
-
Adds a Molecule to the list of templates use by this TemplateHandler.
- addMolecule(IMolecule) - Method in class org.openscience.cdk.MoleculeSet
-
Adds an molecule to this container.
- addMolecule(IMolecule) - Method in class org.openscience.cdk.silent.MoleculeSet
-
Adds an molecule to this container.
- addNeighbor(NodeBuilder) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Adds neighbor to the Neighbors List.
- addNeighbor(NodeBuilder) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Adds neighbor to the Neighbors List.
- addNode(RNode) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Adds a new node to the RGraph.
- addNode(CDKRNode) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Adds a new node to the CDKRGraph.
- addNode(VFAtomMatcher, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Add and return a node for a query atom
- addNTerminus(IAtom) - Method in class org.openscience.cdk.AminoAcid
-
Add an Atom and makes it the N-terminus atom.
- addNTerminus(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addNTerminus(IAtom) - Method in interface org.openscience.cdk.interfaces.IAminoAcid
-
Add an Atom and makes it the N-terminus atom.
- addNTerminus(IAtom) - Method in class org.openscience.cdk.silent.AminoAcid
-
Add an Atom and makes it the N-terminus atom.
- addOK(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport
-
Adds a validation test which did not find a problem.
- addParameter(List<String>) - Method in class org.openscience.cdk.dict.EntryReact
-
Add a IParameterReact's of the reaction.
- addProduct(IMolecule) - Method in class org.openscience.cdk.debug.DebugReaction
-
- addProduct(IMolecule, Double) - Method in class org.openscience.cdk.debug.DebugReaction
-
- addProduct(IMolecule) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a product to this reaction.
- addProduct(IMolecule, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a product to this reaction.
- addProduct(IMolecule) - Method in class org.openscience.cdk.Reaction
-
Adds a product to this reaction.
- addProduct(IMolecule, Double) - Method in class org.openscience.cdk.Reaction
-
Adds a product to this reaction.
- addProduct(IMolecule) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a product to this reaction.
- addProduct(IMolecule, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a product to this reaction.
- addReactant(IMolecule) - Method in class org.openscience.cdk.debug.DebugReaction
-
- addReactant(IMolecule, Double) - Method in class org.openscience.cdk.debug.DebugReaction
-
- addReactant(IMolecule) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a reactant to this reaction.
- addReactant(IMolecule, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a reactant to this reaction with a stoichiometry coefficient.
- addReactant(IMolecule) - Method in class org.openscience.cdk.Reaction
-
Adds a reactant to this reaction.
- addReactant(IMolecule, Double) - Method in class org.openscience.cdk.Reaction
-
Adds a reactant to this reaction with a stoichiometry coefficient.
- addReactant(IMolecule) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a reactant to this reaction.
- addReactant(IMolecule, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a reactant to this reaction with a stoichiometry coefficient.
- addReaction(IReaction) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- addReaction(IReaction) - Method in interface org.openscience.cdk.interfaces.IReactionSet
-
Adds an reaction to this container.
- addReaction(IReaction, int) - Method in class org.openscience.cdk.reaction.ReactionChain
-
Added a IReaction for this chain in position.
- addReaction(IReaction) - Method in class org.openscience.cdk.ReactionSet
-
Adds an reaction to this container.
- addReaction(IReaction) - Method in class org.openscience.cdk.silent.ReactionSet
-
Adds an reaction to this container.
- addReport(ValidationReport) - Method in class org.openscience.cdk.validate.ValidationReport
-
Merges the tests with the tests in this ValidationReport.
- addResidue(Residue) - Method in class org.openscience.cdk.libio.md.MDMolecule
-
Add a Residue to the MDMolecule if not already present
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer
-
Adds a LonePair to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing
-
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a LonePair to this Atom.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.AtomContainer
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugRing
-
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugStrand
-
- addStereoElement(IStereoElement) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a stereo element to this container.
- addStructure(IPDBStructure) - Method in class org.openscience.cdk.debug.DebugPDBPolymer
-
- addStructure(IPDBStructure) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
-
Adds the PDBStructure structure a this PDBPolymer.
- addStructure(IPDBStructure) - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
- addStructure(IPDBStructure) - Method in class org.openscience.cdk.silent.PDBPolymer
-
- addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
Add a symbol to this QueryAtom
- addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Add a symbol to this QueryAtom
- addTuple(Bspt.Tuple) - Method in class org.openscience.cdk.graph.rebond.Bspt
-
- AdductFormula - Class in org.openscience.cdk.formula
-
Class defining an adduct object in a MolecularFormula.
- AdductFormula() - Constructor for class org.openscience.cdk.formula.AdductFormula
-
Constructs an empty AdductFormula.
- AdductFormula(IMolecularFormula) - Constructor for class org.openscience.cdk.formula.AdductFormula
-
Constructs an AdductFormula with a copy AdductFormula of another
AdductFormula (A shallow copy, i.e., with the same objects as in
the original AdductFormula).
- AdductFormula - Class in org.openscience.cdk.silent
-
Class defining an adduct object in a MolecularFormula.
- AdductFormula() - Constructor for class org.openscience.cdk.silent.AdductFormula
-
Constructs an empty AdductFormula.
- AdductFormula(IMolecularFormula) - Constructor for class org.openscience.cdk.silent.AdductFormula
-
Constructs an AdductFormula with a copy AdductFormula of another
AdductFormula (A shallow copy, i.e., with the same objects as in
the original AdductFormula).
- AdductionLPMechanism - Class in org.openscience.cdk.reaction.mechanism
-
This mechanism adduct together two fragments.
- AdductionLPMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.AdductionLPMechanism
-
- AdductionPBMechanism - Class in org.openscience.cdk.reaction.mechanism
-
This mechanism adduct together two fragments due to a double bond.
- AdductionPBMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.AdductionPBMechanism
-
- AdductionProtonLPReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which produces a protonation.
- AdductionProtonLPReaction() - Constructor for class org.openscience.cdk.reaction.type.AdductionProtonLPReaction
-
Constructor of the AdductionProtonLPReaction object.
- AdductionProtonPBReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which produces a protonation to double bond.
- AdductionProtonPBReaction() - Constructor for class org.openscience.cdk.reaction.type.AdductionProtonPBReaction
-
Constructor of the AdductionProtonPBReaction object.
- AdductionSodiumLPReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which produces an adduction of the Sodium.
- AdductionSodiumLPReaction() - Constructor for class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction
-
Constructor of the AdductionSodiumLPReaction object.
- addValidator(IValidator) - Method in class org.openscience.cdk.validate.ValidatorEngine
-
- addWarning(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport
-
Adds a validation test which indicate a possible problem.
- ADFFormat - Class in org.openscience.cdk.io.formats
-
- AdjacencyMatrix - Class in org.openscience.cdk.graph.matrix
-
Calculator for a adjacency matrix representation of this AtomContainer.
- AdjacencyMatrix() - Constructor for class org.openscience.cdk.graph.matrix.AdjacencyMatrix
-
- adjustBeginLineColumn(int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Method to adjust line and column numbers for the start of a token.
- adjustBeginLineColumn(int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Method to adjust line and column numbers for the start of a token.
- AG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- AL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- AL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- AlchemyFormat - Class in org.openscience.cdk.io.formats
-
- Algorithm - Enum in org.openscience.cdk.smsd.interfaces
-
This class represents various algorithm type supported by SMSD.
- align() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
-
Perform an alignment.
- alignment - Variable in class org.openscience.cdk.renderer.elements.AtomSymbolElement
-
The hydrogen alignment.
- Aliphatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AliphaticAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matcher any non-aromatic atom.
- AliphaticAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom
-
Creates a new instance
- AliphaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This smarts atom matches aliphatic atom with element symbol specified
- AliphaticSymbolAtom(String) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom
-
Creates a new instance
- ALL_RINGS - Static variable in class org.openscience.cdk.CDKConstants
-
A set of all rings computed for this molecule.
- allBaseNumbers() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
The usual numbers .
- allCoplanar(Vector3d, Point3d, Point3d...) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Check that all the points in the list are coplanar (in the same plane)
as the plane defined by the planeNormal and the pointInPlane.
- allHeavyAtomsPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
True is all the atoms in the given AtomContainer have been placed
- allPlaced(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer
-
True is all the atoms in the given AtomContainer have been placed
- allPlaced(IRingSet) - Method in class org.openscience.cdk.layout.RingPlacer
-
True if coordinates have been assigned to all atoms in all rings.
- AllRingsFinder - Class in org.openscience.cdk.ringsearch
-
Finds the Set of all Rings.
- AllRingsFinder(boolean) - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder
-
Constructor for the AllRingsFinder.
- AllRingsFinder() - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder
-
Constructor for the AllRingsFinder with logging.
- AllRingsFinderMod - Class in org.openscience.cdk.ringsearch
-
Finds the Set of all Rings.
- AllRingsFinderMod(boolean) - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinderMod
-
Constructor for the AllRingsFinder.
- AllRingsFinderMod() - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinderMod
-
Constructor for the AllRingsFinder with logging.
- allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
-
Determines of all atoms on the AtomContainer have
the right number the lone pair electrons.
- allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
- allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
- ALOGPDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
This class calculates ALOGP (Ghose-Crippen LogKow) and the
Ghose-Crippen molar refractivity .
- ALOGPDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- alogpfrag - Variable in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- ALUMINIUM - Static variable in class org.openscience.cdk.config.Elements
-
- ALUMINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- ALUMINO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- AM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- AMERCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- AMERICIUM - Static variable in class org.openscience.cdk.config.Elements
-
- AMIDE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- AMINE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- AMINO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- AminoAcid - Class in org.openscience.cdk
-
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
- AminoAcid() - Constructor for class org.openscience.cdk.AminoAcid
-
Constructs a new AminoAcid.
- AminoAcid - Class in org.openscience.cdk.silent
-
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
- AminoAcid() - Constructor for class org.openscience.cdk.silent.AminoAcid
-
Constructs a new AminoAcid.
- AminoAcidCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Class that returns the number of each amino acid in an atom container.
- AminoAcidCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Constructor for the AromaticAtomsCountDescriptor object.
- AminoAcidManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods to manipulate
AminoAcid's.
- AminoAcidManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AminoAcidManipulator
-
- AminoAcids - Class in org.openscience.cdk.templates
-
Tool that provides templates for the (natural) amino acids.
- AminoAcids() - Constructor for class org.openscience.cdk.templates.AminoAcids
-
- AN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- ANGSTROM_UNIT - Static variable in class org.openscience.cdk.io.GamessReader
-
Boolean constant used to specify that the coordinates are given in Ångstrom units.
- AngularMomentum - Class in org.openscience.cdk.math.qm
-
This class is used to calculate angular momentum states.
- AngularMomentum(double) - Constructor for class org.openscience.cdk.math.qm.AngularMomentum
-
- ANNOTATIONS - Static variable in class org.openscience.cdk.CDKConstants
-
A List of annotation remarks.
- ANTIMONY - Static variable in class org.openscience.cdk.config.Elements
-
- ANTIMONY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- ANY_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- AnyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matcher any Atom.
- AnyAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom
-
Creates a new instance
- AnyAtom() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AnyOrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matches a bond of any order
- AnyOrderQueryBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
-
- AnyOrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
-
Creates a new instance
- APolDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Sum of the atomic polarizabilities (including implicit hydrogens).
- APolDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Constructor for the APolDescriptor object.
- AR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- AR_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- areIntersected(IBond, IBond) - Method in class org.openscience.cdk.layout.OverlapResolver
-
Checks if two bonds cross each other.
- areRootAtomsDefined() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Checks validity of RGroupQuery.
- areRootAtomsDefined() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- areSubstituentsDefined() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Checks validity of the RGroupQuery.
- areSubstituentsDefined() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- ARGON - Static variable in class org.openscience.cdk.config.Elements
-
- Aromatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AromaticAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matcher any aromatic atom.
- AromaticAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom
-
Creates a new instance
- AromaticAtomsCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Class that returns the number of aromatic atoms in an atom container.
- AromaticAtomsCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Constructor for the AromaticAtomsCountDescriptor object.
- AromaticBondsCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
This Class contains a method that returns the number of aromatic atoms in an AtomContainer.
- AromaticBondsCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Constructor for the AromaticBondsCountDescriptor object.
- AromaticityCalculator - Class in org.openscience.cdk.aromaticity
-
- AromaticityCalculator() - Constructor for class org.openscience.cdk.aromaticity.AromaticityCalculator
-
- AromaticOrSingleQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matches an aromatic or a single bond, used when no bond is specified between an atom
- AromaticOrSingleQueryBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
-
Creates a new instance
- AromaticOrSingleQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
-
Creates a new instance
- AromaticQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matches an aromatic bond
- AromaticQueryBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
-
Creates a new instance
- AromaticQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
-
Creates a new instance
- AromaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This class matches aromatic atom with element symbol specified.
- AromaticSymbolAtom(String) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom
-
- aromatizeMolecule(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
- aromatizeMolecule(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
- ArrowElement - Class in org.openscience.cdk.renderer.elements
-
- ArrowElement(double, double, double, double, double, boolean, Color) - Constructor for class org.openscience.cdk.renderer.elements.ArrowElement
-
Constructor for an arrow element, based on starting point, end point, width,
direction, and color.
- ARSENIC - Static variable in class org.openscience.cdk.config.Elements
-
- ARSENIC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- as - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- AS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- assignAtomTypePropertiesToAtom(IMolecule) - Method in class org.openscience.cdk.tools.AtomTypeTools
-
- assignAtomTypePropertiesToAtom(IMolecule, boolean) - Method in class org.openscience.cdk.tools.AtomTypeTools
-
Method assigns certain properties to an atom.
- assignAtomTyps(IMolecule) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Method assigns atom types to atoms (calculates sssr and aromaticity)
- assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Main method which assigns Gasteiger Marisili partial sigma charges
- assignGasteigerPiPartialCharges(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Main method which assigns Gasteiger partial pi charges.
- assignGasteigerSigmaMarsiliFactors(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Method which stores and assigns the factors a,b,c and CHI+
- assignInductivePartialCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.InductivePartialCharges
-
Main method, set charge as atom properties
- assignMMFF94PartialCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.MMFF94PartialCharges
-
Main method which assigns MMFF94 partial charges
- assignProteinToGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method assigns the atoms of a biopolymer to the grid.
- assignrPiMarsilliFactors(IAtomContainerSet) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Method which stores and assigns the factors a,b,c and CHI+
- assignVdWRadiiToProtein() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method which assigns van der Waals radii to the biopolymer
default org/openscience/cdk/config/data/pdb_atomtypes.xml
stored in the variable String vanDerWaalsFile.
- Association - Class in org.openscience.cdk
-
Base class for storing interactions like hydrogen bonds and ionic interactions.
- Association(IAtom, IAtom) - Constructor for class org.openscience.cdk.Association
-
Constructs an association between two Atom's.
- Association() - Constructor for class org.openscience.cdk.Association
-
Constructs an empty association.
- ASTAliphatic - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTAliphatic(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAliphatic
-
Creates a new instance
- ASTAliphatic(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAliphatic
-
Creates a new instance
- ASTAnyAtom - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTAnyAtom(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAnyAtom
-
Creates a new instance
- ASTAnyAtom(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAnyAtom
-
Creates a new instance
- ASTAromatic - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTAromatic(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAromatic
-
Creates a new instance
- ASTAromatic(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAromatic
-
Creates a new instance
- ASTATINE - Static variable in class org.openscience.cdk.config.Elements
-
- ASTAtom - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTAtom(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtom
-
Creates a new instance
- ASTAtom(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtom
-
Creates a new instance
- ASTAtomicMass - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTAtomicMass(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass
-
- ASTAtomicMass(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass
-
- ASTAtomicNumber - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTAtomicNumber(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber
-
Creates a new instance.
- ASTAtomicNumber(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber
-
Creates a new instance.
- ASTCharge - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTCharge(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTCharge
-
Creates a new instance.
- ASTCharge(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTCharge
-
Creates a new instance.
- ASTChirality - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTChirality(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTChirality
-
Creates a new instance
- ASTChirality(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTChirality
-
Creates a new instance
- ASTElement - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTElement(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTElement
-
Creates a new instance.
- ASTElement(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTElement
-
Creates a new instance.
- ASTExplicitAtom - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTExplicitAtom(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom
-
Creates a new instance.
- ASTExplicitAtom(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom
-
Creates a new instance.
- ASTExplicitConnectivity - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTExplicitConnectivity(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity
-
Creates a new instance.
- ASTExplicitConnectivity(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity
-
Creates a new instance.
- ASTExplicitHighAndBond - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTExplicitHighAndBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndBond
-
Creates a new instance.
- ASTExplicitHighAndBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndBond
-
Creates a new instance.
- ASTExplicitHighAndExpression - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTExplicitHighAndExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndExpression
-
Creates a new instance.
- ASTExplicitHighAndExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndExpression
-
Creates a new instance.
- ASTGroup - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTGroup(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTGroup
-
Creates a new instance
- ASTGroup(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTGroup
-
Creates a new instance
- ASTHybrdizationNumber - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTHybrdizationNumber(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber
-
- ASTHybrdizationNumber(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber
-
- ASTImplicitHCount - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTImplicitHCount(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount
-
Creates a new instance.
- ASTImplicitHCount(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount
-
Creates a new instance.
- ASTImplicitHighAndBond - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTImplicitHighAndBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndBond
-
Creates a new instance.
- ASTImplicitHighAndBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndBond
-
Creates a new instance.
- ASTImplicitHighAndExpression - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTImplicitHighAndExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndExpression
-
Creates a new instance.
- ASTImplicitHighAndExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndExpression
-
Creates a new instance.
- ASTLowAndBond - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTLowAndBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTLowAndBond
-
Creates a new instance.
- ASTLowAndBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTLowAndBond
-
Creates a new instance.
- ASTLowAndExpression - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTLowAndExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpression
-
Creates a new instance.
- ASTLowAndExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpression
-
Creates a new instance.
- ASTNonCHHeavyAtom - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTNonCHHeavyAtom(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNonCHHeavyAtom
-
- ASTNonCHHeavyAtom(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNonCHHeavyAtom
-
- ASTNotBond - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTNotBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNotBond
-
Creates a new instance.
- ASTNotBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNotBond
-
Creates a new instance.
- ASTNotExpression - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTNotExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression
-
Creates a new instance.
- ASTNotExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression
-
Creates a new instance.
- ASTOrBond - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTOrBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTOrBond
-
Creates a new instance.
- ASTOrBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTOrBond
-
Creates a new instance.
- ASTOrExpression - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTOrExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTOrExpression
-
Creates a new instance.
- ASTOrExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTOrExpression
-
Creates a new instance.
- ASTPeriodicGroupNumber - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTPeriodicGroupNumber(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber
-
- ASTPeriodicGroupNumber(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber
-
- ASTPrimitiveAtomExpression - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTPrimitiveAtomExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTPrimitiveAtomExpression
-
Creates a new instance.
- ASTPrimitiveAtomExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTPrimitiveAtomExpression
-
Creates a new instance.
- ASTReaction - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTReaction(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTReaction
-
Creates a new instance.
- ASTReaction(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTReaction
-
Creates a new instance.
- ASTRecursiveSmartsExpression - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTRecursiveSmartsExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRecursiveSmartsExpression
-
Creates a new instance.
- ASTRecursiveSmartsExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRecursiveSmartsExpression
-
Creates a new instance.
- ASTRingConnectivity - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTRingConnectivity(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity
-
Creates a new instance/
- ASTRingConnectivity(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity
-
Creates a new instance.
- ASTRingIdentifier - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTRingIdentifier(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier
-
Creates a new instance.
- ASTRingIdentifier(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier
-
Creates a new instance.
- ASTRingMembership - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTRingMembership(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership
-
Creates a new instance.
- ASTRingMembership(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership
-
Creates a new instance.
- ASTSimpleBond - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTSimpleBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond
-
Creates a new instance.
- ASTSimpleBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond
-
Creates a new instance.
- ASTSmallestRingSize - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTSmallestRingSize(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize
-
Creates a new instance.
- ASTSmallestRingSize(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize
-
Creates a new instance.
- ASTSmarts - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTSmarts(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSmarts
-
Creates a new instance.
- ASTSmarts(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSmarts
-
Creates a new instance.
- ASTStart - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTStart(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTStart
-
Creates a new instance
- ASTStart(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTStart
-
Creates a new instance
- ASTTotalConnectivity - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTTotalConnectivity(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity
-
Creates a new instance.
- ASTTotalConnectivity(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity
-
Creates a new instance.
- ASTTotalHCount - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTTotalHCount(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount
-
Creates a new instance.
- ASTTotalHCount(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount
-
Creates a new instance.
- ASTValence - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST node.
- ASTValence(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTValence
-
Creates a new instance.
- ASTValence(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTValence
-
Creates a new instance.
- AT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- atLowerBoundary() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Test the virtual font pointer to see if it is at the lower boundary of
the font size range (0).
- atMax() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Check if the font pointer is as the maximum value.
- atMin() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Check if the font pointer is as the minimum value.
- atof(String) - Static method in class org.openscience.cdk.math.FortranFormat
-
Converts a string of digits to an double
- Atom - Class in org.openscience.cdk
-
Represents the idea of an chemical atom.
- Atom() - Constructor for class org.openscience.cdk.Atom
-
Constructs an completely unset Atom.
- Atom(String) - Constructor for class org.openscience.cdk.Atom
-
Constructs an Atom from a String containing an element symbol.
- Atom(String, Point3d) - Constructor for class org.openscience.cdk.Atom
-
Constructs an Atom from an Element and a Point3d.
- Atom(String, Point2d) - Constructor for class org.openscience.cdk.Atom
-
Constructs an Atom from an Element and a Point2d.
- Atom(IElement) - Constructor for class org.openscience.cdk.Atom
-
Constructs an isotope by copying the symbol, atomic number,
flags, identifier, exact mass, natural abundance, mass
number, maximum bond order, bond order sum, van der Waals
and covalent radii, formal charge, hybridization, electron
valency, formal neighbour count and atom type name from the
given IAtomType.
- ATOM - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- Atom - Class in org.openscience.cdk.silent
-
Represents the idea of an chemical atom.
- Atom() - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an completely unset Atom.
- Atom(String) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an Atom from a String containing an element symbol.
- Atom(String, Point3d) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an Atom from an Element and a Point3d.
- Atom(String, Point2d) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an Atom from an Element and a Point2d.
- Atom(IElement) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an isotope by copying the symbol, atomic number,
flags, identifier, exact mass, natural abundance, mass
number, maximum bond order, bond order sum, van der Waals
and covalent radii, formal charge, hybridization, electron
valency, formal neighbour count and atom type name from the
given IAtomType.
- ATOM_ATOM_MAPPING - Static variable in class org.openscience.cdk.CDKConstants
-
- ATOM_EXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
Lexical state.
- ATOM_NAME_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
-
- AtomContainer - Class in org.openscience.cdk
-
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
- AtomContainer() - Constructor for class org.openscience.cdk.AtomContainer
-
Constructs an empty AtomContainer.
- AtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.AtomContainer
-
Constructs an AtomContainer with a copy of the atoms and electronContainers
of another AtomContainer (A shallow copy, i.e., with the same objects as in
the original AtomContainer).
- AtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.AtomContainer
-
Constructs an empty AtomContainer that will contain a certain number of
atoms and electronContainers.
- AtomContainer - Class in org.openscience.cdk.silent
-
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
- AtomContainer() - Constructor for class org.openscience.cdk.silent.AtomContainer
-
Constructs an empty AtomContainer.
- AtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.silent.AtomContainer
-
Constructs an AtomContainer with a copy of the atoms and electronContainers
of another AtomContainer (A shallow copy, i.e., with the same objects as in
the original AtomContainer).
- AtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.silent.AtomContainer
-
Constructs an empty AtomContainer that will contain a certain number of
atoms and electronContainers.
- AtomContainerAtomPermutor - Class in org.openscience.cdk.graph
-
This class iterates through all possible permutations of the atom order in a
given atom container.
- AtomContainerAtomPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerAtomPermutor
-
- AtomContainerAtomPermutor - Class in org.openscience.cdk.smsd.labelling
-
- AtomContainerAtomPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor
-
- AtomContainerBondPermutor - Class in org.openscience.cdk.graph
-
This class allows to iterate trough the set of all possible
permutations of the bond order in a given atom container.
- AtomContainerBondPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerBondPermutor
-
- AtomContainerBoundsGenerator - Class in org.openscience.cdk.renderer.generators
-
- AtomContainerBoundsGenerator() - Constructor for class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator
-
- AtomContainerComparator - Class in org.openscience.cdk.tools.manipulator
-
Compares two IAtomContainers for order with the following criteria with decreasing priority:
- AtomContainerComparator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerComparator
-
Creates a new instance of AtomContainerComparator
- AtomContainerComparatorBy2DCenter - Class in org.openscience.cdk.tools.manipulator
-
Compares two IAtomContainers based on their 2D position.
- AtomContainerComparatorBy2DCenter() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter
-
- AtomContainerDiff - Class in org.openscience.cdk.tools.diff
-
- AtomContainerManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods to manipulate
AtomContainer's.
- AtomContainerManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- AtomContainerPermutor - Class in org.openscience.cdk.graph
-
The permutation code here is based on a pseudo code example
on a tutorial site created and maintained by Phillip P.
- AtomContainerPermutor() - Constructor for class org.openscience.cdk.graph.AtomContainerPermutor
-
- AtomContainerPrinter - Class in org.openscience.cdk.smsd.labelling
-
- AtomContainerPrinter() - Constructor for class org.openscience.cdk.smsd.labelling.AtomContainerPrinter
-
- AtomContainerRenderer - Class in org.openscience.cdk.renderer
-
- AtomContainerRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.AtomContainerRenderer
-
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
- AtomContainerRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.AtomContainerRenderer
-
- atomContainers() - Method in class org.openscience.cdk.AtomContainerSet
-
Get an iterator for this AtomContainerSet.
- atomContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- atomContainers() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- atomContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Get an Iterable for this AtomContainerSet.
- atomContainers() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Get an iterator for this AtomContainerSet.
- AtomContainerSet - Class in org.openscience.cdk
-
A set of AtomContainers.
- AtomContainerSet() - Constructor for class org.openscience.cdk.AtomContainerSet
-
Constructs an empty AtomContainerSet.
- AtomContainerSet - Class in org.openscience.cdk.silent
-
A set of AtomContainers.
- AtomContainerSet() - Constructor for class org.openscience.cdk.silent.AtomContainerSet
-
Constructs an empty AtomContainerSet.
- AtomContainerSetManipulator - Class in org.openscience.cdk.tools.manipulator
-
- AtomContainerSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- AtomCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
IDescriptor based on the number of atoms of a certain element type.
- AtomCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Constructor for the AtomCountDescriptor object.
- AtomDegreeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class returns the number of not-Hs substituents of an atom, also defined as "atom degree".
- AtomDegreeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
- AtomDiff - Class in org.openscience.cdk.tools.diff
-
Compares two
IAtom
classes.
- AtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AtomHybridizationDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class returns the hybridization of an atom.
- AtomHybridizationDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
- AtomHybridizationVSEPRDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class returns the hybridization of an atom.
- AtomHybridizationVSEPRDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
Constructor for the AtomHybridizationVSEPRDescriptor object
- ATOMIC - Static variable in class org.openscience.cdk.qsar.DescriptorEngine
-
- AtomicMass() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AtomicNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AtomicNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matches an atom using the atomic number.
- AtomicNumberAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom
-
Creates a new instance.
- AtomicNumberDifferenceDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond
-
Describes the imbalance in atomic number of the IBond.
- AtomicNumberDifferenceDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
-
- AtomicProperties - Class in org.openscience.cdk.tools
-
Provides atomic property values for descriptor calculations.
- AtomMappingTools - Class in org.openscience.cdk.isomorphism
-
- AtomMappingTools() - Constructor for class org.openscience.cdk.isomorphism.AtomMappingTools
-
- AtomMassGenerator - Class in org.openscience.cdk.renderer.generators
-
IGenerator
that can render mass number information of atoms.
- AtomMassGenerator() - Constructor for class org.openscience.cdk.renderer.generators.AtomMassGenerator
-
- atomMassNumber - Variable in class org.openscience.cdk.renderer.elements.AtomMassSymbolElement
-
- AtomMassSymbolElement - Class in org.openscience.cdk.renderer.elements
-
Rendering element that shows the
IAtom
mass number information.
- AtomMassSymbolElement(double, double, String, Integer, Integer, int, Integer, Color) - Constructor for class org.openscience.cdk.renderer.elements.AtomMassSymbolElement
-
Constructs a new
TextElement
displaying the atom's mass number information.
- AtomMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers
-
Interface for the AtomMatcher (atoms) in graph.
- AtomNumberGenerator - Class in org.openscience.cdk.renderer.generators
-
- AtomNumberGenerator() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator
-
- AtomNumberGenerator.AtomColorer - Class in org.openscience.cdk.renderer.generators
-
- AtomNumberGenerator.AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer
-
- AtomNumberGenerator.AtomNumberTextColor - Class in org.openscience.cdk.renderer.generators
-
Color to draw the atom numbers with.
- AtomNumberGenerator.AtomNumberTextColor() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor
-
- AtomNumberGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators
-
- AtomNumberGenerator.ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
-
- AtomNumberGenerator.Offset - Class in org.openscience.cdk.renderer.generators
-
Offset vector in screen space coordinates where the atom number label
will be placed.
- AtomNumberGenerator.Offset() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset
-
- AtomNumberGenerator.WillDrawAtomNumbers - Class in org.openscience.cdk.renderer.generators
-
Boolean parameter indicating if atom numbers should be drawn, allowing
this feature to be disabled temporarily.
- AtomNumberGenerator.WillDrawAtomNumbers() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers
-
- ATOMPAIR - Static variable in class org.openscience.cdk.qsar.DescriptorEngine
-
- AtomParity - Class in org.openscience.cdk
-
Represents the concept of an atom parity identifying the stereochemistry
around an atom, given four neighbouring atoms.
- AtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) - Constructor for class org.openscience.cdk.AtomParity
-
Constructs an completely unset AtomParity.
- AtomParity - Class in org.openscience.cdk.silent
-
Represents the concept of an atom parity identifying the stereochemistry
around an atom, given four neighbouring atoms.
- AtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) - Constructor for class org.openscience.cdk.silent.AtomParity
-
Constructs an completely unset AtomParity.
- AtomPlacer - Class in org.openscience.cdk.layout
-
Methods for generating coordinates for atoms in various situations.
- AtomPlacer() - Constructor for class org.openscience.cdk.layout.AtomPlacer
-
Constructor for the AtomPlacer object
- AtomPlacer3D - Class in org.openscience.cdk.modeling.builder3d
-
Place aliphatic chains with Z matrix method.
- atoms() - Method in class org.openscience.cdk.AtomContainer
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.Bond
-
Returns the Iterator to atoms making up this bond.
- atoms() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- atoms() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- atoms() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- atoms() - Method in class org.openscience.cdk.debug.DebugBond
-
- atoms() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- atoms() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- atoms() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- atoms() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- atoms() - Method in class org.openscience.cdk.debug.DebugRing
-
- atoms() - Method in class org.openscience.cdk.debug.DebugStrand
-
- atoms() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the Iterable to atoms making up this bond.
- atoms() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.silent.Bond
-
Returns the Iterator to atoms making up this bond.
- AtomSignature - Class in org.openscience.cdk.signature
-
The signature for a molecule rooted at a particular
atom.
- AtomSignature(int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature
-
Create an atom signature starting at atomIndex
.
- AtomSignature(IAtom, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature
-
Create an atom signature for the atom atom
.
- AtomSignature(int, int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature
-
Create an atom signature starting at atomIndex
and with a
maximum height of height
.
- AtomSignature(IAtom, int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature
-
Create an atom signature for the atom atom
and with a
maximum height of height
.
- AtomSignature(int, int, AbstractVertexSignature.InvariantType, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature
-
Create an atom signature starting at atomIndex
, with maximum
height of height
, and using a particular invariant type.
- AtomSignature(IAtom, int, AbstractVertexSignature.InvariantType, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature
-
Create an atom signature for the atom atom
, with maximum
height of height
, and using a particular invariant type.
- AtomSymbolElement - Class in org.openscience.cdk.renderer.elements
-
A text element with added information.
- AtomSymbolElement(double, double, String, Integer, Integer, int, Color) - Constructor for class org.openscience.cdk.renderer.elements.AtomSymbolElement
-
- AtomTetrahedralLigandPlacer3D - Class in org.openscience.cdk.modeling.builder3d
-
A set of static utility classes for geometric calculations on Atoms.
- AtomTools - Class in org.openscience.cdk.geometry
-
A set of static utility classes for geometric calculations on Atoms.
- AtomTools() - Constructor for class org.openscience.cdk.geometry.AtomTools
-
- AtomType - Class in org.openscience.cdk
-
The base class for atom types.
- AtomType(String) - Constructor for class org.openscience.cdk.AtomType
-
Constructor for the AtomType object.
- AtomType(String, String) - Constructor for class org.openscience.cdk.AtomType
-
Constructor for the AtomType object.
- AtomType(IElement) - Constructor for class org.openscience.cdk.AtomType
-
Constructs an isotope by copying the symbol, atomic number,
flags, identifier, exact mass, natural abundance and mass
number from the given IIsotope.
- ATOMTYPE - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- AtomType - Class in org.openscience.cdk.silent
-
The base class for atom types.
- AtomType(String) - Constructor for class org.openscience.cdk.silent.AtomType
-
Constructor for the AtomType object.
- AtomType(String, String) - Constructor for class org.openscience.cdk.silent.AtomType
-
Constructor for the AtomType object.
- AtomType(IElement) - Constructor for class org.openscience.cdk.silent.AtomType
-
Constructs an isotope by copying the symbol, atomic number,
flags, identifier, exact mass, natural abundance and mass
number from the given IIsotope.
- ATOMTYPE_ID_JMOL - Static variable in class org.openscience.cdk.config.AtomTypeFactory
-
Used as an ID to describe the atom type.
- ATOMTYPE_ID_MODELING - Static variable in class org.openscience.cdk.config.AtomTypeFactory
-
Used as an ID to describe the atom type.
- ATOMTYPE_ID_STRUCTGEN - Static variable in class org.openscience.cdk.config.AtomTypeFactory
-
Used as an ID to describe the atom type.
- AtomTypeCharges - Class in org.openscience.cdk.charges
-
Assigns charges to atom types.
- AtomTypeDiff - Class in org.openscience.cdk.tools.diff
-
- AtomTypeFactory - Class in org.openscience.cdk.config
-
General class for defining AtomTypes.
- AtomTypeHandler - Class in org.openscience.cdk.config.atomtypes
-
SAX Handler for the AtomTypeReader.
- AtomTypeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.atomtypes.AtomTypeHandler
-
Constructs a new AtomTypeHandler and will create IAtomType
implementations using the given IChemObjectBuilder.
- AtomTypeHybridizationDifference - Class in org.openscience.cdk.tools.diff.tree
-
- AtomTypeManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with utilities for the AtomType
class.
- AtomTypeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomTypeManipulator
-
- AtomTypeMapper - Class in org.openscience.cdk.atomtype.mapper
-
An AtomTypeMapper
allows the mapping of atom types between atom type
schemes.
- AtomTypeReader - Class in org.openscience.cdk.config.atomtypes
-
XML Reader for the CDKBasedAtomTypeConfigurator.
- AtomTypeReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.AtomTypeReader
-
Instantiates the XML based AtomTypeReader.
- AtomTypeTools - Class in org.openscience.cdk.tools
-
AtomTypeTools is a helper class for assigning atom types to an atom.
- AtomTypeTools() - Constructor for class org.openscience.cdk.tools.AtomTypeTools
-
Constructor for the MMFF94AtomTypeMatcher object.
- AtomValenceDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class returns the valence of an atom.
- AtomValenceDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
Constructor for the AtomValenceDescriptor object
- AtomValenceTool - Class in org.openscience.cdk.qsar
-
This class returns the valence of an atom.
- AtomValenceTool() - Constructor for class org.openscience.cdk.qsar.AtomValenceTool
-
- AttachedGroup - Class in org.openscience.cdk.iupac.parser
-
Holds data on a specific functional group or substituent.
- AttachedGroup() - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup
-
Creates a new instance of FunctionalGroup
- AttachedGroup(Vector, String) - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup
-
Creates a new instance of AttachedGroup with a Sting denoting the functional group
- AttachedGroup(Vector, int) - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup
-
Creates a new instance of AttachedGroup with an int denoting the length of the substituent chain
- attachLocationSpecified() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
An attach position has been specified using a
comma seperated list followed by a dash
- atUpperBoundary() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Test the virtual font pointer to see if it is at the upper boundary of
the font size range (|fonts| - 1).
- AU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- AutocorrelationDescriptorCharge - Class in org.openscience.cdk.qsar.descriptors.molecular
-
This class calculates ATS autocorrelation descriptor, where the weight equal
to the charges.
- AutocorrelationDescriptorCharge() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- AutocorrelationDescriptorMass - Class in org.openscience.cdk.qsar.descriptors.molecular
-
This class calculates ATS autocorrelation descriptor, where the weight equal
to the scaled atomic mass .
- AutocorrelationDescriptorMass() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- AutocorrelationDescriptorPolarizability - Class in org.openscience.cdk.qsar.descriptors.molecular
-
This class calculates ATS autocorrelation descriptor, where the weight equal
to the charges.
- AutocorrelationDescriptorPolarizability() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- AUTONOMNAME - Static variable in class org.openscience.cdk.CDKConstants
-
The IUPAC compatible name generated with AutoNom.
- AverageBondLengthCalculator - Class in org.openscience.cdk.renderer
-
Utility class for calculating the average bond length for various
IChemObject subtypes : IReaction, IMoleculeSet, IChemModel, and IReactionSet.
- AverageBondLengthCalculator() - Constructor for class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
- AWTDrawVisitor - Class in org.openscience.cdk.renderer.visitor
-
Implementation of the
IDrawVisitor
interface for the AWT
widget toolkit, allowing molecules to be rendered with toolkits based on
AWT, like the Java reference graphics platform Swing.
- AWTDrawVisitor(Graphics2D) - Constructor for class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
Constructs a new
IDrawVisitor
using the AWT widget toolkit,
taking a
Graphics2D
object to which the chemical content
is drawn.
- AWTFontManager - Class in org.openscience.cdk.renderer.font
-
AWT-specific font manager.
- AWTFontManager() - Constructor for class org.openscience.cdk.renderer.font.AWTFontManager
-
Make a manager for fonts in AWT, with a minimum font size of 9.
- axisScanX(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method performs a scan; works only for cubic grids!
- axisScanY(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method performs a scan; works only for cubic grids!
- axisScanZ(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method performs a scan; works only for cubic grids!
- c - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- C - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CacaoCartesianFormat - Class in org.openscience.cdk.io.formats
-
- CacaoInternalFormat - Class in org.openscience.cdk.io.formats
-
- cacheDescriptorValue(IAtom, IAtomContainer, IDescriptorResult) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor
-
Caches a DescriptorValue for a given IAtom.
- cacheDescriptorValue(IBond, IAtomContainer, IDescriptorResult) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor
-
Caches a DescriptorValue for a given IBond.
- CACheFormat - Class in org.openscience.cdk.io.formats
-
- CADMIUM - Static variable in class org.openscience.cdk.config.Elements
-
- CADMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CAESIUM - Static variable in class org.openscience.cdk.config.Elements
-
- calcD(double, double, double, double, Vector, Vector) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
- calcG(int, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Transfer equation for the calculation of core potentials
- calcG(int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Transfer equation for a four center integral.
- calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- calcI(int, int, int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Transfer equation for a four center integral.
- calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
- calcI(int, int, int, int) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates a two eletron fout center integral
I = <chi_i chi_j | 1/r12 | chi_k chi_l >.
- calcInvertedAxes(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
-
Inverts three cell axes.
- CALCIUM - Static variable in class org.openscience.cdk.config.Elements
-
- CALCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- calcJ(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- calcJ(int, int, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Transfer equation the the calculation of the impulse
- calcJ(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
- calcJ(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates the impulse J = -<d/dr chi_i | d/dr chi_j>.
- calcS(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- calcS(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
- calcS(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculate the overlap integral S = <phi_i|phi_j>.
- calculate(IAtom, IAtom) - Method in interface org.openscience.cdk.geometry.IRDFWeightFunction
-
Calculates the weight for the interaction between the two atoms.
- calculate(IAtomContainer, IAtom) - Method in class org.openscience.cdk.geometry.RDFCalculator
-
Calculates a RDF for Atom
atom in the environment
of the atoms in the AtomContainer
.
- calculate(IMolecule) - Static method in class org.openscience.cdk.geometry.volume.VABCVolume
-
Calculates the volume for the given
IMolecule
.
- calculate() - Method in class org.openscience.cdk.math.qm.ClosedShellJob
-
- calculate() - Method in class org.openscience.cdk.math.qm.OneElectronJob
-
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
This method calculates the number of not-H substituents of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
This method calculates the hybridization of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
This method calculates the hybridization of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
This method calculates the valence of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
This method calculate the number of bonds on the shortest path between two atoms.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
This method calculate the Covalent radius of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
This method calculate the 3D distance between two atoms.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
The method calculates the Effective Atom Polarizability of a given atom
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
It is needed to call the addExplicitHydrogensToSatisfyValency method from
the class tools.HydrogenAdder, and 3D coordinates.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
It is needed to call the addExplicitHydrogensToSatisfyValency method from
the class tools.HydrogenAdder, and 3D coordinates.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
This method calculates the ionization potential of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
This method calculates the ionization potential of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
-
The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
-
The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
-
The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
-
The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
-
The method returns partial charges assigned to an heavy atom through MMFF94 method.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
-
The method returns partial total charges assigned to an heavy atom through PEOE method.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
-
This method calculates the period of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
-
The method calculates the pi electronegativity of a given atom
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
-
This method calculates the protonation affinity of an atom.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
-
The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
-
- calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
-
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
-
- calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
-
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
-
- calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
-
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
-
- calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
-
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
-
- calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
-
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
The method calculates the sigma electronegativity of a given atom
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
The method calculates the stabilization of charge of a given atom
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
-
This method calculate the Van der Waals radius of an atom.
- calculate(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
-
The method returns if two atoms have pi-contact.
- calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
-
- calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
-
The method calculates the bond-pi Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
-
The method calculates the bond-sigma Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
-
The method calculates the bond total Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
-
The method calculates the sigma electronegativity of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
- calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
-
This method calculates the ionization potential of a bond.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Calculates the descriptor value for the given IAtomContainer.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
The AlogP descriptor.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Determine the number of amino acids groups the supplied
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
This method calculate the number of atoms of a given type in an
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
This method calculate the ATS Autocorrelation descriptor.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
This method calculate the ATS Autocorrelation descriptor.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Calculates the descriptor value for the given IAtomContainer.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Calculates the three classes of BCUT descriptors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
This method calculate the number of bonds of a given type in an atomContainer
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
This method calculate the sum of the absolute value of
the difference between atomic polarizabilities of all bonded atoms in the molecule
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Calculates the 9 carbon types descriptors
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Calculates the eccentric connectivity
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Calculates the 9 gravitational indices.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Calculates the number of H bond acceptors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Calculates the number of H bond donors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
It calculates the first ionization energy of a molecule.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
calculates the kier shape indices for an atom container
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
This method calculates occurrences of the Kier & Hall E-state fragments.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Calculate the count of atoms of the largest chain in the supplied
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Calculate the count of atoms of the largest pi system in the supplied
AtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Evaluate the descriptor for the molecule.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Calculate the count of atoms of the longest aliphatic chain in the supplied
AtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Calculates the Mannhold LogP for an atom container.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Calculate the weight of specified element type in the supplied
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Calculates the 3 MI's, 3 ration and the R_gyr value.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Evaluate the descriptor for the molecule.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Calculates the two Petitjean shape indices.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
The method calculates the number of rotatable bonds of an atom container.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
the method take a boolean checkAromaticity: if the boolean is true, it means that
aromaticity has to be checked.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Calculates the TPSA for an atom container.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Calculates the descriptor value using the
VABCVolume
class.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
calculates the VAdjMa descriptor for an atom container
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Calculate the weight of specified element type in the supplied
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Calculates the weighted path descriptors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Calculates 11 directional and 6 non-directional WHIM descriptors for.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Calculate the Wiener numbers.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Calculates the xlogP for an atom container.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Evaluate the Zagreb Index for a molecule.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Calculates the 147 TAE descriptors for amino acids.
- calculate(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IAtomicDescriptor
-
Calculates the descriptor value for the given IAtom.
- calculate(IAtom, IAtom, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IAtomPairDescriptor
-
Calculates the descriptor value for the given IAtom.
- calculate(IBond, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IBondDescriptor
-
Calculates the descriptor value for the given IBond.
- calculate(IAtomContainer) - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor
-
Calculates the descriptor value for the given IAtomContainer.
- calculate(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment
-
Evaluate the 3D similarity between two molecules.
- calculate(BitSet, BitSet) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluates Tanimoto coefficient for two bit sets.
- calculate(double[], double[]) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluates the continuous Tanimoto coefficient for two real valued vectors.
- calculate3DCoordinates0(Point3d, int, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Calculates substituent points.
- calculate3DCoordinates0(Point3d, int, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculates substituent points.
- calculate3DCoordinates1(Point3d, Point3d, Point3d, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Calculate new point(s) X in a B-A system to form B-A-X.
- calculate3DCoordinates1(Point3d, Point3d, Point3d, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate new point(s) X in a B-A system to form B-A-X.
- calculate3DCoordinates2(Point3d, Point3d, Point3d, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Calculate new point(s) X in a B-A-C system.
- calculate3DCoordinates2(Point3d, Point3d, Point3d, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate new point(s) X in a B-A-C system, it forms a B-A(-C)-X
system.
- calculate3DCoordinates3(Point3d, Point3d, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Calculate new point X in a B-A(-D)-C system.
- calculate3DCoordinates3(Point3d, Point3d, Point3d, Point3d, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate new point X in a B-A(-D)-C system.
- calculate3DCoordinatesForLigands(AtomContainer, IAtom, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
- calculate3DCoordinatesSP2_1(Point3d, Point3d, Point3d, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate new point in B-A-C system.
