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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

a - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
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 class org.openscience.cdk.stereo.Octahedral
 
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 method in class org.openscience.cdk.smiles.SmilesGenerator
Create a absolute SMILES generator.
Absolute - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output canonical SMILES with stereochemistry, atomic masses.
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
Implements the common parts of the IFontManager interface.
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
Abstract class to provide the base functionality for IGeneratorParameter implementations.
AbstractGeneratorParameter() - Constructor for class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
 
AbstractMCS - Class in org.openscience.cdk.smsd.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AbstractMCS() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
 
AbstractMCSAlgorithm - Class in org.openscience.cdk.smsd.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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
An abstract selection of IChemObjects.
AbstractSelection() - Constructor for class org.openscience.cdk.renderer.selection.AbstractSelection
 
AbstractSubGraph - Class in org.openscience.cdk.smsd.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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) - Method in class org.openscience.cdk.io.VASPReader
 
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(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(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
 
accepts(Class<? extends 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(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<? 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
 
accepts(IChemObject) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
 
accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNReader
Deprecated.
 
accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
 
accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
 
accepts(IChemObject) - Method in class org.openscience.cdk.io.Mol2Reader
 
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
actArray(int[], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Performing the permutation action on an int array.
Actinium - Enum constant in enum class org.openscience.cdk.config.Elements
 
ACTINIUM - Static variable in enum class 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(double) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
 
add(double, double) - Method in class org.openscience.cdk.renderer.elements.Bounds
Ensure the point x,y is included in the bounding box.
add(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
 
add(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
 
add(String) - Method in class org.openscience.cdk.depict.Abbreviations
Convenience method to add an abbreviation from a SMILES string.
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
add(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Addition from two matrices.
add(IAtomContainer) - Method in class org.openscience.cdk.AtomContainer
Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
Add a conformer to the end of the list.
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(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(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(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing
Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand
Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.ICrystal
Adds the atoms in the AtomContainer as cell content.
add(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer
Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer, String) - Method in class org.openscience.cdk.depict.Abbreviations
Add an abbreviation to the factory.
add(IAtomContainerSet) - Method in class org.openscience.cdk.AtomContainerSet
Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugSubstance
Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.silent.AtomContainerSet
Adds all atomContainers in the AtomContainerSet to this container.
add(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader
 
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(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormula
Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormula
Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugAdductFormula
Adds all molecularFormulas in the AdductFormula to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.AdductFormula
Adds all molecularFormulas in the AdductFormula to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(IMolecularFormulaSet) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.AdductFormula
Adds all molecularFormulas in the AdductFormula to this chemObject.
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.debug.DebugReactionScheme
Add a Scheme of Reactions.
add(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme
Add a scheme of reactions.
add(IReactionScheme) - Method in class org.openscience.cdk.ReactionScheme
Add a Scheme of Reactions.
add(IReactionScheme) - Method in class org.openscience.cdk.silent.ReactionScheme
Add a Scheme of Reactions.
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(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(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(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(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(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.Bounds
Add the specified element bounds.
add(IRenderingElement) - Method in class org.openscience.cdk.renderer.elements.ElementGroup
Add a new element to the group.
add(T) - Method in class org.openscience.cdk.io.setting.SettingManager
Add a setting to the manager and return the instance to use.
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(int, Collection<? extends IAtomContainer>) - Method in class org.openscience.cdk.ConformerContainer
 
