- 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.
- Abbreviations - Class in org.openscience.cdk.depict
-
Utility class for abbreviating (sub)structures.
- Abbreviations() - Constructor for class org.openscience.cdk.depict.Abbreviations
-
- ABINITFormat - Class in org.openscience.cdk.io.formats
-
- ABINITFormat() - Constructor for class org.openscience.cdk.io.formats.ABINITFormat
-
- abortOnErrors - Variable in class org.openscience.cdk.io.cml.CMLErrorHandler
-
- Absolute - Static variable in class org.openscience.cdk.smiles.SmiFlavor
-
Output canonical SMILES with stereochemistry, atomic masses.
- absolute() - Static method in class org.openscience.cdk.smiles.SmilesGenerator
-
Create a absolute SMILES generator.
- 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
-
- AbstractAtomPairDescriptor - Class in org.openscience.cdk.qsar
-
A super class for atom pair descriptors allowing default implementations for
interface methods.
- AbstractAtomPairDescriptor() - Constructor for class org.openscience.cdk.qsar.AbstractAtomPairDescriptor
-
- 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.
- AbstractDifference() - Constructor for class org.openscience.cdk.tools.diff.tree.AbstractDifference
-
- AbstractDifferenceList - Class in org.openscience.cdk.tools.diff.tree
-
Diff between two IChemObjects.
- AbstractDifferenceList() - Constructor for class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
-
- AbstractFingerprinter - Class in org.openscience.cdk.fingerprint
-
- AbstractFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.AbstractFingerprinter
-
- 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
-
- AbstractMCS() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Deprecated.
- AbstractMCSAlgorithm - Class in org.openscience.cdk.smsd.interfaces
-
- AbstractMCSAlgorithm() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
-
Deprecated.
- AbstractMolecularDescriptor - Class in org.openscience.cdk.qsar
-
A super class for molecular descriptors allowing default implementations for
interface methods.
- AbstractMolecularDescriptor() - Constructor for class org.openscience.cdk.qsar.AbstractMolecularDescriptor
-
- AbstractReactionLabeller - Class in org.openscience.cdk.smsd.labelling
-
- AbstractReactionLabeller() - Constructor for class org.openscience.cdk.smsd.labelling.AbstractReactionLabeller
-
Deprecated.
- 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
-
- AbstractResourceFormat - Class in org.openscience.cdk.io.formats
-
- AbstractResourceFormat() - Constructor for class org.openscience.cdk.io.formats.AbstractResourceFormat
-
- 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
-
- AbstractSubGraph() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractSubGraph
-
Deprecated.
- 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.interfaces.IElement
-
- 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.Bounds
-
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.MarkedElement
-
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<? extends IChemObject>) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CIFReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CMLReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CMLWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CrystClustReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CrystClustWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CTXReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.GamessReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Gaussian98Reader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.HINReader
-
- accepts(Class<? extends IChemObject>) - 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<? extends IChemObject>) - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.INChIReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLReader
-
Deprecated.
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV3000Writer
-
Returns whether the given
IChemObject
can be read or written.
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mol2Reader
-
- accepts(IChemObject) - Method in class org.openscience.cdk.io.Mol2Reader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mol2Writer
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mopac7Reader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MoSSOutputReader
-
Returns whether the given
IChemObject
can be read or written.
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PDBReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PDBWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PMPReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.program.Mopac7Writer
-
- accepts(Class<? extends IChemObject>) - 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<? extends IChemObject>) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Returns whether the given
IChemObject
can be read or written.
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Returns true for accepted input types.
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RssWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SDFWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.ShelXReader
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.ShelXWriter
-
- accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SMILESReader
-
- accepts(Class<? extends IChemObject>) - 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<? extends IChemObject>) - Method in class org.openscience.cdk.io.XYZWriter
-
- accepts(Class<? extends IChemObject>) - 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.
- ACDLABS_LABEL - Static variable in class org.openscience.cdk.CDKConstants
-
Atom number/label that can be applied using the Manual Numbering
Tool in ACD/ChemSketch.
- Aces2Format - Class in org.openscience.cdk.io.formats
-
- Aces2Format() - Constructor for class org.openscience.cdk.io.formats.Aces2Format
-
- 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 enum org.openscience.cdk.config.Elements
-
- ACTINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- activity - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
-
- 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(IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Protected methods only to be used by classes extending this class to add
an IIsotope.
- 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
-
Adds all molecularFormulas in the AdductFormula to this chemObject.
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Adds all atomContainers in the AtomContainerSet to this container.
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Adds an molecularFormula to this MolecularFormula.
- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IReactionScheme) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Add a Scheme of Reactions.
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IRingSet) - Method in class org.openscience.cdk.debug.DebugRingSet
-
Adds all rings of another RingSet if they are not already part of this ring set.
- add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Adds all atomContainers in the AtomContainerSet to this container.
- add(String) - Method in class org.openscience.cdk.depict.Abbreviations
-
Convenience method to add an abbreviation from a SMILES string.
- add(IAtomContainer, String) - Method in class org.openscience.cdk.depict.Abbreviations
-
Add an abbreviation to the factory.
- 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(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(T) - Method in class org.openscience.cdk.io.setting.SettingManager
-
Add a setting to the manager and return the instance to use.
- add(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- 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(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.Bounds
-
Add the specified element bounds.
- add(double, double) - Method in class org.openscience.cdk.renderer.elements.Bounds
-
Ensure the point x,y is included in the bounding box.
- add(Bounds) - Method in class org.openscience.cdk.renderer.elements.Bounds
-
Add one bounds to another.
- 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(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
-
Deprecated.
Adds mapping to the mapping list
- add(Map<Integer, Integer>) - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Deprecated.
Adds mapping to the mapping list
- add3DCoordinates1(IAtomContainer) - 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(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction
-
Adds an agent to this reaction.
- addAgent(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds an agent to this reaction.
- addAgent(IAtomContainer) - Method in class org.openscience.cdk.Reaction
-
Adds an agent to this reaction.
- addAgent(IAtomContainer) - 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(IBioPolymer, IAminoAcid, IStrand, IAminoAcid) - 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(IBioPolymer, IAminoAcid, IStrand, IAminoAcid) - 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.
- addArrayElementsTo(List<String>, String) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- 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
-
Adds an atom to this container.
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds an atom to this container.
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds an atom to this container.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
- addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds the atom to a specified Strand and a specified Monomer.
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds an atom to this container.
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds an atom to this container.
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds an atom to this container.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds an atom to this container.
- addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds the atom oAtom without specifying a Monomer or a Strand.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds the atom oAtom to a specific Monomer.
- 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
-
Adds an atom to this container.
- 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(IAtom) - Method in class org.openscience.cdk.sgroup.Sgroup
-
Add an atom to this Sgroup.
- 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
-
Adds an atomContainer to this container.
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Adds an atomContainer to this container with the given
multiplier.
- addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Adds an atomContainer to this container.
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Adds an atomContainer to this container with the given
multiplier.
- 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.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.
- 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
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a bond to this container.
- 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
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a bond to this container.
- addBond(IBond) - Method in class org.openscience.cdk.sgroup.Sgroup
-
Add a bond to this Sgroup.
- 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.
- addBracket(SgroupBracket) - Method in class org.openscience.cdk.sgroup.Sgroup
-
Add a bracket for this Sgroup.
- 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.
- addCell(int...) - Method in class org.openscience.cdk.group.Partition
-
Adds a new cell to the end of the partition containing these elements.
- addCell(Collection<Integer>) - Method in class org.openscience.cdk.group.Partition
-
Adds a new cell to the end of the partition.
- 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
-
Adds an chemModel to this container.
- 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.ChemObjectIO
-
- addChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO
-
- 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
-
Adds a ChemSequence to this container.
- 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
-
Add an Atom and makes it the C-terminus atom.
- 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
-
Deprecated.
Adds edge to the edge list.
- addEdge(EdgeBuilder) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Deprecated.
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
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a ElectronContainer to this AtomContainer.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
-
Adds a ElectronContainer to this AtomContainer.
- addError(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport
-
Adds a validation test which gives serious errors.
- addEscapes(String) - Static method in error org.openscience.cdk.iupac.parser.TokenMgrError
-
Replaces unprintable characters by their escaped (or unicode escaped)
equivalents in the given string
- addEscapes(String) - Static method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError
-
Replaces unprintable characters by their escaped (or unicode escaped)
equivalents in the given string
- addExampleReaction(String) - Method in class org.openscience.cdk.dict.EntryReact
-
add a example for this reaction.
- addFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Add a formula to this isotope container.
- 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
-
Adds an Isotope to this MolecularFormula one time.
- addIsotope(IIsotope, int) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Adds an Isotope to this MolecularFormula in a number of occurrences.
- 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
-
Deprecated.
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
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtom
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBond
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElement
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMapping
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReaction
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugRing
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugStrand
-
Use this to add yourself to this IChemObject as a listener.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Use this to add yourself to this IChemObject as a listener.
- 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.isomorphism.matchers.QueryChemObject
-
Use this to add yourself to this IChemObject as a listener.
- 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
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a LonePair to this Atom.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a LonePair to this Atom.
- 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.isomorphism.matchers.QueryAtomContainer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
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
-
Adds an molecularFormula to this chemObject.
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
Adds an molecularFormula to this chemObject.
- 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(IAtomContainer, boolean) - Method in class org.openscience.cdk.fingerprint.model.Bayesian
-
Appends a new row to the model source data, which consists of a molecule and whether or not it
is considered active.
- addMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
-
Adds a Molecule to the list of templates use by this TemplateHandler.
- addNeighbor(NodeBuilder) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Deprecated.
Adds neighbor to the Neighbors List.
- addNeighbor(NodeBuilder) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Deprecated.
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
-
Deprecated.
Adds a new node to the CDKRGraph.
- addNode(VFAtomMatcher, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Deprecated.
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
-
Add an Atom and makes it the N-terminus atom.
- 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.
- addParent(Sgroup) - Method in class org.openscience.cdk.sgroup.Sgroup
-
Add a parent Sgroup.
- addProduct(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction
-
Adds a product to this reaction.
- addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction
-
Adds a product to this reaction.
- addProduct(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a product to this reaction.
- addProduct(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a product to this reaction.
- addProduct(IAtomContainer) - Method in class org.openscience.cdk.Reaction
-
Adds a product to this reaction.
- addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction
-
Adds a product to this reaction.
- addProduct(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a product to this reaction.
- addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a product to this reaction.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElement
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMapping
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugRing
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Add properties to this object, duplicate keys will replace any existing
value.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Sets the properties of this object.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets the properties of this object.
- addReactant(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction
-
Adds a reactant to this reaction.
- addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction
-
Adds a reactant to this reaction with a stoichiometry coefficient.
- addReactant(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a reactant to this reaction.
- addReactant(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Adds a reactant to this reaction with a stoichiometry coefficient.
- addReactant(IAtomContainer) - Method in class org.openscience.cdk.Reaction
-
Adds a reactant to this reaction.
- addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction
-
Adds a reactant to this reaction with a stoichiometry coefficient.
- addReactant(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a reactant to this reaction.
- addReactant(IAtomContainer, 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
-
Adds an reaction to this container.
- 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.
- addSetting(IOSetting) - Method in class org.openscience.cdk.io.ChemObjectIO
-
Add an IOSetting to the reader/writer.
- addSetting(IOSetting) - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Add an IOSetting to the reader/writer.
- addSettings(Collection<IOSetting>) - Method in class org.openscience.cdk.io.ChemObjectIO
-
Adds a collection of
IOSetting
s to the reader/writer.
- addSettings(Collection<IOSetting>) - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Adds a collection of
IOSetting
s to the reader/writer.
- 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 SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Adds a SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a SingleElectron to this Atom.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a SingleElectron to this Atom.
- 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.isomorphism.matchers.QueryAtomContainer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a LonePair 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 SingleElectron to this Atom.
- addSingletonCell(int) - Method in class org.openscience.cdk.group.Partition
-
Add a new singleton cell to the end of the partition containing only
this element.
- 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
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugRing
-
Adds a stereo element to this container.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugStrand
-
Adds a stereo element to this container.
- 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.isomorphism.matchers.QueryAtomContainer
-
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
-
Adds the PDBStructure structure a this PDBPolymer.
- 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
-
Deprecated.
Add a symbol to this QueryAtom
- addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Deprecated.
Add a symbol to this QueryAtom
- addToAtomContainer(IAtomContainer, IChemObject) - Method in class org.openscience.cdk.renderer.selection.AbstractSelection
-
- addToCell(int, int) - Method in class org.openscience.cdk.group.Partition
-
Add an element to a particular cell.
- 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
-
- ADFFormat() - Constructor for class org.openscience.cdk.io.formats.ADFFormat
-
- 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.
- adjustProtonation(IMolecularFormula, int) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Adjust the protonation of a molecular formula.
- Ag - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- AG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- agents - Variable in class org.openscience.cdk.Reaction
-
These are the used solvent, catalysts etc that normally appear above
the reaction arrow
- agents - Variable in class org.openscience.cdk.silent.Reaction
-
These are the used solvent, catalysts etc that normally appear above
the reaction arrow
- Al - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- AL - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
-
ExtendedTetrahedral a.k.a.
- 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
-
- AlchemyFormat() - Constructor for class org.openscience.cdk.io.formats.AlchemyFormat
-
- Algorithm - Enum in org.openscience.cdk.smsd.interfaces
-
- 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
-
Deprecated.
- AliphaticAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom
-
Deprecated.
Creates a new instance
- AliphaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Deprecated.
- AliphaticSymbolAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom
-
Deprecated.
Creates a new instance.
- all() - Static method in class org.openscience.cdk.graph.Cycles
-
Create a cycle finder which will compute all simple cycles in a molecule.
- all(int) - Static method in class org.openscience.cdk.graph.Cycles
-
All cycles of smaller than or equal to the specified length.
- all(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
-
Find all simple cycles in a molecule.
- all(IAtomContainer, int) - Static method in class org.openscience.cdk.graph.Cycles
-
All cycles of smaller than or equal to the specified length.
- all() - Method in class org.openscience.cdk.group.PermutationGroup
-
Generate the whole group from the compact list of permutations.
- all(SymbolVisibility) - Static method in class org.openscience.cdk.renderer.generators.standard.SelectionVisibility
-
Display the atom symbol if is selected, otherwise use the provided visibility.
- all() - Static method in class org.openscience.cdk.renderer.SymbolVisibility
-
All atom symbols are visible.
- 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
-
Deprecated.
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.
- AllCycles - Class in org.openscience.cdk.graph
-
Compute all simple cycles (rings) in a graph.
- AllCycles(int[][], int, int) - Constructor for class org.openscience.cdk.graph.AllCycles
-
Compute all simple cycles up to given maxCycleSize in the provided
graph.
- Allenal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
-
ExtendedTetrahedral (e.g.
- allHeavyAtomsPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
True is all the atoms in the given AtomContainer have been placed.
- allOrVertexShort() - Static method in class org.openscience.cdk.graph.Cycles
-
- AllPairsShortestPaths - Class in org.openscience.cdk.graph
-
Utility to determine the shortest paths between all pairs of atoms in a
molecule.
- AllPairsShortestPaths(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AllPairsShortestPaths
-
- allPlaced(IAtomContainer) - Static 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
-
Compute the set of all rings in a molecule.
- AllRingsFinder(boolean) - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder
-
- AllRingsFinder() - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder
-
- AllRingsFinder.Threshold - Enum in org.openscience.cdk.ringsearch
-
The threshold values provide a limit at which the computation stops.
- 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
-
- 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 enum 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.interfaces.IElement
-
- 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 enum 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.
- and(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- and(IBitFingerprint) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Performs a logical AND of the bits in this target bit set with
the bits in the argument fingerprint.
- and(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- and(IntArrayFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- and(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr
-
Utility, combine this expression with another, using conjunction.
- and(IQueryAtom, IQueryAtom) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
Deprecated.
Conjunction the provided expressions.
- 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
-
- ANNOTATION_LABEL - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
-
Defines the annotation label(s) of a chem object in a depiction.
- AnnotationColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor
-
- AnnotationDistance() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance
-
- AnnotationFontScale() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale
-
- ANNOTATIONS - Static variable in class org.openscience.cdk.CDKConstants
-
A List of annotation remarks.
- anonymise(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Anonymise the provided container to single-bonded carbon atoms.
- ANTIMONY - Static variable in enum 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
-
Deprecated.
- AnyAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom
-
Deprecated.
Creates a new instance
- AnyAtom() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AnyOrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Deprecated.
- AnyOrderQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
-
Deprecated.
- AnyOrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
-
Deprecated.
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.
- apply(IAtomContainer) - Method in class org.openscience.cdk.aromaticity.Aromaticity
-
Apply this aromaticity model to a molecule.
- apply(IAtomContainer) - Method in class org.openscience.cdk.depict.Abbreviations
-
Generates and assigns abbreviations to a molecule.
- apply(PermutationGroup.Backtracker) - Method in class org.openscience.cdk.group.PermutationGroup
-
Apply the backtracker to all permutations in the larger group.
- apply(int[]) - Method in class org.openscience.cdk.isomorphism.SmartsStereoMatch
-
Deprecated.
Backwards compatible method from when we used GUAVA predicates.
- applyTo(Permutation) - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker
-
Do something to the permutation
- Ar - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- 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
-
Deprecated.
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 enum org.openscience.cdk.config.Elements
-
- Aromatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- aromatic() - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
- AromaticAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Deprecated.
- AromaticAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom
-
Deprecated.
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.
- Aromaticity - Class in org.openscience.cdk.aromaticity
-
A configurable model to perceive aromatic systems.
- Aromaticity(ElectronDonation, CycleFinder) - Constructor for class org.openscience.cdk.aromaticity.Aromaticity
-
Create an aromaticity model using the specified electron donation model
which is tested on the cycles
.
- AromaticityCalculator - Class in org.openscience.cdk.aromaticity
-
- AromaticityCalculator() - Constructor for class org.openscience.cdk.aromaticity.AromaticityCalculator
-
Deprecated.
- AromaticOrSingleQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Deprecated.
- AromaticOrSingleQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
-
Deprecated.
Creates a new instance.
- AromaticOrSingleQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
-
Deprecated.
Creates a new instance
- AromaticQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Deprecated.
- AromaticQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
-
Deprecated.
Creates a new instance.
- AromaticQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
-
Deprecated.
Creates a new instance
- AromaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Deprecated.
- AromaticSymbolAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom
-
Deprecated.
- aromatizeMolecule(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
Deprecated.
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
-
Deprecated.
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.
- ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
-
- ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
-
- ARSENIC - Static variable in enum 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.interfaces.IElement
-
- 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.
- asBitSet() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- asBitSet() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Returns a BitSet
representation of the fingerprint.
- asBitSet() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- assignAtomTypePropertiesToAtom(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeTools
-
- assignAtomTypePropertiesToAtom(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.AtomTypeTools
-
Method assigns certain properties to an atom.
- assignAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff
-
Assign MMFF Symbolic atom types.
- assignAtomTyps(IAtomContainer) - 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.
- ASTATINE - Static variable in enum org.openscience.cdk.config.Elements
-
- At - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- AT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
-
Atropisomeric (e.g.
- AT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- atLeast(int) - Method in class org.openscience.cdk.isomorphism.Mappings
-
Efficiently determine if there are at least 'n' matches
- 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(int) - Constructor for class org.openscience.cdk.Atom
-
Create a new atom with of the specified element.
- Atom(int, int) - Constructor for class org.openscience.cdk.Atom
-
Create a new atom with of the specified element and hydrogen count.
- Atom(int, int, int) - Constructor for class org.openscience.cdk.Atom
-
Create a new atom with of the specified element, hydrogen count, and formal charge.
- Atom(String) - Constructor for class org.openscience.cdk.Atom
-
Constructs an Atom from a string containing an element symbol and optionally
the atomic mass, hydrogen count, and formal charge.
- 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 - Variable in class org.openscience.cdk.LonePair
-
The atom with which this lone pair is associated.
- 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(int) - Constructor for class org.openscience.cdk.silent.Atom
-
Create a new atom with of the specified element.
- Atom(int, int) - Constructor for class org.openscience.cdk.silent.Atom
-
Create a new atom with of the specified element and hydrogen count.
- Atom(int, int, int) - Constructor for class org.openscience.cdk.silent.Atom
-
Create a new atom with of the specified element, hydrogen count, and formal charge.