- calculate3DCoordinatesSP2_2(Point3d, Point3d, Point3d, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate two new points in B-A system.
- calculateAverageBondLength(IReaction) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
Calculate the average bond length for the bonds in a reaction.
- calculateAverageBondLength(IMoleculeSet) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
Calculate the average bond length for the bonds in a molecule set.
- calculateAverageBondLength(IChemModel) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
Calculate the average bond length for the bonds in a chem model.
- calculateAverageBondLength(IReactionSet) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
Calculate the average bond length for the bonds in a reaction set.
- calculateBondPolarizability(IAtomContainer, IBond) - Method in class org.openscience.cdk.charges.Polarizability
-
calculate bond polarizability
- calculateBounds(IChemModel) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for a chem model.
- calculateBounds(IReactionSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for a reaction set.
- calculateBounds(IReaction) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for a reaction.
- calculateBounds(IMoleculeSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for a molecule set.
- calculateBounds(IAtomContainer) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for an atom container.
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.AtomTypeCharges
-
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
- calculateCharges(IAtomContainer) - Method in interface org.openscience.cdk.charges.IElectronicPropertyCalculator
-
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.InductivePartialCharges
-
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.MMFF94PartialCharges
-
- calculateDiagramBounds(IAtomContainer) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateDiagramBounds(IChemModel) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
Given a chem model, calculates the bounding rectangle in screen space.
- calculateDiagramBounds(T) - Method in interface org.openscience.cdk.renderer.IRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateDiagramBounds(IMoleculeSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateDiagramBounds(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateDiagramBounds(IReactionSet) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.charges.Polarizability
-
calculate effective atom polarizability
- calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, boolean, int[][]) - Method in class org.openscience.cdk.charges.Polarizability
-
calculate effective atom polarizability
- calculateIsomorphs(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
- calculateKJMeanMolecularPolarizability(IAtomContainer) - Method in class org.openscience.cdk.charges.Polarizability
-
calculates the mean molecular polarizability as described in paper of Kang and Jhorn
- calculateMaxRank() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Calculate the max possible rank for permutations of N numbers.
- calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Calculate the number of missing hydrogens by substracting the number of
bonds for the atom from the expected number of bonds.
- calculateNumberOfImplicitHydrogens(IAtom) - Method in class org.openscience.cdk.tools.SaturationChecker
-
- calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker
-
- calculateNumberOfImplicitHydrogens(IAtom, double, double, List, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Calculate the number of missing hydrogens by substracting the number of
bonds for the atom from the expected number of bonds.
- calculateNumberOfImplicitHydrogens(IAtom, double, IBond.Order, int) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Calculates the number of hydrogens that can be added to the given atom to fullfil
the atom's valency.
- calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
- calculateOrbits() - Method in class org.openscience.cdk.signature.MoleculeSignature
-
Calculates the orbits of the atoms of the molecule.
- calculateOverlapsAndReduce(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates all the possible combinations of MCS
- calculateOverlapsAndReduceExactMatch(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
- calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Determines the normalized vector orthogonal on the vector p1->p2.
- calculatePiElectronegativity(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.PiElectronegativity
-
calculate the electronegativity of orbitals pi.
- calculatePiElectronegativity(IAtomContainer, IAtom, int, int) - Method in class org.openscience.cdk.charges.PiElectronegativity
-
calculate the electronegativity of orbitals pi.
- calculatePlus(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
It calculates the 1,2,..
- calculatePositive(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.StabilizationCharges
-
calculate the stabilization of orbitals when they contain deficiency of charge.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Calculate the scale to convert the model bonds into bonds of the length
supplied.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScreenBounds(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Converts a bounding rectangle in 'model space' into the equivalent
bounds in 'screen space'.
- calculateSigmaElectronegativity(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Electronegativity
-
calculate the electronegativity of orbitals sigma.
- calculateSigmaElectronegativity(IAtomContainer, IAtom, int, int) - Method in class org.openscience.cdk.charges.Electronegativity
-
calculate the electronegativity of orbitals sigma.
- calculateSubGraphs(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
- calculateSurface() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Evaluate the surface.
- calcV(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- calcV(int, int, Vector, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Calculates the core potential.
- calcV(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Calculates the core potential.
- calcV(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates the potential V = <chi_i | 1/r | chi_j>.
- CALIFORNIUM - Static variable in class org.openscience.cdk.config.Elements
-
- CALIFORNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CANONICAL_LABEL - Static variable in class org.openscience.cdk.smiles.InvPair
-
- CanonicalLabeler - Class in org.openscience.cdk.graph.invariant
-
Canonically labels an atom container implementing
the algorithm published in David Weininger et.al.
- CanonicalLabeler() - Constructor for class org.openscience.cdk.graph.invariant.CanonicalLabeler
-
- CanonicalLabellingAdaptor - Class in org.openscience.cdk.smsd.labelling
-
- CanonicalLabellingAdaptor() - Constructor for class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
-
- canonLabel(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.CanonicalLabeler
-
Canonically label the fragment.
- CARBON - Static variable in class org.openscience.cdk.config.Elements
-
- CarbonTypesDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Topological descriptor characterizing the carbon connectivity.
- CarbonTypesDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
- CarbonylEliminationReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate mass spectrum process.
- CarbonylEliminationReaction() - Constructor for class org.openscience.cdk.reaction.type.CarbonylEliminationReaction
-
Constructor of the CarbonylEliminationReaction object.
- CARET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- cartesianToFractional(Vector3d, Vector3d, Vector3d, Point3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
-
- cartesianToNotional(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
-
- CASNumber - Class in org.openscience.cdk.index
-
Tools to work with CAS registry numbers.
- CASNumber() - Constructor for class org.openscience.cdk.index.CASNumber
-
- CASRN - Static variable in class org.openscience.cdk.CDKConstants
-
The CAS Registry Number.
- CD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CDK - Class in org.openscience.cdk
-
Helper class to provide general information about this CDK library.
- CDK() - Constructor for class org.openscience.cdk.CDK
-
- CDK - Class in org.openscience.cdk.libio.jena
-
Helper class to provide a Java API to the CDK OWL ontology, following the design of similar namespace
classes in the Jena library, like RDF
.
- CDK() - Constructor for class org.openscience.cdk.libio.jena.CDK
-
- CDK2DAtomColors - Class in org.openscience.cdk.renderer.color
-
Gives a short table of atom colors for 2D display.
- CDK2DAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CDK2DAtomColors
-
- CDKAtomColors - Class in org.openscience.cdk.renderer.color
-
Gives a short table of atom colors for 3D display.
- CDKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CDKAtomColors
-
- cdkAtomContainerToCMLMolecule(IAtomContainer) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkAtomToCMLAtom(IAtom) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkAtomToCMLAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKAtomTypeMatcher - Class in org.openscience.cdk.atomtype
-
Atom Type matcher that perceives atom types as defined in the CDK atom type list
org/openscience/cdk/dict/data/cdk-atom-types.owl
.
- CDKBasedAtomTypeConfigurator - Class in org.openscience.cdk.config
-
AtomType resource that reads the atom type configuration from an XML file.
- CDKBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator
-
- cdkBondToCMLBond(IBond) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkChemFileToCMLList(IChemFile) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkChemModelToCMLList(IChemModel) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkChemSequenceToCMLList(IChemSequence) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKConstants - Class in org.openscience.cdk
-
An interface providing predefined values for a number of
constants used throughout the CDK.
- CDKConstants() - Constructor for class org.openscience.cdk.CDKConstants
-
- CDKConvention - Class in org.openscience.cdk.io.cml
-
This is an implementation for the CDK convention.
- CDKConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CDKConvention
-
- CDKConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CDKConvention
-
- cdkCrystalToCMLMolecule(ICrystal) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKDictionaryReferences - Class in org.openscience.cdk.dict
-
This class transforms implicit references to dictionary of CDK
objects into explicit references.
- CDKDictionaryReferences() - Constructor for class org.openscience.cdk.dict.CDKDictionaryReferences
-
- CDKException - Exception in org.openscience.cdk.exception
-
Exception that is thrown by CDK classes when some problem has occured.
- CDKException(String) - Constructor for exception org.openscience.cdk.exception.CDKException
-
Constructs a new CDKException with the given message.
- CDKException(String, Throwable) - Constructor for exception org.openscience.cdk.exception.CDKException
-
Constructs a new CDKException with the given message and the
Exception as cause.
- CDKHueckelAromaticityDetector - Class in org.openscience.cdk.aromaticity
-
This aromaticity detector detects the aromaticity based on the Hückel
4n+2 pi-electrons rule applied to isolated ring systems.
- CDKHueckelAromaticityDetector() - Constructor for class org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector
-
- CDKHydrogenAdder - Class in org.openscience.cdk.tools
-
Adds implicit hydrogens based on atom type definitions.
- CDKMCS - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This class implements atom multipurpose structure comparison tool.
- CDKMCS() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
- CDKMCSHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This class acts as a handler class for
CDKMCS
algorithm.
- CDKMCSHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
- cdkMoleculeSetToCMLList(IMoleculeSet) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkMoleculeToCMLMolecule(IMolecule) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkMonomerToCMLMolecule(IMonomer) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKOWLFormat - Class in org.openscience.cdk.io.formats
-
Serializes a CDK model into the Web Ontology Language using the
N3 format.
- CDKOWLReader - Class in org.openscience.cdk.io.rdf
-
Reads content from a CDK OWL serialization.
- CDKOWLReader(Reader) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader
-
Creates a new CDKOWLReader sending output to the given Writer.
- CDKOWLReader() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader
-
Creates a new CDKOWLReader with an undefined input.
- CDKOWLWriter - Class in org.openscience.cdk.io.rdf
-
Serializes the data model into CDK OWL.
- CDKOWLWriter(Writer) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Creates a new CDKOWLWriter sending output to the given Writer.
- CDKOWLWriter() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Creates a new CDKOWLWriter with an undefined output.
- cdkPDBPolymerToCMLMolecule(IPDBPolymer) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKPopupMenu - Class in org.openscience.cdk.controller
-
Basically, identical to the JPopupMenu class, except that this menu
can also contain the source for which it was popped up.
- CDKPopupMenu() - Constructor for class org.openscience.cdk.controller.CDKPopupMenu
-
- cdkReactionSchemeToCMLReactionScheme(IReactionScheme) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionSetToCMLReactionList(IReactionSet) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionToCMLReaction(IReaction) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionToCMLReactionStep(IReaction) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKRGraph - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This class implements the Resolution Graph (CDKRGraph).
- CDKRGraph() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Constructor for the CDKRGraph object and creates an empty CDKRGraph.
- CDKRMap - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
An CDKRMap implements the association between an edge (bond) in G1 and an edge
(bond) in G2, G1 and G2 being the compared graphs in a RGraph context.
- CDKRMap(int, int) - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Constructor for the CDKRMap
- CDKRMapHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This algorithm derives from the algorithm described in
[Tonnelier, C.
- CDKRMapHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
- CDKRNode - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
Node of the resolution graphe (RGraph) An CDKRNode represents an association
betwwen two edges of the source graphs G1 and G2 that are compared.
- CDKRNode(int, int) - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Constructor for the RNode object
- CDKSourceCodeFormat - Class in org.openscience.cdk.io.formats
-
- CDKSourceCodeWriter - Class in org.openscience.cdk.io
-
Converts a Molecule into CDK source code that would build the same
molecule.
- CDKSourceCodeWriter(Writer) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
-
Constructs a new CDKSourceCodeWriter.
- CDKSourceCodeWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
-
- CDKSourceCodeWriter() - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
-
- CDKSubGraphHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This class acts as a handler class for
CDKMCS
algorithm.
- CDKSubGraphHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
- CDKUtilities - Class in org.openscience.cdk.tools
-
Utility class written by Todd Martin, for help in his QSAR descriptors and SMILES
parser.
- CDKUtilities() - Constructor for class org.openscience.cdk.tools.CDKUtilities
-
- CDKValencyChecker - Class in org.openscience.cdk.tools
-
Assumes CDK atom types to be detected and adds missing hydrogens based on the
atom typing.
- CDKValidator - Class in org.openscience.cdk.validate
-
This Validator tests the internal datastructures, and
tries to detect inconsistencies in it.
- CDKValidator() - Constructor for class org.openscience.cdk.validate.CDKValidator
-
- CE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- center(IAtomContainer, Dimension) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Centers the molecule in the given area
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
- CERIUM - Static variable in class org.openscience.cdk.config.Elements
-
- CERIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CESIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- chainPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
A list of known tokens denoting a chain's length.
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.CDKConvention
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- characterData(CMLStack, char[], int, int) - Method in interface org.openscience.cdk.io.cml.ICMLModule
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.MDLMolConvention
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.PDBConvention
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.PMPConvention
-
- characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
-
- characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
-
- characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
-
- characters(char[], int, int) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
-
- characters(char[], int, int) - Method in class org.openscience.cdk.dict.DictionaryHandler
-
- characters(char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLHandler
-
Implementation of the characters() procedure overwriting the DefaultHandler interface.
- characters(char[], int, int) - Method in class org.openscience.cdk.io.inchi.INChIHandler
-
Implementation of the characters() procedure overwriting the
DefaultHandler interface.
- Charge() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- ChargeGroup - Class in org.openscience.cdk.libio.md
-
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
- ChargeGroup() - Constructor for class org.openscience.cdk.libio.md.ChargeGroup
-
Empty constructor.
- ChargeGroup(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.ChargeGroup
-
Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.
- ChargeRule - Class in org.openscience.cdk.formula.rules
-
This class validate if the charge in the IMolecularFormula correspond with
a specific value.
- ChargeRule() - Constructor for class org.openscience.cdk.formula.rules.ChargeRule
-
Constructor for the ChargeRule object.
- checkAndCleanMolecule(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.MoleculeSanityCheck
-
Modules for cleaning a molecule
- checkAndMarkPlaced(IRingSet) - Method in class org.openscience.cdk.layout.RingPlacer
-
Walks throught the atoms of each ring in a ring set and marks
a ring as PLACED if all of its atoms have been placed.
- checkConsistency() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
-
- checkDiffNumber(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Get different number of the given number
- checkForceFieldType(String) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the forceFieldType attribute of the ForceFieldConfigurator object
- checkIfAllLigandsAreDifferent(ILigand[]) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
- checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Checks for single atom cases before doing subgraph/isomorphism search.
- checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Checks for single atom cases before doing subgraph/isomorphism search
- checkTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
-
Checks if the timeout has been reached and throws an
exception if so.
- checkTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinderMod
-
Checks if the timeout has been reached and throws an
exception if so.
- Chem3D_Cartesian_1Format - Class in org.openscience.cdk.io.formats
-
- Chem3D_Cartesian_2Format - Class in org.openscience.cdk.io.formats
-
- ChemDrawFormat - Class in org.openscience.cdk.io.formats
-
- ChemFile - Class in org.openscience.cdk
-
A Object containing a number of ChemSequences.
- ChemFile() - Constructor for class org.openscience.cdk.ChemFile
-
Constructs an empty ChemFile.
- ChemFile - Class in org.openscience.cdk.silent
-
A Object containing a number of ChemSequences.
- ChemFile() - Constructor for class org.openscience.cdk.silent.ChemFile
-
Constructs an empty ChemFile.
- ChemFileManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemFile.
- ChemFileManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
- ChemGraph - Class in org.openscience.cdk.structgen.stochastic.operator
-
- ChemGraph(IAtomContainer) - Constructor for class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- CHEMICAL_GROUP_CONSTANT - Static variable in class org.openscience.cdk.CDKConstants
-
Used as property key for indicating the chemical group of a certain atom type.
- ChemicalFilters - Class in org.openscience.cdk.smsd.filters
-
Class that ranks MCS final solution according to the chemical rules.
- ChemicalFilters(List<Map<Integer, Integer>>, List<Map<IAtom, IAtom>>, Map<Integer, Integer>, Map<IAtom, IAtom>, IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.smsd.filters.ChemicalFilters
-
This class has all the three chemical filters supported by the SMSD.
- ChemModel - Class in org.openscience.cdk
-
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
- ChemModel() - Constructor for class org.openscience.cdk.ChemModel
-
Constructs an new ChemModel with a null setOfMolecules.
- ChemModel - Class in org.openscience.cdk.silent
-
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
- ChemModel() - Constructor for class org.openscience.cdk.silent.ChemModel
-
Constructs an new ChemModel with a null setOfMolecules.
- ChemModelManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemModel.
- ChemModelManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
- ChemModelRenderer - Class in org.openscience.cdk.renderer
-
- ChemModelRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer
-
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
- ChemModelRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer
-
- chemModels() - Method in class org.openscience.cdk.ChemSequence
-
Returns an Iterable to ChemModels in this container.
- chemModels() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- chemModels() - Method in interface org.openscience.cdk.interfaces.IChemSequence
-
Returns an Iterable to ChemModels in this container.
- chemModels() - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns an Iterable to ChemModels in this container.
- ChemObject - Class in org.openscience.cdk
-
The base class for all chemical objects in this cdk.
- ChemObject() - Constructor for class org.openscience.cdk.ChemObject
-
Constructs a new IChemObject.
- ChemObject(IChemObject) - Constructor for class org.openscience.cdk.ChemObject
-
Constructs a new IChemObject by copying the flags, and the
identifier.
- CHEMOBJECT - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- ChemObject - Class in org.openscience.cdk.silent
-
The base class for all chemical objects in this cdk.
- ChemObject() - Constructor for class org.openscience.cdk.silent.ChemObject
-
Constructs a new IChemObject.
- ChemObject(IChemObject) - Constructor for class org.openscience.cdk.silent.ChemObject
-
Constructs a new IChemObject by copying the flags, and the
identifier.
- ChemObjectChangeEvent - Class in org.openscience.cdk.event
-
Event fired by cdk classes to their registered listeners
in case something changes within them.
- ChemObjectChangeEvent(Object) - Constructor for class org.openscience.cdk.event.ChemObjectChangeEvent
-
Constructs a ChemObjectChangeEvent with a reference
to the object where it originated.
- ChemObjectDiff - Class in org.openscience.cdk.tools.diff
-
- ChemObjectDifference - Class in org.openscience.cdk.tools.diff.tree
-
- ChemObjectDifference(String) - Constructor for class org.openscience.cdk.tools.diff.tree.ChemObjectDifference
-
- ChemSequence - Class in org.openscience.cdk
-
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
- ChemSequence() - Constructor for class org.openscience.cdk.ChemSequence
-
Constructs an empty ChemSequence.
- ChemSequence - Class in org.openscience.cdk.silent
-
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
- ChemSequence() - Constructor for class org.openscience.cdk.silent.ChemSequence
-
Constructs an empty ChemSequence.
- ChemSequenceManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemSequence.
- ChemSequenceManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
- chemSequences() - Method in class org.openscience.cdk.ChemFile
-
Returns the Iterable to ChemSequences of this container.
- chemSequences() - Method in class org.openscience.cdk.debug.DebugChemFile
-
- chemSequences() - Method in interface org.openscience.cdk.interfaces.IChemFile
-
Returns the
Iterable
to ChemSequences of this container.
- chemSequences() - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the Iterable to ChemSequences of this container.
- ChemtoolFormat - Class in org.openscience.cdk.io.formats
-
- ChiChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Evaluates chi chain descriptors.
- ChiChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- ChiClusterDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Evaluates chi cluster descriptors.
- ChiClusterDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- childCount() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
-
- childCount() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
-
- children - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement
-
The child text elements.
- childrenAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode
-
Accept the visitor.
- ChiPathClusterDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Evaluates chi path cluster descriptors.
- ChiPathClusterDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- ChiPathDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Evaluates chi path descriptors.
- ChiPathDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- Chirality() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- ChiralityAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matches an atom with chirality property.
- ChiralityAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
Creates a new instance
- CHLORINE - Static variable in class org.openscience.cdk.config.Elements
-
- CHLORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CHROMIUM - Static variable in class org.openscience.cdk.config.Elements
-
- CHROMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CIFFormat - Class in org.openscience.cdk.io.formats
-
- CIFReader - Class in org.openscience.cdk.io
-
This is not a reader for the CIF and mmCIF crystallographic formats.
- CIFReader(Reader) - Constructor for class org.openscience.cdk.io.CIFReader
-
Create an CIF like file reader.
- CIFReader(InputStream) - Constructor for class org.openscience.cdk.io.CIFReader
-
- CIFReader() - Constructor for class org.openscience.cdk.io.CIFReader
-
- CIPLigandRule - Class in org.openscience.cdk.geometry.cip.rules
-
Compares to
ILigand
s based on CIP sequences sub rules.
- CIPLigandRule() - Constructor for class org.openscience.cdk.geometry.cip.rules.CIPLigandRule
-
- CIPTool - Class in org.openscience.cdk.geometry.cip
-
Tool to help determine the R,S and stereochemistry definitions of a subset of the
CIP rules .
- CIPTool() - Constructor for class org.openscience.cdk.geometry.cip.CIPTool
-
- CIPTool.CIP_CHIRALITY - Enum in org.openscience.cdk.geometry.cip
-
- CL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- cleanDataSet(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
-
- clear() - Method in class org.openscience.cdk.ConformerContainer
-
Get rid of all the conformers but keeps atom and bond information.
- clear() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Reinitialisation of the TGraph.
- clear() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- clear() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Reinitialisation of the TGraph.
- clear() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
clear the mapping
- clear() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
clear the mapping
- clearAtomConfigurations(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
This method will reset all atom configuration to UNSET.
- clearNodeScope(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
-
- clone() - Method in class org.openscience.cdk.AminoAcid
-
Clones this AminoAcid object.
- clone() - Method in class org.openscience.cdk.Atom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.AtomContainer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.AtomContainerSet
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.AtomParity
-
Clones this AtomParity object.
- clone() - Method in class org.openscience.cdk.AtomType
-
- clone() - Method in class org.openscience.cdk.BioPolymer
-
- clone() - Method in class org.openscience.cdk.Bond
-
Clones this bond object, including clones of the atoms between which the
bond is defined.
- clone() - Method in class org.openscience.cdk.ChemFile
-
Allows for getting an clone of this object.
- clone() - Method in class org.openscience.cdk.ChemModel
-
Clones this ChemModel
and its content.
- clone() - Method in class org.openscience.cdk.ChemObject
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.ChemSequence
-
- clone() - Method in class org.openscience.cdk.Crystal
-
Makes a clone of this crystal.
- clone() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- clone() - Method in class org.openscience.cdk.debug.DebugAtom
-
- clone() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- clone() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- clone() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- clone() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- clone() - Method in class org.openscience.cdk.debug.DebugBond
-
- clone() - Method in class org.openscience.cdk.debug.DebugChemFile
-
- clone() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- clone() - Method in class org.openscience.cdk.debug.DebugChemObject
-
- clone() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- clone() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- clone() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- clone() - Method in class org.openscience.cdk.debug.DebugElement
-
- clone() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- clone() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- clone() - Method in class org.openscience.cdk.debug.DebugLonePair
-
- clone() - Method in class org.openscience.cdk.debug.DebugMapping
-
- clone() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- clone() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- clone() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- clone() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- clone() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- clone() - Method in class org.openscience.cdk.debug.DebugReaction
-
- clone() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- clone() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- clone() - Method in class org.openscience.cdk.debug.DebugRing
-
- clone() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- clone() - Method in class org.openscience.cdk.debug.DebugStrand
-
- clone() - Method in class org.openscience.cdk.ElectronContainer
-
- clone() - Method in class org.openscience.cdk.Element
-
- clone() - Method in class org.openscience.cdk.formula.AdductFormula
-
Clones this AdductFormula object and its content.
- clone() - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Clones this IsotopeContainer object and its content.
- clone() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Clones this IsotopePattern object and its content.
- clone() - Method in class org.openscience.cdk.formula.MolecularFormula
-
Clones this MolecularFormula object and its content.
- clone() - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Clones this MolecularFormulaExpand object and its content.
- clone() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Clones this MolecularFormulaSet object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Clones this IAdductFormula object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IAminoAcid
-
- clone() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
- clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Clones this MolecularFormula object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
Clones this IMolecularFormulaSet object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IMolecule
-
- clone() - Method in interface org.openscience.cdk.interfaces.IMonomer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IPolymer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IReactionScheme
-
Clones this IReactionScheme object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IRing
-
- clone() - Method in interface org.openscience.cdk.interfaces.IStrand
-
- clone() - Method in class org.openscience.cdk.Isotope
-
- clone() - Method in class org.openscience.cdk.LonePair
-
Clones this LonePair object, including a clone of the atom for which the
lone pair is defined.
- clone() - Method in class org.openscience.cdk.Mapping
-
Clones this Mapping
and the mapped IChemObject
s.
- clone() - Method in class org.openscience.cdk.Molecule
-
- clone() - Method in class org.openscience.cdk.MoleculeSet
-
Clones this MoleculeSet and its content.
- clone() - Method in class org.openscience.cdk.Monomer
-
- clone() - Method in class org.openscience.cdk.Polymer
-
- clone() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- clone() - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
- clone() - Method in class org.openscience.cdk.PseudoAtom
-
- clone() - Method in class org.openscience.cdk.Reaction
-
Clones this Reaction
and its content.
- clone() - Method in class org.openscience.cdk.ReactionScheme
-
Clones this ReactionScheme object and its content.
- clone() - Method in class org.openscience.cdk.ReactionSet
-
Clones this ReactionSet
and the contained Reaction
s
too.
- clone() - Method in class org.openscience.cdk.Ring
-
- clone() - Method in class org.openscience.cdk.RingSet
-
Clones this RingSet
including the Rings.
- clone() - Method in class org.openscience.cdk.signature.Orbit
- clone() - Method in class org.openscience.cdk.silent.AdductFormula
-
Clones this AdductFormula object and its content.
- clone() - Method in class org.openscience.cdk.silent.AminoAcid
-
Clones this AminoAcid object.
- clone() - Method in class org.openscience.cdk.silent.Atom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.silent.AtomContainer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.silent.AtomParity
-
Clones this AtomParity object.
- clone() - Method in class org.openscience.cdk.silent.AtomType
-
- clone() - Method in class org.openscience.cdk.silent.BioPolymer
-
- clone() - Method in class org.openscience.cdk.silent.Bond
-
Clones this bond object, including clones of the atoms between which the
bond is defined.
- clone() - Method in class org.openscience.cdk.silent.ChemFile
-
Allows for getting an clone of this object.
- clone() - Method in class org.openscience.cdk.silent.ChemModel
-
Clones this ChemModel
and its content.
- clone() - Method in class org.openscience.cdk.silent.ChemObject
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.silent.ChemSequence
-
- clone() - Method in class org.openscience.cdk.silent.Crystal
-
Makes a clone of this crystal.
- clone() - Method in class org.openscience.cdk.silent.ElectronContainer
-
- clone() - Method in class org.openscience.cdk.silent.Element
-
- clone() - Method in class org.openscience.cdk.silent.Isotope
-
- clone() - Method in class org.openscience.cdk.silent.LonePair
-
Clones this LonePair object, including a clone of the atom for which the
lone pair is defined.
- clone() - Method in class org.openscience.cdk.silent.Mapping
-
Clones this Mapping
and the mapped IChemObject
s.
- clone() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Clones this MolecularFormula object and its content.
- clone() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Clones this MolecularFormulaSet object and its content.
- clone() - Method in class org.openscience.cdk.silent.Molecule
-
- clone() - Method in class org.openscience.cdk.silent.MoleculeSet
-
Clones this MoleculeSet and its content.
- clone() - Method in class org.openscience.cdk.silent.Monomer
-
- clone() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- clone() - Method in class org.openscience.cdk.silent.PDBPolymer
-
- clone() - Method in class org.openscience.cdk.silent.Polymer
-
- clone() - Method in class org.openscience.cdk.silent.PseudoAtom
-
- clone() - Method in class org.openscience.cdk.silent.Reaction
-
Clones this Reaction
and its content.
- clone() - Method in class org.openscience.cdk.silent.ReactionScheme
-
Clones this ReactionScheme object and its content.
- clone() - Method in class org.openscience.cdk.silent.ReactionSet
-
Clones this ReactionSet
and the contained Reaction
s
too.
- clone() - Method in class org.openscience.cdk.silent.Ring
-
- clone() - Method in class org.openscience.cdk.silent.RingSet
-
Clones this RingSet
including the Rings.
- clone() - Method in class org.openscience.cdk.silent.SingleElectron
-
Clones this SingleElectron object, including a clone of the atom for which the
SingleElectron is defined.
- clone() - Method in class org.openscience.cdk.silent.Strand
-
- clone() - Method in class org.openscience.cdk.SingleElectron
-
Clones this SingleElectron object, including a clone of the atom for which the
SingleElectron is defined.
- clone() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode
-
- clone() - Method in class org.openscience.cdk.Strand
-
- close() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.CIFReader
-
- close() - Method in class org.openscience.cdk.io.CMLReader
-
- close() - Method in class org.openscience.cdk.io.CMLWriter
-
Flushes the output and closes this object
- close() - Method in class org.openscience.cdk.io.CrystClustReader
-
- close() - Method in class org.openscience.cdk.io.CrystClustWriter
-
Flushes the output and closes this object
- close() - Method in class org.openscience.cdk.io.CTXReader
-
- close() - Method in class org.openscience.cdk.io.GamessReader
-
- close() - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- close() - Method in class org.openscience.cdk.io.Gaussian98Reader
-
- close() - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- close() - Method in class org.openscience.cdk.io.HINReader
-
- close() - Method in class org.openscience.cdk.io.HINWriter
-
Flushes the output and closes this object.
- close() - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Closes this IChemObjectIO's resources.
- close() - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- close() - Method in class org.openscience.cdk.io.INChIReader
-
- close() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Close the reader.
- close() - Method in class org.openscience.cdk.io.MDLReader
-
- close() - Method in class org.openscience.cdk.io.MDLRXNReader
-
- close() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- close() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- close() - Method in class org.openscience.cdk.io.MDLRXNWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- close() - Method in class org.openscience.cdk.io.MDLV2000Writer
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- close() - Method in class org.openscience.cdk.io.Mol2Reader
-
- close() - Method in class org.openscience.cdk.io.Mol2Writer
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.MoSSOutputReader
-
Closes this IChemObjectIO's resources.
- close() - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- close() - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- close() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- close() - Method in class org.openscience.cdk.io.PDBReader
-
- close() - Method in class org.openscience.cdk.io.PDBWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.PMPReader
-
- close() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- close() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- close() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
Closes this IChemObjectIO's resources.
- close() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Closes this IChemObjectIO's resources.
- close() - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- close() - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.RssWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.SDFWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.ShelXReader
-
- close() - Method in class org.openscience.cdk.io.ShelXWriter
-
Flushes the output and closes this object
- close() - Method in class org.openscience.cdk.io.SMILESReader
-
- close() - Method in class org.openscience.cdk.io.SMILESWriter
-
Flushes the output and closes this object
- close() - Method in class org.openscience.cdk.io.VASPReader
-
- close() - Method in class org.openscience.cdk.io.XYZReader
-
- close() - Method in class org.openscience.cdk.io.XYZWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.ZMatrixReader
-
- Close - Class in org.openscience.cdk.renderer.elements.path
-
Indicates the closing point of the path.
- Close() - Constructor for class org.openscience.cdk.renderer.elements.path.Close
-
Make a Close PathElement.
- close() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
-
Close the path.
- ClosedShellJob - Class in org.openscience.cdk.math.qm
-
Calculates the orbitals and orbital energies of electron systems
with closed shells
- ClosedShellJob(Orbitals) - Constructor for class org.openscience.cdk.math.qm.ClosedShellJob
-
- closeEnoughToBond(IAtom, IAtom, double) - Static method in class org.openscience.cdk.geometry.BondTools
-
Returns true if the two atoms are within the distance fudge
factor of each other.
- closeNodeScope(Node, int) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
-
- closeNodeScope(Node, boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
-
- clusterPSPPocket(Point3d, List<Point3d>, int[]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method performs the clustering, is called by findPockets().
- CM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CMLCoreModule - Class in org.openscience.cdk.io.cml
-
Core CML 1.x and 2.x elements are parsed by this class.
- CMLCoreModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLCoreModule
-
- CMLCoreModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLCoreModule
-
- CMLErrorHandler - Class in org.openscience.cdk.io.cml
-
CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document.
- CMLErrorHandler() - Constructor for class org.openscience.cdk.io.cml.CMLErrorHandler
-
Constructor a SAX2 ErrorHandler that uses the cdk.tools.LoggingTool
class to output errors and warnings to.
- CMLFormat - Class in org.openscience.cdk.io.formats
-
- CMLHandler - Class in org.openscience.cdk.io.cml
-
SAX2 implementation for CML XML fragment reading.
- CMLHandler(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLHandler
-
Constructor for the CMLHandler.
- CMLReactionModule - Class in org.openscience.cdk.io.cml
-
- CMLReactionModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule
-
- CMLReactionModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule
-
- CMLReader - Class in org.openscience.cdk.io
-
Reads a molecule in CML 1.x and 2.0 format.
- CMLReader(InputStream) - Constructor for class org.openscience.cdk.io.CMLReader
-
Reads CML from an java.io.InputStream, for example the FileInputStream.
- CMLReader() - Constructor for class org.openscience.cdk.io.CMLReader
-
- CMLReader(String) - Constructor for class org.openscience.cdk.io.CMLReader
-
Define this CMLReader to take the input from a java.io.Reader
class.
- CMLResolver - Class in org.openscience.cdk.io.cml
-
This class resolves DOCTYPE declaration for Chemical Markup Language (CML)
files and uses a local version for validation.
- CMLResolver() - Constructor for class org.openscience.cdk.io.cml.CMLResolver
-
- CMLRSSFormat - Class in org.openscience.cdk.io.formats
-
- CMLStack - Class in org.openscience.cdk.io.cml
-
Low weigth alternative to Sun's Stack class.
- CMLStack() - Constructor for class org.openscience.cdk.io.cml.CMLStack
-
- CMLWriter - Class in org.openscience.cdk.io
-
- CMLWriter(Writer) - Constructor for class org.openscience.cdk.io.CMLWriter
-
Constructs a new CMLWriter class.
- CMLWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CMLWriter
-
- CMLWriter() - Constructor for class org.openscience.cdk.io.CMLWriter
-
- CO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- COBALT - Static variable in class org.openscience.cdk.config.Elements
-
- COBALT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- color - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
-
- color - Variable in class org.openscience.cdk.renderer.elements.GeneralPath
-
The color of the path.
- color - Variable in class org.openscience.cdk.renderer.elements.LineElement
-
The color of the line.
- color - Variable in class org.openscience.cdk.renderer.elements.OvalElement
-
The color to draw the oval.
- color(Color) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
-
Sets the color if this path.
- color - Variable in class org.openscience.cdk.renderer.elements.PathElement
-
The color of the path.
- color - Variable in class org.openscience.cdk.renderer.elements.RectangleElement
-
The color of the rectangle.
- color - Variable in class org.openscience.cdk.renderer.elements.TextElement
-
The color of the text.
- columns - Variable in class org.openscience.cdk.math.IMatrix
-
the count of columns of the matrix
- columns - Variable in class org.openscience.cdk.math.Matrix
-
the number of columns of this matrix
- COMMA - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- COMMENT - Static variable in class org.openscience.cdk.CDKConstants
-
A String comment.
- commit() - Method in class org.openscience.cdk.smiles.InvPair
-
- compare(Object) - Method in class org.openscience.cdk.Atom
-
Compares a atom with this atom.
- compare(Object) - Method in class org.openscience.cdk.AtomType
-
Compares a atom type with this atom type.
- compare(Object) - Method in class org.openscience.cdk.Bond
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.ChemObject
-
Compares a IChemObject with this IChemObject.
- compare(Object) - Method in class org.openscience.cdk.debug.DebugBond
-
- compare(Object) - Method in class org.openscience.cdk.Element
-
Compares an Element with this Element.
- compare(IsotopePattern, IsotopePattern) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity
-
Compare the IMolecularFormula with a isotope
abundance pattern.
- compare(ILigand, ILigand) - Method in class org.openscience.cdk.geometry.cip.rules.CIPLigandRule
-
Compares two ligands according to the particular sequence sub rule.
- compare(ILigand, ILigand) - Method in interface org.openscience.cdk.geometry.cip.rules.ISequenceSubRule
-
Compares two ligands according to the particular sequence sub rule.
- compare(Object) - Method in interface org.openscience.cdk.interfaces.IBond
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.Isotope
-
Compares a atom type with this atom type.
- compare(Object) - Method in class org.openscience.cdk.silent.Atom
-
Compares a atom with this atom.
- compare(Object) - Method in class org.openscience.cdk.silent.AtomType
-
Compares a atom type with this atom type.
- compare(Object) - Method in class org.openscience.cdk.silent.Bond
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Compares a IChemObject with this IChemObject.
- compare(Object) - Method in class org.openscience.cdk.silent.Element
-
Compares an Element with this Element.
- compare(Object) - Method in class org.openscience.cdk.silent.Isotope
-
Compares a atom type with this atom type.
- compare(Object, Object) - Method in class org.openscience.cdk.tools.ElementComparator
-
Returns a negative if o1 comes before o2 in a molecular formula,
returns zero if they are identical, and positive if o1 comes
after o2 in the formula.
- compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparator
-
- compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter
-
Compare two AtomContainers based on their 2D position.
- compare(IMolecularFormula, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Compare two IMolecularFormula looking at type and number of IIsotope and
charge of the formula.
- compare(IRing, IRing) - Method in class org.openscience.cdk.tools.manipulator.RingSizeComparator
-
- compareTo(Algorithm) - Method in enum org.openscience.cdk.smsd.interfaces.Algorithm
-
Compares algorithm types.
- compile() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQueryCompiler
-
Parse and build a query graph from the query moleucle.
- compile() - Method in class org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler
-
Parse and build a query graph from the query moleucle.
- completeChemicalName() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
The general form all chemical names must follow.
- Complex - Class in org.openscience.cdk.math
-
This class handles complex values.
- Complex(double, double) - Constructor for class org.openscience.cdk.math.Complex
-
Creates a complex number
- Complex(Complex) - Constructor for class org.openscience.cdk.math.Complex
-
Creates a copy of a complex object
- computeFloydAPSP(int[][]) - Static method in class org.openscience.cdk.graph.PathTools
-
All-Pairs-Shortest-Path computation based on Floyd's
algorithm .
- computeFloydAPSP(double[][]) - Static method in class org.openscience.cdk.graph.PathTools
-
All-Pairs-Shortest-Path computation based on Floyd's
algorithm .
- configure(IAtom) - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Configures an atom.
- configure(IAtom) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Configures an atom.
- configure(IAtom, IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Configures an atom to have all the data of the
given isotope.
- configure(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.MoleculeSanityCheck
-
Fixes Aromaticity of the molecule
i.e.
- configure(IAtom, IAtomType) - Static method in class org.openscience.cdk.tools.manipulator.AtomTypeManipulator
-
Method that assign properties to an atom given a particular atomType.
- configureAtom(IAtom, String, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
- configureAtoms(IAtomContainer) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Configures atoms in an AtomContainer to
carry all the correct data according to their element type.
- configureLog4j() - Static method in class org.openscience.cdk.tools.LoggingTool
-
Forces the LoggingTool
to configurate the Log4J toolkit.
- configureMM2BasedAtom(IAtom, String, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Configures an atom to a mm2 based atom type
- configureMMFF94BasedAtom(IAtom, String, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Configures an atom to a mmff94 based atom type
- configureUnsetProperties(IAtom, IAtomType) - Static method in class org.openscience.cdk.tools.manipulator.AtomTypeManipulator
-
Method that assign properties to an atom given a particular atomType.
- ConformerContainer - Class in org.openscience.cdk
-
A memory-efficient data structure to store conformers for a single molecule.
- ConformerContainer() - Constructor for class org.openscience.cdk.ConformerContainer
-
- ConformerContainer(IAtomContainer) - Constructor for class org.openscience.cdk.ConformerContainer
-
Create a ConformerContainer object from a single molecule object.
- ConformerContainer(IAtomContainer[]) - Constructor for class org.openscience.cdk.ConformerContainer
-
Create a ConformerContainer from an array of molecules.
- ConjugatedPiSystemsDetector - Class in org.openscience.cdk.graph.invariant
-
- ConjugatedPiSystemsDetector() - Constructor for class org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector
-
- connect(INode, INode, VFBondMatcher) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Construct and return an edge for a given query and target node
- connectingFunctionalGroupsConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
The layout of a functional group(s) which can connect anywhere.
- connectingFunctionalGroupSuffix() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Functional groups suffixs for groups which can be connected anywhere
along the main chain.
- ConnectionCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matcher checks the total valency of the Atom.
- ConnectionCountAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ConnectionCountAtom
-
Creates a new instance
- ConnectionMatrix - Class in org.openscience.cdk.graph.matrix
-
Calculator for a connection matrix representation of this AtomContainer.
- ConnectionMatrix() - Constructor for class org.openscience.cdk.graph.matrix.ConnectionMatrix
-
- ConnectivityChecker - Class in org.openscience.cdk.graph
-
Tool class for checking whether the (sub)structure in an
AtomContainer is connected.
- ConnectivityChecker() - Constructor for class org.openscience.cdk.graph.ConnectivityChecker
-
- CONSTANT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- construct(String, IAtomType.Hybridization, IAtomType.Hybridization) - Static method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference
-
- construct(String, IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.diff.tree.BondOrderDifference
-
- construct(String, boolean[], boolean[]) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanArrayDifference
-
- construct(String, Boolean, Boolean) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanDifference
-
- construct(String, Double, Double) - Static method in class org.openscience.cdk.tools.diff.tree.DoubleDifference
-
- construct(String, Integer, Integer) - Static method in class org.openscience.cdk.tools.diff.tree.IntegerDifference
-
- construct(String, Point2d, Point2d) - Static method in class org.openscience.cdk.tools.diff.tree.Point2dDifference
-
- construct(String, Point3d, Point3d) - Static method in class org.openscience.cdk.tools.diff.tree.Point3dDifference
-
- construct(String, String, String) - Static method in class org.openscience.cdk.tools.diff.tree.StringDifference
-
- CONT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- contains(IAtom) - Method in class org.openscience.cdk.Association
-
Returns true if the given atom participates in this Association.
- contains(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.Bond
-
Returns true if the given atom participates in this bond.
- contains(Object) - Method in class org.openscience.cdk.ConformerContainer
-
Checks to see whether the specified conformer is currently stored.
- contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBond
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugRing
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
-
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
-
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
-
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand
-
- contains(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula
-
True, if the AdductFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula
-
True, if the AdductFormula contains the given IMolecularFormula object.
- contains(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
- contains(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
True, if the MolecularFormulaExpand contains the given IIsotope.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
- contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
True, if the AdductFormula contains the given IIsotope object.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns true if the given atom participates in this bond.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object.
- contains(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
True, if the IMolecularFormulaSet contains the given IMolecularFormula object.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
True, if this set contains the IAtomContainer.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- contains(IAtom) - Method in class org.openscience.cdk.LonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IChemObject) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
-
Determines if the
IChemObject
is part of the current selection.
- contains(IAtom) - Method in class org.openscience.cdk.RingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtomContainer) - Method in class org.openscience.cdk.RingSet
-
Checks for presence of a ring in this RingSet.
- contains(int) - Method in class org.openscience.cdk.signature.Orbit
-
Checks to see if the orbit contains this atom index.
- contains(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula
-
True, if the AdductFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula
-
True, if the AdductFormula contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.silent.Bond
-
Returns true if the given atom participates in this bond.
- contains(IAtom) - Method in class org.openscience.cdk.silent.LonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.silent.RingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtomContainer) - Method in class org.openscience.cdk.silent.RingSet
-
Checks for presence of a ring in this RingSet.
- contains(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- contains(IAtom) - Method in class org.openscience.cdk.SingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- contains(IMolecularFormulaSet, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
-
True, if the IMolecularFormulaSet contains the given IMolecularFormula but not
as object.
- containsAll(Collection<?>) - Method in class org.openscience.cdk.ConformerContainer
-
- containsByID(IAtomContainerSet, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
Tells if an AtomContainerSet contains at least one AtomContainer with the
same ID as atomContainer.
- containsElement(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
True, if the MolecularFormula contains the given element as IIsotope object.
- contraction() - Method in class org.openscience.cdk.math.IMatrix
-
Calculates the contraction from a matrix
- contraction() - Method in class org.openscience.cdk.math.Matrix
-
- convertBondOrder(IBond) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Get bond order value as int
value.
- convertBondStereo(IBond) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Get stereo value as integer
- convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
Returns IAtomContainer without Hydrogen.
- convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
Returns IAtomContainer without Hydrogen.
- convertImplicitToExplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Adds explicit hydrogens (without coordinates) to the IAtomContainer,
equaling the number of set implicit hydrogens.
- convertOneLetterCodeToThreeLetterCode(String) - Static method in class org.openscience.cdk.templates.AminoAcids
-
Returns the three letter code of an amino acid given a one letter code.
- Convertor - Class in org.openscience.cdk.libio.cml
-
- Convertor(boolean, String) - Constructor for class org.openscience.cdk.libio.cml.Convertor
-
Constructs a CML convertor.
- Convertor - Class in org.openscience.cdk.libio.jena
-
Helper class that converts a CDK
IChemObject
into RDF using a
Jena model and the CDK data model ontology.
- Convertor() - Constructor for class org.openscience.cdk.libio.jena.Convertor
-
- convertOrder(double) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
- convertStereo(int) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Get stereo value as Stereo enum
- convertThreeLetterCodeToOneLetterCode(String) - Static method in class org.openscience.cdk.templates.AminoAcids
-
Returns the one letter code of an amino acid given a three letter code.
- convertToAtomContainer(IRingSet) - Static method in class org.openscience.cdk.ringsearch.RingPartitioner
-
Converts a RingSet to an AtomContainer.
- COPPER - Static variable in class org.openscience.cdk.config.Elements
-
- COPPER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- COS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- couldMatchAtomType(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Determines if the atom can be of type AtomType.
- couldMatchAtomType(IAtom, double, IBond.Order, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Determines if the atom can be of type AtomType.
- couldMatchAtomType(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Determines if the atom can be of type AtomType.
- count() - Method in enum org.openscience.cdk.renderer.elements.LineElement.LineType
-
Returns the count for this line type.
- countEdges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns edge count.
- countEdges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns edge count.
- countExplicitHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Count explicit hydrogens.
- countHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- countMaps(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns solution map count.
- countMaps(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns solution map count.
- countMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns solution map count.
- countMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns solution map count.
- countMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns solution map count.
- countMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns solution map count.
- countMatches() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Returns the number of times the pattern was found in the target molecule.
- countNeighbors() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Returns Neighbors count.
- countNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- countNeighbors() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Returns Neighbors count.
- countNodes() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns node count.
- countNodes() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns node count.
- CovalentRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class return the covalent radius of a given atom.
- CovalentRadiusDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
Constructor for the CovalentRadiusDescriptor object.
- cp - Variable in class org.openscience.cdk.renderer.elements.path.QuadTo
-
control point of the curve.
- cp1 - Variable in class org.openscience.cdk.renderer.elements.path.CubicTo
-
first control point in the cubic.
- cp2 - Variable in class org.openscience.cdk.renderer.elements.path.CubicTo
-
second control point in the cubic.
- CPKAtomColors - Class in org.openscience.cdk.renderer.color
-
Colors atoms using CPK color scheme .
- CPKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CPKAtomColors
-
- CPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Calculates 29 Charged Partial Surface Area (CPSA) descriptors.
- CPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
- CR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- create(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingTool
-
- create(Class<?>) - Static method in class org.openscience.cdk.tools.SystemOutLoggingTool
-
- createAAs() - Static method in class org.openscience.cdk.templates.AminoAcids
-
Creates amino acid AminoAcid objects.
- createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Generates a cloned atomcontainer with all atoms being carbon, all bonds being single non-aromatic
- createAnyAtomAnyBondContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with wildcard atoms and wildcard bonds.
- createAnyAtomAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
-
- createAnyAtomContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with AnyAtoms / Aromatic Atoms and OrderQueryBonds / AromaticQueryBonds.
- createAnyAtomForPseudoAtomQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's and
OrderQueryBond's.
- createBasicQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's, AromaticQueryBond's and
OrderQueryBond's.
- createBondOrder(double) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Convenience method to convert a double into an IBond.Order.
- createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- createChiralSMILES(IAtomContainer, boolean[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Generate canonical and chiral SMILES from the molecule
.
- createCubicGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method creates a cubic grid with the grid generator class.
- createIDs(IChemObject) - Static method in class org.openscience.cdk.tools.IDCreator
-
Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2
scheme often used in CML.
- createLoggingTool(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory
-
Dynamically create a
ILoggingTool
for the given
sourceClass
.
- createNewMolecule(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Adds a new Molecule to the MoleculeSet inside a given ChemModel.
- createPath() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
-
Create and return the final path.
- createProtein(String) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool
-
Creates a BioPolymer from a sequence of amino acid as identified by a
the sequence of their one letter codes.
- createReactionScheme(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Create a IReactionScheme give a IReactionSet object.
- createReader(InputStream) - Method in class org.openscience.cdk.io.ReaderFactory
-
Detects the format of the Reader input, and if known, it will return
a CDK Reader to read the format, or null when the reader is not
implemented.
- createReader(IChemFormat) - Method in class org.openscience.cdk.io.ReaderFactory
-
Creates a new IChemObjectReader based on the given IChemFormat.
- createReader(Reader) - Method in class org.openscience.cdk.io.ReaderFactory
-
Detects the format of the Reader input, and if known, it will return
a CDK Reader to read the format.
- createSMILES(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Generate canonical SMILES from the molecule
.
- createSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Generate a SMILES for the given Reaction
.
- createSMILES(IAtomContainer, boolean, boolean[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Generate canonical SMILES from the molecule
.
- createSMILESWithoutCheckForMultipleMolecules(IAtomContainer, boolean, boolean[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Generate canonical SMILES from the molecule
.
- createSymbolAndBondOrderQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.
- createSymbolAndChargeQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolAncChargeQueryAtom's and
OrderQueryBond's.
- createSymbolChargeIDQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
- createWriter(IChemFormat) - Method in class org.openscience.cdk.io.WriterFactory
-
Creates a new IChemObjectWriter based on the given IChemFormat.
- CRK2DFormat - Class in org.openscience.cdk.io.formats
-
- CRK3DFormat - Class in org.openscience.cdk.io.formats
-
- cross(Vector) - Method in class org.openscience.cdk.math.Vector
-
Cross product, only well definited in R^3
- CrossoverMachine - Class in org.openscience.cdk.structgen.stochastic.operator
-
Modified molecular structures by applying crossover operator on a pair of parent structures
and generate a pair of offspring structures.
- CrossoverMachine() - Constructor for class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
-
Constructs a new CrossoverMachine operator.
- Crystal - Class in org.openscience.cdk
-
Class representing a molecular crystal.
- Crystal() - Constructor for class org.openscience.cdk.Crystal
-
Constructs a new crystal with zero length cell axis.
- Crystal(IAtomContainer) - Constructor for class org.openscience.cdk.Crystal
-
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
- Crystal - Class in org.openscience.cdk.silent
-
Class representing a molecular crystal.
- Crystal() - Constructor for class org.openscience.cdk.silent.Crystal
-
Constructs a new crystal with zero length cell axis.
- Crystal(IAtomContainer) - Constructor for class org.openscience.cdk.silent.Crystal
-
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
- CrystalGeometryTools - Class in org.openscience.cdk.geometry
-
A set of static methods for working with crystal coordinates.
- CrystalGeometryTools() - Constructor for class org.openscience.cdk.geometry.CrystalGeometryTools
-
- CrystClustFormat - Class in org.openscience.cdk.io.formats
-
- CrystClustReader - Class in org.openscience.cdk.io
-
- CrystClustReader() - Constructor for class org.openscience.cdk.io.CrystClustReader
-
- CrystClustReader(Reader) - Constructor for class org.openscience.cdk.io.CrystClustReader
-
- CrystClustReader(InputStream) - Constructor for class org.openscience.cdk.io.CrystClustReader
-
- CrystClustWriter - Class in org.openscience.cdk.io
-
Rather stupid file format used for storing crystal information.
- CrystClustWriter(Writer) - Constructor for class org.openscience.cdk.io.CrystClustWriter
-
Constructs a new CrystClustWriter class.
- CrystClustWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CrystClustWriter
-
- CrystClustWriter() - Constructor for class org.openscience.cdk.io.CrystClustWriter
-
- CS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CTXFormat - Class in org.openscience.cdk.io.formats
-
- CTXReader - Class in org.openscience.cdk.io
-
Reader that extracts information from the IDENT, NAME, ATOMS and BONDS
blocks in CTX files.
- CTXReader() - Constructor for class org.openscience.cdk.io.CTXReader
-
- CTXReader(Reader) - Constructor for class org.openscience.cdk.io.CTXReader
-
- CTXReader(InputStream) - Constructor for class org.openscience.cdk.io.CTXReader
-
- CU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CubicTo - Class in org.openscience.cdk.renderer.elements.path
-
A cubic curve in the path.
- CubicTo(Point2d, Point2d, Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo
-
Make a cubic curve path element.
- cubicTo(Point2d, Point2d, Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
-
Make a cubic curve in the path, with two control points.
- CURIUM - Static variable in class org.openscience.cdk.config.Elements
-
- CURIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- current() - Method in class org.openscience.cdk.io.cml.CMLStack
-
Returns the last added entry.
- currentToken - Variable in exception org.openscience.cdk.iupac.parser.ParseException
-
This is the last token that has been consumed successfully.
- currentToken - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException
-
This is the last token that has been consumed successfully.
- customize(IAtom, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
-
Customized the nodeToAdd for the given Atom.
- customize(IBond, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
-
Customized the nodeToAdd for the given IBond.
- customize(IAtomContainer, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
-
Customized the nodeToAdd for the given Molecule.
- customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
-
No customization for bonds
- customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
-
Customize Atom
- customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
-
Customize Molecule
- customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
-
- customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
-
- customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
-
- customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
-
- customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
-
- customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
-
- customizeJob() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader
-
- customizeJob() - Method in class org.openscience.cdk.io.MDLReader
-
- customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- customizeJob() - Method in class org.openscience.cdk.io.PDBReader
-
- customizeJob() - Method in class org.openscience.cdk.io.SDFWriter
-
- customizeJob() - Method in class org.openscience.cdk.io.SMILESWriter
-
- CustomSerializer - Class in org.openscience.cdk.io.cml
-
Custom Serializer
with the sole purpose and functionality to not
output the XML declaration.
- CustomSerializer(OutputStream) - Constructor for class org.openscience.cdk.io.cml.CustomSerializer
-
Instantiates a new
CustomSerializer
using the matching
Serializer.Serializer(OutputStream)
.
- CustomSerializer(OutputStream, String) - Constructor for class org.openscience.cdk.io.cml.CustomSerializer
-
Instantiates a new
CustomSerializer
using the matching
Serializer.Serializer(OutputStream, String)
.
- cycle() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deals with cyclic main chains.
- CycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis
-
A minimum basis of all cycles in a graph.
- CycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
-
Constructs a minimum cycle basis of a graph.
- cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
-
Returns the cycles that form the cycle basis.
- cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
-
- CYCLO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- G - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- GA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- GADOLINIUM - Static variable in class org.openscience.cdk.config.Elements
-
- GADOLINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- GALLIUM - Static variable in class org.openscience.cdk.config.Elements
-
- GALLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- GamessFormat - Class in org.openscience.cdk.io.formats
-
- GamessReader - Class in org.openscience.cdk.io
-
A reader for GAMESS log file.
- GamessReader(Reader) - Constructor for class org.openscience.cdk.io.GamessReader
-
Constructs a new "GamessReader" object given a "Reader" object as input.
- GamessReader(InputStream) - Constructor for class org.openscience.cdk.io.GamessReader
-
- GamessReader() - Constructor for class org.openscience.cdk.io.GamessReader
-
- GasteigerMarsiliPartialCharges - Class in org.openscience.cdk.charges
-
The calculation of the Gasteiger Marsili (PEOE) partial charges is based on
.
- GasteigerMarsiliPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Constructor for the GasteigerMarsiliPartialCharges object
- GasteigerPEPEPartialCharges - Class in org.openscience.cdk.charges
-
The calculation of the Gasteiger (PEPE) partial charges is based on
.
- GasteigerPEPEPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Constructor for the GasteigerPEPEPartialCharges object
- Gaussian03Format - Class in org.openscience.cdk.io.formats
-
- Gaussian03Reader - Class in org.openscience.cdk.io
-
A reader for Gaussian03 output.
- Gaussian03Reader(Reader) - Constructor for class org.openscience.cdk.io.Gaussian03Reader
-
- Gaussian03Reader(InputStream) - Constructor for class org.openscience.cdk.io.Gaussian03Reader
-
- Gaussian03Reader() - Constructor for class org.openscience.cdk.io.Gaussian03Reader
-
- Gaussian90Format - Class in org.openscience.cdk.io.formats
-
- Gaussian92Format - Class in org.openscience.cdk.io.formats
-
- Gaussian94Format - Class in org.openscience.cdk.io.formats
-
- Gaussian95Format - Class in org.openscience.cdk.io.formats
-
- Gaussian98Format - Class in org.openscience.cdk.io.formats
-
- Gaussian98Reader - Class in org.openscience.cdk.io
-
A reader for Gaussian98 output.
- Gaussian98Reader() - Constructor for class org.openscience.cdk.io.Gaussian98Reader
-
Constructor for the Gaussian98Reader object
- Gaussian98Reader(InputStream) - Constructor for class org.openscience.cdk.io.Gaussian98Reader
-
- Gaussian98Reader(Reader) - Constructor for class org.openscience.cdk.io.Gaussian98Reader
-
Create an Gaussian98 output reader.
- gaussianDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Generates a random double from a Gaussian distribution with the specified
deviation.
- gaussianFloat(float) - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Generates a random float from a Gaussian distribution with the specified
deviation.
- GaussianInputFormat - Class in org.openscience.cdk.io.formats
-
- GaussianInputWriter - Class in org.openscience.cdk.io.program
-
File writer thats generates input files for Gaussian calculation
jobs.
- GaussianInputWriter(Writer) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
-
Constructs a new writer that produces input files to run a
Gaussian QM job.
- GaussianInputWriter(OutputStream) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
-
- GaussianInputWriter() - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
-
- GaussiansBasis - Class in org.openscience.cdk.math.qm
-
This class contains the information to use gauss function as a base
for calculation of quantum mechanics.
- GaussiansBasis() - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis
-
- GaussiansBasis(int[], int[], int[], double[], Vector[], IAtom[]) - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis
-
Set up basis with gauss funktions
f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).
- GaussJordan() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Gauss-Jordan algorithm.
- GD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- GE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- GeneralPath - Class in org.openscience.cdk.renderer.elements
-
A path of rendering elements from the elements.path package.
- GeneralPath(List<PathElement>, Color) - Constructor for class org.openscience.cdk.renderer.elements.GeneralPath
-
Make a path from a list of path elements.
- generate(double) - Method in class org.openscience.cdk.formula.MassToFormulaTool
-
Method that actually does the work of extracting the molecular formula.
- generate(String) - Static method in class org.openscience.cdk.iupac.parser.NomParser
-
Parses the chemical name and returns the built molecule.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Generate the rendering element(s) for a particular atom.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate rendering element(s) for the current bond, including ring
elements if this bond is part of a ring.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
-
Generate the rendering element(s) for a particular atom.
- generate(T, RendererModel) - Method in interface org.openscience.cdk.renderer.generators.IGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.MappingGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate() - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator
-
Generates a random structure based on the atoms in the given IAtomContainer.
- generate(IAtomContainerSet) - Method in class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger
-
Randomly generates a single, connected, correctly bonded structure from
a number of fragments.
- generate3DCoordinates(IMolecule, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
Generate 3D coordinates with force field information.
- generateBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate stereo or bond elements for this bond.
- generateBondElement(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate rendering elements for a bond, without ring elements but
considering the type of the bond (single, double, triple).
- generateBondElement(IBond, IBond.Order, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate a LineElement or an ElementGroup of LineElements for this bond.
- generateCompactElement(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Generate a compact element for an atom, such as a circle or a square,
rather than text element.
- GenerateCompatibilityGraph - Class in org.openscience.cdk.smsd.algorithm.mcsplus
-
This class generates compatibility graph between query and target molecule.
- GenerateCompatibilityGraph() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Default constructor added
- GenerateCompatibilityGraph(IAtomContainer, IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Generates a compatibility graph between two molecules
- generateCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
The main method of this StructurDiagramGenerator.
- generateCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
The main method of this StructurDiagramGenerator.
- generateDiagram(T) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
The main method of the renderer, that uses each of the generators
to create a different set of
IRenderingElement
s grouped
together into a tree.
- generateDiagram(T) - Method in interface org.openscience.cdk.renderer.IRenderer
-
Internal method to generate the intermediate format.
- generateDiagram(IMoleculeSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
The main method of the renderer, that uses each of the generators
to create a different set of
IRenderingElement
s grouped
together into a tree.
- generateDiagram(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
The main method of the renderer, that uses each of the generators
to create a different set of
IRenderingElement
s grouped
together into a tree.
- generateElement(IAtom, int, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Generate an atom symbol element.
- generateExperimentalCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
This method uses generateCoordinates, but it removes the hydrogens first,
lays out the structuren and then adds them again.
- generateExperimentalCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Generates 2D coordinates on the non-hydrogen skeleton, after which
coordinates for the hydrogens are calculated.
- generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
-
Generate fragments for the input molecule.
- generateFragments(IAtomContainer) - Method in interface org.openscience.cdk.fragment.IFragmenter
-
Generate fragments for the input molecule.
- generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
Perform the fragmentation procedure.
- generateGrid() - Method in class org.openscience.cdk.tools.GridGenerator
-
Main method creates a grid between given boundaries (dimensions).
- generateInnerElement(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Make the inner ring bond, which is slightly shorter than the outer bond.
- generateMoments(IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment
-
Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.
- generateOrderEle() - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the Elements ordered according to (approximate) probability of occurrence.
- generateParseException() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Generate ParseException.
- generateParseException() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Generate ParseException.
- generateRingElements(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate ring elements, such as inner-ring bonds or ring stereo elements.
- generateRingElements(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.RingGenerator
-
Generate ring elements, such as inner-ring bonds or ring stereo elements.
- geometricCenterAllPlacedAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Calculates the geometric center of all placed atoms in the atomcontainer
- Geometry3DValidator - Class in org.openscience.cdk.validate
-
Validates the 3D geometry of the model.
- Geometry3DValidator() - Constructor for class org.openscience.cdk.validate.Geometry3DValidator
-
- GeometryTools - Class in org.openscience.cdk.geometry
-
A set of static utility classes for geometric calculations and operations.
- GeometryTools() - Constructor for class org.openscience.cdk.geometry.GeometryTools
-
- GERMAINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- GERMANIUM - Static variable in class org.openscience.cdk.config.Elements
-
- get(int) - Method in class org.openscience.cdk.ConformerContainer
-
Get the conformer at a specified position.
- get(int) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
-
The first double is at index = 0;
- get(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
-
The first int is at index = 0;
- get(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
-
- get2DCenter() - Method in class org.openscience.cdk.Bond
-
Returns the geometric 2D center of the bond.
- get2DCenter() - Method in class org.openscience.cdk.debug.DebugBond
-
- get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the center of the given atoms and returns it as a Point2d
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
- get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the center of the given atoms and returns it as a Point2d
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
- get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the geometric center of all the rings in this ringset.
- get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the geometric center of all the atoms in the atomContainer.
- get2DCenter() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the geometric 2D center of the bond.
- get2DCenter() - Method in class org.openscience.cdk.silent.Bond
-
Returns the geometric 2D center of the bond.
- get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the center of mass for the Atom
s in the
AtomContainer for the 2D coordinates.
- get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the java.awt.Dimension of a molecule
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
- get3DCenter() - Method in class org.openscience.cdk.Bond
-
Returns the geometric 3D center of the bond.
- get3DCenter() - Method in class org.openscience.cdk.debug.DebugBond
-
- get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the geometric center of all the atoms in this atomContainer.
- get3DCenter() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the geometric 3D center of the bond.
- get3DCenter() - Method in class org.openscience.cdk.silent.Bond
-
Returns the geometric 3D center of the bond.
- get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the center of mass for the Atom
s in the
AtomContainer for the 2D coordinates.
- get3DCoordinatesForLigands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
- get3DCoordinatesForSP2Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Main method for the calculation of the ligand coordinates for sp2 atoms.
- get3DCoordinatesForSP3Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Main method for the calculation of the ligand coordinates for sp3 atoms.
- get3DCoordinatesForSPLigands(IAtom, IAtomContainer, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
- getA() - Method in class org.openscience.cdk.Crystal
-
Gets the A unit cell axes in Cartesian coordinates
as a three element double array.
- getA() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getA() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the A unit cell axes in carthesian coordinates
as a three element double array.
- getA() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the A unit cell axes in Cartesian coordinates
as a three element double array.
- getAction(JFrame, String, boolean) - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Gets the action attribute of the JCPAction class
- getAction(JFrame, String) - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Gets the action attribute of the JCPAction class
- getAgents() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getAgents() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns a IMoleculeSet containing the agents in this reaction.
- getAgents() - Method in class org.openscience.cdk.Reaction
-
Returns a MoleculeSet containing the agents in this reaction.
- getAgents() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the agents in this reaction.
- getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
Returns all the AtomContainer's of a MoleculeSet.
- getAllAtomContainers(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Returns all the AtomContainer's of a ChemFile.
- getAllAtomContainers(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Returns all the AtomContainer's of a ChemModel.
- getAllAtomContainers(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
Returns all the AtomContainer's of a ChemSequence.
- getAllAtomContainers(IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
Returns all the AtomContainer's of a MoleculeSet.
- getAllAtomContainers(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
Returns all the AtomContainer's of a Reaction.
- getAllAtomContainers(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Returns all the AtomContainer's of a Reaction.
- getAllAtomContainers(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Returns all the AtomContainer's in a RingSet.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence of the mappings
between query and target molecule i.e.
- getAllAtomMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence of the mappings
between query and target molecule i.e.
- getAllAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Return the RMSD between the 2 aligned molecules.
- getAllAtomTypes() - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Gets the allAtomTypes attribute of the AtomTypeFactory object.
- getAllBondMaps() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- getAllChemModels(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Get a list of all ChemModels inside an IChemFile.
- getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
Does not recursively return the contents of the AtomContainer.
- getAllChemObjects(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Returns a List of all IChemObject inside a ChemFile.
- getAllChemObjects(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Retrieve a List of all ChemObject objects within an IChemModel.
- getAllChemObjects(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
Returns a List of all IChemObject inside a ChemSequence.
- getAllChemObjects(IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getAllChemObjects(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getAllChemObjects(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getAllConfigurations() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Produces all combinations of the root structure (scaffold) with the R-groups
substituted in valid ways, using each R-group's definitions and conditions.
- getAllConfigurations() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getAllIDs(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getAllIDs(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
- getAllIDs(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
- getAllIDs(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
- getAllIDs(IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getAllIDs(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getAllIDs(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Get all ID of this IReactionSet.
- getAllIDs(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getAllInOneContainer(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Puts all rings of a ringSet in a single atomContainer
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence index of the mappings
between query and target molecule i.e.
- getAllMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence index of the mappings
between query and target molecule i.e.
- getAllMolecules(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
get all molecule of a IReaction.
- getAllMolecules(IReactionScheme, IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Get all Molecules object from a set of Reactions given a IMoleculeSet to add.
- getAllMolecules(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
get all Molecules object from a set of Reactions.
- getAllMolecules(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
get all Molecules object from a set of Reactions.
- getAllPaths(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools
-
Get a list of all the paths between two atoms.
- getAllProducts(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
get all products of a IReaction
- getAllReactants(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
get all reactants of a IReaction
- getAllReactions(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Get a list of all IReaction inside an IChemFile.
- getAllReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Get all IReaction's object from a given IReactionScheme.
- getAllRgroupQueryAtoms() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
Returns all R# type atoms (pseudo atoms) found in the root structure.
- getAllRings() - Method in class org.openscience.cdk.graph.SpanningTree
-
- getAllSurfaceAreas() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get an array containing the accessible surface area for each atom.
- getAllSurfacePoints() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get an array of all the points on the molecular surface.
- getAltLoc() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getAltLoc() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Alternate location indicator of this atom.
- getAltLoc() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Alternate location indicator of this atom.
- getAltLoc() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Alternate location indicator of this atom.
- getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Gets the angle attribute of the GeometryTools class
- getAngleData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the angle parameter set.
- getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Return the variation of each angle value between the 2 aligned molecules.
- getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the angleKey attribute of the AtomPlacer3D object
- getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Gets the angleKey attribute of the AtomPlacer3D object
- getArrayValue() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the internal representation of the matrix, that is an array of double objects.
- getAtom(int) - Method in class org.openscience.cdk.AtomContainer
-
Get the atom at position number
in [0,..].
- getAtom() - Method in class org.openscience.cdk.AtomParity
-
Returns the atom for which this parity is defined.
- getAtom(int) - Method in class org.openscience.cdk.Bond
-
Returns an Atom from this bond.
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getAtom() - Method in class org.openscience.cdk.debug.DebugAtomParity
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugBond
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getAtom() - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugRing
-
- getAtom() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Get the atom at position number
in [0,..].
- getAtom() - Method in interface org.openscience.cdk.interfaces.IAtomParity
-
Returns the atom for which this parity is defined.
- getAtom(int) - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns an Atom from this bond.
- getAtom() - Method in interface org.openscience.cdk.interfaces.ILonePair
-
Returns the associated Atom.
- getAtom() - Method in interface org.openscience.cdk.interfaces.ISingleElectron
-
Returns the associated Atom.
- getAtom() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
-
- getAtom() - Method in class org.openscience.cdk.LonePair
-
Returns the associated Atom.
- getAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Get the atom at position number
in [0,..].
- getAtom() - Method in class org.openscience.cdk.silent.AtomParity
-
Returns the atom for which this parity is defined.
- getAtom(int) - Method in class org.openscience.cdk.silent.Bond
-
Returns an Atom from this bond.
- getAtom() - Method in class org.openscience.cdk.silent.LonePair
-
Returns the associated Atom.
- getAtom() - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns the associated Atom.
- getAtom() - Method in class org.openscience.cdk.SingleElectron
-
Returns the associated Atom.
- getAtom() - Method in class org.openscience.cdk.smiles.InvPair
-
- getAtom(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- getAtom(INode) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns an atom associated with this node.
- getAtom(INode) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns an atom associated with this node.
- getAtomArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Atom objects from an AtomContainer.
- getAtomArray(List<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Atom objects from a List of Atom objects.
- getAtomArray(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Constructs an array of Atom objects from Bond.
- getAtomAt(int) - Method in class org.openscience.cdk.Association
-
Returns an Atom from this Association.
- getAtomById(IAtomContainer, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returna an atom in an atomcontainer identified by id
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors
-
Returns the CDK 2D color for the given atom's element.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors
-
Returns the CDK 2D color for the given atom's element, or
defaults to the given color if no color is defined.
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors
-
Returns the CDK scheme color for the given atom's element.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors
-
Returns the CDK scheme color for the given atom's element, or
defaults to the given color if no color is defined.
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors
-
Returns the font color for atom given atom.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors
-
Returns the font color for atom given atom.
- getAtomColor(IAtom) - Method in interface org.openscience.cdk.renderer.color.IAtomColorer
-
Returns the color for a certain atom type.
- getAtomColor(IAtom, Color) - Method in interface org.openscience.cdk.renderer.color.IAtomColorer
-
Returns the color for a certain atom type, and uses the
given default color if it fails to identify the atom type.
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.PartialAtomicChargeColors
-
Returns the a color reflecting the given atom's partial charge.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.PartialAtomicChargeColors
-
Returns the a color reflecting the given atom's partial charge, or
defaults to the given color if no color is defined.
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.RasmolColors
-
Returns the Rasmol color for the given atom's element.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.RasmolColors
-
Returns the Rasmol color for the given atom's element, or
defaults to the given color if no color is defined.
- getAtomContainer(int) - Method in class org.openscience.cdk.AtomContainerSet
-
Returns the AtomContainer at position number
in the
container.
- getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getAtomContainer() - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
- getAtomContainer() - Method in class org.openscience.cdk.geometry.cip.Ligand
-
- getAtomContainer() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Returns generated molecule.
- getAtomContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns the AtomContainer at position number
in the
container.
- getAtomContainer() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
- getAtomContainer() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
- getAtomContainer() - Method in interface org.openscience.cdk.io.iterator.event.IEventChemObjectReader
-
- getAtomContainer() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom
-
Returns local copy of IAtomContainer.
- getAtomContainer() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom
-
- getAtomContainer() - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
-
Gets the atom container.
- getAtomContainer(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the AtomContainer at position number
in the
container.
- getAtomContainer(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer.
- getAtomContainer(IMolecularFormula, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer given a IAtomContainer.
- getAtomContainerCount() - Method in class org.openscience.cdk.AtomContainerSet
-
Returns the number of AtomContainers in this Container.
- getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getAtomContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns the number of AtomContainers in this Container.
- getAtomContainerCount() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Return the total number of atom containers (count the root plus all substituents).
- getAtomContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getAtomContainerCount() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the number of AtomContainers in this Container.
- getAtomCount() - Method in class org.openscience.cdk.Association
-
Returns the number of Atoms in this Association.
- getAtomCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.Bond
-
Returns the number of Atoms in this Bond.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugBond
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugRing
-
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getAtomCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the number of Atoms in this Bond.
- getAtomCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.silent.Bond
-
Returns the number of Atoms in this Bond.
- getAtomCount() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getAtomCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Get the total number of atoms inside an IChemFile.
- getAtomCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Get the total number of atoms inside an IChemModel.
- getAtomCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
Get the total number of atoms inside an IChemSequence.
- getAtomCount(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Checks a set of Nodes for the occurrence of each isotopes
instance in the molecular formula.
- getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getAtomCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getAtomCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getAtomCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Return the total number of atoms over all the rings in the colllection.
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugElement
-
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getAtomicNumber() - Method in class org.openscience.cdk.Element
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in interface org.openscience.cdk.interfaces.IElement
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.silent.Element
-
Returns the atomic number of this element.
- getAtomicNumber(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the atomic number of the element.
- getAtomicSoftnessCore(IAtomContainer, int) - Method in class org.openscience.cdk.charges.InductivePartialCharges
-
Gets the atomicSoftnessCore attribute of the InductivePartialCharges object
- getAtomIndices() - Method in class org.openscience.cdk.signature.Orbit
-
Gets all the atom indices as a list.
- getAtomLayers(int[][]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
-
- getAtomMatcher() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Returns Query Atom.
- getAtomMatcher() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Returns Query Atom.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getAtomNumber(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
-
Calculates a score based on the overlap of atoms.
- getAtomParity(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Helper methods that works through the stereo elements of the given atom container
and returns if the atom parity for the given atom, if one is defined.
- getAtomPlacer() - Method in class org.openscience.cdk.layout.RingPlacer
-
- getAtoms() - Method in class org.openscience.cdk.Association
-
Returns the array of atoms making up this Association.
- getAtoms() - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- getAtomsByLinePosition() - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- getAtomType(String) - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Get an AtomType with the given ID.
- getAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
-
Returns a
Map
with atom type mappings.
- getAtomTypeName() - Method in class org.openscience.cdk.AtomType
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getAtomTypeName() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the id attribute of the AtomType object.
- getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedAtomTypePattern
-
Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object
- getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedAtomTypePattern
-
Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object
- getAtomTypes(String) - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Get an array of all atomTypes known to the AtomTypeFactory for the given
element symbol and atomtype class.
- getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
-
Returns a List with read IAtomType's.
- getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
-
Returns a List with read IAtomType's.
- getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Gets the atomTypes attribute of the ForceFieldConfigurator object
- getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
-
- getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
-
- getAtomVector(int) - Method in class org.openscience.cdk.Vibration
-
Gets a atom vector at index given.
- getAtomVectorCount() - Method in class org.openscience.cdk.Vibration
-
Gets the number of atom vectors in the vibration.
- getAtomVectors() - Method in class org.openscience.cdk.Vibration
-
Returns an Enumeration of the atom vectors of this vibration.
- getAtomWeights(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
-
- getAuxInfo() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets auxillary information.
- getAvailableDictionaryClasses() - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Get the all the unique dictionary classes that the descriptors belong to.
- getB() - Method in class org.openscience.cdk.Crystal
-
Gets the B unit cell axes in Cartesian coordinates
as a three element double array.
- getB() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getB() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the B unit cell axes in carthesian coordinates
as a three element double array.
- getB() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the B unit cell axes in Cartesian coordinates
as a three element double array.
- getBasicRings() - Method in class org.openscience.cdk.graph.SpanningTree
-
- getBasis() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Returns the basis set of this orbitals
- getBeginColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token beginning column number.
- getBeginColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token beginning column number.
- getBeginLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token beginning line number.
- getBeginLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token beginning line number.
- getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Determines the best alignment for the label of an atom in 2D space.
- getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Determines the best alignment for the label of an atom in 2D space.
- getBibData() - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
-
- getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Transforms an AtomContainer into a
BitSet
(which's size = number of bond
in the atomContainer, all the bit are set to true).
- getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Transforms an AtomContainer into atom BitSet (which's size = number of bondA1
in the atomContainer, all the bit are set to true).
- getBitSetFromFile(StringTokenizer) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
- getBond(int) - Method in class org.openscience.cdk.AtomContainer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getBond(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getBond(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getBond(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getBond(int) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getBond(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getBond(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getBond(int) - Method in class org.openscience.cdk.debug.DebugRing
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getBond(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the bond that connectes the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the bond that connects the two given atoms.
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- getBondAngleInteractionData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the bond-angle interaction parameter set.
- getBondArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Bond objects from an AtomContainer.
- getBondArray(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Atom objects from a List of Atom objects.
- getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Writes the coordinates of the atoms participating the given bond into an
array.
- getBondCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getBondCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getBondCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getBondCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getBondCount() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getBondCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getBondCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getBondCount() - Method in class org.openscience.cdk.debug.DebugRing
-
- getBondCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of Bonds in this Container.
- getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getBondCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Get the total number of bonds inside an IChemFile.
- getBondCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Get the total number of bonds inside an IChemModel.
- getBondCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
Get the total number of bonds inside an IChemSequence.
- getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getBondCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getBondCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getBondCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Return the total number of bonds over all the rings in the colllection.
- getBondData(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the bond parameter set.
- getBondInSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
get timeout in mins for bond insensitive searches
- getBondInSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
-
get timeout in mins for bond insensitive searches
- getBondLength() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Returns the bond length used for laying out the molecule.
- getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond
-
Get the angle between the three pharmacophore groups that make up the constraint.
- getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreBond
-
Get the distance between the two pharmacophore groups that make up the constraint.
- getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
An average of all 2D bond length values is produced.
- getBondLengthAverage(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
- getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
An average of all 3D bond length values is produced, using point3ds in atoms.
- getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Return the RMSD of bonds length between the 2 aligned molecules.
- getBondLengthValue(String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the distanceValue attribute of the parameter set
- getBondMatcher() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
-
Returns bond matcher.
- getBondMatcher() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
-
Returns bond matcher.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugRing
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getBondNumber(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of a given bond in the electronContainers array.
- getBondOrder() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
-
Returns the bond order for this bond type energy.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
- getBondOrderSum() - Method in class org.openscience.cdk.AtomType
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugRing
-
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getBondOrderSum(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IRing
-
Returns the sum of all bond orders in the ring.
- getBondOrderSum() - Method in class org.openscience.cdk.Ring
-
Returns the sum of all bond orders in the ring.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
- getBondOrderSum() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum() - Method in class org.openscience.cdk.silent.Ring
-
Returns the sum of all bond orders in the ring.
- getBondOrderSum(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns the sum of the bond order equivalents for a given IAtom.
- getBondOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
-
Calculates a score based on the intersection of bonds.
- getBonds() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
-
Returns an array of ligand bonds around the double bond.
- getBonds() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
Returns an array of ligand bonds around the double bond.
- getBondsAcyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree
-
- getBondsCyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree
-
- getBondSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
get timeout in mins for bond sensitive searches
- getBondSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
-
get timeout in mins for bond sensitive searches
- getBondType() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond
-
Returns type of bond.
- getBuilder() - Method in class org.openscience.cdk.AtomParity
-
- getBuilder() - Method in class org.openscience.cdk.ChemObject
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugBond
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugElement
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugMapping
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugRing
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getBuilder() - Method in class org.openscience.cdk.formula.AdductFormula
-
- getBuilder() - Method in class org.openscience.cdk.formula.MolecularFormula
-
- getBuilder() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
- getBuilder() - Method in interface org.openscience.cdk.interfaces.ICDKObject
-
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNAdductFormula
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNAminoAcid
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNAtom
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNAtomContainer
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNAtomContainerSet
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNAtomType
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNBioPolymer
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNBond
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNChemFile
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNChemModel
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNChemObject
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNChemSequence
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNCrystal
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNElectronContainer
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNElement
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNFragmentAtom
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNIsotope
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNLonePair
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNMapping
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNMolecularFormula
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNMolecularFormulaSet
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNMolecule
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNMoleculeSet
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNMonomer
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNPDBAtom
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNPDBMonomer
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNPDBPolymer
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNPDBStructure
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNPolymer
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNPseudoAtom
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNReaction
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNReactionScheme
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNReactionSet
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNRing
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNRingSet
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNSingleElectron
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.nonotify.NNStrand
-
Deprecated.
- getBuilder() - Method in class org.openscience.cdk.silent.AdductFormula
-
- getBuilder() - Method in class org.openscience.cdk.silent.AtomParity
-
- getBuilder() - Method in class org.openscience.cdk.silent.ChemObject
-
- getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormula
-
- getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
- getBuilder() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
- getBuilder() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
- getC() - Method in class org.openscience.cdk.Crystal
-
Gets the C unit cell axes in Cartesian coordinates
as a three element double array.
- getC() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getC() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the C unit cell axes in carthesian coordinates
as a three element double array.
- getC() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the C unit cell axes in Cartesian coordinates
as a three element double array.
- getCachedDescriptorValue(IAtom) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor
-
Returns the cached DescriptorValue for the given IAtom.
- getCachedDescriptorValue(IBond) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor
-
Returns the cached DescriptorValue for the given IBond.
- getCanonicalMolecule(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
- getCanonicalMolecule(IAtomContainer) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller
-
- getCanonicalMolecule(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor
- getCanonicalPermutation(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
- getCanonicalPermutation(IAtomContainer) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller
-
- getCanonicalPermutation(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor
- getCanonicalReaction(IReaction) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalReactionLabeller
-
Convert a reaction into a canonical form by canonizing each of the
structures in the reaction in turn.
- getCanonicalReaction(IReaction) - Method in class org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser
-
Convert a reaction into a canonical form by canonizing each of the
structures in the reaction in turn.
- getCanonicalReaction(IReaction) - Method in class org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser
-
Convert a reaction into a canonical form by canonizing each of the
structures in the reaction in turn.
- getCASId(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the CAS ID for an element.
- getCC(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ConnectionCountAtom
-
Returns the connection count of an atom.
- getCDKErrorCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of CDK errors.
- getCDKErrors() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns an array of ValidationTest indicating CDK problems.
- getCEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- getCenterOfMass() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
-
Returns the center of mass for the first molecule or fragment used in the calculation.
- getCentralAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
The central
IAtom
to which this ligand is connected via one
IBond
.
- getCentralAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand
-
The central
IAtom
to which this ligand is connected via one
IBond
.
- getChainID() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getChainID() - Method in class org.openscience.cdk.debug.DebugPDBMonomer
-
- getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Chain identifier of this atom.
- getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Gets the Chain ID of this monomer.
- getChainID() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Chain identifier of this atom.
- getChainID() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- getChainID() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Chain identifier of this atom.
- getChainID() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getCharge() - Method in class org.openscience.cdk.Atom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- getCharge() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getCharge() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- getCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getCharge() - Method in class org.openscience.cdk.formula.AdductFormula
-
Returns the partial charge of this Adduct.
- getCharge() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Get the charge in this pattern.
- getCharge() - Method in class org.openscience.cdk.formula.MolecularFormula
-
Returns the partial charge of this IMolecularFormula.
- getCharge() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Returns the partial charge of this Adduct.
- getCharge() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns the partial charge of this atom.
- getCharge() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Returns the partial charge of this IMolecularFormula.
- getCharge() - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the partial charge of this Adduct.
- getCharge() - Method in class org.openscience.cdk.silent.Atom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Returns the partial charge of this IMolecularFormula.
- getCharge() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge
-
Returns the charge value.
- getChargeGroups() - Method in class org.openscience.cdk.libio.md.MDMolecule
-
- getChemFile() - Method in class org.openscience.cdk.io.inchi.INChIHandler
-
- getChemicalSeries(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the chemical series for an element.
- getChemModel(int) - Method in class org.openscience.cdk.ChemSequence
-
Returns the ChemModel at position number
in the
container.
- getChemModel(int) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence
-
Returns the ChemModel at position number
in the
container.
- getChemModel(int) - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns the ChemModel at position number
in the
container.
- getChemModelCount() - Method in class org.openscience.cdk.ChemSequence
-
Returns the number of ChemModels in this Container.
- getChemModelCount() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getChemModelCount() - Method in interface org.openscience.cdk.interfaces.IChemSequence
-
Returns the number of ChemModels in this Container.
- getChemModelCount() - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns the number of ChemModels in this Container.
- getChemObject(int) - Method in class org.openscience.cdk.debug.DebugMapping
-
- getChemObject(int) - Method in interface org.openscience.cdk.interfaces.IMapping
-
Retrieve the first or second of the related IChemObjects.
- getChemObject(int) - Method in class org.openscience.cdk.Mapping
-
Retrieves the first or second of the related IChemObjects.
- getChemObject(int) - Method in class org.openscience.cdk.silent.Mapping
-
Retrieves the first or second of the related IChemObjects.
- getChemObject() - Method in class org.openscience.cdk.validate.ValidationTest
-
- getChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- getChemSequence(int) - Method in class org.openscience.cdk.ChemFile
-
Returns the ChemSequence at position number
in the container.
- getChemSequence(int) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile
-
Returns the ChemSequence at position number
in the container.
- getChemSequence(int) - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the ChemSequence at position number
in the container.
- getChemSequenceCount() - Method in class org.openscience.cdk.ChemFile
-
Returns the number of ChemSequences in this Container.
- getChemSequenceCount() - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getChemSequenceCount() - Method in interface org.openscience.cdk.interfaces.IChemFile
-
Returns the number of ChemSequences in this Container.
- getChemSequenceCount() - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the number of ChemSequences in this Container.
- getChiCatHydrogen() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation
- getChildren() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
-
- getChildren() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
-
- getChiralAtom() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
-
Atom that is the chirality center.
- getChiralAtom() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
Atom that is the chirality center.
- getCID(XmlPullParser) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
-
- getCIPChirality(LigancyFourChirality) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
Returns the R or S chirality according to the CIP rules, based on the given
chirality information.
- getCIPChirality(IAtomContainer, ITetrahedralChirality) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
Returns the R or S chirality according to the CIP rules, based on the given
chirality information.
- getClassName() - Method in class org.openscience.cdk.dict.Entry
-
- getClipboardContent() - Method in class org.openscience.cdk.renderer.RendererModel
-
Returns the atoms and bonds on the Renderer2D clipboard.
- getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the atom of the given molecule that is closest to the given
coordinates.
- getClosestAtom(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the atom of the given molecule that is closest to the given atom
(excluding itself).
- getClosestAtom(double, double, IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the atom of the given molecule that is closest to the given
coordinates and is not the atom.
- getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the atom of the given molecule that is closest to the given
coordinates.
- getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the bond of the given molecule that is closest to the given
coordinates.
- getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the bond of the given molecule that is closest to the given
coordinates.
- getCoefficients() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Get the coefficient matrix
- getColorForBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Determine the color of a bond, returning either the default color,
the override color or whatever is in the color hash for that bond.
- getColumn(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the column-matrix at the given line index
- getColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Deprecated.
- getColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Deprecated.
- getColumns() - Method in class org.openscience.cdk.math.IMatrix
-
Returns the count of columns
- getColumns() - Method in class org.openscience.cdk.math.Matrix
-
Returns the number of columns.
- getConfidenceLimit(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
-
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.Bond
-
Returns the atom connected to the given atom.
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBond
-
- getConnectedAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the atom connected to the given atom.
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.silent.Bond
-
Returns the atom connected to the given atom.
- getConnectedAtomContainer() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
-
Make an IAtomContainer where all the bonds
only have atoms that are in the selection.
- getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.Bond
-
Returns all the atoms in the bond connected to the specified atom.
- getConnectedAtoms(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns all the atoms in the bond connected to the given atom.
- getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.silent.Bond
-
Returns all the atoms in the bond connected to the specified atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedAtomsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedAtomsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(int) - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of connected atoms (degree) to the given atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedBondsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of connected atoms (degree) to the given atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of connected atoms (degree) to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedBondsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedElectronContainersList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedLonePairsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedLonePairsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedRings(IRing) - Method in class org.openscience.cdk.debug.DebugRingSet
-
- getConnectedRings(IRing) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
- getConnectedRings(IRing) - Method in class org.openscience.cdk.RingSet
-
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
- getConnectedRings(IRing) - Method in class org.openscience.cdk.silent.RingSet
-
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedSingleElectronsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getConnectedSingleElectronsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getContainer(IMolecule, IAtom) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the container which the atom is found on resonance from a IMolecule.
- getContainer(IMolecule, IBond) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the container which the bond is found on resonance from a IMolecule.
- getContainers(IMolecule) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the container which is found resonance from a IMolecule.
- getCoordinatesFromGridPoint(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method calculates coordiantes from a given grid point.
- getCoordinatesFromGridPoint(int) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method calculates coordiantes from a given grid array position.
- getCount() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount
-
Returns implicit H count.
- getCount() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount
-
Returns total H count.
- getCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of CDK errors.
- getCountBasis() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Set the count of bases
- getCountElectrons() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Gets the count of electrons, which occupies the orbitals
- getCountOrbitals() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Returns the count of orbitals
- getCovalentRadius() - Method in class org.openscience.cdk.AtomType
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getCovalentRadius() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the covalent radius for this AtomType.
- getCovalentRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the covalent radius for an element.
- getCreatormap() - Method in class org.openscience.cdk.io.RssWriter
-
- getCrystal() - Method in class org.openscience.cdk.ChemModel
-
Gets the Crystal contained in this ChemModel.
- getCrystal() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getCrystal() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Gets the Crystal contained in this ChemModel.
- getCrystal() - Method in class org.openscience.cdk.silent.ChemModel
-
Gets the Crystal contained in this ChemModel.
- getCTerminus() - Method in class org.openscience.cdk.AminoAcid
-
Retrieves the C-terminus atom.
- getCTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getCTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid
-
Retrieves the C-terminus atom.
- getCTerminus() - Method in class org.openscience.cdk.silent.AminoAcid
-
Retrieves the C-terminus atom.
- getCurr() - Method in class org.openscience.cdk.smiles.InvPair
-
Get the current seed.
- getCurrentMaxBondOrder(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Returns the currently maximum formable bond order for this atom.
- getCurrentPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Get the permutation that is currently being used.
- getCurrentRecord() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- getCyclicFragmentsContainer() - Method in class org.openscience.cdk.graph.SpanningTree
-
Returns an IAtomContainer which contains all the atoms and bonds which
are involved in ring systems.
- getDatemap() - Method in class org.openscience.cdk.io.RssWriter
-
- getDBE(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the number of double bond equivalents in this molecule.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.KekuleStructure
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowEndCarbons
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowExplicitHydrogens
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondLength
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.DefaultBondColor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.TowardsRingCenterProportion
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
-
Returns the default arrow head width.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FitToScreen
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FontName
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ForegroundColor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowMoleculeTitle
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowTooltip
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UsedFontStyle
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowAtomTypeNames
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowImplicitHydrogens
-
Gets the default value for this parameter.
- getDefault() - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.MappingLineWidth
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.ShowAtomAtomMapping
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ShowReactionBoxes
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.RingProportion
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.ShowAromaticity
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.ColorHash
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.ExternalHighlightColor
-
Gets the default value for this parameter.