- Atom(String) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an Atom from a string containing an element symbol and optionally
the atomic mass, hydrogen count, and formal charge.
- 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 - Variable in class org.openscience.cdk.silent.LonePair
-
The atom with which this lone pair is associated.
- atom - Variable in class org.openscience.cdk.silent.SingleElectron
-
The atom with which this single electron is associated.
- atom - Variable in class org.openscience.cdk.SingleElectron
-
The atom with which this single electron is associated.
- 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
-
- atomAromaticities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- AtomAtomMap - Static variable in class org.openscience.cdk.smiles.SmiFlavor
-
Output atom-atom mapping for reactions and atom classes for molecules.
- AtomAtomMappingLineColor() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor
-
- AtomAtomMapRenumber - Static variable in class org.openscience.cdk.smiles.SmiFlavor
-
Renumber AtomAtomMaps during canonical generation
- AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor
-
- AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor
-
- AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer
-
- AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer
-
- 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 - Variable in class org.openscience.cdk.graph.AtomContainerPermutor
-
The atom container that is permuted at each step.
- atomContainer - Variable in class org.openscience.cdk.inchi.InChIGenerator
-
AtomContainer instance refers to.
- 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.
- atomContainer - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
The molecular structure on which we work
- AtomContainerAtomPermutor - Class in org.openscience.cdk.graph
-
An atom container atom permutor that uses ranking and unranking to calculate
the next permutation in the series.
- AtomContainerAtomPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerAtomPermutor
-
A permutor wraps the original atom container, and produces cloned
(and permuted!) copies on demand.
- AtomContainerAtomPermutor - Class in org.openscience.cdk.smsd.labelling
-
- AtomContainerAtomPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor
-
Deprecated.
- AtomContainerBondPermutor - Class in org.openscience.cdk.graph
-
This class allows the user to iterate through 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
-
A permutor wraps the original atom container, and produces cloned
(and permuted!) copies on demand.
- 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
-
- atomContainerCount - Variable in class org.openscience.cdk.AtomContainerSet
-
Number of AtomContainers contained by this container.
- atomContainerCount - Variable in class org.openscience.cdk.silent.AtomContainerSet
-
Number of AtomContainers contained by this container.
- AtomContainerDiff - Class in org.openscience.cdk.tools.diff
-
- AtomContainerDiscretePartitionRefiner - Interface in org.openscience.cdk.group
-
A tool for determining the automorphism group of the atoms in a molecule, or
for checking for a canonical form of a molecule.
- 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 base class for permutors of atom containers, with a single abstract
method containerFromPermutation
that should be implemented in
concrete derived classes.
- AtomContainerPermutor(int, IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerPermutor
-
Start the permutor off with an initial atom container, and the size of
the permutation.
- AtomContainerPrinter - Class in org.openscience.cdk.smsd.labelling
-
- AtomContainerPrinter() - Constructor for class org.openscience.cdk.smsd.labelling.AtomContainerPrinter
-
Deprecated.
- 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 - Variable in class org.openscience.cdk.AtomContainerSet
-
Array of AtomContainers.
- atomContainers() - Method in class org.openscience.cdk.AtomContainerSet
-
Get an iterator for this AtomContainerSet.
- atomContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Get an iterator for this AtomContainerSet.
- atomContainers() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Get an iterator for this AtomContainerSet.
- atomContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Get an Iterable for this AtomContainerSet.
- atomContainers - Variable in class org.openscience.cdk.silent.AtomContainerSet
-
Array of AtomContainers.
- 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
-
- atomCount - Variable in class org.openscience.cdk.Association
-
- atomCount - Variable in class org.openscience.cdk.AtomContainer
-
Number of atoms contained by this object.
- atomCount - Variable in class org.openscience.cdk.Bond
-
Number of atoms contained by this object.
- atomCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Number of atoms contained by this object.
- atomCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Number of atoms contained by this object.
- atomCount - Variable in class org.openscience.cdk.silent.AtomContainer
-
Number of atoms contained by this object.
- atomCount - Variable in class org.openscience.cdk.silent.Bond
-
Number of atoms contained by this object.
- 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.
- atomCounter - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- atomCustomProperty - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- 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
-
- atomDictRefs - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- AtomDiff - Class in org.openscience.cdk.tools.diff
-
Compares two
IAtom
classes.
- AtomEncoder - Interface in org.openscience.cdk.hash
-
An encoder for invariant atom properties.
- atomEnumeration - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- AtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AtomHashGenerator - Interface in org.openscience.cdk.hash
-
A hash function which generates 64-bit hash codes for the atoms of a
molecule.
- 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() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
-
- AtomicMass - Static variable in class org.openscience.cdk.graph.invariant.CanonOpts
-
Distinguish atoms based on atomic mass.
- AtomicMass() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AtomicMass - Static variable in class org.openscience.cdk.smiles.SmiFlavor
-
Output atomic mass on atoms.
- AtomicMassStrict - Static variable in class org.openscience.cdk.smiles.SmiFlavor
-
- atomicNumber - Variable in class org.openscience.cdk.Element
-
The atomic number for this element giving their position in the periodic table.
- atomicNumber - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The atomic number for this element giving their position in the periodic table.
- atomicNumber - Variable in class org.openscience.cdk.silent.Element
-
The atomic number for this element giving their position in the periodic table.
- AtomicNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- AtomicNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Deprecated.
- AtomicNumberAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom
-
Deprecated.
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
-
- atomicNumbers - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- 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 - Class in org.openscience.cdk.isomorphism
-
Defines compatibility checking of atoms for (subgraph)-isomorphism mapping.
- AtomMatcher() - Constructor for class org.openscience.cdk.isomorphism.AtomMatcher
-
- AtomMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers
-
- 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.AtomNumberTextColor - Class in org.openscience.cdk.renderer.generators
-
Color to draw the atom numbers with.
- AtomNumberGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators
-
- AtomNumberGenerator.Offset - Class in org.openscience.cdk.renderer.generators
-
Offset vector in screen space coordinates where the atom number label
will be placed.
- 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.
- AtomNumberTextColor() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor
-
- AtomPairs2DFingerprinter - Class in org.openscience.cdk.fingerprint
-
- AtomPairs2DFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
-
- atomParities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- 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.
- AtomRadius() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius
-
- AtomRef - Class in org.openscience.cdk
-
An atom ref, references a CDK
IAtom
indirectly.
- AtomRef(IAtom) - Constructor for class org.openscience.cdk.AtomRef
-
Create a pointer for the provided atom.
- AtomRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
-
- atoms - Variable in class org.openscience.cdk.Association
-
The atoms which take part in the association.
- atoms - Variable in class org.openscience.cdk.AtomContainer
-
Internal array of atoms.
- atoms() - Method in class org.openscience.cdk.AtomContainer
-
Returns an Iterable for looping over all atoms in this container.
- atoms - Variable in class org.openscience.cdk.Bond
-
A list of atoms participating in this bond.
- atoms() - Method in class org.openscience.cdk.Bond
-
Returns the Iterator to atoms making up this bond.
- atoms() - Method in class org.openscience.cdk.BondRef
-
Returns the Iterable to atoms making up this bond.
- atoms() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the Iterator to atoms making up this bond.
- atoms() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns an Iterable for looping over all atoms in this container.
- atoms() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns an Iterable for looping over all atoms in this container.
- atoms - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
-
- 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 - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Internal array of atoms.
- atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an Iterable for looping over all atoms in this container.
- atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
A list of atoms participating in this query bond.
- atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the Iterator to atoms making up this query bond.
- atoms - Variable in class org.openscience.cdk.silent.AtomContainer
-
Internal array of atoms.
- atoms() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an Iterable for looping over all atoms in this container.
- atoms - Variable in class org.openscience.cdk.silent.Bond
-
A list of atoms participating in this bond.
- 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 (
Faulon, J. L., Visco, D. P., and Pophale, R. S.. Journal of Chemical Information and Computer
Sciences. 2003. 43,
Faulon, J. L., Collins, M. J., and Carr, R. D.. Journal of Chemical Information and Computer
Sciences. 2004. 44) 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.
- atomsTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths
-
Reconstruct a shortest path to the provided end vertex.
- atomsTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths
-
Reconstruct a shortest path to the provided end atom.
- 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.
- AtomTypeAwareSaturationChecker - Class in org.openscience.cdk.tools
-
This class tries to figure out the bond order of the bonds that has the flag
SINGLE_OR_DOUBLE
raised (i.e.
- AtomTypeAwareSaturationChecker() - Constructor for class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
-
- 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
IAtomType
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
-
- Atropisomeric - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
-
Atropisomeric (e.g.
- Atropisomeric - Class in org.openscience.cdk.stereo
-
Restricted axial rotation around Aryl-Aryl bonds.
- Atropisomeric(IBond, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.Atropisomeric
-
Define a new atropisomer using the focus bond and the carrier atoms.
- 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(List<Token>, String) - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup
-
Creates a new instance of AttachedGroup with a Sting denoting the functional group
- AttachedGroup(List<Token>, 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
-
Deprecated.
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.interfaces.IElement
-
- 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
-
- 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
-
- AUTOMATIC - Static variable in class org.openscience.cdk.depict.DepictionGenerator
-
Magic value for indicating automatic parameters.
- 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, IAtomContainerSet, 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!
- B - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- b - Variable in class org.openscience.cdk.io.random.RandomAccessReader
-
- B - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- Ba - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- BA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- BackgroundColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor
-
- backTrack() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
-
Deprecated.
Returns this IState's atom map to its original condition.
- backTrack() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
-
Deprecated.
Returns this IState's atom map to its original condition.
- backup(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Backup a number of characters.
- backup(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Backup a number of characters.
- BAD_SMILES_INPUT - Static variable in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Store the problem input as a property.
- BadMatrixFormatException - Exception in org.openscience.cdk.graph.invariant.exception
-
- BadMatrixFormatException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.BadMatrixFormatException
-
- BARIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- BARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- BasicAtomEncoder - Enum in org.openscience.cdk.hash
-
Enumeration of atom encoders for seeding atomic hash codes.
- BasicAtomGenerator - Class in org.openscience.cdk.renderer.generators
-
- BasicAtomGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
An empty constructor necessary for reflection.
- BasicAtomGenerator.AtomColor - Class in org.openscience.cdk.renderer.generators
-
Class to hold the color by which atom labels are drawn.