- getDefault(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
-
- getDefaultSetting() - Method in class org.openscience.cdk.io.setting.IOSetting
-
- getDefaultStretchBendData(int, int, int) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the bond-angle interaction parameter set.
- getDefinition() - Method in class org.openscience.cdk.dict.Entry
-
- getDegree() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- getDegree() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality
-
- getDescription() - Method in class org.openscience.cdk.dict.Entry
-
- getDescriptorClassNameByInterface(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns a list containing the classes that implement a specific interface.
- getDescriptorClassNameByPackage(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns a list containing the classes found in the specified descriptor package.
- getDescriptorClassNames() - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns a list containing the names of the classes implementing the descriptors.
- getDescriptorInstances() - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns a List containing the instantiated descriptor classes.
- getDescriptorMetadata() - Method in class org.openscience.cdk.dict.Entry
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Returns an array of names for each descriptor value calculated.
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns an array of names for each descriptor value calculated.
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns an array of names for each descriptor value calculated.
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
- getDescriptorNames() - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Returns an array of names for each descriptor value calculated.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns the specific type of the FMF descriptor value.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Returns a type of return value calculated by this descriptor.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorSpecifications() - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the DescriptorSpecification objects for all available descriptors.
- getDetails() - Method in class org.openscience.cdk.validate.ValidationTest
-
- getDictionary(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
-
- getDictionary() - Method in class org.openscience.cdk.dict.DictionaryHandler
-
- getDictionaryClass(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the class(es) of the decsriptor as defined in the descriptor dictionary.
- getDictionaryClass(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the class(es) of the descriptor as defined in the descriptor dictionary.
- getDictionaryDefinition(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Gets the definition of the descriptor.
- getDictionaryDefinition(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Gets the definition of the descriptor.
- getDictionaryEntries(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
-
Returns a String[] with the id's of all entries in the specified database.
- getDictionaryEntry(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
-
- getDictionaryNames() - Method in class org.openscience.cdk.dict.DictionaryDatabase
-
Returns a String[] with the names of the known dictionaries.
- getDictionaryTitle(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Gets the label (title) of the descriptor.
- getDictionaryTitle(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Gets the label (title) of the descriptor.
- getDictionaryType(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the type of the descriptor as defined in the descriptor dictionary.
- getDictionaryType(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the type of the descriptor as defined in the descriptor dictionary.
- getDim() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getDimValue(int) - Method in interface org.openscience.cdk.graph.rebond.Bspt.Tuple
-
- getDimValue(int) - Method in class org.openscience.cdk.graph.rebond.Point
-
- getDirection() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getDirection() - Method in interface org.openscience.cdk.interfaces.IReaction
-
- getDirection() - Method in class org.openscience.cdk.Reaction
-
Returns the direction of the reaction.
- getDirection() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the direction of the reaction.
- getDisplayMode() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the display mode
- getDrawCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Get the position on screen that the diagram will be drawn.
- getDuration(long, long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife
-
Returns a string reporting the time passed between startTime and endTime, both given in milliseconds, in hours, minutes, seconds and milliseconds
- getDuration(long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife
-
Returns a String reporting the time passed during a given number of milliseconds.
- getEAIDNumber(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
-
Calculates the extended adjacency matrix index.
- getEdge(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns an edge of the query mol at a given position.
- getEdge(INode, INode) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns an edge associated between two nodes.
- getEdge(int) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns an edge of the query mol at a given position.
- getEdge(INode, INode) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns an edge associated between two nodes.
- getEdges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Returns List of Edges.
- getEdges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Returns List of Edges.
- getElapsedTimeInHours() - Method in class org.openscience.cdk.smsd.tools.TimeManager
-
Returns Elapsed Time In Hours
- getElapsedTimeInMilliSeconds() - Method in class org.openscience.cdk.smsd.tools.TimeManager
-
Returns Elapsed Time In Mill Seconds
- getElapsedTimeInMinutes() - Method in class org.openscience.cdk.smsd.tools.TimeManager
-
Returns Elapsed Time In Minutes
- getElapsedTimeInSeconds() - Method in class org.openscience.cdk.smsd.tools.TimeManager
-
Return Elapsed Time In Seconds
- getElectronContainer(int) - Method in class org.openscience.cdk.AtomContainer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugRing
-
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getElectronContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainerArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Bond objects from an AtomContainer.
- getElectronContainerArray(List<IElectronContainer>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Atom objects from a List of Atom objects.
- getElectronContainerCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugRing
-
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getElectronContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronCount() - Method in class org.openscience.cdk.Association
-
Returns the number of electrons in a Association.
- getElectronCount() - Method in class org.openscience.cdk.debug.DebugBond
-
- getElectronCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- getElectronCount() - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getElectronCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getElectronCount() - Method in class org.openscience.cdk.ElectronContainer
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in interface org.openscience.cdk.interfaces.IElectronContainer
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in class org.openscience.cdk.LonePair
-
Returns the number of electrons in a LonePair.
- getElectronCount() - Method in class org.openscience.cdk.silent.ElectronContainer
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in class org.openscience.cdk.silent.LonePair
-
Returns the number of electrons in a LonePair.
- getElectronCount() - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns the number of electrons in this SingleElectron.
- getElectronCount() - Method in class org.openscience.cdk.SingleElectron
-
Returns the number of electrons in this SingleElectron.
- getElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getElement(String) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns an Element with a given element symbol.
- getElement(int) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns an element according to a given atomic number.
- getElementCount(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Checks a set of Nodes for the occurrence of the isotopes in the
molecular formula from a particular IElement.
- getElementCount() - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Return the number of elements currently considered in the periodic table.
- getElements(String) - Static method in class org.openscience.cdk.tools.HOSECodeAnalyser
-
- getElementSymbol(int) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns the symbol matching the element with the given atomic number.
- getEndChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- getEndChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get the ending Chain identifier of this structure.
- getEndChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get the ending Chain identifier of this structure.
- getEndChainID() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending Chain identifier of this structure.
- getEndColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token end column number.
- getEndColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token end column number.
- getEndInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- getEndInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get the ending Code for insertion of residues of this structure.
- getEndInsertionCode() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get the ending Code for insertion of residues of this structure.
- getEndInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending Code for insertion of residues of this structure.
- getEndLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token end line number.
- getEndLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token end line number.
- getEndSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- getEndSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get the ending sequence number of this structure.
- getEndSequenceNumber() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get the ending sequence number of this structure.
- getEndSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending sequence number of this structure.
- getEnergies() - Method in class org.openscience.cdk.math.qm.ClosedShellJob
-
- getEnergies() - Method in class org.openscience.cdk.math.qm.OneElectronJob
-
Returns the energies of the orbitals
- getEnergies(IAtom, IAtom, IBond.Order) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
-
Returns bond energy for a bond type, given atoms and bond type
- getEnergies(String, String, IBond.Order) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
-
Returns bond energy for a bond type, given atoms and bond type
- getEnergies(IBond) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
-
Returns bond energy for a bond type, given atoms and bond type
- getEnergy() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
-
Returns the energy for this bond type.
- getEnergyScore(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns summation energy score of the disorder if the MCS is removed
from the target and query graph.
- getEnergyScore(int) - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns summation energy score of the disorder if the MCS is removed
from the target and query graph.
- getEntries() - Method in class org.openscience.cdk.dict.Dictionary
-
- getEntry(String) - Method in class org.openscience.cdk.dict.Dictionary
-
- getEqual() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Returns equal node
- getEquivalenceClassesSizeVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
-
Returns a vector containing the size of the "interchangeability" equivalence classes.
- getEquivalentClass(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Get the final equivalent class
- getError() - Method in class org.openscience.cdk.validate.ValidationTest
-
- getErrorCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of failed tests.
- getErrors() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns an array of ValidationTest errors.
- getEuclideanDistance() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns Euclidean Distance between query and target molecule.
- getEuclideanDistance() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns Euclidean Distance between query and target molecule.
- getExactMass() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getExactMass() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getExactMass() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getExactMass() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getExactMass() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getExactMass() - Method in class org.openscience.cdk.FragmentAtom
-
The exact mass of an FragmentAtom is defined as the sum of exact masses
of the IAtom's in the fragment.
- getExactMass() - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.Isotope
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.silent.FragmentAtom
-
The exact mass of an FragmentAtom is defined as the sum of exact masses
of the IAtom's in the fragment.
- getExactMass() - Method in class org.openscience.cdk.silent.Isotope
-
Gets the ExactMass attribute of the Isotope object.
- getExampleReactions() - Method in class org.openscience.cdk.dict.EntryReact
-
- getException() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
Returns The number of explicit hydrogens for a given IAtom.
- getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
Returns The number of explicit hydrogens for a given IAtom.
- getExtendedAdjacenyMatrix(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
-
- getExtendGrid() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getExtension() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Gets the extension attribute of the RNode object
- getExtension() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Gets the extension attribute of the RNode object
- getExternalSelectedPart() - Method in class org.openscience.cdk.renderer.RendererModel
-
Get externally selected atoms.
- getExternalSubset(String, String) - Method in class org.openscience.cdk.io.cml.CMLResolver
-
Not implemented: always returns null.
- getFarthestAtom(Point3d, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the farthestAtom attribute of the AtomPlacer3D object
- getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
gives a list of possible force field types
- getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
Gives a list of possible force field types.
- getFinalMapping() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Returns the stored mappings
- getFinalMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Returns the stored mappings
- getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
-
Calculates the substructure fingerprint for the given AtomContainer.
- getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
-
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
- getFingerprint(IAtomContainer, IRingSet, List<IRingSet>) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
-
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
- getFingerprint(IAtomContainer, AllRingsFinder) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
Generates a fingerprint of the default size for the given AtomContainer.
- getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
Generates a fingerprint of the default size for the given AtomContainer.
- getFingerprint(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
- getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
Generates a fingerprint of the default size for the given AtomContainer.
- getFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
-
Returns the fingerprint for the given IAtomContainer.
- getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
-
Calculates the substructure fingerprint for the given AtomContainer.
- getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
-
Calculate 881 bit Pubchem fingerprint for a molecule.
- getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
Calculates the substructure fingerprint for the given AtomContainer.
- getFingerprintAsBytes() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
-
Returns the fingerprint generated for a molecule as a byte[].
- getFirstAtom() - Method in class org.openscience.cdk.AtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugRing
-
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getFirstAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.signature.Orbit
-
Gets the first atom index of the orbit.
- getFirstAtom() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns one of the best matches with atoms mapped.
- getFirstAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getFirstBondMap() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- getFirstGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the size of the first of the two
compared graphs.
- getFirstGraphSize() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the size of the first of the two
compared graphs.
- getFirstMap(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns first solution map.
- getFirstMap(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns first solution map.
- getFirstMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns first solution map.
- getFirstMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns first solution map.
- getFirstMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns first solution map.
- getFirstMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns first solution map.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns one of the best matches with atom indexes mapped.
- getFlag(int) - Method in class org.openscience.cdk.ChemObject
-
Returns the value of some flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtom
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugBond
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugElement
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugMapping
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugReaction
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugRing
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getFlag(int) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the value of some flag.
- getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
- getFlag(int) - Method in class org.openscience.cdk.silent.ChemObject
-
Returns the value of some flag.
- getFlags() - Method in class org.openscience.cdk.ChemObject
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugBond
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugElement
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugMapping
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugRing
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getFlags() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getFlags() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns the whole set of flags.
- getFont() - Method in class org.openscience.cdk.renderer.font.AWTFontManager
-
Get the current font.
- getFontName() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Get the font family name used in this font manager.
- getFontStyle() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
- getForbidden() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Gets the forbidden attribute of the RNode object
- getForbidden() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Gets the forbidden attribute of the RNode object
- getFormalCharge() - Method in class org.openscience.cdk.AtomType
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getFormalCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getFormalCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getFormalCharge() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the formal charge of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.AtomType
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getFormalNeighbourCount() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the formal neighbour count of this atom.
- getFormat() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- getFormat() - Method in class org.openscience.cdk.io.CIFReader
-
- getFormat() - Method in class org.openscience.cdk.io.CMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.CMLWriter
-
- getFormat() - Method in class org.openscience.cdk.io.CrystClustReader
-
- getFormat() - Method in class org.openscience.cdk.io.CrystClustWriter
-
- getFormat() - Method in class org.openscience.cdk.io.CTXReader
-
- getFormat() - Method in class org.openscience.cdk.io.GamessReader
-
- getFormat() - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- getFormat() - Method in class org.openscience.cdk.io.Gaussian98Reader
-
- getFormat() - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- getFormat() - Method in class org.openscience.cdk.io.HINReader
-
- getFormat() - Method in class org.openscience.cdk.io.HINWriter
-
- getFormat() - Method in interface org.openscience.cdk.io.IChemObjectIO
-
- getFormat() - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- getFormat() - Method in class org.openscience.cdk.io.INChIReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Get the format for this reader.
- getFormat() - Method in class org.openscience.cdk.io.MDLReader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLRXNReader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- getFormat() - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- getFormat() - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- getFormat() - Method in class org.openscience.cdk.io.Mol2Reader
-
- getFormat() - Method in class org.openscience.cdk.io.Mol2Writer
-
- getFormat() - Method in class org.openscience.cdk.io.MoSSOutputReader
-
- getFormat() - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- getFormat() - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.PDBReader
-
- getFormat() - Method in class org.openscience.cdk.io.PDBWriter
-
- getFormat() - Method in class org.openscience.cdk.io.PMPReader
-
- getFormat() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- getFormat() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
- getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
- getFormat() - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- getFormat() - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Returns output format.
- getFormat() - Method in class org.openscience.cdk.io.RssWriter
-
- getFormat() - Method in class org.openscience.cdk.io.SDFWriter
-
- getFormat() - Method in class org.openscience.cdk.io.ShelXReader
-
- getFormat() - Method in class org.openscience.cdk.io.ShelXWriter
-
- getFormat() - Method in class org.openscience.cdk.io.SMILESReader
-
- getFormat() - Method in class org.openscience.cdk.io.SMILESWriter
-
- getFormat() - Method in class org.openscience.cdk.io.VASPReader
-
- getFormat() - Method in class org.openscience.cdk.io.XYZReader
-
- getFormat() - Method in class org.openscience.cdk.io.XYZWriter
-
- getFormat() - Method in class org.openscience.cdk.io.ZMatrixReader
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getFormatName() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getFormats() - Method in class org.openscience.cdk.io.FormatFactory
-
Returns the list of recognizable formats.
- getFormats() - Method in class org.openscience.cdk.io.ReaderFactory
-
- getFormula() - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Get the IMolecularFormula object of this container.
- getFractionalPoint3d() - Method in class org.openscience.cdk.Atom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getFractionalPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFractionalPoint3d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFragment() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getFragment() - Method in class org.openscience.cdk.FragmentAtom
-
- getFragment() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
-
Returns the fully expended form of the IFragmentAtom.
- getFragment() - Method in class org.openscience.cdk.silent.FragmentAtom
-
- getFragments() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
-
Get the fragments generated as SMILES strings.
- getFragments() - Method in interface org.openscience.cdk.fragment.IFragmenter
-
Get the fragments generated as SMILES strings.
- getFragments() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
This returns the frameworks and ring systems from a Murcko fragmentation.
- getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
-
- getFragmentsAsContainers() - Method in interface org.openscience.cdk.fragment.IFragmenter
-
- getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
- getFragmentSize(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns number of fragment generated in the solution space,
if the MCS is removed from the target and query graph.
- getFragmentSize(int) - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns number of fragment generated in the solution space,
if the MCS is removed from the target and query graph.
- getFrameworks() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
Get frameworks as SMILES strings.
- getFrameworksAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
- getFunction(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get a function from this set
- getFunctionalGroupSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets
-
- getFunctionColor(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get a color from a function in this set
- getFunctionsSize() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the count of functions in this set
- getGenerators() - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
- getGenerators() - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
- getGenerators() - Method in interface org.openscience.cdk.renderer.IRenderer
-
- getGenerators() - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
- getGenerators() - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
- getGenerators() - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
- getGraph() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the graph object of this RGraph.
- getGraph() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the graph object of this CDKRGraph.
- getGraphics() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
- getGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getGrid() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getGridArray() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getGridPointFrom3dCoordinates(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method calculates the nearest grid point from given coordinates.
- getGroup() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getGroup(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the group of the element.
- getGroupNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber
-
Get the periodic table group number for this element.
- getHandedness(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Gets the tetrahedral handedness of four atoms - three of which form the
'base' of the tetrahedron, and the other the apex.
- getHashMapBySingleCharCode() - Static method in class org.openscience.cdk.templates.AminoAcids
-
Returns a HashMap where the key is one of G, A, V, L, I, S, T, C, M, D,
N, E, Q, R, K, H, F, Y, W and P.
- getHashMapByThreeLetterCode() - Static method in class org.openscience.cdk.templates.AminoAcids
-
Returns a HashMap where the key is one of GLY, ALA, VAL, LEU, ILE, SER,
THR, CYS, MET, ASP, ASN, GLU, GLN, ARG, LYS, HIS, PHE, TYR, TRP AND PRO.
- getHC(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom
-
- getHeaviestRing(IRingSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
We define the heaviest ring as the one with the highest number of double bonds.
- getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Return the RMSD of the heavy atoms between the 2 aligned molecules.
- getHeavyAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns a set of nodes excluding all the hydrogens.
- getHeavyElements(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns a set of nodes excluding all the hydrogens
- getHeight() - Method in class org.openscience.cdk.signature.Orbit
-
Gets the height of the signature label.
- getHetAtom() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getHetAtom() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Determine whether this is a heteroatom or not.
- getHetAtom() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
- getHetAtom() - Method in class org.openscience.cdk.silent.PDBAtom
-
- getHighlightedAtom() - Method in class org.openscience.cdk.renderer.RendererModel
-
Returns the atom currently highlighted.
- getHighlightedBond() - Method in class org.openscience.cdk.renderer.RendererModel
-
Returns the Bond currently highlighted.
- getHillString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
- getHOSECode(IAtomContainer, IAtom, int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
-
- getHOSECode(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
-
- getHTML(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula based on Hill
System with numbers wrapped in <sub></sub> tags.
- getHTML(IMolecularFormula, boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula based on Hill
System with numbers wrapped in <sub></sub> tags and the
isotope of each Element in <sup></sup> tags and the total
charge of IMolecularFormula in <sup></sup> tags.
- getHybridization() - Method in class org.openscience.cdk.AtomType
-
Returns the hybridization of this atom.
- getHybridization() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getHybridization() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getHybridization() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getHybridization() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getHybridization() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Returns the hybridization of this atom.
- getHybridization() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the hybridization of this atom.
- getHybridizationNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber
-
- getHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
The summed implicit + explicit hydrogens of the given IAtom.
- getHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
The summed implicit + explicit hydrogens of the given IAtom.
- getICode() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getICode() - Method in class org.openscience.cdk.debug.DebugPDBMonomer
-
- getICode() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get Code for insertion of residues of this atom.
- getICode() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Gets the ICode of this monomer.
- getICode() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get Code for insertion of residues of this atom.
- getICode() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- getICode() - Method in class org.openscience.cdk.silent.PDBAtom
-
get Code for insertion of residues of this atom.
- getICode() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getID() - Method in class org.openscience.cdk.ChemObject
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getID() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getID() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getID() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getID() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getID() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getID() - Method in class org.openscience.cdk.debug.DebugBond
-
- getID() - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getID() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getID() - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getID() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getID() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getID() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- getID() - Method in class org.openscience.cdk.debug.DebugElement
-
- getID() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getID() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getID() - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getID() - Method in class org.openscience.cdk.debug.DebugMapping
-
- getID() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getID() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getID() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getID() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getID() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getID() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getID() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- getID() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getID() - Method in class org.openscience.cdk.debug.DebugRing
-
- getID() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getID() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getID() - Method in class org.openscience.cdk.dict.Entry
-
- getID() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns the identifier (ID) of this object.
- getId() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode
-
- getId1() - Method in class org.openscience.cdk.isomorphism.mcss.RMap
-
Gets the id1 attribute of the RMap object
- getId1() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Gets the id1 attribute of the CDKRMap object
- getId2() - Method in class org.openscience.cdk.isomorphism.mcss.RMap
-
Gets the id2 attribute of the RMap object
- getId2() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Gets the id2 attribute of the CDKRMap object
- GetImage() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token literal value.
- GetImage() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token literal value.
- getImaginaryPart() - Method in class org.openscience.cdk.math.Complex
-
Gets the imaginary part of this value
- getIminus() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the I- operator
- getImplementationIdentifier() - Method in interface org.openscience.cdk.IImplementationSpecification
-
Identifier for this implementation which must include
version information.
- getImplementationIdentifier() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
-
- getImplementationIdentifier() - Method in class org.openscience.cdk.reaction.ReactionSpecification
-
- getImplementationTitle() - Method in interface org.openscience.cdk.IImplementationSpecification
-
Human-readable name for the implementation for the algorithm
specified by the reference.
- getImplementationTitle() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
-
- getImplementationTitle() - Method in class org.openscience.cdk.reaction.ReactionSpecification
-
- getImplementationVendor() - Method in interface org.openscience.cdk.IImplementationSpecification
-
Human-readable name for the vendor that holds copyright for this
implementation.
- getImplementationVendor() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
-
- getImplementationVendor() - Method in class org.openscience.cdk.reaction.ReactionSpecification
-
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.Atom
-
Returns the hydrogen count of this atom.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getImplicitHydrogenCount() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns the implicit hydrogen count of this atom.
- getImplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
Returns The number of Implicit Hydrogen Count for a given IAtom.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.silent.Atom
-
Returns the hydrogen count of this atom.
- getImplicitHydrogenCount(IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
Returns The number of Implicit Hydrogen Count for a given IAtom.
- getInchi() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets generated InChI string.
- getInChIGenerator(IAtomContainer) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
- getInChIGenerator(IAtomContainer, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets InChI generator for CDK IAtomContainer.
- getInChIGenerator(IAtomContainer, List<INCHI_OPTION>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets InChI generator for CDK IAtomContainer.
- getInchiKey() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets generated InChIKey string.
- getInchimap() - Method in class org.openscience.cdk.io.RssWriter
-
- getInChIToStructure(String, IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets structure generator for an InChI string.
- getInChIToStructure(String, IChemObjectBuilder, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets structure generator for an InChI string.
- getInChIToStructure(String, IChemObjectBuilder, List<String>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets structure generator for an InChI string.
- getIndexFile(String) - Static method in class org.openscience.cdk.io.random.RandomAccessReader
-
Opens the file index _cdk.index in a temporary folder, as specified by "java.io.tmpdir" property.
- getInitialLongestChain(IMolecule) - Method in class org.openscience.cdk.layout.AtomPlacer
-
Search an aliphatic molecule for the longest chain.
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
-
- getInstance(IChemObjectBuilder, int) - Static method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
-
- getInstance(String) - Static method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
-
Instantiates an atom type to atom type mapping, based on the given mapping file.
- getInstance(String, InputStream) - Static method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
-
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher
-
- getInstance(InputStream, String, IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
-
Method to create a default AtomTypeFactory, using the given InputStream.
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
-
Method to create a default AtomTypeFactory, using the structgen atom type list.
- getInstance(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
-
Method to create a specialized AtomTypeFactory.
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.IsotopeFactory
-
Returns an IsotopeFactory instance.
- getInstance() - Static method in class org.openscience.cdk.debug.DebugChemObjectBuilder
-
- getInstance() - Static method in class org.openscience.cdk.DefaultChemObjectBuilder
-
- getInstance() - Static method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gives the one InChIGeneratorFactory
instance,
if needed also creates it.
- getInstance() - Static method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Aces2Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ADFFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.BGFFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.BSFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CACheFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CIFFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CTXFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.DMol3Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GamessFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.HINFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.INChIFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.JMEFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MMODFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Mol2Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PDBFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PMPFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.POVRayFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.QChemFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SDFFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SVGFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.VASPFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.XEDFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.XYZFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getInstance(TemplateHandler3D, String) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
- getInstance() - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
- getInstance() - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
- getInstance() - Static method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder
-
Deprecated.
- getInstance() - Static method in class org.openscience.cdk.silent.SilentChemObjectBuilder
-
- getInstance() - Static method in class org.openscience.cdk.smsd.global.TimeOut
-
Get Instance of the timeout.
- getInstance() - Static method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Stores mapping solutions
- getInstance() - Static method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Create ids from atom labels
- getInstance() - Static method in class org.openscience.cdk.smsd.tools.BondEnergies
-
Returns Singleton pattern instance for the Bond Energy class
- getInstance() - Static method in class org.openscience.cdk.tools.AtomicProperties
-
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKHydrogenAdder
-
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKValencyChecker
-
- getInt2DColumnSum(int[][]) - Static method in class org.openscience.cdk.graph.PathTools
-
Sums up the columns in a 2D int matrix
- getIntensity() - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Get the intensity value of this container.
- getIntersection(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Compares this AtomContainer with another given AtomContainer and returns
the Intersection between them.
- getIntersectionSize(Path) - Method in class org.openscience.cdk.ringsearch.Path
-
- getIOSettings() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- getIOSettings() - Method in class org.openscience.cdk.io.CMLWriter
-
- getIOSettings() - Method in class org.openscience.cdk.io.DefaultChemObjectReader
-
- getIOSettings() - Method in class org.openscience.cdk.io.DefaultChemObjectWriter
-
- getIOSettings() - Method in class org.openscience.cdk.io.Gaussian98Reader
-
Gets the iOSettings attribute of the Gaussian98Reader object
- getIOSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Returns an array of
IOSetting
s defined by this IChemObjectIO class.
- getIOSettings() - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
-
- getIOSettings() - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
-
- getIOSettings() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader
-
- getIOSettings() - Method in class org.openscience.cdk.io.MDLReader
-
- getIOSettings() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- getIOSettings() - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- getIOSettings() - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- getIOSettings() - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- getIOSettings() - Method in class org.openscience.cdk.io.PDBReader
-
- getIOSettings() - Method in class org.openscience.cdk.io.PDBWriter
-
- getIOSettings() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- getIOSettings() - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
-
- getIOSettings() - Method in class org.openscience.cdk.io.SDFWriter
-
- getIOSettings() - Method in class org.openscience.cdk.io.SMILESWriter
-
- getIplus() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the I+ operator
- getIsobutane() - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
-
- getIsohexane() - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
-
- getIsomorphAtomsMap(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns the first isomorph 'atom mapping' found for g2 in g1.
- getIsomorphAtomsMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
- getIsomorphMap(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns the first isomorph mapping found or null.
- getIsomorphMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns the first isomorph mapping found or null.
- getIsomorphMaps(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns all the isomorph 'mappings' found between two
atom containers.
- getIsomorphMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns all the isomorph 'mappings' found between two
atom containers.
- getIsopentane() - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
-
- getIsotope(String, int) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Get isotope based on element symbol and mass number.
- getIsotope(int) - Method in class org.openscience.cdk.formula.IsotopePattern
-
Returns the a isotopes given a specific position.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- getIsotopeCount() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- getIsotopeCount() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.formula.AdductFormula
-
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.formula.MolecularFormula
-
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
- getIsotopeCount() - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Checks a set of Nodes for the number of different isotopes in the
MolecularFormulaExpand.
- getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
- getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
- getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
- getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.silent.AdductFormula
-
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
- getIsotopeCountMax(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Checks a set of Nodes for the maximal occurrence of the isotope in the
MolecularFormulaExpand from a particular isotope.
- getIsotopeCountMin(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Checks a set of Nodes for the minimal occurrence of the isotope in the
MolecularFormulaExpand from a particular isotope.
- getIsotopes(String) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Gets an array of all isotopes known to the IsotopeFactory for the given
element symbol.
- getIsotopes() - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
-
Returns the isotopes read from the XML file.
- getIsotopes() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Returns the all isotopes that form this isotope pattern.
- getIsotopes(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator
-
Get all combinatorial chemical isotopes given a structure.
- getIsotopes(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get a list of IIsotope from a given IElement which is contained
molecular.
- getIterator() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Returns a mapping Iterator
- getIterator() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Returns a mapping Iterator
- getIx() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the Ix operator
- getIy() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the Iy operator
- getIz() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the Iz operator
- getLabel() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getLabel() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getLabel() - Method in class org.openscience.cdk.dict.Entry
-
- getLabel() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
-
Returns the label of this PseudoAtom.
- getLabel() - Method in class org.openscience.cdk.PseudoAtom
-
Returns the label of this PseudoAtom.
- getLabel() - Method in class org.openscience.cdk.signature.Orbit
-
Gets the label of the orbit.
- getLabel() - Method in class org.openscience.cdk.silent.PseudoAtom
-
Returns the label of this PseudoAtom.
- getLabel(Integer) - Method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Returns Label of a given ID
- getLabel() - Method in class org.openscience.cdk.Vibration
-
Gets the label identifying this vibration.
- getLabelID(String) - Method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Returns label ID
- getLargestRingSet(List<IRingSet>) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
Returns the largest (number of atoms) ring set in a molecule
- getLargestRingSet(List<IRingSet>) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Returns the largest (number of atoms) ring set in a molecule
- getLast() - Method in class org.openscience.cdk.smiles.InvPair
-
- getLastAtom() - Method in class org.openscience.cdk.AtomContainer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugRing
-
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getLastAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the atom at the last position in the container.
- getLatticeConstant() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getLatticeConstant() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
- getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- getLength() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Getter for property length.
- getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the geometric length of this bond in 2D space.
- getLevel() - Method in class org.openscience.cdk.io.setting.IOSetting
-
- getLigandAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
- getLigandAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand
-
- getLigandLigands(ILigand) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
Returns a CIP-expanded array of side chains of a ligand.
- getLigands() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
-
Returns an array of ligand atoms around the chiral atom.
- getLigands() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
Returns an array of ligand atoms around the chiral atom.
- getLine(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the line-matrix at the given line index
- getLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Deprecated.
- getLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Deprecated.
- getLinkageRadius() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getLinkmap() - Method in class org.openscience.cdk.io.RssWriter
-
- getListenerCount() - Method in class org.openscience.cdk.ChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugBond
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugElement
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugMapping
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugRing
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getListenerCount() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getLocations() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Getter for property locations.
- getLog() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets generated log.
- getLog() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Gets generated log.
- getLoggingToolClass() - Static method in class org.openscience.cdk.tools.LoggingToolFactory
-
- getLonePair(int) - Method in class org.openscience.cdk.AtomContainer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing
-
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Get the lone pair at position number
in [0,..].
- getLonePairCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugRing
-
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getLonePairCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
-
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getLonePairNumber(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getLongestUnplacedChain(IMolecule, IAtom) - Method in class org.openscience.cdk.layout.AtomPlacer
-
Search a molecule for the longest unplaced, aliphatic chain in it.
- getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
-
- getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
-
- getMajorIsotope(int) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns the most abundant (major) isotope with a given atomic number.
- getMajorIsotope(String) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns the most abundant (major) isotope whose symbol equals element.
- getMajorIsotopeMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed major isotopic mass of all elements from an MolecularFormula.
- getMajorIsotopeMolecularFormula(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Construct an instance of IMolecularFormula, initialized with a molecular
formula string.
- getMap() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
-
Returns the current mapping of query atoms onto target atoms.
- getMap() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
-
Returns the current mapping of query atoms onto target atoms.
- getMappedChemObject(IReaction, IChemObject) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
get the IAtom which is mapped
- getMappedSubstructures(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
-
Checks if one of the loaded templates is a substructure in the given
Molecule and returns all matched substructures in a IAtomContainerSet.
- getMapping() - Method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
-
- getMapping(int) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Retrieves a mapping between the reactant and product side to this
Reaction.
- getMapping(int) - Method in class org.openscience.cdk.Reaction
-
Retrieves a mapping between the reactant and product side to this
Reaction.
- getMapping(int) - Method in class org.openscience.cdk.silent.Reaction
-
Retrieves a mapping between the reactant and product side to this
Reaction.
- getMappingCount() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Get the number of mappings between the reactant and product side to this
Reaction.
- getMappingCount() - Method in class org.openscience.cdk.Reaction
-
Get the number of mappings between the reactant and product side to this
Reaction.
- getMappingCount() - Method in class org.openscience.cdk.silent.Reaction
-
Get the number of mappings between the reactant and product side to this
Reaction.
- getMappings() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Returns computed mappings.
- getMappings() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Returns mapping solutions
- getMaps(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns all solution map.
- getMaps(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns all solution map.
- getMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns all solution map.
- getMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns all solution map.
- getMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns all solution map.
- getMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns all solution map.
- getMass() - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Get the mass value of this container.
- getMass() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass
-
Returns the mass value.
- getMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getMassNumber() - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.Isotope
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.silent.Isotope
-
Returns the atomic mass of this element.
- getMatchingAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
-
Get the atoms of a target molecule that correspond to this group.
- getMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Get the atoms in the target molecule that match the query pattern.
- getMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Get the matching pharmacophore groups.
- getMatchingPharmacophoreBonds() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Get the matching pharmacophore constraints.
- getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.AdjacencyMatrix
-
Returns the adjacency matrix for the given AtomContainer.
- getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.ConnectionMatrix
-
Returns the connection matrix representation of this AtomContainer.
- getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.TopologicalMatrix
-
Returns the topological matrix for the given AtomContainer.
- getMaxBondOrder() - Method in class org.openscience.cdk.AtomType
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getMaxBondOrder() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxGasteigerDamp() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges
object
- getMaxGasteigerIters() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges
object
- getMaxGasteigerIters() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Gets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges
object
- getMaximalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
-
Returns the maximal occurrence of the IIsotope into IMolecularFormula
from this MolelecularFormulaRange.
- getMaximalStructures() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the number maximal of resonance structures to be found.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getMaximumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- getMaximumBondOrder(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the maximum bond order for a List of bonds.
- getMaximumBondOrder(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the maximum bond order for a List of bonds, given an iterator to the list.
- getMaxIterations() - Method in class org.openscience.cdk.charges.Electronegativity
-
get the maximal number of Iterations.
- getMaxIterations() - Method in class org.openscience.cdk.charges.PiElectronegativity
-
get the maximal number of Iterations.
- getMaxOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
-
Extract from a set of MolecularFormula the maximum occurrence of each element found and
put the element and occurrence in a new IMolecularFormula.
- getMaxResonStruc() - Method in class org.openscience.cdk.charges.Electronegativity
-
get the maximal number of resonance structures.
- getMaxResonStruc() - Method in class org.openscience.cdk.charges.PiElectronegativity
-
get the maximal number of resonance structures.
- getMaxResoStruc() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Gets the maximum resonance structures to be searched
- getMaxX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMaxX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxX() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxx() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMaxY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMaxY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxY() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxy() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMaxZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMaxZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxZ() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxz() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMCSSize() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Returns MCS size.
- getMechanism() - Method in class org.openscience.cdk.dict.EntryReact
-
Get the mechanism of this reaction.
- getMerge() - Method in class org.openscience.cdk.renderer.RendererModel
-
This is the central facility for handling "merges" of atoms.
- getMessage() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets generated (error/warning) messages.
- getMessage() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Gets generated (error/warning) messages.
- getMessage() - Method in error org.openscience.cdk.iupac.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- getMessage() - Method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getMIMEType() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getMinimalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
-
Returns the minimal occurrence of the IIsotope into IMolecularFormula
from this MolelecularFormulaRange.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getMinimumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the minimum bond order for a List of bonds.
- getMinimumBondOrder(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the minimum bond order for a List of bonds, given an iterator
to the list.
- getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the minimum and maximum X and Y coordinates of the atoms in the
AtomContainer.
- getMinOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
-
Extract from a set of MolecularFormula the minimal occurrence of each element found and
put the element and occurrence in a new IMolecularFormula.
- getMinPSCluster() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getMinPSPocket() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getMinX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMinX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMinX() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMinx() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMinY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMinY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMinY() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMiny() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMinZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMinZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMinZ() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMinz() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getModelCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Get the center of the model.
- getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
- getMolecularFormula(int) - Method in class org.openscience.cdk.formula.AdductFormula
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
Returns the IMolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Construct an instance of IMolecularFormula, initialized with a molecular
formula string.
- getMolecularFormula(String, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
add in a instance of IMolecularFormula the elements extracts form
molecular formula string.
- getMolecularFormula(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Method that actually does the work of convert the atomContainer
to IMolecularFormula.
- getMolecularFormula(IAtomContainer, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Method that actually does the work of convert the atomContainer
to IMolecularFormula given a IMolecularFormula.
- getMolecularGraphDiameter(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
-
Returns the diameter of the molecular graph.
- getMolecularGraphRadius(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
-
Returns the radius of the molecular graph.
- getMolecule(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getMolecule(int) - Method in interface org.openscience.cdk.interfaces.IMoleculeSet
-
Returns the Molecule at position number
in the
container.
- getMolecule() - Method in class org.openscience.cdk.layout.AtomPlacer
-
Return the molecule the AtomPlacer currently works with
- getMolecule() - Method in class org.openscience.cdk.layout.RingPlacer
-
- getMolecule() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Returns the molecule, usually used after a call of generateCoordinates()
- getMolecule(int) - Method in class org.openscience.cdk.MoleculeSet
-
Returns the Molecule at position number
in the
container.
- getMolecule(int) - Method in class org.openscience.cdk.silent.MoleculeSet
-
Returns the Molecule at position number
in the
container.
- getMolecule() - Method in class org.openscience.cdk.smsd.tools.MolHandler
-
Returns the modified container
- getMolecule() - Method in class org.openscience.cdk.structgen.RandomGenerator
-
Returns the molecule which reflects the current state of this
stochastic structure generator.
- getMoleculeCount() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getMoleculeCount() - Method in interface org.openscience.cdk.interfaces.IMoleculeSet
-
Returns the number of Molecules in this Container.
- getMoleculeCount() - Method in class org.openscience.cdk.MoleculeSet
-
Returns the number of Molecules in this Container.
- getMoleculeCount() - Method in class org.openscience.cdk.silent.MoleculeSet
-
Returns the number of Molecules in this Container.
- getMoleculeGraph(IAtomContainer) - Static method in class org.openscience.cdk.graph.MoleculeGraphs
-
Creates a molecule graph for use with jgrapht.
- getMoleculeSet() - Method in class org.openscience.cdk.ChemModel
-
Returns the MoleculeSet of this ChemModel.
- getMoleculeSet() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getMoleculeSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Returns the MoleculeSet of this ChemModel.
- getMoleculeSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Returns the MoleculeSet of this ChemModel.
- getMoleculeSet(IMolecule, IMolecule, IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Extract the list of molecules taking part in the IReactionScheme to originate a
product given a reactant.
- getMonoIsotope() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Returns the mono-isotope peak that form this isotope pattern.
- getMonomer(String, String) - Method in class org.openscience.cdk.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getMonomer(String, String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getMonomer(String) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getMonomer(String) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getMonomer(String, String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Retrieve a Monomer
object by specifying its name.
- getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Retrieve a Monomer object by specifying its name.
- getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IStrand
-
Retrieve a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.Polymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String, String) - Method in class org.openscience.cdk.silent.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.silent.Polymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.silent.Strand
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.Strand
-
Retrieves a Monomer object by specifying its name.
- getMonomerCount() - Method in class org.openscience.cdk.BioPolymer
-
Returns the number of monomers present in BioPolymer.
- getMonomerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getMonomerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getMonomerCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Return the number of monomers present in BioPolymer.
- getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Return the number of monomers present in the Polymer.
- getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Return the number of monomers present in the Strand.
- getMonomerCount() - Method in class org.openscience.cdk.Polymer
-
Returns the number of monomers present in the Polymer.
- getMonomerCount() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns the number of monomers present in BioPolymer.
- getMonomerCount() - Method in class org.openscience.cdk.silent.Polymer
-
Returns the number of monomers present in the Polymer.
- getMonomerCount() - Method in class org.openscience.cdk.silent.Strand
-
Returns the number of monomers present in the Strand.
- getMonomerCount() - Method in class org.openscience.cdk.Strand
-
Returns the number of monomers present in the Strand.
- getMonomerName() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getMonomerName() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getMonomerName() - Method in interface org.openscience.cdk.interfaces.IMonomer
-
Retrieve the monomer name.
- getMonomerName() - Method in class org.openscience.cdk.Monomer
-
Retrieves the monomer name.
- getMonomerName() - Method in class org.openscience.cdk.silent.Monomer
-
Retrieves the monomer name.
- getMonomerNames() - Method in class org.openscience.cdk.BioPolymer
-
Returns a collection of the names of all Monomer
s in this
BioPolymer.
- getMonomerNames() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getMonomerNames() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getMonomerNames() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Returns a collection of the names of all Monomer
s in this
BioPolymer.
- getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.Polymer
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns a collection of the names of all Monomer
s in this
BioPolymer.
- getMonomerNames() - Method in class org.openscience.cdk.silent.Polymer
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.silent.Strand
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.Strand
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
Returns the monomer names in the order in which they were added.
- getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.protein.data.PDBStrand
-
Returns the monomer names in the order in which they were added.
- getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.silent.PDBPolymer
-
Returns the monomer names in the order in which they were added.
- getMonomers() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getMonomers() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Returns the monomers in this strand.
- getMonomers() - Method in class org.openscience.cdk.silent.Strand
-
Returns a hashtable containing the monomers in the strand.
- getMonomers() - Method in class org.openscience.cdk.Strand
-
Returns a hashtable containing the monomers in the strand.
- getMonomerType() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getMonomerType() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getMonomerType() - Method in interface org.openscience.cdk.interfaces.IMonomer
-
Retrieve the monomer type.
- getMonomerType() - Method in class org.openscience.cdk.Monomer
-
Retrieves the monomer type.
- getMonomerType() - Method in class org.openscience.cdk.silent.Monomer
-
Retrieves the monomer type.
- getMorganNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools
-
Makes an array containing the morgan numbers of the atoms of atomContainer.
- getMorganNumbersWithElementSymbol(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools
-
Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer.
- getMostComplexRing(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Returns the ring with the highest numbers of other rings attached to it.
- getMultiMap() - Method in class org.openscience.cdk.io.RssWriter
-
- getMultiplier(int) - Method in class org.openscience.cdk.AtomContainerSet
-
Returns the multiplier for the AtomContainer at position number
in the
container.
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet
-
Returns the multiplier of the given AtomContainer.
- getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getMultiplier(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns the multiplier for the AtomContainer at position number
in the
container.
- getMultiplier(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns the multiplier of the given AtomContainer.
- getMultiplier(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the multiplier for the AtomContainer at position number
in the
container.
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the multiplier of the given AtomContainer.
- getMultipliers() - Method in class org.openscience.cdk.AtomContainerSet
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getMultipliers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getMultipliers() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getMultipliers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getMultipliers() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getName() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Atom name of this atom.
- getName() - Method in class org.openscience.cdk.io.setting.IOSetting
-
- getName() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Getter for property name.
- getName() - Method in class org.openscience.cdk.libio.md.Residue
-
- getName() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Atom name of this atom.
- getName() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Atom name of this atom.
- getName(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the name of the element.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getNameExtensions() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getNames() - Static method in class org.openscience.cdk.config.fragments.EStateFragments
-
Get the fragment names.
- getNames() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
Returns an array of names for each descriptor value calculated.
- getNativeRingRadius(IRing, double) - Method in class org.openscience.cdk.layout.RingPlacer
-
Returns the ring radius of a perfect polygons of size ring.getAtomCount()
The ring radius is the distance of each atom to the ringcenter.
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getNaturalAbundance() - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.Isotope
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.silent.Isotope
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns the molecular mass of the IAtomContainer.
- getNaturalExactMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed natural mass of all elements from an MolecularFormula.
- getNaturalMass(IElement) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Gets the natural mass of this element, defined as average of masses of isotopes,
weighted by abundance.
- getNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList
-
- getNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- getNextBond(IBond, IAtom) - Method in interface org.openscience.cdk.interfaces.IRing
-
Returns the next bond in order, relative to a given bond and atom.
- getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.Ring
-
Returns the next bond in order, relative to a given bond and atom.
- getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.silent.Ring
-
Returns the next bond in order, relative to a given bond and atom.
- getNextBondVector(IAtom, IAtom, Point2d, boolean) - Method in class org.openscience.cdk.layout.AtomPlacer
-
Returns the next bond vector needed for drawing an extended linear chain of
atoms.
- getNextPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Get the next permutation in the list.
- getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule
- getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object
- getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Get the next Token.
- getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
-
Get the next Token.
- getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Get the next Token.
- getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Get the next Token.
- getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule
- getNode(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns a node of the query mol at a given position.
- getNode(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Return a node for a given atom else return null
- getNode(int) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns a node of the query mol at a given position.
- getNodesInSphere(int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
-
- getNormal(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Given three points (A, B, C), makes the vectors A-B and A-C, and makes
the cross product of these two vectors; this has the effect of making a
third vector at right angles to AB and AC.
- getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the normalization factor in order to get an average bond length
of 1.5.
- getNormalizedElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getNormalizedMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getNormalizedPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getNormalizedVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getNotEqual() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Returns not equal node
- getNotification() - Method in class org.openscience.cdk.ChemObject
-
- getNotification() - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getNotification() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the flag that indicates whether notification messages are sent around.
- getNotification() - Method in class org.openscience.cdk.renderer.RendererModel
-
Determines if the model sends around change notifications.
- getNotification() - Method in class org.openscience.cdk.silent.ChemObject
-
- getNS() - Method in class org.openscience.cdk.dict.Dictionary
-
- getNTerminus() - Method in class org.openscience.cdk.AminoAcid
-
Retrieves the N-terminus atom.
- getNTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getNTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid
-
Retrieves the N-terminus atom.
- getNTerminus() - Method in class org.openscience.cdk.silent.AminoAcid
-
Retrieves the N-terminus atom.
- getNumAtoms() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- getNumber() - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- getNumber() - Method in class org.openscience.cdk.libio.md.Residue
-
- getNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber
-
Returns the atomic number.
- getNumberOfFontSizes() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Get the number of font sizes used.
- getNumberOfIsotopes() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Returns the number of isotopes in this pattern.
- getNumberOfNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList
-
- getNumberOfTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate
-
- getNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools
-
Makes an array containing the InChI atom numbers of the non-hydrogen
atoms in the atomContainer.
- getNumOfConnection() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom
-
Returns number of explicit connections.
- getNumOfConnection() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity
-
Returns the number of explicit connections.
- getNumOfConnection() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity
-
Returns the number of ring connections.
- getNumOfConnection() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity
-
Returns the number of total connections.
- getNumOfMembership() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership
-
Returns the number of SSSR rings this atom is in.
- getOccupancy() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getOccupancy() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Occupancy of this atom.
- getOccupancy() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Occupancy of this atom.
- getOccupancy() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Occupancy of this atom.
- getOccurrence() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Returns the occurrence value.
- getOKCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of tests without errors.
- getOKs() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns an array of ValidationTest which did not find problems.
- getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
- getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- getOptions() - Method in class org.openscience.cdk.io.setting.OptionIOSetting
-
Returns a Vector of Strings containing all possible options.
- getOrder() - Method in class org.openscience.cdk.Bond
-
Returns the bond order of this bond.
- getOrder() - Method in class org.openscience.cdk.debug.DebugBond
-
- getOrder() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the bond order of this bond.
- getOrder() - Method in class org.openscience.cdk.silent.Bond
-
Returns the bond order of this bond.
- getOrder() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTValence
-
Returns valence order.
- getOtherBondAtom(IAtom, IBond) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Returns the other atom of the bond.
- getOverlaps(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns all the maximal common substructure between twp atom containers.
- getOverlaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns all the maximal common substructure between 2 atom containers.
- getOverlapScore(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
-
Calculates a score based on the overlap of atoms and intersection of bonds.
- getOxt() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getOxt() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
- getOxt() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
- getOxt() - Method in class org.openscience.cdk.silent.PDBAtom
-
- getParameter(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
-
- getParameterClass() - Method in class org.openscience.cdk.dict.EntryReact
-
Get the IParameterReact's of the reaction.
- getParameterClass(Class<?>) - Method in interface org.openscience.cdk.reaction.IReactionProcess
-
Return the IParameterReact if it exists given the class.
- getParameterClass(Class<?>) - Method in class org.openscience.cdk.reaction.ReactionEngine
-
Return the IParameterReact if it exists given the class.
- getParameterList() - Method in interface org.openscience.cdk.reaction.IReactionProcess
-
Returns the current parameter values.
- getParameterList() - Method in class org.openscience.cdk.reaction.ReactionEngine
-
Returns the current parameter values.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
Gets the parameterNames attribute of the AtomDegreeDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
Gets the parameterNames attribute of the BondsToAtomDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
Gets the parameterNames attribute of the DistanceToAtomDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
Gets the parameterNames attribute of the EffectiveAtomPolarizabilityDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
Gets the parameterNames attribute of the InductiveAtomicHardnessDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
Gets the parameterNames attribute of the IPAtomicHOSEDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
Gets the parameterNames attribute of the IPAtomicLearningDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
-
Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
-
Gets the parameterNames attribute of the
IsProtonInConjugatedPiSystemDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
-
Gets the parameterNames attribute of the PartialPiChargeDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
-
Gets the parameterNames attribute of the PartialSigmaChargeDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
-
Gets the parameterNames attribute of the PartialTChargeMMFF94Descriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
-
Gets the parameterNames attribute of the PartialTChargePEOEDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
-
Gets the parameterNames attribute of the PeriodicTablePositionDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
-
Gets the parameterNames attribute of the SigmaElectronegativityDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
-
Gets the parameterNames attribute of the ProtonAffinityDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
-
Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
-
Gets the parameterNames attribute of the RDFProtonDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
-
Gets the parameterNames attribute of the RDFProtonDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
-
Gets the parameterNames attribute of the RDFProtonDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
-
Gets the parameterNames attribute of the RDFProtonDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
-
Gets the parameterNames attribute of the RDFProtonDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
Gets the parameterNames attribute of the SigmaElectronegativityDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
Gets the parameterNames attribute of the StabilizationPlusChargeDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
-
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
-
Gets the parameterNames attribute of the PiContactDetectionDescriptor
object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
-
Gets the parameterNames attribute of the BondPartialPiChargeDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
-
Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
-
Gets the parameterNames attribute of the BondPartialTChargeDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
-
Gets the parameterNames attribute of the BondSigmaElectronegativityDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
-
Gets the parameterNames attribute of the IPBondLearningDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Gets the parameterNames attribute of the APolDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Gets the parameterNames attribute of the AromaticBondsCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Gets the parameterNames attribute of the AtomCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Gets the parameterNames attribute of the BCUTDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Gets the parameterNames attribute of the BondCountDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Gets the parameterNames attribute of the BPolDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Gets the parameterNames attribute of the CPSADescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Gets the parameterNames attribute of the EccentricConnectivityIndexDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Gets the parameterNames attribute of the FragmentComplexityDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Gets the parameterNames attribute of the HBondAcceptorCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Gets the parameterNames of the HBondDonorCountDescriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Gets the parameterNames attribute of the HybridizationRatioDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Gets the parameterNames attribute of the IPMolecularLearningDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Gets the parameterNames attribute of the
KappaShapeIndicesDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Gets the parameterNames attribute of the descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Gets the parameterNames attribute of the LongestAliphaticChainDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Gets the parameterNames attribute for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Gets the parameterNames attribute of the WeightDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Gets the parameterNames attribute of the MomentOfInertiaDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Gets the parameterNames attribute of the PetitjeanShapeIndexDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Gets the parameterNames attribute of the RotatableBondsCountDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Gets the parameterNames attribute of the RuleOfFiveDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Gets the parameterNames attribute of the TPSADescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Gets the parameterNames attribute of the VAdjMaDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Gets the parameterNames attribute of the WeightDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Gets the parameterNames attribute of the WeightedPathDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Gets the parameterNames attribute of the WHIMDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Gets the parameterNames attribute of the WienerNumbersDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Gets the parameterNames attribute of the XLogPDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Gets the parameterNames attribute of the ZagrebIndexDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Gets the parameterNames attribute of the TaeAminOAcidDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getParameterNames() - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameters() - Method in class org.openscience.cdk.dict.EntryReact
-
Get the parameters of the reaction.
- getParameters() - Method in class org.openscience.cdk.formula.rules.ChargeRule
-
Gets the parameters attribute of the ChargeRule object.
- getParameters() - Method in class org.openscience.cdk.formula.rules.ElementRule
-
Gets the parameters attribute of the ElementRule object.
- getParameters() - Method in interface org.openscience.cdk.formula.rules.IRule
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule
-
Gets the parameters attribute of the IsotopePatternRule object.
- getParameters() - Method in class org.openscience.cdk.formula.rules.MMElementRule
-
Gets the parameters attribute of the MMElementRule object.
- getParameters() - Method in class org.openscience.cdk.formula.rules.NitrogenRule
-
Gets the parameters attribute of the NitrogenRule object.
- getParameters() - Method in class org.openscience.cdk.formula.rules.RDBERule
-
Gets the parameters attribute of the RDBRule object.
- getParameters() - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule
-
Gets the parameters attribute of the ToleranceRangeRule object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
Gets the parameters attribute of the AtomDegreeDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
Gets the parameters attribute of the VdWRadiusDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
Gets the parameters attribute of the VdWRadiusDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
Gets the parameters attribute of the BondsToAtomDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
Gets the parameters attribute of the VdWRadiusDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
Gets the parameters attribute of the DistanceToAtomDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
Gets the parameters attribute of the EffectiveAtomPolarizabilityDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
Gets the parameters attribute of the InductiveAtomicHardnessDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
Gets the parameters attribute of the IPAtomicHOSEDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
Gets the parameters attribute of the IPAtomicLearningDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
-
Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
-
Gets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
-
Gets the parameters attribute of the PartialPiChargeDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
-
Gets the parameters attribute of the PartialSigmaChargeDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
-
Gets the parameters attribute of the PartialTChargeMMFF94Descriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
-
Gets the parameters attribute of the PartialTChargePEOEDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
-
Gets the parameters attribute of the PeriodicTablePositionDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
-
Gets the parameters attribute of the PiElectronegativityDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
-
Gets the parameters attribute of the ProtonAffinityDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
-
Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
-
Gets the parameters attribute of the RDFProtonDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
-
Gets the parameters attribute of the RDFProtonDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
-
Gets the parameters attribute of the RDFProtonDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
-
Gets the parameters attribute of the RDFProtonDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
-
Gets the parameters attribute of the RDFProtonDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
Gets the parameters attribute of the SigmaElectronegativityDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
Gets the parameters attribute of the StabilizationPlusChargeDescriptor
object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
-
Gets the parameters attribute of the VdWRadiusDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
-
Gets the parameters attribute of the PiContactDetectionDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
-
Gets the parameters attribute of the BondPartialPiChargeDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
-
Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
-
Gets the parameters attribute of the BondPartialTChargeDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
-
Gets the parameters attribute of the BondSigmaElectronegativityDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
-
Gets the parameters attribute of the IPBondLearningDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Gets the parameters attribute of the AminoAcidsCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Gets the parameters attribute of the APolDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Gets the parameters attribute of the AromaticAtomsCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Gets the parameters attribute of the AromaticBondsCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Gets the parameters attribute of the AtomCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Gets the parameters attribute of the BCUTDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Gets the parameters attribute of the BondCountDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Gets the parameters attribute of the BPolDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Gets the parameters attribute of the GravitationalIndexDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Gets the parameters attribute of the CPSADescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Gets the parameters attribute of the EccentricConnectivityIndexDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Gets the parameters attribute of the FragmentComplexityDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Gets the parameters attribute of the GravitationalIndexDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Gets the parameters attribute of the HBondAcceptorCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Gets the parameters of the HBondDonorCountDescriptor instance.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Gets the parameters attribute of the HybridizationRatioDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Gets the parameters attribute of the IPMolecularLearningDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Gets the parameters attribute of the
KappaShapeIndicesDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Gets the parameters attribute of the descriptor.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Gets the parameters attribute of the LargestChainDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Gets the parameters attribute of the LargestPiSystemDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Gets the parameters attribute of the PetitjeanNumberDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Gets the parameters attribute of the LongestAliphaticChainDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Gets the parameters attribute of the MannholdLogPDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Gets the parameters attribute of the WeightDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Gets the parameters attribute of the MomentOfInertiaDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Gets the parameters attribute of the PetitjeanNumberDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Gets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Gets the parameters attribute of the RotatableBondsCountDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Gets the parameters attribute of the RuleOfFiveDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Gets the parameters attribute of the TPSADescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Gets the parameters attribute of the VAdjMaDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Gets the parameters attribute of the WeightDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Gets the parameters attribute of the WeightedPathDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Gets the parameters attribute of the WHIMDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Gets the parameters attribute of the WienerNumbersDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Gets the parameters attribute of the XLogPDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Gets the parameters attribute of the ZagrebIndexDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Gets the parameters attribute of the TaeAminoAcidDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getParameters() - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
-
- getParameters() - Method in interface org.openscience.cdk.renderer.generators.IGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.RingGenerator
-
- getParameterSet() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Gets the parameterSet attribute of the ForceFieldConfigurator object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
Gets the parameterType attribute of the AtomDegreeDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
Gets the parameterType attribute of the VdWRadiusDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
Gets the parameterType attribute of the VdWRadiusDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
Gets the parameterType attribute of the BondsToAtomDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
Gets the parameterType attribute of the VdWRadiusDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
Gets the parameterType attribute of the DistanceToAtomDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
Gets the parameterType attribute of the EffectiveAtomPolarizabilityDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
Gets the parameterType attribute of the InductiveAtomicHardnessDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
Gets the parameterType attribute of the IPAtomicHOSEDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
Gets the parameterType attribute of the IPAtomicLearningDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
-
Gets the parameterType attribute of the IsProtonInAromaticSystemDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
-
Gets the parameterType attribute of the
IsProtonInConjugatedPiSystemDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
-
Gets the parameterType attribute of the PartialPiChargeDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
-
Gets the parameterType attribute of the PartialSigmaChargeDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
-
Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
-
Gets the parameterType attribute of the PartialTChargePEOEDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
-
Gets the parameterType attribute of the PeriodicTablePositionDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
-
Gets the parameterType attribute of the SigmaElectronegativityDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
-
Gets the parameterType attribute of the ProtonAffinityDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
-
Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
-
Gets the parameterType attribute of the RDFProtonDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
-
Gets the parameterType attribute of the RDFProtonDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
-
Gets the parameterType attribute of the RDFProtonDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
-
Gets the parameterType attribute of the RDFProtonDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
-
Gets the parameterType attribute of the RDFProtonDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
Gets the parameterType attribute of the SigmaElectronegativityDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
Gets the parameterType attribute of the StabilizationPlusChargeDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
-
Gets the parameterType attribute of the VdWRadiusDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
-
Gets the parameterType attribute of the PiContactDetectionDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
-
Gets the parameterType attribute of the BondPartialPiChargeDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
-
Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
-
Gets the parameterType attribute of the BondPartialTChargeDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
-
Gets the parameterType attribute of the BondSigmaElectronegativityDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
-
Gets the parameterType attribute of the IPBondLearningDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Gets the parameterType attribute of the APolDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Gets the parameterType attribute of the AromaticBondsCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Gets the parameterType attribute of the AtomCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Gets the parameterType attribute of the BCUTDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Gets the parameterType attribute of the BondCountDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Gets the parameterType attribute of the BPolDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Gets the parameterType attribute of the GravitationalIndexDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Gets the parameterType attribute of the CPSADescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Gets the parameterType attribute of the EccentricConnectivityIndexDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Gets the parameterType attribute of the FragmentComplexityDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Gets the parameterType attribute of the GravitationalIndexDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Gets the parameterType of the HBondDonorCountDescriptor.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Gets the parameterType attribute of the HybridizationRatioDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Gets the parameterType attribute of the IPMolecularLearningDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Gets the parameterType attribute of the
KappaShapeIndicesDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Gets the parameterType attribute of the descriptor.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Gets the parameterType attribute of the LargestChainDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Gets the parameterType attribute of the LargestPiSystemDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Gets the parameterType attribute of the PetitjeanNumberDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Gets the parameterType attribute for a given parameter name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Gets the parameterType attribute of the WeightDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Gets the parameterType attribute of the MomentOfInertiaDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Gets the parameterType attribute of the PetitjeanNumberDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Gets the parameterType attribute of the PetitjeanShapeIndexDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Gets the parameterType attribute of the RotatableBondsCountDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Gets the parameterType attribute of the RuleOfFiveDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Gets the parameterType attribute of the TPSADescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Gets the parameterType attribute of the VAdjMaDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Gets the parameterType attribute of the WeightDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Gets the parameterType attribute of the WeightedPathDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Gets the parameterType attribute of the WHIMDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Gets the parameterType attribute of the WienerNumbersDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Gets the parameterType attribute of the XLogPDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Gets the parameterType attribute of the ZagrebIndexDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Gets the parameterType attribute of the TaeAminoAcidDescriptor object.
- getParameterType(String) - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterValue() - Method in class org.openscience.cdk.dict.EntryReact
-
Get the parameter value of the reaction.
- getParamterSet() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
-
- getParamterSet() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
-
- getParentMolecule() - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- getParentMolecule() - Method in class org.openscience.cdk.libio.md.Residue
-
- getParity() - Method in class org.openscience.cdk.AtomParity
-
Returns the parity value.
- getParity() - Method in class org.openscience.cdk.debug.DebugAtomParity
-
- getParity() - Method in interface org.openscience.cdk.interfaces.IAtomParity
-
Returns the parity value.
- getParity() - Method in class org.openscience.cdk.silent.AtomParity
-
Returns the parity value.
- getParser() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode
-
- getPath(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.graph.SpanningTree
-
- getPathsOfLength(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Get the paths starting from an atom of specified length.
- getPathsOfLengthUpto(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Get all the paths starting from an atom of length 0 upto the specified length.
- getPaulingElectronegativities(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.InductivePartialCharges
-
Gets the paulingElectronegativities attribute of the
InductivePartialCharges object
- getPaulingElectronegativity(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the Pauling electronegativity of an element.
- getPeriod(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the period of the element.
- getPharmacophoreQuery() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Get the query pharmacophore
- getPhase(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the phase of the element.
- getPlacedAtoms(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer
-
Get all the placed atoms in an AtomContainer
- getPlacedAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Gets all placed neighbouring atoms of a atom
- getPlacedHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Returns a placed atom connected to a given atom
- getPlacedHeavyAtom(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the first placed Heavy Atom around atomA which is not atomB
- getPlacedHeavyAtomInAtomContainer(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Returns a placed neighbouring atom of a central atom atomA, which is not
atomB
- getPlacedHeavyAtoms(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the placed Heavy Atoms connected to an atom.
- getPockets() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getPocketSize() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getPoint2d() - Method in class org.openscience.cdk.Atom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint2d() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getPoint2d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getPoint2d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getPoint2d() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint2d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint3d() - Method in class org.openscience.cdk.Atom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPoint3d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPolarizabilitiyFactorForAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Polarizability
-
Gets the polarizabilitiyFactorForAtom
- getPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getPosition(int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the position of a base.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getPreferredNameExtension() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getPrime() - Method in class org.openscience.cdk.smiles.InvPair
-
Get the current prime number.
- getPrimeAt(int) - Static method in class org.openscience.cdk.math.Primes
-
Returns the i-th prime number in the sequence of
all prime numbers below 19700.
- getProductCoefficient(IMolecule) - Method in class org.openscience.cdk.debug.DebugReaction
-
- getProductCoefficient(IMolecule) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns the stoichiometry coefficient of the given product.
- getProductCoefficient(IMolecule) - Method in class org.openscience.cdk.Reaction
-
Returns the stoichiometry coefficient of the given product.
- getProductCoefficient(IMolecule) - Method in class org.openscience.cdk.silent.Reaction
-
Returns the stoichiometry coefficient of the given product.
- getProductCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getProductCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getProductCoefficients() - Method in class org.openscience.cdk.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getProductCoefficients() - Method in class org.openscience.cdk.silent.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getProductCount() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getProductCount() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns the number of products in this reaction.
- getProductCount() - Method in class org.openscience.cdk.Reaction
-
Returns the number of products in this reaction.
- getProductCount() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the number of products in this reaction.
- getProductMolecule() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns modified target molecule on which mapping was
performed.
- getProductMolecule() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns modified target molecule on which mapping was
performed.
- getProducts() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getProducts() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns a IMoleculeSet containing the products of this reaction.
- getProducts() - Method in class org.openscience.cdk.Reaction
-
Returns a MoleculeSet containing the products of this reaction.
- getProducts() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the products of this reaction.
- getProperties() - Method in class org.openscience.cdk.ChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugBond
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugElement
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugMapping
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugRing
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getProperties() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getProperties() - Method in class org.openscience.cdk.formula.MolecularFormula
-
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
- getProperties() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
- getProperties() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.ChemObject
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtom
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBond
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElement
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMapping
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReaction
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugRing
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getProperty(Object) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Returns a property for the IChemObject.
- getProtein() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getProteinInterior() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getQSARs(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool
-
Get the results of 7 qsar descriptors been applied.
- getQSARs(IAtomContainer, IBond) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool
-
Get the results of 7 qsar descriptors been applied.
- getQueryNode() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.Match
-
Return query node
- getQuestion() - Method in class org.openscience.cdk.io.setting.IOSetting
-
- getRandom() - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Returns the instance of Random used by this class.
- getRandomNextPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Randomly skip ahead in the list of permutations.
- getRandomSeed() - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Returns the seed being used by this random number generator.
- getRange(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
-
Extract from a set of MolecularFormula the range of each each element found and
put the element and occurrence in a new MolecularFormulaRange.
- getRank() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
- getRAtom() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getRawContent() - Method in class org.openscience.cdk.dict.Entry
-
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
- getRDBEValue(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule
-
Method to extract the Ring Double Bond Equivalents (RDB) value.
- getReactantCoefficient(IMolecule) - Method in class org.openscience.cdk.debug.DebugReaction
-
- getReactantCoefficient(IMolecule) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns the stoichiometry coefficient of the given reactant.
- getReactantCoefficient(IMolecule) - Method in class org.openscience.cdk.Reaction
-
Returns the stoichiometry coefficient of the given reactant.
- getReactantCoefficient(IMolecule) - Method in class org.openscience.cdk.silent.Reaction
-
Returns the stoichiometry coefficient of the given reactant.
- getReactantCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getReactantCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns an array of double with the stoichiometric coefficients
of the reactants.
- getReactantCoefficients() - Method in class org.openscience.cdk.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the reactants.
- getReactantCoefficients() - Method in class org.openscience.cdk.silent.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the reactants.
- getReactantCount() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getReactantCount() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns the number of reactants in this reaction.
- getReactantCount() - Method in class org.openscience.cdk.Reaction
-
Returns the number of reactants in this reaction.
- getReactantCount() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the number of reactants in this reaction.
- getReactantMolecule() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns modified query molecule on which mapping was
performed.
- getReactantMolecule() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns modified query molecule on which mapping was
performed.
- getReactants() - Method in class org.openscience.cdk.debug.DebugReaction
-
- getReactants() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns a IMoleculeSet containing the reactants in this reaction.
- getReactants() - Method in class org.openscience.cdk.Reaction
-
Returns a MoleculeSet containing the reactants in this reaction.
- getReactants() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the reactants in this reaction.
- getReaction(int) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet
-
Returns the Reaction at position number
in the
container.
- getReaction(int) - Method in class org.openscience.cdk.reaction.ReactionChain
-
Get the reaction of this chain reaction object at the position.
- getReaction(int) - Method in class org.openscience.cdk.ReactionSet
-
Returns the Reaction at position number
in the
container.
- getReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet
-
Returns the Reaction at position number
in the
container.
- getReactionByAtomContainerID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Gets a reaction from a ReactionSet by ID of any product or reactant.
- getReactionByReactionID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Gets a reaction from a ReactionSet by ID.
- getReactionCount() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- getReactionCount() - Method in interface org.openscience.cdk.interfaces.IReactionSet
-
Returns the number of Reactions in this Container.
- getReactionCount() - Method in class org.openscience.cdk.ReactionSet
-
Returns the number of Reactions in this Container.
- getReactionCount() - Method in class org.openscience.cdk.silent.ReactionSet
-
Returns the number of Reactions in this Container.
- getReactionMetadata() - Method in class org.openscience.cdk.dict.EntryReact
-
- getReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the reactions that must be presents in the generation of the resonance.
- getReactionSchemeCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- getReactionSchemeCount() - Method in interface org.openscience.cdk.interfaces.IReactionScheme
-
Returns the number of ReactionScheme in this Scheme.
- getReactionSchemeCount() - Method in class org.openscience.cdk.ReactionScheme
-
Returns the number of ReactionScheme in this Scheme.
- getReactionSchemeCount() - Method in class org.openscience.cdk.silent.ReactionScheme
-
Returns the number of ReactionScheme in this Scheme.
- getReactionSet() - Method in class org.openscience.cdk.ChemModel
-
Gets the ReactionSet contained in this ChemModel.
- getReactionSet() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getReactionSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Gets the ReactionSet contained in this ChemModel.
- getReactionSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Gets the ReactionSet contained in this ChemModel.
- getReactionStep(IReaction) - Method in class org.openscience.cdk.reaction.ReactionChain
-
Get the position of the reaction into this chain reaction object.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- getReaderClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getRealPart() - Method in class org.openscience.cdk.math.Complex
-
Gets the real part of this complex value
- getRecord() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getRecord() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Get one entire line from the PDB entry file which describe the IPDBAtom.
- getRecord() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get one entire line from the PDB entry file which describe the IPDBAtom.
- getRecord() - Method in class org.openscience.cdk.silent.PDBAtom
-
get one entire line from the PDB entry file which describe the IPDBAtom.
- getRectangle2D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the 2D rectangle spanning the space occupied by the atom
container.
- getRecursiveQuery() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom
-
- getReference() - Method in class org.openscience.cdk.dict.DictRef
-
- getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getRelevantAtomContainer(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
This badly named methods tries to determine which AtomContainer in the
ChemModel is best suited to contain added Atom's and Bond's.
- getRelevantAtomContainer(IChemModel, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Retrieves the first IAtomContainer containing a given IBond from an
IChemModel.
- getRelevantAtomContainer(IMoleculeSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getRelevantAtomContainer(IMoleculeSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getRelevantAtomContainer(IReaction, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getRelevantAtomContainer(IReaction, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getRelevantAtomContainer(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getRelevantAtomContainer(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getRelevantReaction(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Retrieves the first IReaction containing a given IAtom from an
IChemModel.
- getRelevantReaction(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getRelevantReaction(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getRelevantReactions(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Get all Reactions object containing a Molecule from a set of Reactions.
- getRelevantReactionsAsProduct(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Get all Reactions object containing a Molecule as a Product from a set of
Reactions.
- getRelevantReactionsAsReactant(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Get all Reactions object containing a Molecule as a Reactant from a set
of Reactions.
- getRemoveHydrogenFlag() - Method in class org.openscience.cdk.smsd.tools.MolHandler
-
Returns true if hydrogens were made implicit else return false
- getRenderer2DModel() - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Get the
RendererModel
used by this renderer, which provides
access to the various parameters used to generate and draw the diagram.
- getRenderer2DModel() - Method in interface org.openscience.cdk.renderer.IRenderer
-
Returns the drawing model, giving access to drawing parameters.
- getRendererModel() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
- getRenderingParameters() - Method in class org.openscience.cdk.renderer.RendererModel
-
- getRepresentations() - Method in class org.openscience.cdk.dict.EntryReact
-
Get the Representation of the reaction.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- getRequiredDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getRequiredRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getResidues() - Method in class org.openscience.cdk.libio.md.MDMolecule
-
- getResName() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getResName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Residue name of this atom.
- getResName() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Residue name of this atom.
- getResName() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Residue name of this atom.
- getResSeq() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Residue sequence number of this atom.
- getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Gets the sequence identifier of this monomer.
- getResSeq() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Residue sequence number of this atom.
- getResSeq() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- getResSeq() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Residue sequence number of this atom.
- getResSeq() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool
-
Get the restrictions that must be presents in the molecular formula.
- getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets return status from InChI process.
- getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Gets return status from InChI process.
- getRGroupDefinitions() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for the R-group definitions (substituents).
- getRGroupDefinitions() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getRgroupQueryAtoms(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
Returns all R# type atoms (pseudo atoms) found in the root structure
for a certain provided RGgroup number.
- getRGroups() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
- getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- getRingBond() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
-
- getRingFinder() - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Returns the current AllRingsFinder instance
- getRingId() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier
-
Returns the ring identifier.
- getRings(IBond) - Method in class org.openscience.cdk.debug.DebugRingSet
-
- getRings(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet
-
- getRings(IBond) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
Returns a vector of all rings that this bond is part of.
- getRings(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
Returns a vector of all rings that this atom is part of.
- getRings(IBond) - Method in class org.openscience.cdk.RingSet
-
Returns a vector of all rings that this bond is part of.
- getRings(IAtom) - Method in class org.openscience.cdk.RingSet
-
Returns a vector of all rings that this atom is part of.
- getRings(IBond) - Method in class org.openscience.cdk.silent.RingSet
-
Returns a vector of all rings that this bond is part of.
- getRings(IAtom) - Method in class org.openscience.cdk.silent.RingSet
-
Returns a vector of all rings that this atom is part of.
- getRingSet() - Method in class org.openscience.cdk.ChemModel
-
Returns the RingSet of this ChemModel.
- getRingSet() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- getRingSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Returns the RingSet of this ChemModel.
- getRingSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Returns the RingSet of this ChemModel.
- getRingSet(IAtomContainer) - Method in class org.openscience.cdk.smsd.ring.HanserRingFinder
-
Returns Ring set based on Hanser Ring Finding method
- getRingSet(IAtomContainer) - Method in interface org.openscience.cdk.smsd.ring.RingFinder
-
Returns CDK object Ring set based on Hanser Ring Finding method
- getRingSize() - Method in class org.openscience.cdk.debug.DebugRing
-
- getRingSize() - Method in interface org.openscience.cdk.interfaces.IRing
-
Returns the number of atoms/bonds in this ring.
- getRingSize() - Method in class org.openscience.cdk.Ring
-
Returns the number of atoms\edges in this ring.
- getRingSize() - Method in class org.openscience.cdk.silent.Ring
-
Returns the number of atoms\edges in this ring.
- getRingSystems() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
Get the ring system fragments as SMILES strings.
- getRingSystemsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
- getRMap() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Gets the rMap attribute of the RNode object
- getRMap() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Gets the rMap attribute of the RNode object
- getrMap() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Returns resolution Map
- getRMSD() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
-
Returns the RMSD from the alignment.
- getRoot(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor
-
- getRootAttachmentPoints() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
- getRootAttachmentPoints() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getRootStructure() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for the root structure of this R-Group.
- getRootStructure() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getRotationMatrix() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
-
Returns the rotation matrix (u).
- getRows() - Method in class org.openscience.cdk.math.IMatrix
-
Returns the count of rows
- getRows() - Method in class org.openscience.cdk.math.Matrix
-
Returns the number of rows.
- getRSolvent() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getRules() - Method in class org.openscience.cdk.formula.MolecularFormulaChecker
-
Get the IRules to be applied to validate the IMolecularFormula.
- getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Determines the scale factor for displaying a structure loaded from disk in
a frame.
- getSearchDepth() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
- getSearchDepth() - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
- getSecondAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getSecondGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the size of the second of the two
compared graphs.
- getSecondGraphSize() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the size of the second of the two
compared graphs.
- getSegID() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getSegID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Segment identifier, left-justified of this atom.
- getSegID() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Segment identifier, left-justified of this atom.
- getSegID() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Segment identifier, left-justified of this atom.
- getSelection() - Method in class org.openscience.cdk.renderer.RendererModel
-
- getSerial() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getSerial() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Atom serial number of this atom.
- getSerial() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Atom serial number of this atom.
- getSerial() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Atom serial number of this atom.
- getSetting() - Method in class org.openscience.cdk.io.setting.IOSetting
-
Sets the setting for a certain question.
- getSettingValue() - Method in class org.openscience.cdk.io.setting.IntegerIOSetting
-
- getShortestPath(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools
-
Returns a list of atoms in the shortest path between two atoms.
- getSID(XmlPullParser) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
-
- getSingleBondEquivalentSum(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns the sum of bond orders, where a single bond counts as one
single bond equivalent, a double as two, etc.
- getSingleBondEquivalentSum(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Get the single bond equivalent (SBE) of a list of bonds.
- getSingleBondEquivalentSum(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.
- getSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing
-
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Get the single electron at position number
in [0,..].
- getSingleElectronCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of the single electrons in this container,
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugRing
-
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getSingleElectronCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of the single electrons in this container,
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
-
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
-
- getSingleElectronNumber(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of a given single electron in the single electron array.
- getSize() - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Returns the number of atom types in this list.
- getSize() - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns the number of isotopes defined by this class.
- getSize() - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
-
- getSize() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
-
- getSize() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
- getSize() - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
- getSize() - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
-
Returns the size of the fingerprints calculated.
- getSize() - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
-
- getSize() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
-
Get the size of the fingerprint.
- getSize() - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
- getSize() - Method in class org.openscience.cdk.math.IVector
-
Return the size from this vector
- getSize() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getSize() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the number of base vectors.
- getSize() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the number of base vectors
- getSize() - Method in class org.openscience.cdk.math.Vector
-
Returns the size of this vector
- getSize() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize
-
Returns the smallest SSSR size.
- getSize() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Returns number of stored mappings
- getSize() - Method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Returns label count
- getSize() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Returns number of stored mappings
- getSmarts() - Static method in class org.openscience.cdk.config.fragments.EStateFragments
-
Get the SMARTS patterns.
- getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
-
Get the SMARTS for the group.
- getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
-
Get the SMARTS pattern for this pharmacophore group.
- getSmarts() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Returns the current SMARTS pattern being used.
- getSolutions() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the list of solutions.
- getSolutions() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the list of solutions.
- getSolvantValue() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getSortedEnergy() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Return sorted energy in ascending order.
- getSortedFragment() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Return sorted fragment in ascending order of the size.
- getSource() - Method in class org.openscience.cdk.controller.CDKPopupMenu
-
- getSource() - Method in interface org.openscience.cdk.interfaces.IChemObjectChangeEvent
-
IChemObject that fired the event.
- getSource(ActionEvent) - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Gets the source attribute of the JCPAction object
- getSource() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Returns source molecule
- getSource() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
-
Returns source Node.
- getSource() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
-
Returns source Node.
- getSource() - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- getSpaceGroup() - Method in class org.openscience.cdk.Crystal
-
Gets the space group of this crystal.
- getSpaceGroup() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getSpaceGroup() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the space group of this crystal.
- getSpaceGroup() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the space group of this crystal.
- getSpanningTree() - Method in class org.openscience.cdk.graph.SpanningTree
-
- getSpanningTreeSize() - Method in class org.openscience.cdk.graph.SpanningTree
-
- getSpatproduct(Vector3d, Vector3d, Vector3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Gets the spatproduct of three vectors
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
Gets the specification attribute of the AtomHybridizationDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
Gets the specification attribute of the AtomValenceDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
Gets the specification attribute of the BondsToAtomDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
Gets the specification attribute of the DistanceToAtomDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
Gets the specification attribute of the EffectiveAtomPolarizabilityDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
Gets the specification attribute of the InductiveAtomicHardnessDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
Gets the specification attribute of the InductiveAtomicSoftnessDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
Gets the specification attribute of the IPAtomicHOSEDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
Gets the specification attribute of the IPAtomicLearningDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
-
Gets the specification attribute of the IsProtonInAromaticSystemDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
-
Gets the specification attribute of the
IsProtonInConjugatedPiSystemDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
-
Gets the specification attribute of the PartialPiChargeDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
-
Gets the specification attribute of the PartialSigmaChargeDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
-
Gets the specification attribute of the PartialTChargeMMFF94Descriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
-
Gets the specification attribute of the PartialTChargePEOEDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
-
Gets the specification attribute of the PeriodicTablePositionDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
-
Gets the specification attribute of the PiElectronegativityDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
-
Gets the specification attribute of the ProtonAffinityDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
-
Gets the specification attribute of the ProtonTotalPartialChargeDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
-
Gets the specification attribute of the RDFProtonDescriptor_G3R object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
-
Gets the specification attribute of the RDFProtonDescriptor_GDR
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
-
Gets the specification attribute of the RDFProtonDescriptor_GHR
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
-
Gets the specification attribute of the RDFProtonDescriptor_GHR_topol
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
-
Gets the specification attribute of the RDFProtonDescriptor_GSR
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
Gets the specification attribute of the SigmaElectronegativityDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
Gets the specification attribute of the StabilizationPlusChargeDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
-
Gets the specification attribute of the PiContactDetectionDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
-
Gets the specification attribute of the BondPartialPiChargeDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
-
Gets the specification attribute of the BondPartialSigmaChargeDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
-
Gets the specification attribute of the BondPartialTChargeDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
-
Gets the specification attribute of the BondSigmaElectronegativityDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
-
Gets the specification attribute of the IPBondLearningDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Gets the specification attribute of the BondCountDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Gets the specification attribute of the HBondAcceptorCountDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Gets the specification attribute of the HBondDonorCountDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Gets the specification attribute of the IPMolecularLearningDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Gets the specification attribute of the
KappaShapeIndicesDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Gets the specification attribute of the PetitjeanNumberDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Gets the specification attribute of the MannholdLogPDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Returns a Map
which specifies which descriptor is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Gets the specification attribute of the PetitjeanNumberDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Gets the specification attribute of the RotatableBondsCountDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Gets the specification attribute of the TPSADescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Gets the specification attribute of the VAdjMaDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Returns a Map
which specifies which descriptor is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Gets the specification attribute of the XLogPDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Gets the specification attribute of the ZagrebIndexDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getSpecification() - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in interface org.openscience.cdk.reaction.IReactionProcess
-
Returns a Map
which specifies which reaction
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction
-
Gets the specification attribute of the AdductionProtonLPReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction
-
Gets the specification attribute of the AdductionProtonPBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction
-
Gets the specification attribute of the AdductionSodiumLPReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction
-
Gets the specification attribute of the CarbonylEliminationReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction
-
Gets the specification attribute of the ElectronImpactNBEReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction
-
Gets the specification attribute of the ElectronImpactPDBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction
-
Gets the specification attribute of the ElectronImpactSDBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction
-
Gets the specification attribute of the HeterolyticCleavagePBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction
-
Gets the specification attribute of the HeterolyticCleavageSBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction
-
Gets the specification attribute of the HomolyticCleavageReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction
-
Gets the specification attribute of the HyperconjugationReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction
-
Gets the specification attribute of the PiBondingMovementReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction
-
Gets the specification attribute of the RadicalChargeSiteInitiationHReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction
-
Gets the specification attribute of the RadicalChargeSiteInitiationReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction
-
Gets the specification attribute of the RadicalSiteHrAlphaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction
-
Gets the specification attribute of the RadicalSiteHrBetaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction
-
Gets the specification attribute of the RadicalSiteHrDeltaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction
-
Gets the specification attribute of the RadicalSiteHrGammaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction
-
Gets the specification attribute of the RadicalSiteInitiationHReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction
-
Gets the specification attribute of the RadicalSiteInitiationReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction
-
Gets the specification attribute of the RadicalSiteRrAlphaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction
-
Gets the specification attribute of the RadicalSiteRrBetaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction
-
Gets the specification attribute of the RadicalSiteRrDeltaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction
-
Gets the specification attribute of the RadicalSiteRrGammaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction
-
Gets the specification attribute of the RearrangementAnionReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction
-
Gets the specification attribute of the RearrangementCationReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction
-
Gets the specification attribute of the RearrangementLonePairReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction
-
Gets the specification attribute of the RearrangementRadicalReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction
-
Gets the specification attribute of the SharingAnionReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction
-
Gets the specification attribute of the SharingChargeDBReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction
-
Gets the specification attribute of the SharingChargeSBReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction
-
Gets the specification attribute of the SharingLonePairReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.TautomerizationReaction
-
Gets the specification attribute of the TautomerizationReaction object.
- getSpecificationReference() - Method in interface org.openscience.cdk.IImplementationSpecification
-
Pointer to a dictionary or ontology describing a unique
algorithm.
- getSpecificationReference() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
-
- getSpecificationReference() - Method in class org.openscience.cdk.reaction.ReactionSpecification
-
- getSpheres(IMolecule, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
-
This method is intended to be used to get the atoms around an atom in spheres.
- getSpinVector(double, double) - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates a spin vector by a direction specified by theta and phi
- getSquarePlanarShape(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Given four atoms (assumed to be in the same plane), returns the
arrangement of those atoms in that plane.
- getSSSRWeightVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
-
Returns a vector containing the lengths of the rings in a SSSR.
- getStartChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- getStartChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get start Chain identifier of this structure.
- getStartChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get start Chain identifier of this structure.
- getStartChainID() - Method in class org.openscience.cdk.silent.PDBStructure
-
get start Chain identifier of this structure.
- getStartInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- getStartInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get start Code for insertion of residues of this structure.
- getStartInsertionCode() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get start Code for insertion of residues of this structure.
- getStartInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure
-
get start Code for insertion of residues of this structure.
- getStartSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- getStartSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get the start sequence number of this structure.
- getStartSequenceNumber() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get the start sequence number of this structure.
- getStartSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the start sequence number of this structure.
- getStepSize() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Get the StepSize attribute of the GasteigerMarsiliPartialCharges
object
- getStepSize() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Get the StepSize attribute of the GasteigerMarsiliPartialCharges
object
- getStereo() - Method in class org.openscience.cdk.Bond
-
Returns the stereo descriptor for this bond.
- getStereo() - Method in class org.openscience.cdk.debug.DebugBond
-
- getStereo() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the stereo descriptor for this bond.
- getStereo() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
-
Defines the stereochemistry around the double bond.
- getStereo() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
-
Defines the stereochemistry around the chiral atom.
- getStereo() - Method in class org.openscience.cdk.silent.Bond
-
Returns the stereo descriptor for this bond.
- getStereo() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
Defines the stereochemistry around the double bond.
- getStereo(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.
- getStereo() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
Defines the stereochemistry around the chiral atom.
- getStereoBond() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
-
IBond
that is the stereo center.
- getStereoBond() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
IBond
that is the stereo center.
- getStereoMatches() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Return Stereo matches in descending order.
- getStereoParity() - Method in class org.openscience.cdk.Atom
-
Returns the stereo parity of this atom.
- getStereoParity() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getStereoParity() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getStereoParity() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getStereoParity() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns the stereo parity of this atom.
- getStereoParity() - Method in class org.openscience.cdk.silent.Atom
-
Returns the stereo parity of this atom.
- getStereoScore(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns a number which denotes the quality of the mcs.
- getStereoScore(int) - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns a number which denotes the quality of the mcs.
- getStrand(String) - Method in class org.openscience.cdk.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getStrand(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Retrieve a Monomer object by specifying its name.
- getStrand(String) - Method in class org.openscience.cdk.silent.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getStrandCount() - Method in class org.openscience.cdk.BioPolymer
-
Returns the number of strands present in the BioPolymer.
- getStrandCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getStrandCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Return the number of strands present in the BioPolymer.
- getStrandCount() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns the number of strands present in the BioPolymer.
- getStrandName() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getStrandName() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Retrieve the strand name.
- getStrandName() - Method in class org.openscience.cdk.silent.Strand
-
Retrieves the strand name.
- getStrandName() - Method in class org.openscience.cdk.Strand
-
Retrieves the strand name.
- getStrandNames() - Method in class org.openscience.cdk.BioPolymer
-
Returns a collection of the names of all Strand
s in this
BioPolymer.
- getStrandNames() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getStrandNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Returns a collection of the names of all Strand
s in this
BioPolymer.
- getStrandNames() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns a collection of the names of all Strand
s in this
BioPolymer.
- getStrands() - Method in class org.openscience.cdk.BioPolymer
-
- getStrands() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- getStrands() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Returns a Map containing the strands in the Polymer.
- getStrands() - Method in class org.openscience.cdk.silent.BioPolymer
-
- getStrandType() - Method in class org.openscience.cdk.debug.DebugStrand
-
- getStrandType() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Retrieve the strand type.
- getStrandType() - Method in class org.openscience.cdk.silent.Strand
-
Retrieves the strand type.
- getStrandType() - Method in class org.openscience.cdk.Strand
-
Retrieves the strand type.
- getString(IMolecularFormula, String[], boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula.
- getString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula.
- getString(IMolecularFormula, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula.
- getStrokeMap() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
Returns the current stroke map.
- getStructures() - Method in class org.openscience.cdk.debug.DebugPDBPolymer
-
- getStructures() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
-
Returns a Collection containing the PDBStructure in the PDBPolymer.
- getStructures() - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
- getStructures() - Method in class org.openscience.cdk.silent.PDBPolymer
-
- getStructures(IMolecule) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the resonance structures from an IMolecule.
- getStructureType() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- getStructureType() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get Structure Type of this structure.
- getStructureType() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get Structure Type of this structure.
- getStructureType() - Method in class org.openscience.cdk.silent.PDBStructure
-
get Structure Type of this structure.
- getSubgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- getSubgraphAtomsMap(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure
of g1.
- getSubgraphAtomsMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
- getSubgraphAtomsMaps(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure
of g1.
- getSubgraphAtomsMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
- getSubgraphMap(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns the first subgraph 'bond mapping' found for g2 in g1.
- getSubgraphMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
- getSubgraphMaps(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns all the subgraph 'bond mappings' found for g2 in g1.
- getSubgraphMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.
- getSubstituents() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Return all the substituent atom containers, in other words the atom containers
defined in this RGroupQuery except for the root structure.
- getSubstituents() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getSubstructure(int) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
Retrieves the SMARTS representation of a substructure for a given
bit in the fingerprint.
- GetSuffix(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get the suffix.
- GetSuffix(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get the suffix.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- getSupportedDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getSupportedDataFeatures(IMolecule) - Static method in class org.openscience.cdk.tools.DataFeaturesTool
-
Determines the features present in the given IMolecule.
- getSurfaceArea(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get the surface area for the specified atom.
- getSurfacePoints(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get an array of the points on the accessible surface of a specific atom.
- getSurroundingAtoms() - Method in class org.openscience.cdk.AtomParity
-
Returns the four atoms that define the stereochemistry for
this parity.
- getSurroundingAtoms() - Method in class org.openscience.cdk.debug.DebugAtomParity
-
- getSurroundingAtoms() - Method in interface org.openscience.cdk.interfaces.IAtomParity
-
Returns the four atoms that define the stereochemistry for
this parity.
- getSurroundingAtoms() - Method in class org.openscience.cdk.silent.AtomParity
-
Returns the four atoms that define the stereochemistry for
this parity.
- getSwitchingAtom() - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- getSymbol() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getSymbol() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getSymbol() - Method in class org.openscience.cdk.debug.DebugElement
-
- getSymbol() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getSymbol() - Method in class org.openscience.cdk.debug.DebugIsotope
-
- getSymbol() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getSymbol() - Method in class org.openscience.cdk.Element
-
Returns the element symbol of this element.
- getSymbol() - Method in interface org.openscience.cdk.interfaces.IElement
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.silent.Element
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTElement
-
Returns the element symbol.
- getSymbol() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom
-
Returns the element symbol.
- getSymbol(int) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
- getSymbolFirstAtom() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
-
Returns the element symbol of the first atom.
- getSymbolSecondAtom() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
-
Returns the element symbol of the second atom.
- getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
Retrieve the Set of symbols
- getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Retrieve the Set of symbols
- getTanimotoAtomSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- getTanimotoBondSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- getTanimotoSimilarity() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns Tanimoto similarity between query and target molecules
(Score is between 0-min and 1-max).
- getTanimotoSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns Tanimoto similarity between query and target molecules
(Score is between 0-min and 1-max).
- getTarget() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Returns target molecule
- getTarget() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
-
Returns target Node.
- getTarget() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
-
Returns target Node.
- getTarget() - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- getTargetAtom() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.Match
-
Return Target Atom
- getTargetQueryBondMappings() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Return a list of HashMap's that allows one to get the query constraint for a given pharmacophore bond.