- BasicAtomGenerator.AtomColorer - Class in org.openscience.cdk.renderer.generators
-
- BasicAtomGenerator.AtomRadius - Class in org.openscience.cdk.renderer.generators
-
Magic number with unknown units that defines the radius
around an atom, e.g.
- BasicAtomGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators
-
Boolean property that triggers atoms to be colored by type
when set to true.
- BasicAtomGenerator.CompactAtom - Class in org.openscience.cdk.renderer.generators
-
Boolean parameters that will cause atoms to be drawn as
filled shapes when set to true.
- BasicAtomGenerator.CompactShape - Class in org.openscience.cdk.renderer.generators
-
- BasicAtomGenerator.KekuleStructure - Class in org.openscience.cdk.renderer.generators
-
Determines whether structures should be drawn as Kekule structures, thus
giving each carbon element explicitly, instead of not displaying the
element symbol.
- BasicAtomGenerator.Shape - Enum in org.openscience.cdk.renderer.generators
-
When atoms are selected or in compact mode, they will
be covered by a shape determined by this enumeration.
- BasicAtomGenerator.ShowEndCarbons - Class in org.openscience.cdk.renderer.generators
-
Boolean parameters that will show carbons with only one
(non-hydrogen) neighbor to be drawn with an element symbol.
- BasicAtomGenerator.ShowExplicitHydrogens - Class in org.openscience.cdk.renderer.generators
-
Boolean property that triggers explicit hydrogens to be
drawn if set to true.
- BasicBondGenerator - Class in org.openscience.cdk.renderer.generators
-
Generator for elements from bonds.
- BasicBondGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
An empty constructor necessary for reflection.
- BasicBondGenerator.BondDistance - Class in org.openscience.cdk.renderer.generators
-
The gap between double and triple bond lines on the screen.
- BasicBondGenerator.BondWidth - Class in org.openscience.cdk.renderer.generators
-
The width on screen of a bond.
- BasicBondGenerator.DefaultBondColor - Class in org.openscience.cdk.renderer.generators
-
The color to draw bonds if not other color is given.
- BasicBondGenerator.TowardsRingCenterProportion - Class in org.openscience.cdk.renderer.generators
-
The proportion to move in towards the ring center.
- BasicBondGenerator.WedgeWidth - Class in org.openscience.cdk.renderer.generators
-
The width on screen of the fat end of a wedge bond.
- BasicCreator(Class<T>) - Constructor for class org.openscience.cdk.DynamicFactory.BasicCreator
-
Create a basic constructor with a given declaring class.
- BasicGenerator - Class in org.openscience.cdk.renderer.generators
-
Combination generator for basic drawing of molecules.
- BasicGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicGenerator
-
Make a basic generator that creates elements for atoms and bonds.
- BasicGroupCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Returns the number of basic groups.
- BasicGroupCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
- basicInvariants(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon
-
- basicInvariants(IAtomContainer, int[][], int) - Static method in class org.openscience.cdk.graph.invariant.Canon
-
Generate the initial invariants for each atom in the container
.
- BasicSceneGenerator - Class in org.openscience.cdk.renderer.generators
-
This generator does not create any elements, but acts as a holding place
for various generator parameters used by most drawings, such as the zoom,
background color, margin, etc.
- BasicSceneGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator
-
An empty constructor necessary for reflection.
- BasicSceneGenerator.ArrowHeadWidth - Class in org.openscience.cdk.renderer.generators
-
The width of the head of arrows.
- BasicSceneGenerator.BackgroundColor - Class in org.openscience.cdk.renderer.generators
-
The background color of the drawn image.
- BasicSceneGenerator.BondLength - Class in org.openscience.cdk.renderer.generators
-
The length on the screen of a typical bond.
- BasicSceneGenerator.FitToScreen - Class in org.openscience.cdk.renderer.generators
-
If true, the scale is set such that the diagram
fills the whole screen.
- BasicSceneGenerator.FontName - Class in org.openscience.cdk.renderer.generators
-
Font to use for text.
- BasicSceneGenerator.ForegroundColor - Class in org.openscience.cdk.renderer.generators
-
The foreground color, with which objects are drawn.
- BasicSceneGenerator.Margin - Class in org.openscience.cdk.renderer.generators
-
Area on each of the four margins to keep empty.
- BasicSceneGenerator.Scale - Class in org.openscience.cdk.renderer.generators
-
The scale is the factor to multiply model coordinates by to convert the
coordinates to screen space coordinate, such that the entire structure
fits the visible screen dimension.
- BasicSceneGenerator.ShowMoleculeTitle - Class in org.openscience.cdk.renderer.generators
-
Determines if the molecule's title is depicted.
- BasicSceneGenerator.ShowReactionTitle - Class in org.openscience.cdk.renderer.generators
-
Determines if the reaction's title is depicted.
- BasicSceneGenerator.ShowTooltip - Class in org.openscience.cdk.renderer.generators
-
Determines if tooltips are to be shown.
- BasicSceneGenerator.UseAntiAliasing - Class in org.openscience.cdk.renderer.generators
-
If set to true, uses anti-aliasing for drawing.
- BasicSceneGenerator.UsedFontStyle - Class in org.openscience.cdk.renderer.generators
-
The font style to use for text.
- BasicSceneGenerator.ZoomFactor - Class in org.openscience.cdk.renderer.generators
-
The zoom factor which is a user oriented parameter allowing the
user to zoom in on parts of the molecule.
- BasicValidator - Class in org.openscience.cdk.validate
-
Validator which tests a number of basic chemical semantics.
- BasicValidator() - Constructor for class org.openscience.cdk.validate.BasicValidator
-
- Bayesian - Class in org.openscience.cdk.fingerprint.model
-
Bayesian models using fingerprints: provides model creation, analysis, prediction and
serialisation.
Uses a variation of the classic Bayesian model, using a Laplacian correction, which sums log
values of ratios rather than multiplying them together.
- Bayesian(int) - Constructor for class org.openscience.cdk.fingerprint.model.Bayesian
-
Instantiate a Bayesian model with no data.
- Bayesian(int, int) - Constructor for class org.openscience.cdk.fingerprint.model.Bayesian
-
Instantiate a Bayesian model with no data.
- BCUTDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Eigenvalue based descriptor noted for its utility in chemical diversity.
- BCUTDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
- Be - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- BE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- beginColumn - Variable in class org.openscience.cdk.iupac.parser.Token
-
The column number of the first character of this Token.
- beginColumn - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
-
The column number of the first character of this Token.
- beginLine - Variable in class org.openscience.cdk.iupac.parser.Token
-
The line number of the first character of this Token.
- beginLine - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
-
The line number of the first character of this Token.
- BeginToken() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Start.
- BeginToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Start.
- BEILSTEINRN - Static variable in class org.openscience.cdk.CDKConstants
-
The Beilstein Registry Number.
- BELOWAREA - Static variable in class org.openscience.cdk.renderer.GraphRendererModel
-
Paints the area below the function
- BENZENE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
-
- BERKELIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- BERKELIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- BERYLLIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- BERYLLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- BFSShortestPath - Class in org.openscience.cdk.graph
-
- BGFFormat - Class in org.openscience.cdk.io.formats
-
- BGFFormat() - Constructor for class org.openscience.cdk.io.formats.BGFFormat
-
- Bh - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- Bi - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- BI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- biconnectedSets() - Method in class org.openscience.cdk.graph.BiconnectivityInspector
-
Deprecated.
Returns a list of Set
s, where each set contains all edge that are
in the same biconnected component.
- BiconnectivityInspector - Class in org.openscience.cdk.graph
-
- BiconnectivityInspector(UndirectedGraph) - Constructor for class org.openscience.cdk.graph.BiconnectivityInspector
-
Deprecated.
Creates a biconnectivity inspector for the specified undirected graph.
- BinaryTree - Class in org.openscience.cdk.smsd.helper
-
- BinaryTree(int) - Constructor for class org.openscience.cdk.smsd.helper.BinaryTree
-
Deprecated.
Creates a new instance of BinaryTree.
- BINDSATOM - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- bindsHydrogen(IBond) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Check to see if any of the atoms in this bond are hydrogen atoms.
- BioPolymer - Class in org.openscience.cdk
-
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
- BioPolymer() - Constructor for class org.openscience.cdk.BioPolymer
-
Constructs a new Polymer to store the Strands.
- BioPolymer - Class in org.openscience.cdk.silent
-
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
- BioPolymer() - Constructor for class org.openscience.cdk.silent.BioPolymer
-
Constructs a new Polymer to store the Strands.
- BISMUTH - Static variable in enum org.openscience.cdk.config.Elements
-
- BISMUTH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- BitSetFingerprint - Class in org.openscience.cdk.fingerprint
-
- BitSetFingerprint(BitSet) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- BitSetFingerprint() - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- BitSetFingerprint(int) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- BitSetFingerprint(IBitFingerprint) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- bitSetToRMap(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Converts a RGraph bitset (set of RNode)
to a list of RMap that represents the
mapping between to substructures in G1 and G2
(the projection of the RGraph bitset on G1
and G2).
- bitSetToRMap(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Deprecated.
Converts a CDKRGraph bitset (set of CDKRNode)
to a list of CDKRMap that represents the
mapping between to substructures in G1 and G2
(the projection of the CDKRGraph bitset on G1
and G2).
- Bk - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- BK - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- BKKCKCF - Class in org.openscience.cdk.smsd.algorithm.mcsplus
-
- BKKCKCF(List<Integer>, List<Integer>, List<Integer>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF
-
Deprecated.
Creates index new instance of Bron Kerbosch Cazals Karande Koch Clique Finder
This class implements Bron-Kerbosch clique detection algorithm as it is
described in [F.
- BOHR_TO_ANGSTROM - Static variable in class org.openscience.cdk.io.GamessReader
-
Double constant that contains the conversion factor from Bohr unit to
Ångstrom unit.
- BOHR_TO_ANGSTROM - Static variable in class org.openscience.cdk.PhysicalConstants
-
Factor for the conversion of Bohr's to Angstrom's.
- BOHR_UNIT - Static variable in class org.openscience.cdk.io.GamessReader
-
Boolean constant used to specify that the coordinates are given in Bohr units.
- BOHRIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- BOHRIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- Bond - Class in org.openscience.cdk
-
Implements the concept of a covalent bond between two or more atoms.