- getTautomers(IAtomContainer) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator
-
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by jniinchi.
- getTautomers(IAtomContainer, String) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator
-
- getTC(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom
-
This returns the total connection of an atom.
- getTempFactor() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- getTempFactor() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Temperature factor of this atom.
- getTempFactor() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Temperature factor of this atom.
- getTempFactor() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Temperature factor of this atom.
- getTemplateAt(int) - Method in class org.openscience.cdk.layout.TemplateHandler
-
Gets the templateAt attribute of the TemplateHandler object
- getTemplateAt(int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
Gets the templateAt attribute of the TemplateHandler object
- getTemplateCount() - Method in class org.openscience.cdk.layout.TemplateHandler
-
Gets the templateCount attribute of the TemplateHandler object
- getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
Returns the number of loaded templates.
- getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
Gets the templateCount attribute of the TemplateHandler object
- getTemplateHandler() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Gets the templateHandler attribute of the StructureDiagramGenerator object
- getTessAsPoint3ds() - Method in class org.openscience.cdk.geometry.surface.Tessellate
-
- getTessAsTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate
-
- getTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
-
Gets the timeout values in milliseconds of the AllRingsFinder object
- getTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinderMod
-
Gets the timeout values in milliseconds of the AllRingsFinder object
- getTimeOut() - Method in class org.openscience.cdk.smsd.global.TimeOut
-
Return cutoff value for time out.
- getTitle() - Method in class org.openscience.cdk.ConformerContainer
-
Get the title of the conformers.
- getTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the main title
- getTitlemap() - Method in class org.openscience.cdk.io.RssWriter
-
- getToken(int) - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Get the specific Token.
- getToken(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Get the specific Token.
- getTolerance() - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity
-
Get the tolerance of the mass accuracy.
- getToolTipText(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel
-
Gets the toolTipText for atom certain atom.
- getToolTipTextMap() - Method in class org.openscience.cdk.renderer.RendererModel
-
Gets the toolTipTextMap.
- getTopoEquivClassbyHuXu(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Get the topological equivalent class of the molecule
- getTorsionAngle(Point3d, Point3d, Point3d, Point3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculates the torsionAngle of a-b-c-d
- getTorsionData(String, String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the bond parameter set.
- getTotalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the summed charge of all atoms in an AtomContainer
- getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getTotalCharge(IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getTotalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the summed exact mass of all atoms in an AtomContainer.
- getTotalExactMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed exact mass of all isotopes from an MolecularFormula.
- getTotalFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the total formal charge on a molecule.
- getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getTotalFormalCharge(IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getTotalHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Count the total number of hydrogens (implicit and explicit).
- getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getTotalHydrogenCount(IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getTotalMassNumber(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed mass number of all isotopes from an MolecularFormula.
- getTotalNaturalAbundance(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the summed natural abundance of all atoms in an AtomContainer
- getTotalNaturalAbundance(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed natural abundance of all isotopes from an MolecularFormula.
- getTotalNegativeFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the total formal negative charge on a molecule.
- getTotalPositiveFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the total positive formal charge on a molecule.
- getTotalSurfaceArea() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get the total surface area for the AtomContainer.
- getType() - Method in class org.openscience.cdk.dict.DictRef
-
- getType() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotBond
-
- getType() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression
-
- getUniqueMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Get the atoms in the target molecule that match the query pattern.
- getUniqueMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Get the uniue matching pharmacophore groups.
- getUnplacedRingHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object
- getUnsetAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Gets the unsetAtomsInAtomContainer attribute of the
AtomTetrahedralLigandPlacer3D object
- getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
-
- getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
-
- getUseTemplates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Returns whether the use of templates is enabled or disabled.
- getValence(IAtom) - Static method in class org.openscience.cdk.qsar.AtomValenceTool
-
- getValency() - Method in class org.openscience.cdk.AtomType
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in class org.openscience.cdk.debug.DebugAtom
-
- getValency() - Method in class org.openscience.cdk.debug.DebugAtomType
-
- getValency() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- getValency() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- getValency() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the the exact electron valency of the AtomType object.
- getValue() - Method in class org.openscience.cdk.iupac.parser.Token
-
An optional attribute value of the Token.
- getValue(double, double, double) - Method in interface org.openscience.cdk.math.IFunction
-
Return the function value at (x,y,z)
- getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Calculates the function value an (x,y,z).
- getValue(int, double, double, double) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates the function value an (x,y,z).
- getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.Orbitals
-
Get the function value of a orbital at the position (x,y,z)
- getValue() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getValue() - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
-
Get the value of the parameter.
- getValue() - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
-
Get the value of the parameter.
- getValue() - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
-
Gets the value for this parameter.
- getValue() - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
-
Gets the value for this parameter.
- getValue() - Method in class org.openscience.cdk.smiles.smarts.parser.Token
-
An optional attribute value of the Token.
- getValue() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Return value of the node
- getValueAt(int, int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the value of the given element.
- getValues(Matrix) - Method in interface org.openscience.cdk.math.IFunction
-
Return the function value
The rows of the matrix x are the Parameters like x,y,z
and the columns are the values which must calculated.
- getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Calculates the function values.
- getValues(int, Matrix) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates the function values.
- getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals
-
Get the function value of a orbital
- getVanDerWaalsFile() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getVdwRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the Van der Waals radius for the element in question.
- getVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getVectorFromColumn(int) - Method in class org.openscience.cdk.math.IMatrix
-
Creates a vector with the content of a column from this matrix
- getVectorFromColumn(int) - Method in class org.openscience.cdk.math.Matrix
-
Creates a Vector with the content of a column from this Matrix.
- getVectorFromDiagonal() - Method in class org.openscience.cdk.math.IMatrix
-
Creates a vector with the content of the diagonal elements from this matrix
- getVectorFromDiagonal() - Method in class org.openscience.cdk.math.Matrix
-
Creates a Vector with the content of the diagonal elements from this Matrix.
- getVectorFromRow(int) - Method in class org.openscience.cdk.math.IMatrix
-
Creates a vector with the content of a row from this matrix
- getVectorFromRow(int) - Method in class org.openscience.cdk.math.Matrix
-
Creates a Vector with the content of a row from this Matrix.
- getVersion() - Static method in class org.openscience.cdk.CDK
-
Returns the version of this CDK library.
- getVertexCountAtDistance(IAtomContainer, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Returns the number of vertices that are a distance 'd' apart.
- getVisitedAtoms() - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
Returns a list of visitedAtoms.
- getVisitedAtoms() - Method in class org.openscience.cdk.geometry.cip.Ligand
-
- getWarningCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of tests which gave warnings.
- getWarningFlags() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Returns warning flags, see INCHIDIFF in inchicmp.h.
- getWarnings() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns an array of ValidationTest warnings.
- getWidthForBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Determine the width of a bond, returning either the width defined
in the model, or the override width.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- getWriterClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getXMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- getXMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Gets the function area, which will painted
- getXTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the title of the x axis
- getYMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- getYMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- getYTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the title of the y axis
- getZ() - Method in class org.openscience.cdk.Crystal
-
Gets the number of asymmetric parts in the unit cell.
- getZ() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- getZ() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the number of asymmetric parts in the unit cell.
- getZ() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the number of asymmetric parts in the unit cell.
- GhemicalMMFormat - Class in org.openscience.cdk.io.formats
-
- GhemicalMMReader - Class in org.openscience.cdk.io
-
- GhemicalMMReader(Reader) - Constructor for class org.openscience.cdk.io.GhemicalMMReader
-
- GhemicalMMReader(InputStream) - Constructor for class org.openscience.cdk.io.GhemicalMMReader
-
- GhemicalMMReader() - Constructor for class org.openscience.cdk.io.GhemicalMMReader
-
- GhemicalSPMFormat - Class in org.openscience.cdk.io.formats
-
- GIMatrix - Class in org.openscience.cdk.graph.invariant
-
This class is intended to provide the user an efficient way of implementing matrix of double number and
using normal operations (linear operations, addition, substraction, multiplication, inversion, concatenation)
on them.
- GIMatrix(int[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- GIMatrix(double[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- GIMatrix(int, int) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- GIMatrix(GIMatrix) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- GIMatrix(GIMatrix[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- giveAngle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Calls giveAngleBothMethods with bool = true
- giveAngleBothMethods(IAtom, IAtom, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
-
Gives the angle between two lines starting at atom from and going to to1
and to2.
- giveAngleBothMethods(Point2d, Point2d, Point2d, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
-
- giveAngleFromMiddle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Calls giveAngleBothMethods with bool = false
- GOLD - Static variable in class org.openscience.cdk.config.Elements
-
- GOLD - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- GraphOnlyFingerprinter - Class in org.openscience.cdk.fingerprint
-
Specialized version of the
Fingerprinter
which does not take bond orders
into account.
- GraphOnlyFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
Creates a fingerprint generator of length defaultSize
and with a search depth of defaultSearchDepth
.
- GraphOnlyFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
- GraphOnlyFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
- GraphRendererModel - Class in org.openscience.cdk.renderer
-
This class handles a set of function for the GraphRenderer
- GraphRendererModel() - Constructor for class org.openscience.cdk.renderer.GraphRendererModel
-
- GravitationalIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
IDescriptor characterizing the mass distribution of the molecule.
- GravitationalIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
- GridGenerator - Class in org.openscience.cdk.tools
-
Generates a grid of points in 3D space within given boundaries.
- GridGenerator() - Constructor for class org.openscience.cdk.tools.GridGenerator
-
- GridGenerator(double, double) - Constructor for class org.openscience.cdk.tools.GridGenerator
-
- GridGenerator(double, double, double) - Constructor for class org.openscience.cdk.tools.GridGenerator
-
- GridGenerator(double[], double, boolean) - Constructor for class org.openscience.cdk.tools.GridGenerator
-
- gridToGridArray(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method transforms the grid to an array.
- gridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method writes the grid to pmesh format.
- GROMOS96Format - Class in org.openscience.cdk.io.formats
-
- GroupExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- groupOneMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
- groupTwoMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
- guessFormat(Reader) - Method in class org.openscience.cdk.io.FormatFactory
-
Creates a String of the Class name of the IChemObject
reader
for this file format.
- guessFormat(InputStream) - Method in class org.openscience.cdk.io.FormatFactory
-
- I - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- IAdductFormula - Interface in org.openscience.cdk.interfaces
-
Class defining an adduct object in a MolecularFormula.
- IAminoAcid - Interface in org.openscience.cdk.interfaces
-
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
- IAtom - Interface in org.openscience.cdk.interfaces
-
Represents the idea of an chemical atom.
- IAtomColorer - Interface in org.openscience.cdk.renderer.color
-
Interface to a class for coloring atoms.
- IAtomContainer - Interface in org.openscience.cdk.interfaces
-
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
- IAtomContainerSet - Interface in org.openscience.cdk.interfaces
-
A set of AtomContainers.
- IAtomicDescriptor - Interface in org.openscience.cdk.qsar
-
Classes that implement this interface are QSAR descriptor calculators.
- IAtomPairDescriptor - Interface in org.openscience.cdk.qsar
-
Classes that implement this interface are QSAR descriptor calculators.
- IAtomParity - Interface in org.openscience.cdk.interfaces
-
Represents the concept of an atom parity identifying the stereochemistry
around an atom, given four neighbouring atoms.
- IAtomType - Interface in org.openscience.cdk.interfaces
-
The base class for atom types.
- IAtomType.Hybridization - Enum in org.openscience.cdk.interfaces
-
An enum for the different hybridization states.
- IAtomTypeConfigurator - Interface in org.openscience.cdk.config
-
Interface that allows reading atom type configuration data from some
source.
- IAtomTypeGuesser - Interface in org.openscience.cdk.atomtype
-
Classes that implement this interface are atom type guessers.
- IAtomTypeMatcher - Interface in org.openscience.cdk.atomtype
-
Classes that implement this interface are atom type matchers.
- IBasis - Interface in org.openscience.cdk.math.qm
-
A basis set must implement this class.
- IBioPolymer - Interface in org.openscience.cdk.interfaces
-
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
- IBond - Interface in org.openscience.cdk.interfaces
-
Implements the concept of a covalent bond between two or more atoms.
- IBond.Order - Enum in org.openscience.cdk.interfaces
-
A list of permissible bond orders.
- IBond.Stereo - Enum in org.openscience.cdk.interfaces
-
Enumeration of possible stereo types of two-atom bonds.
- IBondDescriptor - Interface in org.openscience.cdk.qsar
-
Classes that implement this interface are QSAR descriptor calculators.
- ICanonicalMoleculeLabeller - Interface in org.openscience.cdk.smsd.labelling
-
- ICanonicalReactionLabeller - Interface in org.openscience.cdk.smsd.labelling
-
- ICDKChangeListener - Interface in org.openscience.cdk.event
-
A ChangeListener for the CDK, to be independent from the Swing package.
- ICDKObject - Interface in org.openscience.cdk.interfaces
-
The base class for all data objects in this CDK.
- ICDKSelectionChangeListener - Interface in org.openscience.cdk.event
-
A ChangeListener for the CDK, to be independent from the Swing package.
- IChargeCalculator - Interface in org.openscience.cdk.charges
-
Interface for classes that calculate (partial) charges centered
on atom nuclei.
- IChemFile - Interface in org.openscience.cdk.interfaces
-
- IChemFormat - Interface in org.openscience.cdk.io.formats
-
This class is the interface that all ChemFormat's should implement.
- IChemFormatMatcher - Interface in org.openscience.cdk.io.formats
-
This interface is used for classes that are able to match a certain
chemical file format.
- IChemModel - Interface in org.openscience.cdk.interfaces
-
An object containig multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
- IChemObject - Interface in org.openscience.cdk.interfaces
-
The base class for all chemical objects in this cdk.
- IChemObjectBuilder - Interface in org.openscience.cdk.interfaces
-
A helper class to instantiate a
ICDKObject
instance for a specific
implementation.
- IChemObjectChangeEvent - Interface in org.openscience.cdk.interfaces
-
Event fired by CDK IChemObject classes to their registered listeners
in case something changed within them.
- IChemObjectIO - Interface in org.openscience.cdk.io
-
This class is the interface that all IO readers should implement.
- IChemObjectIOListener - Interface in org.openscience.cdk.io.listener
-
Allows monitoring of progress of file reader activities.
- IChemObjectListener - Interface in org.openscience.cdk.interfaces
-
Classes implementing this interface must implement this method
such that they react appropriately to changes in the object they
are interested in.
- IChemObjectReader - Interface in org.openscience.cdk.io
-
This interface specifies the common functionality all IO readers should provide.
- IChemObjectReader.Mode - Enum in org.openscience.cdk.io
-
- IChemObjectReaderErrorHandler - Interface in org.openscience.cdk.io
-
- IChemObjectSelection - Interface in org.openscience.cdk.renderer.selection
-
- IChemObjectWriter - Interface in org.openscience.cdk.io
-
This class is the interface that all IO writers should implement.
- IChemSequence - Interface in org.openscience.cdk.interfaces
-
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
- ICMLConvention - Interface in org.openscience.cdk.io.cml
-
This interface describes the procedures classes must implement to be plugable
into the CMLHandler.
- ICMLCustomizer - Interface in org.openscience.cdk.libio.cml
-
Interface for classes that allow the Convertor to be customized for certain
features.
- ICMLModule - Interface in org.openscience.cdk.io.cml
-
This interface describes the procedures classes must implement to be plugable
into the CMLHandler.
- ICrystal - Interface in org.openscience.cdk.interfaces
-
Class representing a molecular crystal.
- ID - Static variable in class org.openscience.cdk.templates.AminoAcids
-
- IDCreator - Class in org.openscience.cdk.tools
-
Class that provides methods to give unique IDs to ChemObjects.
- IDCreator() - Constructor for class org.openscience.cdk.tools.IDCreator
-
- IDeduceBondOrderTool - Interface in org.openscience.cdk.tools
-
A common interface for tools that deduce bond orders from connectivity
and optionally additional information, like number of implicit or
explicit hydrogens, or hybridization states.
- IDENTIFIER - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- identity(int) - Static method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the identity matrix.
- IDescriptor - Interface in org.openscience.cdk.qsar
-
Classes that implement this interface are QSAR descriptor calculators.
- IDescriptorResult - Interface in org.openscience.cdk.qsar.result
-
Object that provides access to the calculated descriptor value.
- IDifference - Interface in org.openscience.cdk.tools.diff.tree
-
Object that describes the difference between two
Object
s.
- IDifferenceList - Interface in org.openscience.cdk.tools.diff.tree
-
- IDoubleBondStereochemistry - Interface in org.openscience.cdk.interfaces
-
Stereochemistry specification for double bond stereochemistry.
- IDoubleBondStereochemistry.Conformation - Enum in org.openscience.cdk.interfaces
-
Enumeration that defines the two possible values for this stereochemistry type.
- IDrawVisitor - Interface in org.openscience.cdk.renderer.visitor
-
- IEdge - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
-
Interface for the Edges (bonds) in graph.
- IElectronContainer - Interface in org.openscience.cdk.interfaces
-
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
- IElectronicPropertyCalculator - Interface in org.openscience.cdk.charges
-
Interface for classes that calculate (partial) charges centered
on atom nuclei.
- IElement - Interface in org.openscience.cdk.interfaces
-
Implements the idea of an element in the periodic table.
- IEventChemObjectReader - Interface in org.openscience.cdk.io.iterator.event
-
Interface for an iterating molecule reader.
- IFinalMapping - Interface in org.openscience.cdk.smsd.interfaces
-
Interface for mappings.
- IFingerprinter - Interface in org.openscience.cdk.fingerprint
-
Interface for fingerprint calculators.
- IFontManager - Interface in org.openscience.cdk.renderer.font
-
An interface for managing the drawing of fonts at different zoom levels.
- IFontManager.FontStyle - Enum in org.openscience.cdk.renderer.font
-
Style of the font to use to draw text.
- IFragmentAtom - Interface in org.openscience.cdk.interfaces
-
Class to represent an IPseudoAtom which embeds an IAtomContainer.
- IFragmenter - Interface in org.openscience.cdk.fragment
-
An interface for classes implementing fragmentation algorithms.
- IFunction - Interface in org.openscience.cdk.math
-
A class, which has a function value should implement this interface.
- IGenerator<T extends IChemObject> - Interface in org.openscience.cdk.renderer.generators
-
- IGeneratorParameter<T> - Interface in org.openscience.cdk.renderer.generators
-
Parameter from some rendering of the 2D diagram.
- IGraphMatrix - Interface in org.openscience.cdk.graph.matrix
-
Interface describing a molecular graph matrix calculator.
- IImplementationSpecification - Interface in org.openscience.cdk
-
Interface that is used to describe the specification of a certain
implementation of an algorithm.
- IIsotope - Interface in org.openscience.cdk.interfaces
-
Used to store and retrieve data of a particular isotope.
- IIteratingChemObjectReader<T extends IChemObject> - Interface in org.openscience.cdk.io.iterator
-
Interface for an iterating molecule reader.
- ILigand - Interface in org.openscience.cdk.geometry.cip
-
Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can
have precedence over another.
- ILoggingTool - Interface in org.openscience.cdk.tools
-
Useful for logging messages.
- ILonePair - Interface in org.openscience.cdk.interfaces
-
A LonePair is an orbital primarily located with one Atom, containing
two electrons.
- imag - Variable in class org.openscience.cdk.math.Complex
-
The imaginary part of this value
- image - Variable in class org.openscience.cdk.iupac.parser.Token
-
The string image of the token.
- image - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
-
The string image of the token.
- imageSuffix - Static variable in class org.openscience.cdk.renderer.JCPAction2D
-
Description of the Field
- imagmatrix - Variable in class org.openscience.cdk.math.IMatrix
-
the imaginary part of the content
- imagvector - Variable in class org.openscience.cdk.math.IVector
-
The imaginary part of this vector
- IMapper - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
-
Interface for the mappings (mapped objects).
- IMapping - Interface in org.openscience.cdk.interfaces
-
Represents a mapping of two atoms.
- IMatrix - Class in org.openscience.cdk.math
-
This class contains a complex matrix.
- IMatrix(int, int) - Constructor for class org.openscience.cdk.math.IMatrix
-
Creates a complex matrix
- IMatrix(Matrix) - Constructor for class org.openscience.cdk.math.IMatrix
-
Creates a complex copy of a matrix
- IMCSBase - Interface in org.openscience.cdk.smsd.interfaces
-
Interface that holds basic core interface for all MCS algorithm.
- IMolecularDescriptor - Interface in org.openscience.cdk.qsar
-
Classes that implement this interface are QSAR descriptor calculators
for IMolecule
objects.
- IMolecularFormula - Interface in org.openscience.cdk.interfaces
-
Class defining a molecular formula object.
- IMolecularFormulaSet - Interface in org.openscience.cdk.interfaces
-
Class defining a molecular formula object.
- IMolecule - Interface in org.openscience.cdk.interfaces
-
Represents a set of Molecules.
- IMoleculeSet - Interface in org.openscience.cdk.interfaces
-
Represents a set of Molecules.
- IMonomer - Interface in org.openscience.cdk.interfaces
-
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
- IMouseEventRelay - Interface in org.openscience.cdk.controller
-
Widget toolkit-independent interface to relay for mouse events.
- ImplicitHCount() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- ImplicitHCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matcher checks the number of implicit hydrogens of the Atom.
- ImplicitHCountAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom
-
Creates a new instance
- ImplicitHighAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- ImplicitHighAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- ImplicitHydrogenLigand - Class in org.openscience.cdk.geometry.cip
-
Subclass of
Ligand
to which no further recursion must be applied.
- ImplicitHydrogenLigand(IAtomContainer, VisitedAtoms, IAtom) - Constructor for class org.openscience.cdk.geometry.cip.ImplicitHydrogenLigand
-
- IN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- INCHI - Static variable in class org.openscience.cdk.CDKConstants
-
The IUPAC International Chemical Identifier.
- INChIContentProcessorTool - Class in org.openscience.cdk.io.inchi
-
Tool to help process INChI 1.12beta content.
- INChIContentProcessorTool() - Constructor for class org.openscience.cdk.io.inchi.INChIContentProcessorTool
-
- INChIFormat - Class in org.openscience.cdk.io.formats
-
- InChIGenerator - Class in org.openscience.cdk.inchi
-
This class generates the IUPAC International Chemical Identifier (InChI) for
a CDK IAtomContainer.
- InChIGeneratorFactory - Class in org.openscience.cdk.inchi
-
- INChIHandler - Class in org.openscience.cdk.io.inchi
-
SAX2 implementation for INChI XML fragment parsing.
- INChIHandler() - Constructor for class org.openscience.cdk.io.inchi.INChIHandler
-
Constructor for the IChIHandler.
- InChINumbersTools - Class in org.openscience.cdk.graph.invariant
-
Tool for calculating atom numbers using the InChI algorithm.
- InChINumbersTools() - Constructor for class org.openscience.cdk.graph.invariant.InChINumbersTools
-
- INChIPlainTextFormat - Class in org.openscience.cdk.io.formats
-
- INChIPlainTextReader - Class in org.openscience.cdk.io
-
Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text
document.
- INChIPlainTextReader(Reader) - Constructor for class org.openscience.cdk.io.INChIPlainTextReader
-
Construct a INChI reader from a Reader object.
- INChIPlainTextReader(InputStream) - Constructor for class org.openscience.cdk.io.INChIPlainTextReader
-
- INChIPlainTextReader() - Constructor for class org.openscience.cdk.io.INChIPlainTextReader
-
- INChIReader - Class in org.openscience.cdk.io
-
Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document.
- INChIReader(InputStream) - Constructor for class org.openscience.cdk.io.INChIReader
-
Construct a INChI reader from a InputStream object.
- INChIReader() - Constructor for class org.openscience.cdk.io.INChIReader
-
- InChITautomerGenerator - Class in org.openscience.cdk.tautomers
-
Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI.
- InChITautomerGenerator() - Constructor for class org.openscience.cdk.tautomers.InChITautomerGenerator
-
- InChIToStructure - Class in org.openscience.cdk.inchi
-
This class generates a CDK IAtomContainer from an InChI string.
- IncorrectUseOfCDKCoreClassError - Error in org.openscience.cdk.exception
-
Error that is thrown by debug implementations of the core CDK classes.
- IncorrectUseOfCDKCoreClassError(String) - Constructor for error org.openscience.cdk.exception.IncorrectUseOfCDKCoreClassError
-
- increaseBondOrder(IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the IBond.Order one higher.
- increaseBondOrder(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Increment the bond order of this bond.
- increaseFontSize() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Move the font size pointer up.
- indexOf(Object) - Method in class org.openscience.cdk.ConformerContainer
-
Returns the lowest index at which the specific IAtomContainer appears in the list or -1 if is not found.
- IndexOutOfBoundsException - Exception in org.openscience.cdk.graph.invariant.exception
-
- IndexOutOfBoundsException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.IndexOutOfBoundsException
-
- INDIUM - Static variable in class org.openscience.cdk.config.Elements
-
- INDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- InductiveAtomicHardnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
Inductive atomic hardness of an atom in a polyatomic system can be defined
as the "resistance" to a change of the atomic charge.
- InductiveAtomicHardnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
Constructor for the InductiveAtomicHardnessDescriptor object
- InductiveAtomicSoftnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
Inductive atomic softness of an atom in a polyatomic system can be defined
as charge delocalizing ability.
- InductiveAtomicSoftnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
Constructor for the InductiveAtomicSoftnessDescriptor object
- InductivePartialCharges - Class in org.openscience.cdk.charges
-
The calculation of the inductive partial atomic charges and equalization of
effective electronegativities is based on .
- InductivePartialCharges() - Constructor for class org.openscience.cdk.charges.InductivePartialCharges
-
Constructor for the InductivePartialCharges object
- info(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool
-
Shows INFO output for the Object.
- info(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool
-
Shows INFO output for the given Object's.
- info(Object) - Method in class org.openscience.cdk.tools.LoggingTool
-
Shows INFO output for the Object.
- info(Object, Object...) - Method in class org.openscience.cdk.tools.LoggingTool
-
Shows INFO output for the given Object's.
- info(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
-
Shows INFO output for the Object.
- info(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
-
Shows INFO output for the given Object's.
- inherit(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- inherit(ICMLModule) - Method in interface org.openscience.cdk.io.cml.ICMLModule
-
- init(IMolecule, IMolecule, boolean, boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
initialize query and target molecules.
- init(IAtomContainer, IAtomContainer, boolean, boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
initialize query and target molecules.
- init(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
initialize query and target molecules.
- init(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.Isomorphism
-
- init(IMolecule, IMolecule, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
-
initialize query and target molecules.
- init(IAtomContainer, IAtomContainer, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
-
initialize query and target molecules.
- init(String, String, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
-
Initialize the query and targetAtomCount mol via mol files
- initBookkeeping() - Method in class org.openscience.cdk.graph.AtomContainerPermutor
-
- initialize(Map<String, List>) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Initialize the AtomOrder class.
- initializeGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method initialise the given grid points with a value.
- initializeGrid(double[][][], double) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method initialise the given grid points with a value.
- initializeSpecifications(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in interface org.openscience.cdk.reaction.IReactionMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, IMoleculeSet) - Method in interface org.openscience.cdk.reaction.IReactionProcess
-
Initiates the process for the given Reaction.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.AdductionLPMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.AdductionPBMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.TautomerizationMechanism
-
Initiates the process for the given mechanism.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction
-
Initiate process.
- initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.TautomerizationReaction
-
Initiate process.
- initilize(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Initialize the atomPlacer class.
- initObjectArray() - Method in class org.openscience.cdk.graph.AtomContainerAtomPermutor
-
- initObjectArray() - Method in class org.openscience.cdk.graph.AtomContainerBondPermutor
-
- inLower() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Test to see if the lower virtual pointer is in use.
- INode - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
-
Interface for the Node (atomss) in graph.
- inRange() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Check that the font pointer is in the range (0, numberOfFonts - 1).
- inSameAromaticRing(IAtomContainer, IAtom, IAtom, IRingSet) - Static method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
-
- insertLeafChild(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpression
-
- instantiateDescriptors(List<String>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
- IntegerArrayResult - Class in org.openscience.cdk.qsar.result
-
- IntegerArrayResult() - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult
-
- IntegerArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult
-
- IntegerArrayResultType - Class in org.openscience.cdk.qsar.result
-
IDescriptorResult type for booleans.
- IntegerArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResultType
-
- IntegerDifference - Class in org.openscience.cdk.tools.diff.tree
-
- IntegerIOSetting - Class in org.openscience.cdk.io.setting
-
An class for a reader setting which must be of type String.
- IntegerIOSetting(String, int, String, String) - Constructor for class org.openscience.cdk.io.setting.IntegerIOSetting
-
- IntegerResult - Class in org.openscience.cdk.qsar.result
-
Object that provides access to the calculated descriptor value.
- IntegerResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerResult
-
- IntegerResultType - Class in org.openscience.cdk.qsar.result
-
IDescriptorResult type for booleans.
- IntegerResultType() - Constructor for class org.openscience.cdk.qsar.result.IntegerResultType
-
- intValue() - Method in class org.openscience.cdk.qsar.result.IntegerResult
-
- inUpper() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Test to see if the upper virtual pointer is in use.
- InvalidSmilesException - Exception in org.openscience.cdk.exception
-
- InvalidSmilesException(String) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException
-
- InvalidSmilesException(String, Exception) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException
-
- INVARIANCE_PAIR - Static variable in class org.openscience.cdk.smiles.InvPair
-
The description used to set the invariance numbers in the atom's property
- inverse() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the transpose of this matrix.
- InverseSymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
A QueryAtom that matches all symbols but those in this container.
- InverseSymbolSetQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
Constructor for the InverseSymbolSetQueryAtom object
- invertLine(int, int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the resulting matrix of an elementary linear operation that consists of inverting two lines.
- InvPair - Class in org.openscience.cdk.smiles
-
This is used to hold the invariance numbers for the canonical labeling of
IAtomContainer
s.
- InvPair() - Constructor for class org.openscience.cdk.smiles.InvPair
-
- InvPair(long, IAtom) - Constructor for class org.openscience.cdk.smiles.InvPair
-
- IODINE - Static variable in class org.openscience.cdk.config.Elements
-
- IODO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- IonizationPotentialTool - Class in org.openscience.cdk.tools
-
This class contains the necessary information to predict ionization
potential energy.
- IonizationPotentialTool() - Constructor for class org.openscience.cdk.tools.IonizationPotentialTool
-
- IOSetting - Class in org.openscience.cdk.io.setting
-
An interface for reader settings.
- IOSetting(String, int, String, String) - Constructor for class org.openscience.cdk.io.setting.IOSetting
-
The default constructor that sets this field.
- IParameterReact - Interface in org.openscience.cdk.reaction.type.parameters
-
Interface for classes that generate parameters used in reactions.
- IPAtomicHOSEDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class returns the ionization potential of an atom containg lone
pair electrons.
- IPAtomicHOSEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
Constructor for the IPAtomicHOSEDescriptor object.
- IPAtomicLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class returns the ionization potential of an atom containing lone
pair electrons.
- IPAtomicLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
Constructor for the IPAtomicLearningDescriptor object.
- IPBondLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond
-
This class returns the ionization potential of a Bond.
- IPBondLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
-
Constructor for the IPBondLearningDescriptor object
- IPDBAtom - Interface in org.openscience.cdk.interfaces
-
A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
- IPDBMonomer - Interface in org.openscience.cdk.interfaces
-
Represents the idea of an protein monomer as found in PDB files.
- IPDBPolymer - Interface in org.openscience.cdk.interfaces
-
A PDBPolymer is a subclass of a BioPolymer which is supposed to store
additional informations about the BioPolymer which are connected to BioPolymers.
- IPDBStructure - Interface in org.openscience.cdk.interfaces
-
Represents the idea of an chemical structure.
- IPMolecularLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
This class returns the ionization potential of a molecule.
- IPMolecularLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Constructor for the IPMolecularLearningDescriptor object
- IPolymer - Interface in org.openscience.cdk.interfaces
-
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
- IPseudoAtom - Interface in org.openscience.cdk.interfaces
-
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
- IQuery - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
-
Interface for the query molecule/graph.
- IQueryAtom - Interface in org.openscience.cdk.isomorphism.matchers
-
Defines the ability to be matched against
IAtom
's.
- IQueryAtomContainer - Interface in org.openscience.cdk.isomorphism.matchers
-
General concept of a IAtomContainer aimed at doing molecular subgraph
queries using the UniversalIsomorphismTester.
- IQueryBond - Interface in org.openscience.cdk.isomorphism.matchers
-
Defines the abililty to be matched against IBond's.
- IQueryCompiler - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
-
Interface for the query graph generator.
- IR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- IRandomAccessChemObjectReader<T> - Interface in org.openscience.cdk.io.random
-
- IRDFWeightFunction - Interface in org.openscience.cdk.geometry
-
Weight function used in the RDFCalculator
.
- IReaction - Interface in org.openscience.cdk.interfaces
-
Represents the idea of a chemical reaction.
- IReaction.Direction - Enum in org.openscience.cdk.interfaces
-
Permissible reaction directions.
- IReactionMechanism - Interface in org.openscience.cdk.reaction
-
Classes that implement this interface are reaction mechanisms.
- IReactionProcess - Interface in org.openscience.cdk.reaction
-
Classes that implement this interface are Reactions types.
- IReactionScheme - Interface in org.openscience.cdk.interfaces
-
Classes that implement this interface of a scheme.
- IReactionSet - Interface in org.openscience.cdk.interfaces
-
A set of reactions, for example those taking part in a reaction.
- IReaderListener - Interface in org.openscience.cdk.io.listener
-
Allows monitoring of progress of file reader activities.
- IRenderer<T extends IChemObject> - Interface in org.openscience.cdk.renderer
-
Interface that all 2D renderers implement.
- IRenderingElement - Interface in org.openscience.cdk.renderer.elements
-
Widget toolkit-independent, abstract definition of something to be drawn.
- IRenderingVisitor - Interface in org.openscience.cdk.renderer.elements
-
An
IRenderingVisitor
is responsible of converting an abstract
chemical drawing into a widget set specific drawing.
- IResourceFormat - Interface in org.openscience.cdk.io.formats
-
This class is the interface that all ResourceFormat's should implement.
- IRGroupQuery - Interface in org.openscience.cdk.isomorphism.matchers
-
Interface definition for Rgroup query classes.
- IRIDIUM - Static variable in class org.openscience.cdk.config.Elements
-
- IRIDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- IRing - Interface in org.openscience.cdk.interfaces
-
Class representing a ring structure in a molecule.
- IRingSet - Interface in org.openscience.cdk.interfaces
-
Maintains a set of Ring objects.
- IRON - Static variable in class org.openscience.cdk.config.Elements
-
- IRON - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- IRule - Interface in org.openscience.cdk.formula.rules
-
Interface which groups all method that validate a IMolecularFormula.
- IS_HYDROGENBOND_ACCEPTOR - Static variable in class org.openscience.cdk.CDKConstants
-
Sets to true if the atom is an hydrogen bond acceptor.
- IS_HYDROGENBOND_DONOR - Static variable in class org.openscience.cdk.CDKConstants
-
Sets to true if the atom is an hydrogen bond donor.
- IS_TYPEABLE - Static variable in class org.openscience.cdk.CDKConstants
-
Flag is set if an atom could be typed.
- ISALIPHATIC - Static variable in class org.openscience.cdk.CDKConstants
-
Flag that is set if a chemobject is part of an aliphatic chain.
- isAntisymmetric() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Verifies if the matrix is antisymmetric, that is if the matrix is equal to the opposite of
it's transpose.
- isAromatic(IRing, IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.AromaticityCalculator
-
Tests the ring
in the molecule
for aromaticity.
- ISAROMATIC - Static variable in class org.openscience.cdk.CDKConstants
-
Flag is set if chemobject is part of an aromatic system.
- isAtomMatch(AtomMatcher, AtomMatcher, IAtomContainer, IBond, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher
-
- isBondMatch(BondMatcher, IAtomContainer, IBond, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher
-
- isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
-
- isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
-
- isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
-
- isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
-
- isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
-
- isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
- isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
- isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
- isCachedAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor
-
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
- isCachedAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor
-
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
- isCisTrans(IAtom, IAtom, IAtom, IAtom, IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools
-
Says if two atoms are in cis or trans position around a double bond.
- isClockwise() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- isClockwise() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality
-
- isColinear(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Checks the three supplied points to see if they fall on the same line.
- ISCONJUGATED - Static variable in class org.openscience.cdk.CDKConstants
-
Flag is set if chemobject is part of a conjugated system.
- isConnected(IAtomContainer) - Static method in class org.openscience.cdk.graph.ConnectivityChecker
-
- isConnected(int, int) - Method in class org.openscience.cdk.signature.SignatureQuotientGraph
-
- isConnectedTo(IBond) - Method in class org.openscience.cdk.Bond
-
Checks whether a bond is connected to another one.
- isConnectedTo(IBond) - Method in class org.openscience.cdk.debug.DebugBond
-
- isConnectedTo(IBond) - Method in interface org.openscience.cdk.interfaces.IBond
-
Checks whether a bond is connected to another one.
- isConnectedTo(IBond) - Method in class org.openscience.cdk.silent.Bond
-
Checks whether a bond is connected to another one.
- isCycle() - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- isDashed - Variable in class org.openscience.cdk.renderer.elements.WedgeLineElement
-
If true, the wedge should be rendered as a dashed triangle.
- isDead() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
-
Returns true if no match will come from this IState.
- isDead() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
-
Returns true if no match will come from this IState.
- isDebugEnabled() - Method in interface org.openscience.cdk.tools.ILoggingTool
-
Use this method for computational demanding debug info.
- isDebugEnabled() - Method in class org.openscience.cdk.tools.LoggingTool
-
Use this method for computational demanding debug info.
- isDebugEnabled() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
-
Use this method for computational demanding debug info.
- isDiagonal() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Verifies whether or not the matrix is diagonal.
- isDisconnected() - Method in class org.openscience.cdk.graph.SpanningTree
-
- isElement(String) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Checks whether the given element exists.
- isEmpty() - Method in class org.openscience.cdk.AtomContainer
-
- isEmpty() - Method in class org.openscience.cdk.AtomContainerSet
-
- isEmpty() - Method in class org.openscience.cdk.ChemModel
-
- isEmpty() - Method in class org.openscience.cdk.ConformerContainer
-
Checks whether any conformers are stored or not.
- isEmpty() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- isEmpty() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- isEmpty() - Method in class org.openscience.cdk.debug.DebugChemModel
-
- isEmpty() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- isEmpty() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- isEmpty() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Indicates whether this container is empty.
- isEmpty() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns true if this IAtomContainerSet is empty.
- isEmpty() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Returns true if this ChemModel is empty.
- isEmpty() - Method in interface org.openscience.cdk.interfaces.IReactionSet
-
Returns true if this IReactionSet is empty.
- isEmpty() - Method in interface org.openscience.cdk.interfaces.IRingSet
-
Returns true if this IRingSet has no atoms.
- isEmpty() - Method in class org.openscience.cdk.ReactionSet
-
- isEmpty() - Method in class org.openscience.cdk.signature.Orbit
-
Checks to see if the orbit is empty.
- isEmpty() - Method in class org.openscience.cdk.silent.AtomContainer
-
- isEmpty() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
- isEmpty() - Method in class org.openscience.cdk.silent.ChemModel
-
- isEmpty() - Method in class org.openscience.cdk.silent.ReactionSet
-
- isEnabled() - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Is this action runnable?
- ISequenceSubRule<ILigand> - Interface in org.openscience.cdk.geometry.cip.rules
-
Sequence sub rule used in the CIP method to decide which of the two ligands takes
precedence .
- isEven(int) - Static method in class org.openscience.cdk.math.MathTools
-
- isExpanded() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- isExpanded() - Method in class org.openscience.cdk.FragmentAtom
-
- isExpanded() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
-
Helper method to indicate that the method should be drawn fully, and not
just the abbreviated form.
- isExpanded() - Method in class org.openscience.cdk.silent.FragmentAtom
-
- isFilled() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
-
The opposite of a method like "isEmpty"
- isGoal() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
-
Returns true if all atoms in the query molecule have been
mapped.
- isGoal() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
-
Returns true if all atoms in the query molecule have been
mapped.
- isHigherOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns true if the first bond has a higher bond order than the second bond.
- ISimpleChemObjectReader - Interface in org.openscience.cdk.io
-
This class is the interface that all IO readers should implement.
- isIndexCreated() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- ISingleElectron - Interface in org.openscience.cdk.interfaces
-
A Single Electron is an orbital which is occupied by only one electron.
- ISINRING - Static variable in class org.openscience.cdk.CDKConstants
-
Flag that is set when the chemobject is part of a ring.
- isInterrupted() - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool
-
Returns if the next or running calculation should be interrupted.
- isInterrupted() - Method in class org.openscience.cdk.smiles.FixBondOrdersTool
-
Returns if the next or running calculation should be interrupted.
- isInvertible() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Verifies if the matrix is invertible or not by asking for its determinant.
- isIsomorph(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Tests if g1 and g2 are isomorph.
- isIsomorph(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Tests if sourceGraph and targetGraph are isomorph.
- isIsomorphic(IMolecule, IMolecule) - Method in class org.openscience.cdk.isomorphism.IsomorphismTester
-
Checks whether a given molecule is isomorphic with the one
that has been assigned to this IsomorphismTester at contruction time
- isIsomorphic(IMolecule) - Method in class org.openscience.cdk.isomorphism.IsomorphismTester
-
Checks whether a given molecule is isomorphic with the one
that has been assigned to this IsomorphismTester at contruction time
- isLeft(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Says if an atom is on the left side of a another atom seen from a certain
atom or not
- isLowerOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns true if the first bond has a lower bond order than the second bond.
- isMatchBond() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- isMatchBonds() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- isMatchFeasible(Match) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
-
Returns true if the given match will work with the current
map, or false otherwise.
- isMatchFeasible(Match) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
-
Returns true if the given match will work with the current
map, or false otherwise.
- isNewMatrix() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Checks if its a new Matrix.
- ISNOTINRING - Static variable in class org.openscience.cdk.CDKConstants
-
Flag that is set when the chemobject is part of a ring.
- IsoAlkanes - Class in org.openscience.cdk.templates.saturatedhydrocarbons
-
This class contains methods for generating simple organic alkanes.
- IsoAlkanes() - Constructor for class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
-
- isOctahedral(IAtom, IAtom, IAtom, IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Checks these 7 atoms to see if they are at the points of an octahedron.
- isOdd(int) - Static method in class org.openscience.cdk.math.MathTools
-
- isOK(IMolecule) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool
-
Determines if, according to the algorithms implemented in this class, the given
molecule has properly distributed double bonds.
- Isomorphism - Class in org.openscience.cdk.smsd
-
This class implements the Isomorphism- a multipurpose structure comparison tool.
- Isomorphism(Algorithm, boolean) - Constructor for class org.openscience.cdk.smsd.Isomorphism
-
This is the algorithm factory and entry port for all the MCS algorithm in the Isomorphism
supported algorithm
Algorithm
types:
- 0: Default,
- 1: MCSPlus,
- 2: VFLibMCS,
- 3: CDKMCS,
- 4: SubStructure
- IsomorphismTester - Class in org.openscience.cdk.isomorphism
-
A too simplistic implementation of an isomorphism test for chemical graphs.
- IsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester
-
Constructor for the IsomorphismTester object
- IsomorphismTester(IMolecule) - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester
-
Constructor for the IsomorphismTester object
- Isotope - Class in org.openscience.cdk
-
Used to store and retrieve data of a particular isotope.
- Isotope(String) - Constructor for class org.openscience.cdk.Isotope
-
Constructor for the Isotope object.
- Isotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.Isotope
-
Constructor for the Isotope object.
- Isotope(int, String, double, double) - Constructor for class org.openscience.cdk.Isotope
-
Constructor for the Isotope object.
- Isotope(String, int) - Constructor for class org.openscience.cdk.Isotope
-
Constructor for the Isotope object.
- Isotope(IElement) - Constructor for class org.openscience.cdk.Isotope
-
Constructs an empty by copying the symbol, atomic number,
flags, and identifier from the given IElement.
- ISOTOPE - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- Isotope - Class in org.openscience.cdk.silent
-
Used to store and retrieve data of a particular isotope.
- Isotope(String) - Constructor for class org.openscience.cdk.silent.Isotope
-
Constructor for the Isotope object.
- Isotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.silent.Isotope
-
Constructor for the Isotope object.
- Isotope(int, String, double, double) - Constructor for class org.openscience.cdk.silent.Isotope
-
Constructor for the Isotope object.
- Isotope(String, int) - Constructor for class org.openscience.cdk.silent.Isotope
-
Constructor for the Isotope object.
- Isotope(IElement) - Constructor for class org.openscience.cdk.silent.Isotope
-
Constructs an empty by copying the symbol, atomic number,
flags, and identifier from the given IElement.
- IsotopeContainer - Class in org.openscience.cdk.formula
-
This class defines a isotope container.
- IsotopeContainer() - Constructor for class org.openscience.cdk.formula.IsotopeContainer
-
Constructor of the IsotopeContainer object.
- IsotopeContainer(IMolecularFormula, double) - Constructor for class org.openscience.cdk.formula.IsotopeContainer
-
Constructor of the IsotopeContainer object setting a IMolecularFormula
object and intensity value.
- IsotopeContainer(double, double) - Constructor for class org.openscience.cdk.formula.IsotopeContainer
-
Constructor of the IsotopeContainer object setting a mass
and intensity value.
- IsotopeDiff - Class in org.openscience.cdk.tools.diff
-
- IsotopeFactory - Class in org.openscience.cdk.config
-
Used to store and return data of a particular isotope.
- IsotopeHandler - Class in org.openscience.cdk.config.isotopes
-
Reads an isotope list in CML2 format.
- IsotopeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.isotopes.IsotopeHandler
-
Constructs an IsotopeHandler used by the IsotopeReader.
- IsotopePattern - Class in org.openscience.cdk.formula
-
This class defines the properties of a deisotoped
pattern distribution.
- IsotopePattern() - Constructor for class org.openscience.cdk.formula.IsotopePattern
-
Constructor of the IsotopePattern object.
- IsotopePatternGenerator - Class in org.openscience.cdk.formula
-
Generates all Combinatorial chemical isotopes given a structure.
- IsotopePatternGenerator() - Constructor for class org.openscience.cdk.formula.IsotopePatternGenerator
-
Constructor for the IsotopeGenerator.
- IsotopePatternGenerator(double) - Constructor for class org.openscience.cdk.formula.IsotopePatternGenerator
-
Constructor for the IsotopeGenerator.
- IsotopePatternManipulator - Class in org.openscience.cdk.formula
-
Class to manipulate IsotopePattern objects.
- IsotopePatternManipulator() - Constructor for class org.openscience.cdk.formula.IsotopePatternManipulator
-
- IsotopePatternRule - Class in org.openscience.cdk.formula.rules
-
This class validate if the Isotope Pattern from a given IMolecularFormula
correspond with other to compare.
- IsotopePatternRule() - Constructor for class org.openscience.cdk.formula.rules.IsotopePatternRule
-
Constructor for the IsotopePatternRule object.
- IsotopePatternSimilarity - Class in org.openscience.cdk.formula
-
This class gives a score hit of similarity between two different
isotope abundance pattern.
- IsotopePatternSimilarity() - Constructor for class org.openscience.cdk.formula.IsotopePatternSimilarity
-
Constructor for the IsotopePatternSimilarity object.
- IsotopeReader - Class in org.openscience.cdk.config.isotopes
-
Reader that instantiates an XML parser and customized handler to process
the isotope information in the CML2 isotope data file.
- IsotopeReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.isotopes.IsotopeReader
-
Instantiates a new reader that parses the XML from the given input
.
- isotopes() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- isotopes() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- isotopes() - Method in class org.openscience.cdk.formula.AdductFormula
-
Returns an Iterator for looping over all isotopes in this adduct formula.
- isotopes() - Method in class org.openscience.cdk.formula.MolecularFormula
-
Returns an Iterator for looping over all isotopes in this IMolecularFormula.
- isotopes() - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Returns an Iterator for looping over all isotopes in this MolecularFormulaExpand.
- isotopes() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Returns an Iterator for looping over all isotopes in this adduct formula.
- isotopes() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Returns an
Iterable
for looping over all isotopes in this IMolecularFormula.
- isotopes() - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns an Iterator for looping over all isotopes in this adduct formula.
- isotopes() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Returns an Iterator for looping over all isotopes in this IMolecularFormula.
- ISOTROPIC_SHIELDING - Static variable in class org.openscience.cdk.CDKConstants
-
The Isotropic Shielding, usually calculated by
a quantum chemistry program like Gaussian.
- isOverSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Checks if the current atom has exceeded its bond order sum value.
- ISPLACED - Static variable in class org.openscience.cdk.CDKConstants
-
Flag that is set if the chemobject is placed (somewhere).
- isPopupAction() - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Gets the popupAction attribute of the JCPAction object
- isPositive() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge
-
Returns true if charge is positive.
- isPreservingAromaticity() - Method in class org.openscience.cdk.smiles.SmilesParser
-
Gets the (default false) setting to preserve aromaticity as provided in the Smiles itself.
- IsProtonInAromaticSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This descriptor returns 1 if the protons is directly bonded to an aromatic system,
it returns 2 if the distance between aromatic system and proton is 2 bonds,
and it return 0 for other positions.
- IsProtonInAromaticSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
-
Constructor for the IsProtonInAromaticSystemDescriptor object
- IsProtonInConjugatedPiSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class evaluates if a proton is joined to a conjugated system.
- IsProtonInConjugatedPiSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
-
Constructor for the IsProtonInConjugatedPiSystemDescriptor object
- isReady() - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- isRestH() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- isSameRing(IRingSet, IAtom, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Checks if atom1
and atom2
share membership in the same ring or ring system.
- isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.CDKValencyChecker
-
- isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.CDKValencyChecker
-
- isSaturated(IAtomContainer) - Method in interface org.openscience.cdk.tools.IValencyChecker
-
- isSaturated(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.tools.IValencyChecker
-
- isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
-
Determines of all atoms on the AtomContainer have the
right number the lone pair electrons.
- isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
-
Checks if an Atom is saturated their lone pair electrons
by comparing it with known AtomTypes.
- isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Determines of all atoms on the AtomContainer are saturated.
- isSaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Returns whether a bond is saturated.
- isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Checks whether an Atom is saturated by comparing it with known AtomTypes.
- isSaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Returns whether a bond is saturated.
- isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Determines of all atoms on the AtomContainer are saturated.
- isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Checks whether an Atom is saturated by comparing it with known AtomTypes.
- isSet() - Method in class org.openscience.cdk.io.setting.BooleanIOSetting
-
- isSetParameter() - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
-
Get if this parameter needs to take account.
- isSetParameter() - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
-
Get if this parameter needs to take account.
- isSquare() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Verifies if the matrix is square, that is if it has an equal number of lines and columns.
- isSquarePlanar(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Says if an atom as a center of a square planar chirality.
- isSquarePlanar(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Checks these four atoms for square planarity.
- isStereo(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Says if an atom as a center of any valid stereo configuration or not.
- isStereoMisMatch() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns true if mols have different stereo
chemistry else false if no stereo mismatch.
- isStereoMisMatch() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns true if mols have different stereo
chemistry else false if no stereo mismatch.
- isSubgraph(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Tests if g2 a subgraph of g1.
- isSubgraph(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Tests if targetGraph atom subgraph of sourceGraph.
- isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Initialise the Subgraph search algorithm.
- isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
- isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
- isSubgraph() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Checks if query is a subgraph of the target.
- isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractSubGraph
-
Initialise the Subgraph search algorithm.
- isSubgraph() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Checks if query is a subgraph of the target.
- isSubset(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool
-
Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1.
- isSymmetric() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Verifies if the matrix is symmetric, that is if the matrix is equal to it's transpose.
- IState - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
-
Interface for the storing the states of the mapping in the VF algorithm.
- IStereoElement - Interface in org.openscience.cdk.interfaces
-
Represents the concept of a stereo element in the molecule.
- isTetrahedral(IAtomContainer, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
-
Says if an atom as a center of a tetrahedral chirality.
- isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
-
- isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
- isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
- isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
- isTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- isTimeoutFlag() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Returns true if a time out occured else false
- isTimeOutFlag() - Method in class org.openscience.cdk.smsd.global.TimeOut
-
Return true if its a timeout else return false.
- IStrand - Interface in org.openscience.cdk.interfaces
-
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
- isTriangularInferior() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Verifies if the matrix is triangular inferior or not.
- isTriangularSuperior() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Verifies if the matrix is triangular superior or not.
- isTrigonalBipyramidal(IAtom, IAtom, IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Checks these 6 atoms to see if they form a trigonal-bipyramidal shape.
- isTrigonalBipyramidalOrOctahedral(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Says if an atom as a center of a trigonal-bipyramidal or actahedral
chirality.
- IStructureGenerationListener - Interface in org.openscience.cdk.structgen
-
- isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Returns whether a bond is unsaturated.
- isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Returns whether a bond is unsaturated.
- isUnspecified() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- isUnspecified() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality
-
- isValid(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaChecker
-
Validate if a IMolecularFormula is valid.
- isValid(String) - Static method in class org.openscience.cdk.index.CASNumber
-
Checks whether the registry number is valid.
- isValidDoubleBondConfiguration(IAtomContainer, IBond) - Static method in class org.openscience.cdk.geometry.BondTools
-
Tells if a certain bond is center of a valid double bond configuration.
- isValidDoubleBondConfiguration(IAtomContainer, IBond) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Tells if a certain bond is center of a valid double bond configuration.
- isValidOccurrenceSyntax(String) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Validates the occurrence value.
- isValidRgroupQueryLabel(String) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
Validates a Pseudo atom's label to be valid RGroup query label (R1..R32).
- isValidSum(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaChecker
-
Validate if a IMolecularFormula is valid.
- isVisited(IAtom) - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
Returns a true if the atom has been visited before.
- isVisited(IAtom) - Method in class org.openscience.cdk.geometry.cip.Ligand
-
- isVisited(IAtom) - Method in class org.openscience.cdk.geometry.cip.VisitedAtoms
-
Returns true if the given atom already has been visited.
- isXMLBased() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.BSFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.HINFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- isXMLBased() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Indicates if the format is an XML-based language.
- isXMLBased() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Indicates if the format is an XML-based language.
- isXMLBased() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
- isXMLBased() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- IteratingMDLConformerReader - Class in org.openscience.cdk.io.iterator
-
Iterate over conformers of a collection of molecules stored in SDF format.
- IteratingMDLConformerReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
-
- IteratingMDLConformerReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
-
- IteratingMDLReader - Class in org.openscience.cdk.io.iterator
-
Iterating MDL SDF reader.
- IteratingMDLReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLReader
-
Constructs a new IteratingMDLReader that can read Molecule from a given Reader.
- IteratingMDLReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLReader
-
Constructs a new IteratingMDLReader that can read Molecule from a given InputStream.
- IteratingMDLReader(InputStream, IChemObjectBuilder, boolean) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLReader
-
Constructs a new IteratingMDLReader that can read Molecule from a given a
InputStream.
- IteratingMDLReader(Reader, IChemObjectBuilder, boolean) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLReader
-
Constructs a new IteratingMDLReader that can read Molecule from a given a
Reader.
- IteratingPCCompoundASNReader - Class in org.openscience.cdk.io.iterator
-
Iterating PubChem PCCompound ASN reader.
- IteratingPCCompoundASNReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given Reader.
- IteratingPCCompoundASNReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given InputStream and IChemObjectBuilder.
- IteratingPCCompoundXMLReader - Class in org.openscience.cdk.io.iterator
-
Iterating PubChem PCCompound ASN.1 XML reader.
- IteratingPCCompoundXMLReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
Constructs a new IteratingPCCompoundXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
- IteratingPCCompoundXMLReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
Constructs a new IteratingPCCompoundXLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
- IteratingPCSubstancesXMLReader - Class in org.openscience.cdk.io.iterator
-
Iterating PubChem PC-Substances ASN.1 XML reader.
- IteratingPCSubstancesXMLReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
- IteratingPCSubstancesXMLReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
- IteratingSMILESReader - Class in org.openscience.cdk.io.iterator
-
Iterating SMILES file reader.
- IteratingSMILESReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.
- IteratingSMILESReader(InputStream) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream.
- IteratingSMILESReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.
- iterator() - Method in class org.openscience.cdk.ConformerContainer
-
Gets an iterator over the conformers.
- iterator() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- iterator() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
- iterator() - Method in class org.openscience.cdk.formula.AdductFormula
-
Returns an Iterator for looping over all IMolecularFormula
in this adduct formula.
- iterator() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Returns an Iterator for looping over all IMolecularFormula
in this MolecularFormulaSet.
- iterator() - Method in class org.openscience.cdk.renderer.elements.ElementGroup
- iterator() - Method in class org.openscience.cdk.signature.Orbit
- iterator() - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns an Iterator for looping over all IMolecularFormula
in this adduct formula.
- iterator() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Returns an Iterator for looping over all IMolecularFormula
in this MolecularFormulaSet.
- ITetrahedralChirality - Interface in org.openscience.cdk.interfaces
-
Stereochemistry specification for quadrivalent atoms.
- ITetrahedralChirality.Stereo - Enum in org.openscience.cdk.interfaces
-
Enumeration that defines the two possible chiralities for this stereochemistry type.
- IValencyChecker - Interface in org.openscience.cdk.tools
-
A common interface for SaturationChecker and ValencyChecker.
- IValidator - Interface in org.openscience.cdk.validate
-
Interface that Validators need to implement to be used in validation.
- IVector - Class in org.openscience.cdk.math
-
- IVector(int) - Constructor for class org.openscience.cdk.math.IVector
-
Constructs a vector with "size"-elements
- IViewEventRelay - Interface in org.openscience.cdk.controller
-
- IWriterListener - Interface in org.openscience.cdk.io.listener
-
Allows monitoring of progress of writing activities.
- s - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- S - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SAMARIUM - Static variable in class org.openscience.cdk.config.Elements
-
- sample(IMolecule) - Static method in class org.openscience.cdk.structgen.VicinitySampler
-
Choose any possible quadruple of the set of atoms
in ac and establish all of the possible bonding schemes according to
Faulon's equations.
- SANARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- saturate(IAtomContainer) - Method in interface org.openscience.cdk.tools.IDeduceBondOrderTool
-
- saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
-
Saturates a molecule by setting appropriate number lone pair electrons.
- saturate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
-
Saturates an IAtom by adding the appropriate number lone pairs.
- saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
The method is known to fail for certain compounds.
- saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Saturates a molecule by setting appropriate bond orders.
- saturate(IBond[], IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Saturates a set of Bonds in an AtomContainer.
- saturateByIncreasingBondOrder(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Tries to saturate a bond by increasing its bond orders by 1.0.
- saturateRingSystems(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
- SaturationChecker - Class in org.openscience.cdk.tools
-
Provides methods for checking whether an atoms valences are saturated with
respect to a particular atom type.
- SaturationChecker() - Constructor for class org.openscience.cdk.tools.SaturationChecker
-
- SB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- scaleMolecule(IAtomContainer, Dimension, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Scales a molecule such that it fills a given percentage of a given
dimension
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
- scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Multiplies all the coordinates of the atoms of the given molecule with the
scalefactor.
- SCANDIUM - Static variable in class org.openscience.cdk.config.Elements
-
- SCANDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- SDFFormat - Class in org.openscience.cdk.io.formats
-
- SDFWriter - Class in org.openscience.cdk.io
-
Writes MDL SD files ().
- SDFWriter(Writer) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Constructs a new SDFWriter that writes to the given
Writer
.
- SDFWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Constructs a new MDLWriter that can write to a given
OutputStream
.
- SDFWriter() - Constructor for class org.openscience.cdk.io.SDFWriter
-
- se - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SEABORGIUM - Static variable in class org.openscience.cdk.config.Elements
-
- SEABORGIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
General
RGraph
parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input.
- search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
General Rgraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Initialise the MCS search algorithm.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Initialise the MCS search algorithm.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Initialise the MCS search algorithm.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Initialise the MCS search algorithm.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
-
Initialise the MCS search algorithm.
- secondPointX - Variable in class org.openscience.cdk.renderer.elements.LineElement
-
The x-coordinate of the second point.
- secondPointY - Variable in class org.openscience.cdk.renderer.elements.LineElement
-
The y-coordinate of the second point.
- select(IChemModel) - Method in class org.openscience.cdk.renderer.selection.AbstractSelection
-
Perform a selection by some method.
- select(IChemModel) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
-
Perform a selection by some method.
- SELENIUM - Static variable in class org.openscience.cdk.config.Elements
-
- SELENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- SERIAL_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
-
- set(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
-
- set(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- set(Class<T>, S) - Method in class org.openscience.cdk.renderer.RendererModel
-
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Initialise the query and target molecule.
- set(List<Map<Integer, Integer>>) - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Sets mapping list
- set(List<Map<Integer, Integer>>) - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Sets mapping list
- set(MolHandler, MolHandler) - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Initialise the query and target molecule.
- SET_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator
-
Old ID generation policy - to generate IDs unique over the entire set
- setA(Vector3d) - Method in class org.openscience.cdk.Crystal
-
Sets the A unit cell axes in Cartesian coordinates in a
Euclidean space.
- setA(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setA(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the A unit cell axes in carthesian coordinates in a
eucledian space.
- setA(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the A unit cell axes in Cartesian coordinates in a
Euclidean space.
- setAbout(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setAllMap(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the 'finAllMap' option.
- setAllMap(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Sets the 'finAllMap' option.
- setAllStructure(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the 'AllStructres' option.
- setAllStructure(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Sets the 'AllStructres' option.
- setAltLoc(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setAltLoc(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Alternate location indicator of this atom.
- setAltLoc(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Alternate location indicator of this atom.
- setAltLoc(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Alternate location indicator of this atom.
- setArrayValue(double[][]) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Resets the value of the matrix to the given array of double numbers
- setAtom(int, IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Sets the atom at position number
in [0,..].
- setAtom(IAtom, int) - Method in class org.openscience.cdk.Bond
-
Sets an Atom in this bond.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- setAtom(IAtom, int) - Method in class org.openscience.cdk.debug.DebugBond
-
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
- setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setAtom(int, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Set the atom at position number
in [0,..].
- setAtom(IAtom, int) - Method in interface org.openscience.cdk.interfaces.IBond
-
Sets an Atom in this bond.
- setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair
-
Sets the associated Atom.
- setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron
-
Sets the associated Atom.
- setAtom(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
-
- setAtom(IAtom) - Method in class org.openscience.cdk.LonePair
-
Sets the associated Atom.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Sets the atom at position number
in [0,..].
- setAtom(IAtom, int) - Method in class org.openscience.cdk.silent.Bond
-
Sets an Atom in this bond.
- setAtom(IAtom) - Method in class org.openscience.cdk.silent.LonePair
-
Sets the associated Atom.
- setAtom(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron
-
Sets the associated Atom.
- setAtom(IAtom) - Method in class org.openscience.cdk.SingleElectron
-
Sets the associated Atom.
- setAtom(IAtom) - Method in class org.openscience.cdk.smiles.InvPair
-
- setAtomAt(IAtom, int) - Method in class org.openscience.cdk.Association
-
Sets an Atom in this Association.
- setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
-
- setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
-
- setAtomCheckRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.graph.AtomContainerPermutor
-
- setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom
-
Sets IAtomContainer.
- setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom
-
- setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator
-
Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugElement
-
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.Element
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IElement
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.silent.Element
-
Sets the atomic number of this element.
- setAtomPlacer(AtomPlacer) - Method in class org.openscience.cdk.layout.RingPlacer
-
- setAtomProperties(IAtomContainer, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Sets a property on all Atom
s in the given container.
- setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- setAtomProperties(IChemModel, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Sets the AtomProperties of all Atoms inside an IChemModel.
- setAtomProperties(IMoleculeSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- setAtomProperties(IReaction, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- setAtomProperties(IReactionSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.Association
-
Sets the array of atoms making up this Association.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.AtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.Bond
-
Sets the array of atoms making up this bond.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBond
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugRing
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IBond
-
Sets the array of atoms making up this bond.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.AtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.Bond
-
Sets the array of atoms making up this bond.
- setAtomTypeName(String) - Method in class org.openscience.cdk.AtomType
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setAtomTypeName(String) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the if attribute of the AtomType object.
- setAtomTypes(List<IAtomType>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the atomTypes attribute of the ForceFieldConfigurator object
- setB(Vector3d) - Method in class org.openscience.cdk.Crystal
-
Sets the B unit cell axes in Cartesian coordinates.
- setB(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setB(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the B unit cell axes in carthesian coordinates.
- setB(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the B unit cell axes in Cartesian coordinates.
- setBondInSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
set timeout in mins (default 1.00 min) for bond insensitive searches
- setBondInSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.Isomorphism
-
set timeout in mins (default 1.00 min) for bond insensitive searches
- setBondLength(double) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Set the bond length used for laying out the molecule.
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
- setBondOrderSum(Double) - Method in class org.openscience.cdk.AtomType
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setBondOrderSum(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBonds(IBond[]) - Method in class org.openscience.cdk.AtomContainer
-
Sets the array of bonds of this AtomContainer.
- setBonds(IBond[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Sets the array of bonds of this AtomContainer.
- setBonds(IBond[]) - Method in class org.openscience.cdk.silent.AtomContainer
-
Sets the array of bonds of this AtomContainer.
- setBondSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
set timeout in mins (default 0.10 min) for bond sensitive searches
- setBondSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.Isomorphism
-
set timeout in mins (default 0.10 min) for bond sensitive searches
- setBondType(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond
-
Sets type of bond.
- setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
- setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
- setC(Vector3d) - Method in class org.openscience.cdk.Crystal
-
Sets the C unit cell axes in Cartesian coordinates.
- setC(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setC(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the C unit cell axes in carthesian coordinates.
- setC(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the C unit cell axes in Cartesian coordinates.
- setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer
-
- setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Chain identifier of this atom.
- setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Sets the Chain ID of this monomer.
- setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Chain identifier of this atom.
- setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- setChainID(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Chain identifier of this atom.
- setChainID(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setCharge(Double) - Method in class org.openscience.cdk.Atom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- setCharge(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setCharge(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- setCharge(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setCharge(Integer) - Method in class org.openscience.cdk.formula.AdductFormula
-
Deprecated.
- setCharge(double) - Method in class org.openscience.cdk.formula.IsotopePattern
-
Set the charge in this pattern.
- setCharge(Integer) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Sets the partial charge of this IMolecularFormula.
- setCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Sets the partial charge of this adduct formula.
- setCharge(Double) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Sets the partial charge of this IMolecularFormula.
- setCharge(Integer) - Method in class org.openscience.cdk.silent.AdductFormula
-
Deprecated.
- setCharge(Double) - Method in class org.openscience.cdk.silent.Atom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Sets the partial charge of this IMolecularFormula.
- setCharge(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge
-
Sets the charge value.
- setChargeGroups(List) - Method in class org.openscience.cdk.libio.md.MDMolecule
-
- setCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.AtomTypeCharges
-
Sets initial charges for atom types
+1 for cationic atom types
-1 for anionic atom types
carboxylic oxygen -0.5
phosphorylic oxygen -0.66
sulfanilic oxygen -0.5
or to formal charge (which must be determined elsewhere or set manually)
polycations are not handled by this approach
- setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
initialize query and target molecules.
- setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
-
initialize query and target molecules.
- setChemObjectReader(ISimpleChemObjectReader) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- setChiCatHydrogen(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation
- setClassName(String) - Method in class org.openscience.cdk.dict.Entry
-
- setClipboardContent(IAtomContainer) - Method in class org.openscience.cdk.renderer.RendererModel
-
Sets the atoms and bonds on the Renderer2D clipboard.
- setClockwise(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- setClockwise(boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality
-
- setCoefficients(Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals
-
Set a coefficient matrix
- setColumn(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Sets the column of the matrix at the specified index to a new value.
- setCount(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount
-
Set the value of implicit H count.
- setCount(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount
-
Sets total H count.
- setCountElectrons(int) - Method in class org.openscience.cdk.math.qm.Orbitals
-
Sets the count of electrons, which occupies the orbitals
- setCovalentRadius(Double) - Method in class org.openscience.cdk.AtomType
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setCovalentRadius(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the covalent radius for this AtomType.
- setCreator(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setCreatormap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setCrystal(ICrystal) - Method in class org.openscience.cdk.ChemModel
-
Sets the Crystal contained in this ChemModel.
- setCrystal(ICrystal) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setCrystal(ICrystal) - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Sets the Crystal contained in this ChemModel.
- setCrystal(ICrystal) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the Crystal contained in this ChemModel.
- setCurr(long) - Method in class org.openscience.cdk.smiles.InvPair
-
Set the value of the seed.
- setDatemap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setDebugStream(PrintStream) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Set debug output.
- setDefaultReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Set the default reactions that must be presents to generate the resonance.
- setDefaultRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool
-
Set the default restrictions that must be presents in the molecular formula.
- setDefinition(String) - Method in class org.openscience.cdk.dict.Entry
-
- setDegree(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- setDegree(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality
-
- setDescription(String) - Method in class org.openscience.cdk.dict.Entry
-
- setDescription(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setDescriptorInstances(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Set the list of Descriptor
objects.
- setDescriptorMetadata(String) - Method in class org.openscience.cdk.dict.Entry
-
- setDescriptorSpecifications(List<DescriptorSpecification>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Set the list of DescriptorSpecification
objects.
- setDetails(String) - Method in class org.openscience.cdk.validate.ValidationTest
-
- setDim(int[]) - Method in class org.openscience.cdk.tools.GridGenerator
-
- setDimension(double, double) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method sets the maximal 3d dimensions to given min and max values.
- setDimension(double[], boolean) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method sets the maximal 3d dimensions to given min and max values.
- setDimension(double, double, double, double, double, double) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method sets the maximal 3d dimensions to given min and max values.
- setDirection(IReaction.Direction) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setDirection(IReaction.Direction) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the direction of the reaction.
- setDirection(IReaction.Direction) - Method in class org.openscience.cdk.Reaction
-
Sets the direction of the reaction.
- setDirection(IReaction.Direction) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the direction of the reaction.
- setDisplayMode(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Set the display mode
- setDocumentProperty(String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
Procedure required by the CDOInterface.
- setDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Set the point on the screen to draw the diagram.
- setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugBond
-
- setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- setElectronCount(Integer) - Method in class org.openscience.cdk.ElectronContainer
-
Sets the number of electrons in this electron container.
- setElectronCount(Integer) - Method in interface org.openscience.cdk.interfaces.IElectronContainer
-
Sets the number of electrons in this electron container.
- setElectronCount(Integer) - Method in class org.openscience.cdk.silent.ElectronContainer
-
Sets the number of electrons in this electron container.
- setEndChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- setEndChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the ending Chain identifier of this structure.
- setEndChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the ending Chain identifier of this structure.
- setEndChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending Chain identifier of this structure.
- setEndInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- setEndInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the ending Code for insertion of residues of this structure.
- setEndInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the ending Code for insertion of residues of this structure.
- setEndInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending Code for insertion of residues of this structure.
- setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- setEndSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the ending sequence number of this structure.
- setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the ending sequence number of this structure.
- setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending sequence number of this structure.
- setEqual(BinaryTree) - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Set equal node
- setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
-
Sets an error handler that is sent events when file format issues occur.
- setErrorHandler(IChemObjectReaderErrorHandler) - Method in interface org.openscience.cdk.io.IChemObjectReader
-
Sets an error handler that is sent events when file format issues occur.
- setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
-
Sets an error handler that is sent events when file format issues occur.
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setExactMass(Double) - Method in class org.openscience.cdk.FragmentAtom
-
- setExactMass(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.Isotope
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setExactMass(Double) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the ExactMass attribute of the Isotope object.
- setExpanded(boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setExpanded(boolean) - Method in class org.openscience.cdk.FragmentAtom
-
- setExpanded(boolean) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
-
- setExpanded(boolean) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setExtendGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator
-
- setExtension(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Sets the extension attribute of the RNode object
- setExtension(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Sets the extension attribute of the RNode object
- setExternalSelectedPart(IAtomContainer) - Method in class org.openscience.cdk.renderer.RendererModel
-
Set externally selected atoms.
- setFirstAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setFirstGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the size of the first of the two
compared graphs.
- setFirstGraphSize(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Sets the size of the first of the two
compared graphs.
- setFlag(int, boolean) - Method in class org.openscience.cdk.ChemObject
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBond
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElement
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMapping
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugRing
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setFlag(int, boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets the value of some flag.
- setFlags(boolean[]) - Method in class org.openscience.cdk.ChemObject
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBond
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElement
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMapping
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugRing
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setFlags(boolean[]) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets the whole set of flags.
- setFontForZoom(double) - Method in class org.openscience.cdk.renderer.font.AWTFontManager
-
For a particular zoom level, set the appropriate font size to use.
- setFontForZoom(double) - Method in interface org.openscience.cdk.renderer.font.IFontManager
-
For a particular zoom level, set the appropriate font size to use.
- setFontManager(IFontManager) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
The font manager must be set by any renderer that uses this class!
This manager is needed to keep track of fonts of the right size.
- setFontManager(IFontManager) - Method in interface org.openscience.cdk.renderer.visitor.IDrawVisitor
-
- setFontName(String) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Set the font name ('Arial', 'Times New Roman') and so on.
- setFontName(String) - Method in interface org.openscience.cdk.renderer.font.IFontManager
-
Set the font name ('Arial', 'Times New Roman') and so on.
- setFontStyle(IFontManager.FontStyle) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Set the font style.
- setFontStyle(IFontManager.FontStyle) - Method in interface org.openscience.cdk.renderer.font.IFontManager
-
Set the font style.
- setForbidden(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Sets the forbidden attribute of the RNode object
- setForbidden(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Sets the forbidden attribute of the RNode object
- setForceFieldConfigurator(String) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Constructor for the ForceFieldConfigurator object
- setFormalCharge(Integer) - Method in class org.openscience.cdk.AtomType
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setFormalCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the formal charge of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.AtomType
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setFormalNeighbourCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the formal neighbour count of this atom.
- setFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Set IMolecularFormula object of this container.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.Atom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setFractionalPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFragment(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setFragment(IAtomContainer) - Method in class org.openscience.cdk.FragmentAtom
-
- setFragment(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
-
Sets the fully expended form of the IFragmentAtom.
- setFragment(IAtomContainer) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setGrid(double[][][]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setGrid(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator
-
- setGroup(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setGroupNumber(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber
-
Set the periodic table group number for this element.
- setHCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- setHetAtom(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setHetAtom(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Mark the atom as a heteroatom.
- setHetAtom(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
- setHetAtom(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
-
- setHighlightedAtom(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel
-
Sets the atom currently highlighted.
- setHighlightedBond(IBond) - Method in class org.openscience.cdk.renderer.RendererModel
-
Sets the Bond currently highlighted.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.AtomType
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setHybridization(IAtomType.Hybridization) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the hybridization of this atom.
- setHybridizationNumber(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber
-
- setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer
-
- setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Code for insertion of residues of this atom.
- setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Sets the ICode of this monomer.
- setICode(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Code for insertion of residues of this atom.
- setICode(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- setICode(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Code for insertion of residues of this atom.
- setICode(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setID(String) - Method in class org.openscience.cdk.ChemObject
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugBond
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugElement
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugMapping
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugRing
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- setID(String) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setID(String) - Method in class org.openscience.cdk.dict.Entry
-
- setID(String) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets the identifier (ID) of this object.
- setId(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode
-
- setId1(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap
-
Sets the id1 attribute of the RMap object
- setId1(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Sets the id1 attribute of the CDKRMap object
- setId2(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap
-
Sets the id2 attribute of the RMap object
- setId2(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Sets the id2 attribute of the CDKRMap object
- setIDPolicy(int) - Static method in class org.openscience.cdk.tools.IDCreator
-
Alters the policy of ID generation.
- setImagelink(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setImaginaryPart(double) - Method in class org.openscience.cdk.math.Complex
-
Sets the imaginary part of this value
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.Atom
-
Sets the number of implicit hydrogen count of this atom.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setImplicitHydrogenCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets the implicit hydrogen count of this atom.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.silent.Atom
-
Sets the number of implicit hydrogen count of this atom.
- setInchimap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setIndexCreated(boolean) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- setInputReader(Reader) - Method in class org.openscience.cdk.io.listener.TextGUIListener
-
Overwrites the default reader from which the input is taken.
- setInputStream(InputStream) - Method in class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator
-
- setInputStream(InputStream) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator
-
Sets the file containing the config data.
- setInputStream(InputStream) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator
-
- setInputStream(InputStream) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator
-
Sets the file containing the config data.
- setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the inputStream attribute of the ForceFieldConfigurator object
- setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
-
Sets the file containing the config data.
- setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
-
Sets the file containing the config data
- setIntensity(double) - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Set the intensity value of this container.
- setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool
-
Sets if the calculation should be interrupted.
- setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.FixBondOrdersTool
-
Sets if the calculation should be interrupted.
- setIsPopupAction(boolean) - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Sets the isPopupAction attribute of the JCPAction object
- setJChemPaintPanel(JFrame) - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Sets the jChemPaintPanel attribute of the JCPAction object
- setLabel(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setLabel(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setLabel(String) - Method in class org.openscience.cdk.dict.Entry
-
- setLabel(String) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
-
Sets the label of this PseudoAtom.
- setLabel(String) - Method in class org.openscience.cdk.PseudoAtom
-
Sets the label of this PseudoAtom.
- setLabel(String) - Method in class org.openscience.cdk.silent.PseudoAtom
-
Sets the label of this PseudoAtom.
- setLast(long) - Method in class org.openscience.cdk.smiles.InvPair
-
- setLatticeConstant(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setLatticeConstant(double) - Method in class org.openscience.cdk.tools.GridGenerator
-
- setLeft(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
- setLeft(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- setLength(int) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Setter for property length.
- setLevel(int) - Method in class org.openscience.cdk.io.listener.SwingGUIListener
-
- setLevel(int) - Method in class org.openscience.cdk.io.listener.TextGUIListener
-
- setLine(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Sets the line of the matrix at the specified index to a new value.
- setLink(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setLinkageRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setLinkmap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setLocations(Vector) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Setter for property locations.
- setLoggingToolClass(Class<? extends ILoggingTool>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory
-
- setMappings(List<Map<Integer, Integer>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Set mapping solutions
- setMass(double) - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Set the mass value of this container.
- setMass(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass
-
Sets the mass value.
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setMassNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.Isotope
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the atomic mass of this element.
- setMatchBond(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- setMatchBonds(boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
-
- setMatchingAtoms(int[]) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
-
Set the atoms of a target molecule that correspond to this group.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.AtomType
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setMaxBondOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxGasteigerDamp(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges
object
- setMaxGasteigerIters(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges
object
- setMaxGasteigerIters(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges
object
- setMaximalStructures(int) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Set the number maximal of resonance structures to be found.
- setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
-
- setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
-
- setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
-
- setMaxIteration(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the maxIteration for the RGraph parsing.
- setMaxIteration(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Sets the maxIteration for the CDKRGraph parsing.
- setMaxIterations(int) - Method in class org.openscience.cdk.charges.Electronegativity
-
set the maximal number of Iterations.
- setMaxIterations(int) - Method in class org.openscience.cdk.charges.PiElectronegativity
-
set the maximal number of Iterations.
- setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.Electronegativity
-
set the maximal number of resonance structures.
- setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.PiElectronegativity
-
set the maximal number of resonance structures.
- setMaxResoStruc(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Sets the maximum resonance structures to be searched
- setMechanism(String) - Method in class org.openscience.cdk.dict.EntryReact
-
Set the mechanism of this reaction.
- setMinimumFragmentSize(int) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
-
Set the minimum fragment size.
- setMinPSCluster(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setMinPSPocket(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setMM2Parameters() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
- setMMFF94Parameters() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
- setModelCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Set the position of the center of the model.
- setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer
-
Sets the molecule the AtomPlacer currently works with
- setMolecule(IMolecule) - Method in class org.openscience.cdk.layout.RingPlacer
-
- setMolecule(IMolecule, boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Assings a molecule to be layed out.
- setMolecule(IMolecule) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Assings a molecule to be layed out.
- setMolecule(IMolecule) - Method in class org.openscience.cdk.structgen.RandomGenerator
-
Assigns a starting structure to this generator.
- setMolecules(IMolecule[]) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setMolecules(IMolecule[]) - Method in interface org.openscience.cdk.interfaces.IMoleculeSet
-
Sets the molecules in the IMoleculeSet, removing previously added
IMolecule's.
- setMolecules(IMolecule[]) - Method in class org.openscience.cdk.MoleculeSet
-
- setMolecules(IMolecule[]) - Method in class org.openscience.cdk.silent.MoleculeSet
-
- setMoleculeSet(IMoleculeSet) - Method in class org.openscience.cdk.ChemModel
-
Sets the MoleculeSet of this ChemModel.
- setMoleculeSet(IMoleculeSet) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setMoleculeSet(IMoleculeSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Sets the MoleculeSet of this ChemModel.
- setMoleculeSet(IMoleculeSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the MoleculeSet of this ChemModel.
- setMonoIsotope(IsotopeContainer) - Method in class org.openscience.cdk.formula.IsotopePattern
-
Set the mono isotope object.
- setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setMonomerName(String) - Method in interface org.openscience.cdk.interfaces.IMonomer
-
Set the name of the Monomer object.
- setMonomerName(String) - Method in class org.openscience.cdk.Monomer
-
Sets the name of the Monomer object.
- setMonomerName(String) - Method in class org.openscience.cdk.silent.Monomer
-
Sets the name of the Monomer object.
- setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setMonomerType(String) - Method in interface org.openscience.cdk.interfaces.IMonomer
-
Set the type of the Monomer object.
- setMonomerType(String) - Method in class org.openscience.cdk.Monomer
-
Sets the type of the Monomer object.
- setMonomerType(String) - Method in class org.openscience.cdk.silent.Monomer
-
Sets the type of the Monomer object.
- setMultiMap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in class org.openscience.cdk.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setMultiplier(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultipliers(Double[]) - Method in class org.openscience.cdk.AtomContainerSet
-
Sets the multipliers of the AtomContainers.
- setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setMultipliers(Double[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Sets the multipliers of the AtomContainers.
- setMultipliers(Double[]) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the multipliers of the AtomContainers.
- setName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Atom name of this atom.
- setName(String) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Setter for property name.
- setName(String) - Method in class org.openscience.cdk.libio.md.Residue
-
- setName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Atom name of this atom.
- setName(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Atom name of this atom.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setNaturalAbundance(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.Isotope
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNewMatrix(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
set a new Matrix.
- setNotEqual(BinaryTree) - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Set not equal node
- setNotification(boolean) - Method in class org.openscience.cdk.ChemObject
-
- setNotification(boolean) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- setNotification(boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Set a flag to use or not use notification.
- setNotification(boolean) - Method in class org.openscience.cdk.renderer.RendererModel
-
Dis- or enables sending around change notifications.
- setNotification(boolean) - Method in class org.openscience.cdk.silent.ChemObject
-
- setNS(String) - Method in class org.openscience.cdk.dict.Dictionary
-
- setNumAtoms(int) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- setNumber(int) - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- setNumber(int) - Method in class org.openscience.cdk.libio.md.Residue
-
- setNumber(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber
-
Sets the atomic number.
- setNumOfConnection(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom
-
Sets number of explicit connections.
- setNumOfConnection(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity
-
Sets the number of explicit connections.
- setNumOfConnection(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity
-
Sets the number of ring connections.
- setNumOfConnection(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity
-
Sets the number of total connections.
- setNumOfMembership(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership
-
Sets the number of SSSR rings this atom is in.
- setObjectProperty(String, String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
Procedure required by the CDOInterface.
- setOccupancy(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setOccupancy(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Occupancy of this atom.
- setOccupancy(Double) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Occupancy of this atom.
- setOccupancy(Double) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Occupancy of this atom.
- setOccurrence(String) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Picky setter for occurrence fields.
- seTolerance(double) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity
-
Set the tolerance of the mass accuracy.
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
-
- setOrder(IBond.Order) - Method in class org.openscience.cdk.Bond
-
Sets the bond order of this bond.
- setOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugBond
-
- setOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IBond
-
Sets the bond order of this bond.
- setOrder(IBond.Order) - Method in class org.openscience.cdk.silent.Bond
-
Sets the bond order of this bond.
- setOrder(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTValence
-
Sets valence order.
- setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.PropertiesListener
-
Overwrites the default writer to which the output is directed.
- setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.TextGUIListener
-
Overwrites the default writer to which the output is directed.
- setOverrideBondWidth(double) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Set the width to use for all bonds, overriding any standard bond widths.
- setOverrideColor(Color) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Set the color to use for all bonds, overriding the standard bond colors.
- setOxt(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setOxt(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
- setOxt(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
- setOxt(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
-
- setParameter(boolean) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
-
Set the parameter to take account.
- setParameter(boolean) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
-
Set the parameter to take account.
- setParameterList(List<IParameterReact>) - Method in interface org.openscience.cdk.reaction.IReactionProcess
-
Sets the parameters for this reaction.
- setParameterList(List<IParameterReact>) - Method in class org.openscience.cdk.reaction.ReactionEngine
-
Returns the current parameter Map for this reaction.
- setParameters(String, String, String) - Method in class org.openscience.cdk.dict.EntryReact
-
Set the parameters of the reaction.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ChargeRule
-
Sets the parameters attribute of the ChargeRule object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ElementRule
-
Sets the parameters attribute of the ElementRule object.
- setParameters(Object[]) - Method in interface org.openscience.cdk.formula.rules.IRule
-
Sets the parameters for this rule.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule
-
Sets the parameters attribute of the IsotopePatternRule object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.MMElementRule
-
Sets the parameters attribute of the MMElementRule object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.NitrogenRule
-
Sets the parameters attribute of the NitrogenRule object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.RDBERule
-
Sets the parameters attribute of the RDBE object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule
-
Sets the parameters attribute of the ToleranceRangeRule object.
- setParameters(Map<String, Object>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the parameters attribute of the ForceFieldConfigurator object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
This descriptor does not have any parameter to be set.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
Sets the parameters attribute of the BondsToAtomDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
Sets the parameters attribute of the DistanceToAtomDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
-
Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
-
Sets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
-
Sets the parameters attribute of the PartialPiChargeDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
-
Sets the parameters attribute of the PartialSigmaChargeDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
-
This descriptor does not have any parameter to be set.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
-
This descriptor does not have any parameter to be set.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
-
This descriptor does not have any parameter to be set.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
-
Sets the parameters attribute of the PiElectronegativityDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
-
This descriptor does not have any parameter to be set.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
-
Sets the parameters attribute of the RDFProtonDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
-
Sets the parameters attribute of the RDFProtonDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
-
Sets the parameters attribute of the RDFProtonDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
-
Sets the parameters attribute of the RDFProtonDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
-
Sets the parameters attribute of the RDFProtonDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
Sets the parameters attribute of the SigmaElectronegativityDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
Sets the parameters attribute of the StabilizationPlusChargeDescriptor
object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
-
Sets the parameters attribute of the PiContactDetectionDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Sets the parameters attribute of the AminoAcidsCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Sets the parameters attribute of the APolDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Sets the parameters attribute of the AromaticAtomsCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Sets the parameters attribute of the AromaticBondsCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Sets the parameters attribute of the AtomCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Sets the parameters attribute of the BCUTDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Sets the parameters attribute of the BondCountDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Sets the parameters attribute of the BPolDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Sets the parameters attribute of the GravitationalIndexDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Sets the parameters attribute of the CPSADescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Sets the parameters attribute of the EccentricConnectivityIndexDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Sets the parameters attribute of the FragmentComplexityDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Sets the parameters attribute of the GravitationalIndexDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Sets the parameters attribute of the HBondAcceptorCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Sets the parameter of this HBondDonorCountDescriptor instance.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Sets the parameters attribute of the HybridizationRatioDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Sets the parameters attribute of the IPMolecularLearningDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Sets the parameters attribute of the
KappaShapeIndicesDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Sets the parameters attribute of the descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Sets the parameters attribute of the LargestChain object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Sets the parameters attribute of the LargestPiSystemDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Sets the parameters attribute of the PetitjeanNumberDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Sets the parameters attribute of the LongestAliphaticChainDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Sets the parameters attribute of the WeightDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Sets the parameters attribute of the MomentOfInertiaDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Sets the parameters attribute of the PetitjeanNumberDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Sets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Sets the parameters attribute of the RotatableBondsCountDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Sets the parameters attribute of the RuleOfFiveDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Sets the parameters attribute of the TPSADescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Sets the parameters attribute of the VAdjMaDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Sets the parameters attribute of the WeightDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Sets the parameters attribute of the WeightedPathDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Sets the parameters attribute of the WHIMDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Sets the parameters attribute of the WienerNumbersDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Sets the parameters attribute of the XLogPDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Sets the parameters attribute of the ZagrebIndexDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Sets the parameters attribute of the TaeAminoAcidDescriptor object.
- setParameters(Object[]) - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Sets the parameters for this descriptor.
- setParameterSet(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Constructor for the setParameterSet object
- setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.Residue
-
- setParser(SMARTSParser) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode
-
- setPermutation(int[]) - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Set the currently used permutation.
- setPharmacophoreQuery(PharmacophoreQuery) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Set a pharmacophore query
- setPocketSize(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setPoint2d(Point2d) - Method in class org.openscience.cdk.Atom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setPoint2d(Point2d) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint2d(Point2d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.Atom
-
Sets a point specifying the location of this
atom in 3D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets a point specifying the location of this
atom in 3D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in 3D space.
- setPositive(boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge
-
Sets whether the charge is positive.
- setPreservingAromaticity(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser
-
Makes the Smiles parser set aromaticity as provided in the Smiles itself, without detecting it.
- setPrime() - Method in class org.openscience.cdk.smiles.InvPair
-
Sets the prime number based on the current seed.
- setProductCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setProductCoefficient(IMolecule, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the coefficient of a a product to a given value.
- setProductCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.Reaction
-
Sets the coefficient of a a product to a given value.
- setProductCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of a a product to a given value.
- setProductCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setProductCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the coefficient of the products.
- setProductCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction
-
Sets the coefficient of the products.
- setProductCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of the products.
- setProducts(IMoleculeSet) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setProducts(IMoleculeSet) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Assigns a IMoleculeSet to the products of this reaction.
- setProducts(IMoleculeSet) - Method in class org.openscience.cdk.Reaction
-
Assigns a MoleculeSet to the products of this reaction.
- setProducts(IMoleculeSet) - Method in class org.openscience.cdk.silent.Reaction
-
Assigns a MoleculeSet to the products of this reaction.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject
-
Sets the properties of this object.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBond
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElement
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMapping
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugRing
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Sets the properties of this object.
- setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets the properties of this object.
- setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Sets the properties of this object.I should
integrate into ChemObject.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets the properties of this object.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Sets the properties of this object.
- setProperty(Object, Object) - Method in class org.openscience.cdk.ChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBond
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemFile
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElement
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugLonePair
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMapping
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMolecule
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMoleculeSet
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugRing
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setProperty(Object, Object) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Sets a property for a IChemObject.
- setProtein(IBioPolymer) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setProteinInterior(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setPublisher(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setQueryCacheSize(int) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Set the maximum size of the query cache.
- setRandom(Random) - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Sets the base generator to be used by this class.
- setRandomSeed(long) - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Sets the seed of this random number generator using a single
long
seed.
- setRank(int) - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Set the permutation to use, given its rank.
- setRAtom(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setRawContent(Object) - Method in class org.openscience.cdk.dict.Entry
-
- setRdFields(Map) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
Here you can set a map which will be used to build rd fields in the file.
- setReactantCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setReactantCoefficient(IMolecule, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the coefficient of a a reactant to a given value.
- setReactantCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.Reaction
-
Sets the coefficient of a a reactant to a given value.
- setReactantCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of a a reactant to a given value.
- setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setReactantCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the coefficients of the reactants.
- setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction
-
Sets the coefficients of the reactants.
- setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficients of the reactants.
- setReactants(IMoleculeSet) - Method in class org.openscience.cdk.debug.DebugReaction
-
- setReactants(IMoleculeSet) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Assigns a IMoleculeSet to the reactants in this reaction.