- Bond() - Constructor for class org.openscience.cdk.Bond
-
Constructs an empty bond.
- Bond(IAtom, IAtom) - Constructor for class org.openscience.cdk.Bond
-
Constructs a bond with a single bond order..
- Bond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.Bond
-
Constructs a bond with a given order.
- Bond(IAtom[]) - Constructor for class org.openscience.cdk.Bond
-
Constructs a multi-center bond, with undefined order and no stereo information.
- Bond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.Bond
-
Constructs a multi-center bond, with a specified order and no stereo information.
- Bond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class org.openscience.cdk.Bond
-
Constructs a bond with a given order and stereo orientation from an array
of atoms.
- BOND - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- Bond - Class in org.openscience.cdk.silent
-
Implements the concept of a covalent bond between two or more atoms.
- Bond() - Constructor for class org.openscience.cdk.silent.Bond
-
Constructs an empty bond.
- Bond(IAtom, IAtom) - Constructor for class org.openscience.cdk.silent.Bond
-
Constructs a bond with a single bond order..
- Bond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.silent.Bond
-
Constructs a bond with a given order.
- Bond(IAtom[]) - Constructor for class org.openscience.cdk.silent.Bond
-
Constructs a multi-center bond, with undefined order and no stereo information.
- Bond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.silent.Bond
-
Constructs a multi-center bond, with a specified order and no stereo information.
- Bond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class org.openscience.cdk.silent.Bond
-
Constructs a bond with a given order and stereo orientation from an array
of atoms.
- bondARef1 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- bondARef2 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- bondAromaticity - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- bondCount - Variable in class org.openscience.cdk.AtomContainer
-
Number of bonds contained by this object.
- bondCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Number of bonds contained by this object.
- bondCount - Variable in class org.openscience.cdk.silent.AtomContainer
-
Number of bonds contained by this object.
- BondCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
IDescriptor based on the number of bonds of a certain bond order.
- BondCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Constructor for the BondCountDescriptor object
- bondCounter - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- bondCustomProperty - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- bondDictRefs - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- BondDiff - Class in org.openscience.cdk.tools.diff
-
Compares two
IBond
classes.
- BondDistance() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance
-
- bondElid - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- BondEnergies - Class in org.openscience.cdk.smsd.tools
-
- BondEnergies() - Constructor for class org.openscience.cdk.smsd.tools.BondEnergies
-
Deprecated.
- BondEnergy - Class in org.openscience.cdk.smsd.helper
-
- BondEnergy(String, String, IBond.Order, int) - Constructor for class org.openscience.cdk.smsd.helper.BondEnergy
-
Deprecated.
Creates a new bond energy for the given elements and
bond order.
- bondid - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- BondLength() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BondLength
-
- BondManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods to manipulate
AtomContainer's.
- BondManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.BondManipulator
-
- bondMap - Variable in class org.openscience.cdk.stereo.StereoElementFactory
-
A bond map for fast access to bond labels between two atom indices.
- BondMatcher - Class in org.openscience.cdk.isomorphism
-
Defines compatibility checking of bonds for (subgraph)-isomorphism mapping.
- BondMatcher() - Constructor for class org.openscience.cdk.isomorphism.BondMatcher
-
- BondMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers
-
- BONDORDER_DOUBLE - Static variable in class org.openscience.cdk.CDKConstants
-
- BONDORDER_QUADRUPLE - Static variable in class org.openscience.cdk.CDKConstants
-
- BONDORDER_SINGLE - Static variable in class org.openscience.cdk.CDKConstants
-
- BONDORDER_TRIPLE - Static variable in class org.openscience.cdk.CDKConstants
-
- bondOrderCanBeIncreased(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
-
Check if the bond order can be increased.
- BondOrderDifference - Class in org.openscience.cdk.tools.diff.tree
-
- BondPartialPiChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond
-
The calculation of bond-pi Partial charge is calculated
determining the difference the Partial Pi Charge on atoms
A and B of a bond.
- BondPartialPiChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
-
Constructor for the BondPartialPiChargeDescriptor object.
- BondPartialSigmaChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond
-
The calculation of bond-sigma Partial charge is calculated
determining the difference the Partial Sigma Charge on atoms
A and B of a bond.
- BondPartialSigmaChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
-
Constructor for the BondPartialSigmaChargeDescriptor object.
- BondPartialTChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond
-
The calculation of bond total Partial charge is calculated
determining the difference the Partial Total Charge on atoms
A and B of a bond.
- BondPartialTChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
-
Constructor for the BondPartialTChargeDescriptor object.
- BondRef - Class in org.openscience.cdk
-
A bond ref, references a CDK
IBond
indirectly.
- BondRef(IBond) - Constructor for class org.openscience.cdk.BondRef
-
Create a pointer for the provided bond.
- BondRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
-
- bonds() - Method in class org.openscience.cdk.Atom
-
Returns the bonds connected to this atom.
- bonds - Variable in class org.openscience.cdk.AtomContainer
-
Internal array of bonds.
- bonds() - Method in class org.openscience.cdk.AtomContainer
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.AtomRef
-
- bonds() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the bonds connected to this atom.
- bonds() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns the bonds connected to this atom.
- bonds() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the bonds connected to this atom.
- bonds - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Internal array of bonds.
- bonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an Iterable for looping over all bonds in this container.
- bonds() - Method in class org.openscience.cdk.silent.Atom
-
Returns the bonds connected to this atom.
- bonds - Variable in class org.openscience.cdk.silent.AtomContainer
-
Internal array of bonds.
- bonds() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an Iterable for looping over all bonds in this container.
- BondSeparation() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation
-
- BondSigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond
-
The calculation of bond-Polarizability is calculated determining the
difference the Sigma electronegativity on atoms A and B of a bond.
- BondSigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
-
Constructor for the BondSigmaElectronegativityDescriptor object.
- bondsInTree - Variable in class org.openscience.cdk.graph.SpanningTree
-
- bondStereo - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- BondsToAtomDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class returns the number of bonds on the shortest path between two atoms.
- BondsToAtomDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
Constructor for the BondsToAtomDescriptor object
- bondSymbols - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
The bond symbols used for bond orders "single", "double", "triple" and
"aromatic"
- BondTools - Class in org.openscience.cdk.geometry
-
A set of static utility classes for geometric calculations on
IBond
s.
- BondTools() - Constructor for class org.openscience.cdk.geometry.BondTools
-
- bondType() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Tokens which affect the bond order of the first bond.
- BondWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth
-
- BooleanArrayDifference - Class in org.openscience.cdk.tools.diff.tree
-
Difference between two boolean[]'s.
- BooleanDifference - Class in org.openscience.cdk.tools.diff.tree
-
- BooleanIOSetting - Class in org.openscience.cdk.io.setting
-
An class for a reader setting which must be of type String.
- BooleanIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.BooleanIOSetting
-
- BooleanResult - Class in org.openscience.cdk.qsar.result
-
Object that provides access to the calculated descriptor value.
- BooleanResult(boolean) - Constructor for class org.openscience.cdk.qsar.result.BooleanResult
-
- BooleanResultType - Class in org.openscience.cdk.qsar.result
-
IDescriptorResult type for boolean.
- BooleanResultType() - Constructor for class org.openscience.cdk.qsar.result.BooleanResultType
-
- booleanValue() - Method in class org.openscience.cdk.qsar.result.BooleanResult
-
- BORON - Static variable in enum org.openscience.cdk.config.Elements
-
- Bounds - Class in org.openscience.cdk.renderer.elements
-
Defines a bounding box element which the renderer can use to determine the true
drawing limits.
- Bounds(double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.Bounds
-
Specify the min/max coordinates of the bounding box.
- Bounds() - Constructor for class org.openscience.cdk.renderer.elements.Bounds
-
An empty bounding box.
- Bounds(IRenderingElement) - Constructor for class org.openscience.cdk.renderer.elements.Bounds
-
An bounding box around the specified element.
- BoundsCalculator - Class in org.openscience.cdk.renderer
-
Utility class for calculating the 2D bounding rectangles (bounds)
of various IChemObject subtypes - IChemModel, IReactionSet, IReaction,
IAtomContainerSet, and IAtomContainer.
- BoundsCalculator() - Constructor for class org.openscience.cdk.renderer.BoundsCalculator
-
- BoundsColor() - Constructor for class org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor
-
- BoundsGenerator - Class in org.openscience.cdk.renderer.generators
-
Produce a bounding rectangle for various chem objects.
- BoundsGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BoundsGenerator
-
- BoundsGenerator.BoundsColor - Class in org.openscience.cdk.renderer.generators
-
The color of the box drawn at the bounds of a
molecule, molecule set, or reaction.
- boundTo(IAtom, String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
-
- BPolDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Sum of the absolute value of the difference between atomic polarizabilities
of all bonded atoms in the molecule (including implicit hydrogens) with polarizabilities taken from
http://www.sunysccc.edu/academic/mst/ptable/p-table2.htm
This descriptor assumes 2-centered bonds.
- BPolDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Constructor for the APolDescriptor object
- Br - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- BR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- breadthFirstSearch(IAtomContainer, List<IAtom>, IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
-
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
- breadthFirstSearch(IAtomContainer, List<IAtom>, IAtomContainer, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
- breadthFirstSearch(IAtomContainer, List<IAtom>, IAtomContainer[]) - Static method in class org.openscience.cdk.layout.AtomPlacer
-
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom, and searches
for the longest aliphatic chain which is yet unplaced.
- breadthFirstTargetSearch(IAtomContainer, List<IAtom>, IAtom, int, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Performs a breadthFirstTargetSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
- BremserOneSphereHOSECodePredictor - Class in org.openscience.cdk.tools
-
- BremserOneSphereHOSECodePredictor() - Constructor for class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
-
- BROMINE - Static variable in enum org.openscience.cdk.config.Elements
-
- BROMO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- BSFormat - Class in org.openscience.cdk.io.formats
-
- BSFormat() - Constructor for class org.openscience.cdk.io.formats.BSFormat
-
- Bspt - Class in org.openscience.cdk.graph.rebond
-
BSP-Tree stands for Binary Space Partitioning Tree.
- Bspt(int) - Constructor for class org.openscience.cdk.graph.rebond.Bspt
-
- Bspt.Tuple - Interface in org.openscience.cdk.graph.rebond
-
- bufcolumn - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
- bufcolumn - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
- buffer - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
- buffer - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
- bufline - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
- bufline - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
- bufpos - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Position in buffer.