- setReactants(IMoleculeSet) - Method in class org.openscience.cdk.Reaction
-
Assigns a MoleculeSet to the reactants in this reaction.
- setReactants(IMoleculeSet) - Method in class org.openscience.cdk.silent.Reaction
-
Assigns a MoleculeSet to the reactants in this reaction.
- SetReactionCenter - Class in org.openscience.cdk.reaction.type.parameters
-
Class extension of ParameterReact class which defines if a reaction is set already the reaction center
in the reactants.
- SetReactionCenter() - Constructor for class org.openscience.cdk.reaction.type.parameters.SetReactionCenter
-
- setReactionMetadata(String) - Method in class org.openscience.cdk.dict.EntryReact
-
- setReactions(List<IReactionProcess>) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Set the reactions that must be used in the generation of the resonance.
- setReactionSet(IReactionSet) - Method in class org.openscience.cdk.ChemModel
-
Sets the ReactionSet contained in this ChemModel.
- setReactionSet(IReactionSet) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setReactionSet(IReactionSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Sets the ReactionSet contained in this ChemModel.
- setReactionSet(IReactionSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the ReactionSet contained in this ChemModel.
- setReader(Reader) - Method in class org.openscience.cdk.io.CIFReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.CIFReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.CMLReader
-
This method must not be used; XML reading requires the use of an InputStream.
- setReader(InputStream) - Method in class org.openscience.cdk.io.CMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.CrystClustReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.CrystClustReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.CTXReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.CTXReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.GamessReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.GamessReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.Gaussian98Reader
-
Sets the reader attribute of the Gaussian98Reader object
- setReader(InputStream) - Method in class org.openscience.cdk.io.Gaussian98Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.HINReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.HINReader
-
- setReader(Reader) - Method in interface org.openscience.cdk.io.IChemObjectReader
-
Sets the Reader from which this ChemObjectReader should read
the contents.
- setReader(InputStream) - Method in interface org.openscience.cdk.io.IChemObjectReader
-
Sets the InputStream from which this ChemObjectReader should read
the contents.
- setReader(Reader) - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.INChIReader
-
This method must not be used; XML reading requires the use of an InputStream.
- setReader(InputStream) - Method in class org.openscience.cdk.io.INChIReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.Mol2Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.Mol2Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MoSSOutputReader
-
Sets the Reader from which this ChemObjectReader should read
the contents.
- setReader(InputStream) - Method in class org.openscience.cdk.io.MoSSOutputReader
-
Sets the InputStream from which this ChemObjectReader should read
the contents.
- setReader(Reader) - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.PDBReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PDBReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.PMPReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PMPReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
Deprecated.
- setReader(InputStream) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
Sets the InputStream from which this ChemObjectReader should read
the contents.
- setReader(Reader) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
Sets the input Reader.
- setReader(InputStream) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.ShelXReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.ShelXReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.SMILESReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.SMILESReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.VASPReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.VASPReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.XYZReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.XYZReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.ZMatrixReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.ZMatrixReader
-
- setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
-
- setReaderMode(IChemObjectReader.Mode) - Method in interface org.openscience.cdk.io.IChemObjectReader
-
Sets the reader mode.
- setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
-
- setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
-
- setRealPart(double) - Method in class org.openscience.cdk.math.Complex
-
Sets the real part of this complex value
- setRecord(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setRecord(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Set one entire line from the PDB entry file which describe the IPDBAtom.
- setRecord(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set one entire line from the PDB entry file which describe the IPDBAtom.
- setRecord(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set one entire line from the PDB entry file which describe the IPDBAtom.
- setRecursiveQuery(IQueryAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom
-
- setRendererModel(RendererModel) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
- setRendererModel(RendererModel) - Method in interface org.openscience.cdk.renderer.visitor.IDrawVisitor
-
- setRepresentation(String) - Method in class org.openscience.cdk.dict.EntryReact
-
Set the representation of the reaction.
- setRequiredRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setResidues(List) - Method in class org.openscience.cdk.libio.md.MDMolecule
-
- setResName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setResName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Residue name of this atom.
- setResName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Residue name of this atom.
- setResName(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Residue name of this atom.
- setResSeq(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Residue sequence number of this atom.
- setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Sets the sequence identifier of this monomer.
- setResSeq(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Residue sequence number of this atom.
- setResSeq(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- setResSeq(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Residue sequence number of this atom.
- setResSeq(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setRestH(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setRestrictions(List<IRule>) - Method in class org.openscience.cdk.formula.MassToFormulaTool
-
Set the restrictions that must be presents in the molecular formula.
- setRGroupDefinitions(Map<Integer, RGroupList>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for the R-group definitions (substituents).
- setRGroupDefinitions(Map<Integer, RGroupList>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Setter for rGroupNumber, checks for valid range.
- setRGroups(List<RGroup>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setRight(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
- setRight(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- setRingBond(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
-
- setRingFinder(AllRingsFinder) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Sets the current AllRingsFinder instance
Use this if you want to customize the timeout for
the AllRingsFinder.
- setRingId(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier
-
Sets the ring identifier.
- setRings(IRingSet) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Provide a reference to a RingSet that holds ALL rings of the molecule.
During creation of a SMILES the aromaticity of the molecule has to be detected.
- setRingSet(IRingSet) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
-
- setRingSet(IRingSet) - Method in class org.openscience.cdk.ChemModel
-
Sets the RingSet of this ChemModel.
- setRingSet(IRingSet) - Method in class org.openscience.cdk.debug.DebugChemModel
-
- setRingSet(IRingSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Sets the RingSet of this ChemModel.
- setRingSet(IRingSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the RingSet of this ChemModel.
- setRMap(RMap) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Sets the rMap attribute of the RNode object
- setRMap(CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Sets the rMap attribute of the RNode object
- setrMap(CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Sets resolution map/graph
- setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
- setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setRootStructure(IAtomContainer) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for the root structure of this R-Group.
- setRootStructure(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setRSolvent(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setScale(IAtomContainer) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
Set the scale for an IAtomContainer.
- setScale(IChemModel) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
Set the scale for an IChemModel.
- setScale(T) - Method in interface org.openscience.cdk.renderer.IRenderer
-
- setScale(IMoleculeSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
Set the scale for an IMoleculeSet.
- setScale(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
Set the scale for an IReaction.
- setScale(IReactionSet) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
Set the scale for an IReactionSet.
- setSecondAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setSecondGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the size of the second of the two
compared graphs.
- setSecondGraphSize(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the size of the second of the two
compared graphs.
- setSegID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setSegID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Segment identifier, left-justified of this atom.
- setSegID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Segment identifier, left-justified of this atom.
- setSegID(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Segment identifier, left-justified of this atom.
- setSelection(IChemObjectSelection) - Method in class org.openscience.cdk.renderer.RendererModel
-
- setSerial(Integer) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setSerial(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Atom serial number of this atom.
- setSerial(Integer) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Atom serial number of this atom.
- setSerial(Integer) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Atom serial number of this atom.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.BooleanIOSetting
-
Sets the setting for a certain question.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.IntegerIOSetting
-
Sets the setting for a certain question.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.IOSetting
-
Sets the setting for a certain question.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.OptionIOSetting
-
Sets the setting for a certain question.
- setSetting(int) - Method in class org.openscience.cdk.io.setting.OptionIOSetting
-
Sets the setting for a certain question.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.StringIOSetting
-
Sets the setting for a certain question.
- setSize(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize
-
Sets the smallest SSSR size.
- setSkip(boolean) - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader
-
Indicate whether the reader should skip over SDF records
that cause problems.
- setSmarts(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
-
Set the SMARTS for the group.
- setSmarts(String) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Set a new SMARTS pattern.
- setSolvantValue(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setSource(IChemObject) - Method in class org.openscience.cdk.controller.CDKPopupMenu
-
- setSource(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Set source molecule
- setSpaceGroup(String) - Method in class org.openscience.cdk.Crystal
-
Sets the space group of this crystal.
- setSpaceGroup(String) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setSpaceGroup(String) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the space group of this crystal.
- setSpaceGroup(String) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the space group of this crystal.
- setStackLength(int) - Method in interface org.openscience.cdk.tools.ILoggingTool
-
Sets the number of StackTraceElements to be printed in DEBUG mode when
calling debug(Throwable)
.
- setStackLength(int) - Method in class org.openscience.cdk.tools.LoggingTool
-
Sets the number of StackTraceElements to be printed in DEBUG mode when
calling debug(Throwable)
.
- setStackLength(int) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
-
Sets the number of StackTraceElements to be printed in DEBUG mode when
calling debug(Throwable)
.
- setStart(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
- setStartChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- setStartChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the start Chain identifier of this structure.
- setStartChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the start Chain identifier of this structure.
- setStartChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start Chain identifier of this structure.
- setStartInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- setStartInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the start Chain identifier of this structure.
- setStartInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the start Chain identifier of this structure.
- setStartInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start Chain identifier of this structure.
- setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- setStartSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the start sequence number of this structure.
- setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the start sequence number of this structure.
- setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start sequence number of this structure.
- setStepSize(int) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Set the StepSize attribute of the GasteigerMarsiliPartialCharges
object
- setStepSize(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Set the StepSize attribute of the GasteigerMarsiliPartialCharges
object
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.Bond
-
Sets the stereo descriptor for this bond.
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBond
-
- setStereo(IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IBond
-
Sets the stereo descriptor for this bond.
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.silent.Bond
-
Sets the stereo descriptor for this bond.
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.AtomContainer
-
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setStereoElements(List<IStereoElement>) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Set the stereo elements - this will replace the existing instance
with a new instance.
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.silent.AtomContainer
-
- setStereoParity(Integer) - Method in class org.openscience.cdk.Atom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setStereoParity(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.PseudoAtom
-
Dummy method: the stereo parity is undefined, final.
- setStereoParity(Integer) - Method in class org.openscience.cdk.silent.Atom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.silent.PseudoAtom
-
Dummy method: the stereo parity is undefined, final.
- setStrandName(String) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setStrandName(String) - Method in interface org.openscience.cdk.interfaces.IStrand
-
Set the name of the Strand object.
- setStrandName(String) - Method in class org.openscience.cdk.silent.Strand
-
Sets the name of the Strand object.
- setStrandName(String) - Method in class org.openscience.cdk.Strand
-
Sets the name of the Strand object.
- setStrandType(String) - Method in class org.openscience.cdk.debug.DebugStrand
-
- setStrandType(String) - Method in interface org.openscience.cdk.interfaces.IStrand
-
Set the type of the Strand object.
- setStrandType(String) - Method in class org.openscience.cdk.silent.Strand
-
Sets the type of the Strand object.
- setStrandType(String) - Method in class org.openscience.cdk.Strand
-
Sets the type of the Strand object.
- setStructureType(String) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
- setStructureType(String) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the Structure Type of this structure.
- setStructureType(String) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the Structure Type of this structure.
- setStructureType(String) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the Structure Type of this structure.
- setSubgraph(List<Integer>) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- setSwitchingAtom(IAtom) - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugElement
-
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugIsotope
-
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setSymbol(String) - Method in class org.openscience.cdk.Element
-
Sets the element symbol of this element.
- setSymbol(String) - Method in interface org.openscience.cdk.interfaces.IElement
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.silent.Element
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTElement
-
Sets the element symbol.
- setSymbol(String) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom
-
Sets the element symbol.
- setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
-
- setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
-
- setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
-
- setTarget(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Set target molecule
- setTempFactor(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
- setTempFactor(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Temperature factor of this atom.
- setTempFactor(Double) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Temperature factor of this atom.
- setTempFactor(Double) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Temperature factor of this atom.
- setTemplateHandler(TemplateHandler) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Sets the templateHandler attribute of the StructureDiagramGenerator object
- setTimeout(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the time in milliseconds until the substructure search will be breaked.
- setTimeout(long) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Sets the time in milliseconds until the substructure search will be breaked.
- setTimeout(long) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
-
Sets the timeout value in milliseconds of the AllRingsFinder object
This is used to prevent this AllRingsFinder
to run for ages in certain rare cases with ring systems of
large size or special topology
- setTimeout(long) - Method in class org.openscience.cdk.ringsearch.AllRingsFinderMod
-
Sets the timeout value in milliseconds of the AllRingsFinder object
This is used to prevent this AllRingsFinder
to run for ages in certain rare cases with ring systems of
large size or special topology
- setTimeOut(double) - Method in class org.openscience.cdk.smsd.global.TimeOut
-
set cutoff value for time out eg.
- setTimeoutFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Set time out flag
- setTimeOutFlag(boolean) - Method in class org.openscience.cdk.smsd.global.TimeOut
-
Set true if timeout occures else false
- setTimezone(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setTitle(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Set the main title
- setTitlemap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setToolTipTextMap(Map<IAtom, String>) - Method in class org.openscience.cdk.renderer.RendererModel
-
Sets the toolTipTextMap.
- setTransform(AffineTransform) - Method in interface org.openscience.cdk.renderer.elements.IRenderingVisitor
-
Sets the affine transformations used.
- setTransform(AffineTransform) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
-
Sets a new affine transformation to convert world coordinates into
screen coordinates.
- setType(String) - Method in class org.openscience.cdk.renderer.JCPAction2D
-
Sets the type attribute of the JCPAction object
- setType(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotBond
-
- setType(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression
-
- setUnspecified(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- setUnspecified(boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality
-
- setup(IAtomContainer, Rectangle) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
Setup the transformations necessary to draw this Atom Container.
- setup(IChemModel, Rectangle) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
Setup the transformations necessary to draw this Chem Model.
- setup(T, Rectangle) - Method in interface org.openscience.cdk.renderer.IRenderer
-
- setup(IMoleculeSet, Rectangle) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
Setup the transformations necessary to draw this
IMoleculeSet
.
- setup(IReaction, Rectangle) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
Setup the transformations necessary to draw this Reaction.
- setup(IReactionSet, Rectangle) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
Setup the transformations necessary to draw this Reaction Set.
- setUseAromaticityFlag(boolean) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Indicates whether output should be an aromatic SMILES.
- setUseTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Sets whether to use templates or not.
- setValency(Integer) - Method in class org.openscience.cdk.AtomType
-
Sets the the exact electron valency of the AtomType object.
- setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
- setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
- setValency(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
- setValency(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
- setValency(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the the exact electron valency of the AtomType object.
- setValency(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the the exact electron valency of the AtomType object.
- setValue(Object) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
-
Set the value of the parameter.
- setValue(Object) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
-
Set the value of the parameter.
- setValue(T) - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
-
Sets the value for this parameter.
- setValue(T) - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
-
Sets the value for this parameter.
- setValueAt(int, int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Sets the value of the element at the given index.
- setVanDerWaalsFile(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.CMLWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.CMLWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.CrystClustWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.CrystClustWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.HINWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.HINWriter
-
- setWriter(Writer) - Method in interface org.openscience.cdk.io.IChemObjectWriter
-
Sets the Writer from which this ChemObjectWriter should write
the contents.
- setWriter(OutputStream) - Method in interface org.openscience.cdk.io.IChemObjectWriter
-
Sets the OutputStream from which this ChemObjectWriter should write
the contents.
- setWriter(Writer) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.Mol2Writer
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.Mol2Writer
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.PDBWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.PDBWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Sets the Writer from which this ChemObjectWriter should write
the contents.
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Sets the OutputStream from which this ChemObjectWriter should write
the contents.
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Sets the writer to given output stream.
- setWriter(Writer) - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Sets the writer.
- setWriter(Writer) - Method in class org.openscience.cdk.io.RssWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.RssWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.SDFWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.SDFWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.ShelXWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.ShelXWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.SMILESWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.SMILESWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.XYZWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.XYZWriter
-
- setX(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- setXTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Set the title of the x axis
- setY(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- setYTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Set the title of the y axis
- setZ(Integer) - Method in class org.openscience.cdk.Crystal
-
Sets the number of asymmetric parts in the unit cell.
- setZ(Integer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- setZ(Integer) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the number of assymmetric parts in the unit cell.
- setZ(Integer) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the number of asymmetric parts in the unit cell.
- setZoom(double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Set the zoom, where 1.0 is 100% zoom.
- setZoom(double) - Method in interface org.openscience.cdk.renderer.IRenderer
-
Set a new zoom factor.
- setZoomToFit(double, double, double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Calculate and set the zoom factor needed to completely fit the diagram
onto the screen bounds.
- shallowCopy() - Method in class org.openscience.cdk.ChemObject
-
Clones this IChemObject
, but preserves references to Object
s.
- shallowCopy() - Method in class org.openscience.cdk.silent.ChemObject
-
Clones this IChemObject
, but preserves references to Object
s.
- SharingAnionReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate in movement resonance.
- SharingAnionReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingAnionReaction
-
Constructor of the SharingAnionReaction object.
- SharingChargeDBReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate in movement resonance.
- SharingChargeDBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeDBReaction
-
Constructor of the SharingChargeDBReaction object.
- SharingChargeSBReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate in movement resonance.
- SharingChargeSBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeSBReaction
-
Constructor of the SharingChargeSBReaction object.
- SharingElectronMechanism - Class in org.openscience.cdk.reaction.mechanism
-
This mechanism displaces the charge (lonePair) because of
deficiency of charge.
- SharingElectronMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism
-
- SharingLonePairReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate in movement resonance.
- SharingLonePairReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingLonePairReaction
-
Constructor of the SharingLonePairReaction object.
- SHEET - Static variable in class org.openscience.cdk.protein.data.PDBStructure
-
- SHEET - Static variable in class org.openscience.cdk.silent.PDBStructure
-
- ShelXFormat - Class in org.openscience.cdk.io.formats
-
- ShelXReader - Class in org.openscience.cdk.io
-
A reader for ShelX output (RES) files.
- ShelXReader(Reader) - Constructor for class org.openscience.cdk.io.ShelXReader
-
Create an ShelX file reader.
- ShelXReader(InputStream) - Constructor for class org.openscience.cdk.io.ShelXReader
-
- ShelXReader() - Constructor for class org.openscience.cdk.io.ShelXReader
-
- ShelXWriter - Class in org.openscience.cdk.io
-
Serializes a MoleculeSet or a Molecule object to ShelX code.
- ShelXWriter(Writer) - Constructor for class org.openscience.cdk.io.ShelXWriter
-
Constructs a new ShelXWriter class.
- ShelXWriter(OutputStream) - Constructor for class org.openscience.cdk.io.ShelXWriter
-
- ShelXWriter() - Constructor for class org.openscience.cdk.io.ShelXWriter
-
- shift(Rectangle, Rectangle) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Determine the overlap of the diagram with the screen, and shift (if
necessary) the diagram draw center.
- shift(Rectangle, Rectangle) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
Determine the overlap of the diagram with the screen, and shift (if
necessary) the diagram draw center.
- shiftContainer(IAtomContainer, Rectangle2D, Rectangle2D, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Shift the container horizontally to the right to make its bounds not
overlap with the other bounds.
- shiftDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Move the draw center by dx and dy.
- shiftDrawCenter(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer
-
Set a new drawing center in screen coordinates.
- shiftReactionVertical(IReaction, Rectangle2D, Rectangle2D, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Shift the containers in a reaction vertically upwards to not overlap
with the reference Rectangle2D.
- shouldBeLinear(IAtom, IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer
-
- showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomMassGenerator
-
Returns true if the mass number of this element is set and not
equal the mass number of the most abundant isotope of this element.
- SI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity.
- SigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
Constructor for the SigmaElectronegativityDescriptor object
- signatureForVertex(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
-
- SignatureQuotientGraph - Class in org.openscience.cdk.signature
-
A signature quotient graph has a vertex for every signature symmetry class
and an edge for each bond in the molecule between atoms in their class.
- SignatureQuotientGraph(IAtomContainer) - Constructor for class org.openscience.cdk.signature.SignatureQuotientGraph
-
Construct a quotient graph from the symmetry classes generated from the
atom container.
- SignatureQuotientGraph(IAtomContainer, int) - Constructor for class org.openscience.cdk.signature.SignatureQuotientGraph
-
Construct a quotient graph using symmetry classes defined by signatures
of height height
.
- SignatureReactionCanoniser - Class in org.openscience.cdk.smsd.labelling
-
- SignatureReactionCanoniser() - Constructor for class org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser
-
- signatureStringForVertex(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
-
- signatureStringForVertex(int, int) - Method in class org.openscience.cdk.signature.MoleculeSignature
-
- signedDistanceToPlane(Vector3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Given a normalized normal for a plane, any point in that plane, and
a point, will return the distance between the plane and that point.
- SilentChemObjectBuilder - Class in org.openscience.cdk.silent
-
A helper class to instantiate a
ICDKObject
for the original CDK
implementation.
- SILICON - Static variable in class org.openscience.cdk.config.Elements
-
- SILVER - Static variable in class org.openscience.cdk.config.Elements
-
- SILVER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- similar(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Similar transformation
Ut * M * U
- similar(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Similar transformation
Ut * M * U
- similar(Matrix) - Method in class org.openscience.cdk.math.Matrix
-
Similar transformation
Ut * M * U
- SimpleBasisSet - Class in org.openscience.cdk.math.qm
-
This class will generate a simple base set for a atom container.
- SimpleBasisSet(IAtom[]) - Constructor for class org.openscience.cdk.math.qm.SimpleBasisSet
-
Create a base set
- SimpleBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- SimpleCharStream - Class in org.openscience.cdk.iupac.parser
-
An implementation of interface CharStream, where the stream is assumed to
contain only ASCII characters (without unicode processing).
- SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream - Class in org.openscience.cdk.smiles.smarts.parser
-
An implementation of interface CharStream, where the stream is assumed to
contain only ASCII characters (without unicode processing).
- SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCycle - Class in org.openscience.cdk.ringsearch.cyclebasis
-
A cycle in a graph G is a subgraph in which every vertex has even degree.
- SimpleCycle(UndirectedGraph, Collection) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
-
Constructs a cycle in a graph consisting of the specified edges.
- SimpleCycle(UndirectedGraph, Set) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
-
Constructs a cycle in a graph consisting of the specified edges.
- SimpleCycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis
-
Auxiliary class for CycleBasis
.
- SimpleCycleBasis(List<SimpleCycle>, List, UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
-
- SimpleCycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
-
- SimpleNode - Class in org.openscience.cdk.smiles.smarts.parser
-
Basic implementation of AST nodes.
- SimpleNode(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleNode
-
- SimpleNode(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleNode
-
- simplifyMolecularFormula(String) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Simplify the molecular formula.
- SINGLE_ELECTRON_COUNT - Static variable in class org.openscience.cdk.CDKConstants
-
Used as property key for indicating the number of single electrons on the atom type.
- SINGLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- SingleElectron - Class in org.openscience.cdk.silent
-
A Single Electron is an orbital which is occupied by only one electron.
- SingleElectron(IAtom) - Constructor for class org.openscience.cdk.silent.SingleElectron
-
Constructs an single electron orbital on an Atom.
- SingleElectron() - Constructor for class org.openscience.cdk.silent.SingleElectron
-
Constructs an single electron orbital with an associated Atom.
- SingleElectron - Class in org.openscience.cdk
-
A Single Electron is an orbital which is occupied by only one electron.
- SingleElectron(IAtom) - Constructor for class org.openscience.cdk.SingleElectron
-
Constructs an single electron orbital on an Atom.
- SingleElectron() - Constructor for class org.openscience.cdk.SingleElectron
-
Constructs an single electron orbital with an associated Atom.
- SingleElectronDiff - Class in org.openscience.cdk.tools.diff
-
- singleElectrons() - Method in class org.openscience.cdk.AtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugRing
-
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugStrand
-
- singleElectrons() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- SingleMapping - Class in org.openscience.cdk.smsd.algorithm.single
-
This class handles single atom mapping.
- SingleMapping() - Constructor for class org.openscience.cdk.smsd.algorithm.single.SingleMapping
-
Default
- SingleMappingHandler - Class in org.openscience.cdk.smsd.algorithm.single
-
- SingleMappingHandler(boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
- SingleStructureRandomGenerator - Class in org.openscience.cdk.structgen
-
Randomly generates a single, connected, correctly bonded structure for
a given molecular formula.
- SingleStructureRandomGenerator(long) - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator
-
Constructor for the SingleStructureRandomGenerator object.
- SingleStructureRandomGenerator() - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator
-
Constructor for the SingleStructureRandomGenerator object.
- sitefinder() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Main method which calls the methods: assignProteinToGrid,
GridScan, and FindPockets.
- size() - Method in class org.openscience.cdk.ConformerContainer
-
Get the number of conformers stored.
- size() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- size() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
- size() - Method in class org.openscience.cdk.dict.Dictionary
-
- size() - Method in class org.openscience.cdk.formula.AdductFormula
-
Returns the number of MolecularFormulas in this AdductFormula.
- size() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Returns the number of MolecularFormulas in this MolecularFormulaSet.
- size() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
Returns the number of MolecularFormulas in this IMolecularFormulaSet.
- size() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
-
- size() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- size - Variable in class org.openscience.cdk.math.IVector
-
Size of this vector
- size - Variable in class org.openscience.cdk.math.Vector
-
The size of this vector
- size() - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the number of MolecularFormulas in this AdductFormula.
- size() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Returns the number of MolecularFormulas in this MolecularFormulaSet.
- SM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SMALL_FIRST - Static variable in class org.openscience.cdk.RingSet
-
Flag to denote that the set is order with the smallest ring first?
- SMALL_FIRST - Static variable in class org.openscience.cdk.silent.RingSet
-
Flag to denote that the set is order with the smallest ring first?
- SMALL_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator
-
Flag to denote that the set is order with the smallest ring first
- SMALLEST_RINGS - Static variable in class org.openscience.cdk.CDKConstants
-
A smallest set of smallest rings computed for this molecule.
- SmallestRingAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This smarts atom matches any atom with the smallest SSSR size being a
certain value.
- SmallestRingAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom
-
- SmallestRingSize() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- Smarts2MQLVisitor - Class in org.openscience.cdk.smiles.smarts.parser.visitor
-
An AST tree visitor.
- Smarts2MQLVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor
-
- SMARTSAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Abstract smarts atom.
- SMARTSAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
-
- SMARTSBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Abstract smarts bond.
- SMARTSBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond
-
- SMARTSBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond
-
- SmartsDumpVisitor - Class in org.openscience.cdk.smiles.smarts.parser.visitor
-
An AST Tree visitor.
- SmartsDumpVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor
-
- SmartsExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- SMARTSFormat - Class in org.openscience.cdk.io.formats
-
- SMARTSParser - Class in org.openscience.cdk.smiles.smarts.parser
-
This parser implements a nearly complete subset of the SMARTS syntax as defined on
the
Daylight website.
- SMARTSParser(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Constructor with InputStream.
- SMARTSParser(InputStream, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Constructor with InputStream and supplied encoding
- SMARTSParser(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Constructor.
- SMARTSParser(SMARTSParserTokenManager) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Constructor with generated Token Manager.
- SMARTSParserConstants - Interface in org.openscience.cdk.smiles.smarts.parser
-
Token literal values and constants.
- SMARTSParserTokenManager - Class in org.openscience.cdk.smiles.smarts.parser
-
Token Manager.
- SMARTSParserTokenManager(SimpleCharStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Constructor.
- SMARTSParserTokenManager(SimpleCharStream, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Constructor.
- SMARTSParserTreeConstants - Interface in org.openscience.cdk.smiles.smarts.parser
-
- SMARTSParserVisitor - Interface in org.openscience.cdk.smiles.smarts.parser
-
- SMARTSQueryTool - Class in org.openscience.cdk.smiles.smarts
-
This class provides a easy to use wrapper around SMARTS matching functionality.
- SMARTSQueryTool(String) - Constructor for class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
- SmartsQueryVisitor - Class in org.openscience.cdk.smiles.smarts.parser.visitor
-
An AST tree visitor.
- SmartsQueryVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor
-
Creates a new instance
- SMILES - Static variable in class org.openscience.cdk.CDKConstants
-
The Daylight SMILES.
- SMILESFIXFormat - Class in org.openscience.cdk.io.formats
-
- SMILESFormat - Class in org.openscience.cdk.io.formats
-
- SmilesGenerator - Class in org.openscience.cdk.smiles
-
Generates SMILES strings .
- SmilesGenerator() - Constructor for class org.openscience.cdk.smiles.SmilesGenerator
-
Create the SMILES generator.
- SmilesGenerator(boolean) - Constructor for class org.openscience.cdk.smiles.SmilesGenerator
-
Create the SMILES generator.
- SmilesParser - Class in org.openscience.cdk.smiles
-
Parses a SMILES string and an AtomContainer.
- SmilesParser(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.SmilesParser
-
Constructor for the SmilesParser object.
- SmilesReactionCanoniser - Class in org.openscience.cdk.smsd.labelling
-
- SmilesReactionCanoniser() - Constructor for class org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser
-
- SMILESReader - Class in org.openscience.cdk.io
-
This Reader reads files which has one SMILES string on each
line, where the format is given as below:
- SMILESReader(Reader) - Constructor for class org.openscience.cdk.io.SMILESReader
-
- SMILESReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.SMILESReader
-
Construct a new reader from a Reader and a specified builder object.
- SMILESReader(InputStream) - Constructor for class org.openscience.cdk.io.SMILESReader
-
- SMILESReader() - Constructor for class org.openscience.cdk.io.SMILESReader
-
- SmilesValencyChecker - Class in org.openscience.cdk.tools
-
Small customization of ValencyHybridChecker suggested by Todd Martin
specially tuned for SMILES parsing.
- SmilesValencyChecker() - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker
-
- SmilesValencyChecker(String) - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker
-
- SMILESWriter - Class in org.openscience.cdk.io
-
Writes the SMILES strings to a plain text file.
- SMILESWriter(Writer) - Constructor for class org.openscience.cdk.io.SMILESWriter
-
Constructs a new SMILESWriter that can write a list of SMILES to a Writer
- SMILESWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter
-
- SMILESWriter() - Constructor for class org.openscience.cdk.io.SMILESWriter
-
- SMILESWriter(FileOutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter
-
Constructs a new SMILESWriter that can write an list of SMILES to a given OutputStream
- SMSDNormalizer - Class in org.openscience.cdk.normalize
-
This class containes set of modules required to clean a molecule
before subjecting it for MCS search.
- SMSDNormalizer() - Constructor for class org.openscience.cdk.normalize.SMSDNormalizer
-
- SN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SODIUM - Static variable in class org.openscience.cdk.config.Elements
-
- SODIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- sort() - Method in class org.openscience.cdk.signature.Orbit
-
Sorts the atom indices in this orbit
- sort(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
Sorts the IAtomContainers in the given IAtomContainerSet by the following
criteria with decreasing priority:
- sort(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Sorts the rings in the set by size.
- sortAndNormalizedByIntensity(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
-
Return the isotope pattern sorted and normalized by intensity
to the highest abundance.
- sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.AtomContainerSet
-
Sort the AtomContainers and multipliers using a provided Comparator
- sortAtomContainers(Comparator<IAtomContainer>) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Sort the AtomContainers using a provided Comparator.
- sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sort the AtomContainers and multipliers using a provided Comparator
- sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Sorts a Vector of atoms such that the 2D distances of the atom locations
from a given point are smallest for the first atoms in the vector
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
- sortByIntensity(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
-
Return the isotope pattern sorted by intensity
to the highest abundance.
- sortByMass(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
-
Return the isotope pattern sorted by mass
to the highest abundance.
- sortResultsByEnergies() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Sort MCS solution by bond breaking energy.
- sortResultsByFragments() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Sort solution by ascending order of the fragment count.
- sortResultsByStereoAndBondMatch() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Sort MCS solution by stereo and bond type matches.
- SPACE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- SpanningTree - Class in org.openscience.cdk.graph
-
Spanning tree of a molecule.
- SpanningTree(IAtomContainer) - Constructor for class org.openscience.cdk.graph.SpanningTree
-
- SpartanFormat - Class in org.openscience.cdk.io.formats
-
- specialCase() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deal with special cases where the rules don't apply.
- specialToken - Variable in class org.openscience.cdk.iupac.parser.Token
-
This field is used to access special tokens that occur prior to this
token, but after the immediately preceding regular (non-special) token.
- specialToken - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
-
This field is used to access special tokens that occur prior to this
token, but after the immediately preceding regular (non-special) token.
- SPHERICAL_MATCHER - Static variable in class org.openscience.cdk.CDKConstants
-
Used as property key for indicating the HOSE code for a certain atom type.
- splice(PathEdge) - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- SPLIT_MODE_BREADTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
-
Indicates that crossover
is using SPLIT_MODE_BREADTH_FIRST mode.
- SPLIT_MODE_DEPTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
-
Indicates that crossover
is using SPLIT_MODE_DEPTH_FIRST mode.
- SPLIT_MODE_RADNDOM - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
-
Indicates that crossover
is using SPLIT_MODE_RADNDOM mode.
- sqrt() - Method in class org.openscience.cdk.math.Quaternion
-
- SR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SSSRFinder - Class in org.openscience.cdk.ringsearch
-
Finds the Smallest Set of Smallest Rings.
- SSSRFinder(IAtomContainer) - Constructor for class org.openscience.cdk.ringsearch.SSSRFinder
-
Constructs a SSSRFinder for a specified molecule.
- StabilizationCharges - Class in org.openscience.cdk.charges
-
The stabilization of the positive and the negative charge
obtained (e.g in the polar breaking of a bond) is calculated from the sigma- and
lone pair-electronegativity values of the atoms that are in conjugation to the atoms
obtaining the charges.
- StabilizationCharges() - Constructor for class org.openscience.cdk.charges.StabilizationCharges
-
Constructor for the StabilizationCharges object.
- StabilizationPlusChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
The stabilization of the positive charge
(e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and
lone pair-electronegativity values of the atoms that are in conjugation to the atoms
obtaining the charges.
- StabilizationPlusChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
Constructor for the StabilizationPlusChargeDescriptor object
- StandardSubstructureSets - Class in org.openscience.cdk.fingerprint
-
Default sets of atom containers aimed for use with the substructure
- StandardSubstructureSets() - Constructor for class org.openscience.cdk.fingerprint.StandardSubstructureSets
-
- Start() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Start ::=
ReactionExpression ::= (">>" )? |
">" ">" | ">>"
GroupExpression ::= ["("] [")"] ( "." ["("] [")"] )*
SmartsExpression ::= (
( [ ] ( | ) ) |
( "(" [ ] ")" ) )*
AtomExpression ::= ( "[" [ ] "]" ) |
LowAndBond ::= [ ";" ]
OrBond ::= [ "," ]
ExplicitHighAndBond ::= [ "&" ]
ImplicitHighAndBond ::= [ ]
NotBond ::= [ "!" ]
SimpleBond ::= "/" | "\\" | "/?" | "\\?" | "=" | "#" | "~" | "@"
ExplicitAtomExpression ::= [ "B" | "C" | "N" | "O" | "P" | "S" | "F" | "CL" | "BR" | "I"
| "c" | "o" | "n" | "*" | "A" | "a" | "p" | "as" | "se" ]
LowAndExpression ::= ( ";" )?
OrExpression ::= ( "," ) ?
ExplicitHighAndExpression ::= ( "&" )?
ImplicitHighAndExpression ::= ( ) ?
NotExpression ::= "!" ( | )
RecursiveSmartsExpression ::= "$" "(" ")"
PrimitiveAtomExpression ::= | "*" | "A" | "a" | "D" ()? | "H" ()? | "h" ()?
| "R" (+)? | "r" (+)? | "v" (+)? | "#X" | "G" (+)
| "X" (+)? | "x" (+)? | "^" ()
| ("+" | "-") (+)? | "#" (+) | "@" | "@@" | +
Digit ::= ( "0" - "9")
NonHydrogenElement ::= [ "HE" | "LI" | "BE" | "NE" | "NA" | "MG" | "AL" | "SI" | "AR" | "CA" | "SC" |
"TI" | "CR" | "MN" | "FE" | "CO" | "NI" | "CU" | "ZN" | "GA" | "GE" | "AS" |
"SE" | "BR" | "KR" | "RB" | "SR" | "ZR" | "NB" | "MO" | "TC" | "RU" | "RH" |
"PD" | "AG" | "CD" | "IN" | "SN" | "SB" | "TE" | "XE" | "CS" | "BA" | "LA" |
"HF" | "TA" | "RE" | "OS" | "IR" | "PT" | "AU" | "HG" | "TL" | "PB" | "BI" |
"PO" | "AT" | "RN" | "FR" | "RA" | "AC" | "TH" | "PA" |
"B" | "C" | "N" | "O" | "F" | "P" | "S" | "K" | "V" | "Y" | "I" | "U" |
"c" | "o" | "n" | "p" | "as" | "se" ]
- startDocument() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
-
- startDocument() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
-
- startDocument() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
-
- startDocument() - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
-
- startDocument() - Method in class org.openscience.cdk.dict.DictionaryHandler
-
- startDocument() - Method in class org.openscience.cdk.io.cml.CDKConvention
-
- startDocument() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- startDocument() - Method in class org.openscience.cdk.io.cml.CMLHandler
-
- startDocument() - Method in interface org.openscience.cdk.io.cml.ICMLModule
-
- startDocument() - Method in class org.openscience.cdk.io.cml.MDLMolConvention
-
- startDocument() - Method in class org.openscience.cdk.io.cml.PMPConvention
-
- startDocument() - Method in class org.openscience.cdk.io.inchi.INChIHandler
-
- startDocument() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
Procedure required by the CDOInterface.
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
-
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
-
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
-
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
-
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.dict.DictionaryHandler
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CDKConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLHandler
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLReactionModule
-
- startElement(CMLStack, String, String, String, Attributes) - Method in interface org.openscience.cdk.io.cml.ICMLModule
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDLMolConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention
-
Add parsing of elements in mdmolecule:
mdmolecule
chargeGroup
id
cgNumber
atomArray
switchingAtom
residue
id
title
resNumber
atomArray
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PDBConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PMPConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.QSARConvention
-
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.inchi.INChIHandler
-
Implementation of the startElement() procedure overwriting the
DefaultHandler interface.
- startMcGregorIteration(int, Map<Integer, Integer>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Start McGregor search and extend the mappings if possible.
- startMcGregorIteration(int, List<Integer>, List<Integer>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Start McGregor search and extend the mappings if possible.
- startObject(String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
Procedure required by the CDOInterface.
- startX - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
-
- startY - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainer
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainerSet
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemFile
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemModel
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemSequence
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand
-
- stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKChangeListener
-
Invoked when the target of the listener has changed its state.
- stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKSelectionChangeListener
-
Invoked when the target of the listener has changed its state.
- stateChanged(IChemObjectChangeEvent) - Method in interface org.openscience.cdk.interfaces.IChemObjectListener
-
Called by objects to notify objects that implemented this interface
and registered with them as ChemObjectListeners.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.MoleculeSet
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ReactionSet
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainer
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemFile
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemModel
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemSequence
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.MoleculeSet
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ReactionSet
-
- stateChanged(List) - Method in interface org.openscience.cdk.structgen.IStructureGenerationListener
-
- staticFlag - Static variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Whether parser is static.
- staticFlag - Static variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Whether parser is static.
- STDOUT_LOGGING_TOOL_CLASS - Static variable in class org.openscience.cdk.tools.LoggingToolFactory
-
Back-up logging tool.
- STEREO_ATOM_PARITY_MINUS - Static variable in class org.openscience.cdk.CDKConstants
-
A negative atom parity.
- STEREO_ATOM_PARITY_PLUS - Static variable in class org.openscience.cdk.CDKConstants
-
A positive atom parity.
- STEREO_ATOM_PARITY_UNDEFINED - Static variable in class org.openscience.cdk.CDKConstants
-
A undefined atom parity.
- StereoBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This query bond matches bonds with specific stereo type.
- StereoBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond
-
- stereoElements() - Method in class org.openscience.cdk.AtomContainer
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
- stereoElements() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- stereoElements() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
- stereoElements() - Method in class org.openscience.cdk.debug.DebugCrystal
-
- stereoElements() - Method in class org.openscience.cdk.debug.DebugMolecule
-
- stereoElements() - Method in class org.openscience.cdk.debug.DebugMonomer
-
- stereoElements() - Method in class org.openscience.cdk.debug.DebugPolymer
-
- stereoElements() - Method in class org.openscience.cdk.debug.DebugRing
-
- stereoElements() - Method in class org.openscience.cdk.debug.DebugStrand
-
- stereoElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the stereo elements defined for this atom container.
- stereosAreOpposite(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Says if of four atoms connected two one atom the up and down bonds are
opposite or not, i.
- StereoTool - Class in org.openscience.cdk.stereo
-
Methods to determine or check the stereo class of a set of atoms.
- StereoTool() - Constructor for class org.openscience.cdk.stereo.StereoTool
-
- StereoTool.SquarePlanarShape - Enum in org.openscience.cdk.stereo
-
The shape that four atoms take in a plane.
- StereoTool.StereoClass - Enum in org.openscience.cdk.stereo
-
Currently unused, but intended for the StereoTool to indicate what it
'means' by an assignment of some atoms to a class.
- StereoTool.TetrahedralSign - Enum in org.openscience.cdk.stereo
-
The handedness of a tetrahedron, in terms of the point-plane distance
of three of the corners, compared to the fourth.
- Strand - Class in org.openscience.cdk.silent
-
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
- Strand() - Constructor for class org.openscience.cdk.silent.Strand
-
Constructs a new Strand.
- Strand - Class in org.openscience.cdk
-
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
- Strand() - Constructor for class org.openscience.cdk.Strand
-
Constructs a new Strand.
- StringDifference - Class in org.openscience.cdk.tools.diff.tree
-
- StringIOSetting - Class in org.openscience.cdk.io.setting
-
An class for a reader setting which must be of type String.
- StringIOSetting(String, int, String, String) - Constructor for class org.openscience.cdk.io.setting.StringIOSetting
-
- STRONTIUM - Static variable in class org.openscience.cdk.config.Elements
-
- STRONTIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- StructGenAtomTypeGuesser - Class in org.openscience.cdk.atomtype
-
AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
- StructGenAtomTypeGuesser() - Constructor for class org.openscience.cdk.atomtype.StructGenAtomTypeGuesser
-
Constructor for the StructGenMatcher object.
- StructGenMatcher - Class in org.openscience.cdk.atomtype
-
AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
- StructGenMatcher() - Constructor for class org.openscience.cdk.atomtype.StructGenMatcher
-
Constructor for the StructGenMatcher object.
- StructureDiagramGenerator - Class in org.openscience.cdk.layout
-
Generates 2D coordinates for a molecule for which only connectivity is known
or the coordinates have been discarded for some reason.
- StructureDiagramGenerator() - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator
-
The empty constructor.
- StructureDiagramGenerator(IMolecule) - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator
-
Creates an instance of this class while assigning a molecule to be layed
out.
- StructureResonanceGenerator - Class in org.openscience.cdk.tools
-
This class try to generate resonance structure for a determinate molecule.
- StructureResonanceGenerator() - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator
-
Construct an instance of StructureResonanceGenerator.
- StructureResonanceGenerator(boolean) - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator
-
Construct an instance of StructureResonanceGenerator.
- sub(Complex) - Method in class org.openscience.cdk.math.Complex
-
Subtracs a complex value
- sub(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Subtraktion from two matrices
- sub(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Subtraktion from two matrices
- sub(IVector) - Method in class org.openscience.cdk.math.IVector
-
Subtraction from two vectors
- sub(IVector, IVector) - Method in class org.openscience.cdk.math.IVector
-
Subtraction from two vectors
- sub(Matrix) - Method in class org.openscience.cdk.math.Matrix
-
Subtracts from two matrices.
- sub(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
-
- sub(Vector) - Method in class org.openscience.cdk.math.Vector
-
Subtraktion from two vectors
- subChain() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
The substituent part of the prefix
- subList(int, int) - Method in class org.openscience.cdk.ConformerContainer
-
- subscript - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child
-
A subscript (if any) for the child.
- SubstructureFingerprinter - Class in org.openscience.cdk.fingerprint
-
IFingerprinter
that gives a bit set which has a size equal to the number
of substructures it was constructed from.
- SubstructureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
- SubstructureFingerprinter(String[]) - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
Set up the fingerprinter to use a user-defined set of fragments.
- SULFUR - Static variable in class org.openscience.cdk.config.Elements
-
- SVGFormat - Class in org.openscience.cdk.io.formats
-
- SwingEventRelay - Class in org.openscience.cdk.controller
-
- SwingEventRelay(JComponent) - Constructor for class org.openscience.cdk.controller.SwingEventRelay
-
- SwingGUIListener - Class in org.openscience.cdk.io.listener
-
Allows processing of IOSetting quesions which are passed to the user
by using Swing dialogs.
- SwingGUIListener(Component, int) - Constructor for class org.openscience.cdk.io.listener.SwingGUIListener
-
0 = ask no questions
3 = ask all questions
- SwingMouseEventRelay - Class in org.openscience.cdk.controller
-
- SwingMouseEventRelay(IMouseEventRelay) - Constructor for class org.openscience.cdk.controller.SwingMouseEventRelay
-
- SwissArmyKnife - Class in org.openscience.cdk.tools
-
A set of utilities which did not really fit into any other category
- SwissArmyKnife() - Constructor for class org.openscience.cdk.tools.SwissArmyKnife
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- SwitchTo(int) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
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Switch to specified lex state.
- SwitchTo(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
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Switch to specified lex state.
- SybylAtomTypeMatcher - Class in org.openscience.cdk.atomtype
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Atom Type matcher for Sybyl atom types.
- SybylDescriptorFormat - Class in org.openscience.cdk.io.formats
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- SYMBOL - Static variable in class org.openscience.cdk.libio.jena.CDK
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- SymbolAndChargeQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
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- SymbolAndChargeQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
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- SymbolAndChargeQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
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- SymbolChargeIDQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
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- SymbolChargeIDQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
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- SymbolChargeIDQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
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- SymbolQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
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- SymbolQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
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- SymbolQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
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- SymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
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A QueryAtom that matches all symbols in this container.
- SymbolSetQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
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Constructor for the SymbolSetQueryAtom object
- SystemOutLoggingTool - Class in org.openscience.cdk.tools
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- SystemOutLoggingTool(Class<?>) - Constructor for class org.openscience.cdk.tools.SystemOutLoggingTool
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Constructs a ILoggingTool which produces log lines indicating them to be
for the given Class.