- bufpos - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Position in buffer.
- build() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
-
Performs that Bayesian model generation, using the {molecule:activity} pairs that have been submitted up to this
point.
- buildBondMatrix() - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Build bond matrix.
- builder - Variable in class org.openscience.cdk.io.random.RandomAccessReader
-
- buildMolecule(int, List<AttachedGroup>, List<AttachedGroup>, boolean, String) - Method in class org.openscience.cdk.iupac.parser.MoleculeBuilder
-
Start of the process of building a molecule from the parsed data.
- buildNodeMatrix(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Build node Matrix.
- buildRGraph(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Builds the
RGraph
( resolution graph ), from two atomContainer
(description of the two molecules to compare)
This is the interface point between the CDK model and
the generic MCSS algorithm based on the RGRaph.
- buildRGraph(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Deprecated.
Builds the CDKRGraph ( resolution graph ), from two atomContainer
(description of the two molecules to compare)
This is the interface point between the CDK model and
the generic MCSS algorithm based on the RGRaph.
- buildTrialNodeMatrix(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Build trial node Matrix.
- buildWeightMatrix(double[][], double[][]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Build weight array for the given node matrix and bond matrix.
- BUILTIN - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- BUT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- C - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- 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.interfaces.IElement
-
- CA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CacaoCartesianFormat - Class in org.openscience.cdk.io.formats
-
- CacaoCartesianFormat() - Constructor for class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- CacaoInternalFormat - Class in org.openscience.cdk.io.formats
-
- CacaoInternalFormat() - Constructor for class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- cachedDiagram - Variable in class org.openscience.cdk.renderer.AbstractRenderer
-
Used when repainting an unchanged model.
- 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
-
- CACheFormat() - Constructor for class org.openscience.cdk.io.formats.CACheFormat
-
- CADMIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- CADMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CAESIUM - Static variable in enum 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 enum 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>.
- calcLogP(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
-
Given a structure in the correct configuration (explicit H and aromatised) it will return the logP as a Double
or if it is out of domain (encounters an unknown atomtype) it will return Double.NaN
- 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(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Calculates the fingerprints for the given
IAtomContainer
, and stores them for subsequent retrieval.
- 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(IAtomContainer) - Static method in class org.openscience.cdk.geometry.volume.VABCVolume
-
- 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 calculates 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
-
Deprecated.
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
-
Deprecated.
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.FractionalCSP3Descriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
Calculates the topological polar surface area and expresses it as a ratio to molecule size.
- 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
-
Deprecated.
It calculates the first ionization energy of a molecule.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
-
- 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
IAtomContainer
.
- 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
IAtomContainer
.
- 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.SmallRingDescriptor
-
Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped
up into descriptors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor
-
Calculates the descriptor value for the given IAtomContainer.
- 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 natural weight of specified elements 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(ISubstance) - Method in interface org.openscience.cdk.qsar.descriptors.substance.ISubstanceDescriptor
-
Calculates the descriptor value for the given
ISubstance
.
- calculate(ISubstance) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
-
Calculates the descriptor value for the given
ISubstance
.
- 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(Map<String, Integer>, Map<String, Integer>) - Static method in class org.openscience.cdk.similarity.LingoSimilarity
-
Evaluate the LINGO similarity between two key,value sty;e fingerprints.
- calculate(BitSet, BitSet) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluates Tanimoto coefficient for two bit sets.
- calculate(IBitFingerprint, IBitFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluates Tanimoto coefficient for two IBitFingerprint
.
- calculate(double[], double[]) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluates the continuous Tanimoto coefficient for two real valued vectors.
- calculate(Map<String, Integer>, Map<String, Integer>) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluate continuous Tanimoto coefficient for two feature, count fingerprint representations.
- calculate(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluate continuous Tanimoto coefficient for two feature, count fingerprint representations.
- 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(IAtomContainer, 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(IAtomContainerSet) - 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(IAtomContainerSet) - 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(IAtomContainerSet) - 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
-
Deprecated.
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.graph.Permutor
-
Calculate the max possible rank for permutations of N numbers.
- calculateMaxRank() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Deprecated.
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 subtracting 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<IBond>, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Calculate the number of missing hydrogens by subtracting 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
-
Deprecated.
This function calculates all the possible combinations of MCS
- calculateOverlapsAndReduceExactMatch(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Deprecated.
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
-
Deprecated.
Determines the normalized vector orthogonal on the vector p1->p2.
- calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
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
-
Deprecated.
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
-
Deprecated.
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
-
Deprecated.
- 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 enum org.openscience.cdk.config.Elements
-
- CALIFORNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- cancel() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
-
Cancel the current search.
- canDraw(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Checks an atom to see if it should be drawn.
- Canon - Class in org.openscience.cdk.graph.invariant
-
- Canonical - Static variable in class org.openscience.cdk.smiles.SmiFlavor
-
Output SMILES in a canonical order.
- CANONICAL_LABEL - Static variable in class org.openscience.cdk.smiles.InvPair
-
- canonicalizeAtoms(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
-
- CanonicalLabeler - Class in org.openscience.cdk.graph.invariant
-
- CanonicalLabeler() - Constructor for class org.openscience.cdk.graph.invariant.CanonicalLabeler
-
Deprecated.
- CanonicalLabellingAdaptor - Class in org.openscience.cdk.smsd.labelling
-
- CanonicalLabellingAdaptor() - Constructor for class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
-
Deprecated.
- canonLabel(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.CanonicalLabeler
-
Deprecated.
Canonically label the fragment.
- CanonOpts - Class in org.openscience.cdk.graph.invariant
-
Basic flavor options to tweak canonical invariants, note these deliberately mirror some fields
from the
SmiFlavor
settings.
- CanonOpts() - Constructor for class org.openscience.cdk.graph.invariant.CanonOpts
-
- CARBON - Static variable in enum 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
-
- carbonylConjugated(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
-
- 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.
- cardinality() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- cardinality() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Returns the number of bits set to true in the fingerprint.
- cardinality() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- 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
-
- case1(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
Deprecated.
- case2(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
Deprecated.
- case3(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
Deprecated.
- case4(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
Deprecated.
- cases(int, int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
Deprecated.
- 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.interfaces.IElement
-
- CD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- cdk() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation
-
Use the preset CDK atom types to determine the electron contribution of
atoms.
- 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
-
- cdkAllowingExocyclic() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation
-
Use the preset CDK atom types to determine the electron contribution of
atoms.
- cdkAromaticSet() - Static method in class org.openscience.cdk.graph.Cycles
-
Create a cycle finder which will compute a set of cycles traditionally
used by the CDK to test for aromaticity.
- CDKAtomColors - Class in org.openscience.cdk.renderer.color
-
- CDKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CDKAtomColors
-
Deprecated.
- cdkAtomContainerSetToCMLList(IAtomContainerSet) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- 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 occurred.
- 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
-
- CDKHueckelAromaticityDetector() - Constructor for class org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector
-
Deprecated.
- CDKHydrogenAdder - Class in org.openscience.cdk.tools
-
Adds implicit hydrogens based on atom type definitions.
- cdkLegacy() - Static method in class org.openscience.cdk.aromaticity.Aromaticity
-
Access an aromaticity instance that replicates the previously utilised -
CDKHueckelAromaticityDetector.
- CDKMCS - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
- CDKMCS() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Deprecated.
- CDKMCSHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
- CDKMCSHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Deprecated.
- 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.
- CDKOWLFormat() - Constructor for class org.openscience.cdk.io.formats.CDKOWLFormat
-
- 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
-
- 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
-
- CDKRGraph() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Deprecated.
Constructor for the CDKRGraph object and creates an empty CDKRGraph.
- CDKRMap - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
- CDKRMap(int, int) - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Deprecated.
Constructor for the CDKRMap
- CDKRMapHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
- CDKRMapHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Deprecated.
- CDKRNode - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
- CDKRNode(int, int) - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Deprecated.
Constructor for the RNode object
- CDKSourceCodeFormat - Class in org.openscience.cdk.io.formats
-
- CDKSourceCodeFormat() - Constructor for class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- 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
-
- CDKStyleAromaticity() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity
-
- CDKSubGraphHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
- CDKSubGraphHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Deprecated.
- CDKUtilities - Class in org.openscience.cdk.tools
-
- CDKUtilities() - Constructor for class org.openscience.cdk.tools.CDKUtilities
-
Deprecated.
- 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 data structures, and
tries to detect inconsistencies in it.
- CDKValidator() - Constructor for class org.openscience.cdk.validate.CDKValidator
-
- Ce - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- 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
-
Deprecated.
Centers the molecule in the given area.
- center(IAtomContainer, double[]) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Centers the molecule in the given area.
- centerCode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
- CERIUM - Static variable in enum 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.interfaces.IElement
-
- CF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CFG_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
-
- chainPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
A list of known tokens denoting a chain's length.
- changeBase(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup
-
Change the base of the group to the new base newBase
.
- changeCharBonds(int, String, int, IAtomContainer, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
Deprecated.
- changeCharBonds(int, String, int, List<Integer>, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
Deprecated.
- 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
-
Deprecated.
Implementation of the characters() procedure overwriting the
DefaultHandler interface.
- charge - Variable in class org.openscience.cdk.Atom
-
The partial charge of the atom.
- charge - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The partial charge of the atom.
- charge - Variable in class org.openscience.cdk.silent.Atom
-
The partial charge of the atom.
- Charge() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- charged() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
-
Discriminate protonation states.
- 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.
- CHECK_RING_SYSTEM - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
- checkAlphaCarbonyl(IAtom, String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
-
Should be called from the carbonyl oxygen
- checkAndCleanMolecule(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.MoleculeSanityCheck
-
Deprecated.
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
-
Deprecated.
- 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
-
- checkInputParameters(IChemObjectBuilder, double, double, MolecularFormulaRange) - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
-
Checks if input parameters are valid and throws an IllegalArgumentException otherwise.
- 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
-
Deprecated.
Checks for single atom cases before doing subgraph/isomorphism search
- checkSymmetry(boolean) - Method in class org.openscience.cdk.stereo.StereoElementFactory
-
- checkTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
-
- Chem3D_Cartesian_1Format - Class in org.openscience.cdk.io.formats
-
- Chem3D_Cartesian_1Format() - Constructor for class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- Chem3D_Cartesian_2Format - Class in org.openscience.cdk.io.formats
-
- Chem3D_Cartesian_2Format() - Constructor for class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- ChemDrawFormat - Class in org.openscience.cdk.io.formats
-
- ChemDrawFormat() - Constructor for class org.openscience.cdk.io.formats.ChemDrawFormat
-
- 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
-
- 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
-
Deprecated.
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.
- chemModelCount - Variable in class org.openscience.cdk.ChemSequence
-
Number of ChemModels contained by this container.
- chemModelCount - Variable in class org.openscience.cdk.silent.ChemSequence
-
Number of ChemModels contained by this container.
- 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 - Variable in class org.openscience.cdk.ChemSequence
-
Array of ChemModels.
- 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
-
Returns an Iterable to ChemModels in this container.
- chemModels() - Method in interface org.openscience.cdk.interfaces.IChemSequence
-
Returns an Iterable to ChemModels in this container.
- chemModels - Variable in class org.openscience.cdk.silent.ChemSequence
-
Array of ChemModels.
- 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
-
- ChemObjectIO - Class in org.openscience.cdk.io
-
Provides some basic functionality for readers and writers.
- ChemObjectIO() - Constructor for class org.openscience.cdk.io.ChemObjectIO
-
- chemObjectReader - Variable in class org.openscience.cdk.io.random.RandomAccessReader
-
- 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.
- chemSequenceCount - Variable in class org.openscience.cdk.ChemFile
-
Number of ChemSequences contained by this container.
- chemSequenceCount - Variable in class org.openscience.cdk.silent.ChemFile
-
Number of ChemSequences contained by this container.
- 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 - Variable in class org.openscience.cdk.ChemFile
-
Array of ChemSquences.
- 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
-
Returns the Iterable to ChemSequences of this container.
- chemSequences() - Method in interface org.openscience.cdk.interfaces.IChemFile
-
Returns the
Iterable
to ChemSequences of this container.
- chemSequences - Variable in class org.openscience.cdk.silent.ChemFile
-
Array of ChemSquences.
- 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
-
- ChemtoolFormat() - Constructor for class org.openscience.cdk.io.formats.ChemtoolFormat
-
- 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
-
- Child(String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child
-
Make a child element with the specified text and position.
- Child(String, String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child
-
Make a child element with the specified text, subscript, and position.
- 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.
- 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
-
- chiral() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
-
Generate different hash codes for stereoisomers.
- Chirality() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- ChiralityAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Deprecated.
- ChiralityAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
Deprecated.
Creates a new instance
- chiralityMatches(IAtom, int, int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
Deprecated.
Check if the atom-based chirality of the target matches.
- chiralityMatches(IAtom, int, int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
-
Deprecated.
Check if the atom-based chirality of the target matches.
- CHLORINE - Static variable in enum org.openscience.cdk.config.Elements
-
- CHLORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CHROMIUM - Static variable in enum 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
-
- CIFFormat() - Constructor for class org.openscience.cdk.io.formats.CIFFormat
-
- 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
-
- CIP_DESCRIPTOR - Static variable in class org.openscience.cdk.CDKConstants
-
Property key to store the CIP descriptor label for an atom / bond.
- 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
-
- CIPTool() - Constructor for class org.openscience.cdk.geometry.cip.CIPTool
-
- CIPTool.CIP_CHIRALITY - Enum in org.openscience.cdk.geometry.cip
-
Enumeration with the two tetrahedral chiralities defined by the CIP schema.
- CircularFingerprinter - Class in org.openscience.cdk.fingerprint
-
Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6
fingerprints, which are partially described by Rogers et al.
- CircularFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Default constructor: uses the ECFP6 type.
- CircularFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is
for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the
path diameter, and may be 0, 2, 4 or 6.
- CircularFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is
for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the
path diameter, and may be 0, 2, 4 or 6.
- CircularFingerprinter.FP - Class in org.openscience.cdk.fingerprint
-
- CisTrans - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
-
Geometric CisTrans (e.g.
- Cl - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- CL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CLASS_ECFP0 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_ECFP2 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_ECFP4 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_ECFP6 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_FCFP0 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_FCFP2 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_FCFP4 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_FCFP6 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_KEY - Static variable in class org.openscience.cdk.renderer.elements.MarkedElement
-
- 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
-
Deprecated.
- clear() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Deprecated.
Reinitialisation of the TGraph.
- clear() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Deprecated.
clear the mapping
- clear() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Deprecated.
clear the mapping
- clearAtomConfigurations(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
This method will reset all atom configuration to UNSET.
- clearCEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Deprecated.
- clearCompGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Deprecated.
- clearCompGraphNodesCZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Deprecated.
- clearDEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Deprecated.
- clearMajorIsotopes(IAtomContainer) - Static method in class org.openscience.cdk.config.Isotopes
-
Clear the isotope information from atoms that are major isotopes (e.g.
- clearMajorIsotopes(IMolecularFormula) - Static method in class org.openscience.cdk.config.Isotopes
-
Clear the isotope information from istopes that are major (e.g.
- clearNodeScope(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
-
- clearProps(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff
-
Clear all transient properties assigned by this class.
- clearTraining() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
-
Clears out the training set, to free up memory.
- 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 IChemObject
.
- clone() - Method in class org.openscience.cdk.AtomContainerSet
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.AtomRef
-
Returns a deep clone of this IChemObject.
- 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.BondRef
-
Returns a deep clone of this IChemObject.
- 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
-
Clones this AminoAcid object.
- clone() - Method in class org.openscience.cdk.debug.DebugAtom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugBond
-
Clones this bond object, including clones of the atoms between which the
bond is defined.
- clone() - Method in class org.openscience.cdk.debug.DebugChemFile
-
Allows for getting an clone of this object.
- clone() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Clones this ChemModel
and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugChemObject
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Makes a clone of this crystal.
- clone() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugElement
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugLonePair
-
Clones this LonePair object, including a clone of the atom for which the
lone pair is defined.
- clone() - Method in class org.openscience.cdk.debug.DebugMapping
-
Clones this Mapping
and the mapped IChemObject
s.
- clone() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugReaction
-
Clones this Reaction
and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Clones this ReactionScheme object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Clones this ReactionSet
and the contained Reaction
s
too.
- clone() - Method in class org.openscience.cdk.debug.DebugRing
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Clones this SingleElectron object, including a clone of the atom for which the
SingleElectron is defined.
- clone() - Method in class org.openscience.cdk.debug.DebugStrand
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Clones this AtomContainerSet and its content.
- 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 class org.openscience.cdk.FragmentAtom
-
- 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
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns a deep clone of this IChemObject.
- 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
-
Returns a deep clone of this IChemObject.
- 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.IMonomer
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
-
Returns a deep clone of this IChemObject.
- 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
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Returns a deep clone of this IChemObject.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Clones this query bond object, including clones of the atoms between which the
query bond is defined.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
Deprecated.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
Deprecated.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Deprecated.
- 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.Monomer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.Polymer
-
- clone() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.PseudoAtom
-
- clone(IAtomContainer) - Static method in class org.openscience.cdk.qsar.AbstractMolecularDescriptor
-
- 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
-
Clones this IChemObject
.
- 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 IChemObject
.
- clone() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Clones this AtomContainerSet and its content.
- 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.FragmentAtom
-
- 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.Monomer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.silent.PDBMonomer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.silent.PDBPolymer
-
Clones this IChemObject
.
- 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
-
Clones this IChemObject
.
- 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.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.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.IteratingSDFReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Close the reader.
- close() - Method in class org.openscience.cdk.io.MDLReader
-
Deprecated.
- close() - Method in class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- 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.MDLV3000Writer
-
Closes this IChemObjectIO's resources.
- 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.Mopac7Reader
-
- 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.program.Mopac7Writer
-
- 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
-
- CLS_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
-
- 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.interfaces.IElement
-
- CM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CMLCoreModule - Class in org.openscience.cdk.io.cml
-
- 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
-
- CMLFormat() - Constructor for class org.openscience.cdk.io.formats.CMLFormat
-
- 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.
- CMLModuleStack - Class in org.openscience.cdk.io.cml
-
Low weight alternative to Sun's Stack class.
- CMLModuleStack() - Constructor for class org.openscience.cdk.io.cml.CMLModuleStack
-
- 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
-
- CMLRSSFormat() - Constructor for class org.openscience.cdk.io.formats.CMLRSSFormat
-
- 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
-
- Cn - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- Co - Static variable in interface org.openscience.cdk.interfaces.IElement
-
- CO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- COBALT - Static variable in enum 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 of the arrow.
- 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.
- color(int) - Method in interface org.openscience.cdk.renderer.generators.HighlightGenerator.Palette
-
Obtain the color in index, id.
- ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
-
- ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
-
- ColorHash() - Constructor for class org.openscience.cdk.renderer.RendererModel.ColorHash
-
- column - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
- column - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
- 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
- Combinations(Object[], int) - Constructor for class org.openscience.cdk.formula.rules.RDBERule.Combinations
-
Create a Combination to enumerate through all subsets of the
supplied Object array, selecting m at a time.
- 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
-
- CompactAtom() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom
-
- CompactShape() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape
-
- 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.BondRef
-
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
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.Element
-
Compares an Element with this Element.
- compare(IAtom, IAtom) - Method in class org.openscience.cdk.fingerprint.SimpleAtomComparator
-
- 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.isomorphism.matchers.QueryBond
-
Compares a query bond with this query 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 an isotope with this isotope.
- compare(String, String) - 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(DynamicFactory.ConstructorKey) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
-
Orders constructor keys by the number of parameters and then this
name.
- compareTo(IChemFormatMatcher.MatchResult) - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult
-
Compares the match result with another, results with lower position
are ordered before those with higher position.
- compareTo(Algorithm) - Method in enum org.openscience.cdk.smsd.interfaces.Algorithm
-
Deprecated.
Compares algorithm types.
- compatibilityGraph() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Deprecated.
Generate Compatibility Graph Nodes Bond Insensitive
- compatibilityGraphCEdgeZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Deprecated.
compatibilityGraphCEdgeZero is used to
build up of the edges of the
compatibility graph BIS
- compatibilityGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Deprecated.
Generate Compatibility Graph Nodes
- compatibilityGraphNodesIfCEdgeIsZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Deprecated.
compGraphNodesCZero is used to build up of the edges of the compatibility graph
- compile() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQueryCompiler
-
Deprecated.
Parse and build a query graph from the query moleucle.
- compile() - Method in class org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler
-
Deprecated.
Parse and build a query graph from the query moleucle.
- completeChemicalName() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
The general form all chemical names must follow.
- completed() - Method in class org.openscience.cdk.graph.AllCycles
-
Did the cycle perception complete - if not the molecule was considered
impractical and computation was aborted.
- 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
- components() - Method in class org.openscience.cdk.graph.ConnectedComponents
-
Access the components each vertex belongs to.
- computeFloydAPSP(int[][]) - Static method in class org.openscience.cdk.graph.PathTools
-
- computeFloydAPSP(double[][]) - Static method in class org.openscience.cdk.graph.PathTools
-
- 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
-
Deprecated.
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 configure 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
-
Deprecated.
Construct and return an edge for a given query and target node
- ConnectedComponents - Class in org.openscience.cdk.graph
-
Compute the connected components of an adjacency list.
- ConnectedComponents(int[][]) - Constructor for class org.openscience.cdk.graph.ConnectedComponents
-
Compute the connected components of an adjacency list, g
.
- connectingFunctionalGroupsConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
The layout of a functional group(s) which can connect anywhere.
- connectingFunctionalGroupSuffix() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Functional groups suffixs for groups which can be connected anywhere
along the main chain.
- 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
-
- ConstructorKey() - Constructor for class org.openscience.cdk.DynamicFactory.ConstructorKey
-
- CONT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- contab - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- container - Variable in class org.openscience.cdk.stereo.StereoElementFactory
-
Native CDK structure representation.
- containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerAtomPermutor
-
Generate the atom container with this permutation of the atoms.
- containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerBondPermutor
-
- containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerPermutor
-
Convert a permutation (expressed as a list of numbers) into a permuted
atom container.
- 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(IAtom) - Method in class org.openscience.cdk.BondRef
-
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
-
True, if the AdductFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
True, if the AdductFormula contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBond
-
Returns true if the given atom participates in this bond.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given ElectronContainer object.
- 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 interface org.openscience.cdk.interfaces.IStereoElement
-
Does the stereo element contain the provided atom.
- contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns true if the given atom participates in this query bond.
- 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
-
- contribs - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
-
- convertBondOrder(IBond) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Deprecated.
Get bond order value as int
value.
- convertBondStereo(IBond) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Deprecated.
Get stereo value as integer
- convertEdgeLabelToColor(String) - Method in class org.openscience.cdk.signature.AtomSignature
-
- convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
Deprecated.
Returns IAtomContainer without Hydrogen.
- convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
Deprecated.
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
-
Deprecated.
- convertStereo(int) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Deprecated.
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.
- convertToDiagramBounds(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Calculate the bounds of the diagram on screen, given the current scale,
zoom, and margin.
- coords - Variable in class org.openscience.cdk.renderer.elements.path.CubicTo
-
Coordinates of control point 1, control point 2 and end point.
- coords - Variable in class org.openscience.cdk.renderer.elements.path.LineTo
-
The point to make a line to.
- coords - Variable in class org.openscience.cdk.renderer.elements.path.MoveTo
-
The point to move to.
- coords - Variable in class org.openscience.cdk.renderer.elements.path.QuadTo
-
Coordinates of control point and end point.
- COPPER - Static variable in enum org.openscience.cdk.config.Elements
-
- COPPER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- copy(Collection<Sgroup>, Map<? extends IChemObject, ? extends IChemObject>) - Static method in class org.openscience.cdk.tools.manipulator.SgroupManipulator
-
Copy a collection of Sgroups, replacing any
IAtom
/
IBond
references with those present in the provided 'replace' map.
- copyAndSuppressedHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Copy the input container and suppress any explicit hydrogens.
- copyBlock(int) - Method in class org.openscience.cdk.group.Partition
-
Creates and returns a copy of the cell at cell index.
- 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 class org.openscience.cdk.isomorphism.Mappings
-
Convenience method to count the number mappings.
- count() - Method in enum org.openscience.cdk.renderer.elements.LineElement.LineType
-
Returns the count for this line type.
- countArcsLeft(List<Integer>, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
Deprecated.
- countEdges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Deprecated.
Returns edge count.
- countEdges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Deprecated.
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
-
Deprecated.
Returns solution map count.
- countMaps(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Deprecated.
Returns solution map count.
- countMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Deprecated.
Returns solution map count.
- countMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Deprecated.
Returns solution map count.
- countMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Deprecated.
Returns solution map count.
- countMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Deprecated.
Returns solution map count.
- countMatches() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Deprecated.
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
-
Deprecated.
Returns Neighbors count.
- countNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
Deprecated.
- countNeighbors() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Deprecated.
Returns Neighbors count.
- countNodes() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Deprecated.
Returns node count.
- countNodes() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Deprecated.
Returns node count.
- countUnique() - Method in class org.openscience.cdk.isomorphism.Mappings
-
Convenience method to count the number of unique atom mappings.
- covalentRadius() - Method in enum org.openscience.cdk.config.Elements
-
The covalent radius, rcov, is a measure of the
size of an atom that forms part of one covalent bond.
- CovalentRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class returns the covalent radius of a given atom.
- CovalentRadiusDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
Constructor for the CovalentRadiusDescriptor object.
- CPKAtomColors - Class in org.openscience.cdk.renderer.color
-
- CPKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CPKAtomColors
-
Deprecated.
- 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.interfaces.IElement
-
- CR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- create(Object[]) - Method in interface org.openscience.cdk.DynamicFactory.Creator
-
Create a new instance with the provided object parameters.
- create() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
-
- create() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
-
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.DoubleBondElementEncoderFactory
-
Create a stereo-encoder for possible stereo-chemical configurations.
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactory
-
Create a stereo encoder for cumulative double bonds.
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory
-
Create a stereo encoder for all potential 2D and 3D double bond stereo
configurations.
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory
-
Create a stereo encoder for all potential 2D and 3D tetrahedral
elements.
- create(IAtomContainer, int[][]) - Method in interface org.openscience.cdk.hash.stereo.StereoEncoderFactory
-
Create a stereo-encoder for possible stereo-chemical configurations.
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory
-
Create a stereo-encoder for possible stereo-chemical configurations.
- create(IAtomContainer, IAtomContainer, Expr.Type...) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Populate a query from a molecule and a provided set of expressions.
- create(IAtomContainer, Expr.Type...) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Create a query from a molecule and a provided set of expressions.
- create(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smarts.SmartsPattern
-
Create a
Pattern
that will match the given
smarts
query.
- create(String) - Static method in class org.openscience.cdk.smarts.SmartsPattern
-
Default SMARTS pattern constructor, passes in a null chem object builder.
- create(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smiles.smarts.SmartsPattern
-
Deprecated.
Create a
Pattern
that will match the given
smarts
query.
- create(String) - Static method in class org.openscience.cdk.smiles.smarts.SmartsPattern
-
Deprecated.
Default SMARTS pattern constructor, passes in a null chem object builder.
- create(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Generate SMILES for the provided molecule
.
- create(IAtomContainer, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Creates a SMILES string of the flavour specified in the constructor
and write the output order to the provided array.
- create(IAtomContainer, int, int[]) - Static method in class org.openscience.cdk.smiles.SmilesGenerator
-
Creates a SMILES string of the flavour specified as a parameter
and write the output order to the provided array.
- create(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Create a SMILES for a reaction of the flavour specified in the constructor.
- create(IReaction, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Create a SMILES for a reaction of the flavour specified in the constructor and
write the output order to the provided array.
- create(IBond, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.Atropisomeric
- create(IBond, List<IBond>, int) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
- create(IBond, List<IBond>, int) - Method in class org.openscience.cdk.stereo.ExtendedCisTrans
- create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
-
- create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.Octahedral
- create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.SquarePlanar
- create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
- create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.TrigonalBipyramidal
- 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.
- createAll() - Method in class org.openscience.cdk.stereo.StereoElementFactory
-
Creates all stereo elements found by
Stereocenters
using the or
2D/3D coordinates to specify the configuration (clockwise/anticlockwise).
- createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- createAnyAtomAnyBondContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with the following settings:
- 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 the following settings:
- createAnyAtomForPseudoAtomQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with the following settings:
- createAutoGenPalette(float, float, boolean) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create an auto generating palette which will generate colors using the
provided parameters.
- createAutoGenPalette(boolean) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create an auto generating palette which will generate colors using the
provided parameters.
- createAutoPalette(float, float, int) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create an auto generating palette which will generate colors using the
provided parameters.
- createBasicQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with the following settings:
- 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
-
- createComparator(IAtomContainer, int) - Static method in class org.openscience.cdk.smiles.SmilesGenerator
-
- createCubicGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method creates a cubic grid with the grid generator class.
- createFromSubstructure(Pattern, Iterable<IAtomContainer>) - Static method in class org.openscience.cdk.layout.TemplateHandler
-
Create a template from a substructure pattern.
- createFromSubstructure(Pattern, IAtomContainer) - Static method in class org.openscience.cdk.layout.TemplateHandler
-
Create a template from a substructure pattern.
- 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.
- createPalette(Color[]) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create a palette which uses the provided colors.
- createPalette(Color, Color...) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create a palette which uses the provided colors.
- 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.
- createProtein(String, IChemObjectBuilder) - 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.
- createReactionSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
- 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.
- createSingleton(IAtomContainer) - Static method in class org.openscience.cdk.layout.TemplateHandler
-
Singleton template instance, mainly useful for aligning molecules.
- createSMILES(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
- createSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
- createSymbolAndBondOrderQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with the following settings:
- createSymbolAndChargeQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with the following settings:
- 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
-
- CRK2DFormat() - Constructor for class org.openscience.cdk.io.formats.CRK2DFormat
-
- CRK3DFormat - Class in org.openscience.cdk.io.formats
-
- CRK3DFormat() - Constructor for class org.openscience.cdk.io.formats.CRK3DFormat
-
- 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 - Variable in class org.openscience.cdk.ChemModel
-
A Crystal.
- 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 - Variable in class org.openscience.cdk.silent.ChemModel
-
A Crystal.
- 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
-
- crystalScalar - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- CrystClustFormat - Class in org.openscience.cdk.io.formats
-
- CrystClustFormat() - Constructor for class org.openscience.cdk.io.formats.