addAll(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(int) - Method in class org.openscience.cdk.signature.Orbit
Adds an atom index to the orbit.
addAtom(IAtom) - Method in class org.openscience.cdk.AtomContainer
Adds an atom to this container.
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) - 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) - 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) - 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) - Method in interface org.openscience.cdk.interfaces.ICrystal
Adds the atom to the crystal.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IPolymer
Adds the atom oAtom without specifying a Monomer.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IStrand
Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.sgroup.Sgroup
Add an atom to this Sgroup.
addAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.silent.Strand
Adds the atom oAtom without specifying a Monomer or a Strand.
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.debug.DebugBioPolymer
Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugPolymer
Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugStrand
Adds the atom oAtom to a specific Monomer.
addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IPolymer
Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IStrand
Adds the atom oAtom to a specific Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Polymer
Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.protein.data.PDBStrand
Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Polymer
Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Strand
Adds the atom oAtom to a specific Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Strand
Adds the atom oAtom to a specific Monomer.
addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.BioPolymer
Adds the atom to a specified Strand and a specified Monomer.
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, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
Adds the atom to a specified Strand and a specified Monomer.
addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer
Adds the atom to a specified Strand and a specified Monomer.
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, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
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, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
addAtom(IPDBAtom) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IPDBAtom) - Method in class org.openscience.cdk.protein.data.PDBPolymer
Adds the atom oAtom without specifying a IMonomer or a Strand.
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.protein.data.PDBPolymer
Adds the atom oAtom to a specified Monomer.
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 interface org.openscience.cdk.interfaces.IPDBPolymer
Adds the atom to a specified Strand and 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(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.PDBPolymer
Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet
Adds an atomContainer to this container.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Adds an atomContainer to this container.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance
Adds an atomContainer to this container.
addAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Adds an atomContainer to this container.
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.AtomContainerSet
Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugSubstance
Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer, double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Adds an atomContainer to this container with the given multiplier.
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(int, int, IBond.Order) - Method in class org.openscience.cdk.AtomContainer
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(int, int, IBond.Order) - 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.DebugBioPolymer
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(int, int, IBond.Order) - 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.DebugPolymer
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(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugStrand
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(int, int, IBond.Order) - 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.silent.AtomContainer
Adds a bond to this container.
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, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Adds a bond to this container.
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, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Adds a bond to this container.
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, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugMonomer
Adds a bond to this container.
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, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugRing
Adds a bond to this container.
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, IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Adds a bond to this container.
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, IBond.Stereo) - Method in class org.openscience.cdk.silent.AtomContainer
Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.AtomContainer
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Adds a Bond to this AtomContainer.
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.
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
Adds a IChemObjectIOListener to this IChemObjectIO.
addChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO
Adds a IChemObjectIOListener to this 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
Adds an IChemSequence to this container.
addChemSequence(IChemSequence) - Method in class org.openscience.cdk.silent.ChemFile
Adds a ChemSequence to this container.
addChild(String, String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement
Add a child text element with a subscript.
addChild(String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement
Add a child text element.
addChild(IDifference) - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
Adds a new IDifference as child to this tree.
addChild(IDifference) - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
Adds a new IDifference as child to this tree.
addChildren(List<IDifference>) - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
Adds multiple IDifferences as child to this tree.
addChildren(List<IDifference>) - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
Adds multiple IDifferences as child to this tree.
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
addHydrogens(int[][], int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
After generating matrices, adding the hydrogen with respect to the pre-hydrogen distribution.
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(IsotopeContainer) - Method in class org.openscience.cdk.formula.IsotopePattern
Add an isotope object.
addIsotope(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
Adds an Isotope to this MolecularFormula one time.
addIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
Adds an Isotope to this MolecularFormula one time.
addIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Adds an Isotope to this MolecularFormula one time.
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.debug.DebugMolecularFormula
Adds an Isotope to this MolecularFormula in a number of occurrences.
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) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Adds an Isotope to this MolecularFormula in a number of occurrences.
addIsotope(IIsotope, int) - Method in class org.openscience.cdk.silent.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.
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.AtomRef
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(int) - Method in class org.openscience.cdk.AtomContainer
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand
Adds a LonePair to this Atom.
addLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.AtomContainer
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
Adds a lone pair to this AtomContainer.
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) - Method in class org.openscience.cdk.layout.TemplateHandler
Adds a Molecule to the list of templates use by this TemplateHandler.
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.
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(VFAtomMatcher, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
Deprecated.
Add and return a node for a query atom
addNode(CDKRNode) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
Deprecated.
Adds a new node to the CDKRGraph.
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.
addOnes(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Add number of 1s into an ArrayList
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.
addPartition(int, int[], int[][], int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Updating canonical partition list.
addProduct(IAtomContainer) - 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) - 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.debug.DebugReaction
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, Double) - Method in class org.openscience.cdk.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.AtomRef
Add properties to this object, duplicate keys will replace any existing value.
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) - Method in interface org.openscience.cdk.interfaces.IReaction
Adds a reactant to this reaction.
addReactant(IAtomContainer) - Method in class org.openscience.cdk.Reaction
Adds a reactant to this reaction.
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.debug.DebugReaction
Adds a reactant to this reaction with a stoichiometry coefficient.
addReactant(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
Adds a reactant to this reaction with a stoichiometry coefficient.
addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction
Adds a reactant to this reaction with a stoichiometry coefficient.
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) - 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.
addReaction(IReaction, int) - Method in class org.openscience.cdk.reaction.ReactionChain
Added a IReaction for this chain in position.
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 IOSettings to the reader/writer.
addSettings(Collection<IOSetting>) - Method in interface org.openscience.cdk.io.IChemObjectIO
Adds a collection of IOSettings to the reader/writer.
addSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Adds a LonePair to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
Adds a single electron to this AtomContainer.
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
Utility method to add an IChemObject to an IAtomContainer.
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 - Class in org.openscience.cdk.silent
Class defining an adduct object in a MolecularFormula.
AdductFormula() - Constructor for class org.openscience.cdk.formula.AdductFormula
Constructs an empty AdductFormula.
AdductFormula() - Constructor for class org.openscience.cdk.silent.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(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.
Agent - Enum constant in enum class org.openscience.cdk.ReactionRole
 
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 Class in org.openscience.cdk.smsd.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
align() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
Perform an alignment.
alignment - Variable in class org.openscience.cdk.renderer.elements.AtomSymbolElement
The hydrogen alignment.
Aliphatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
ALIPHATIC_ELEMENT - Enum constant in enum class org.openscience.cdk.isomorphism.matchers.Expr.Type
True if the atomic number (IElement.getAtomicNumber() ()}) of an atom equals the specified 'value' and IAtom.isAromatic() is false.
ALIPHATIC_HETERO_SUBSTITUENT_COUNT - Enum constant in enum class org.openscience.cdk.isomorphism.matchers.Expr.Type
True if the number hetero atoms (see Expr.Type.IS_ALIPHATIC_HETERO) this atom is next to is equal to the specified value.
ALIPHATIC_ORDER - Enum constant in enum class org.openscience.cdk.isomorphism.matchers.Expr.Type
True if the bond order IBond.getOrder() equals the specified value and the bond is not marked as aromatic (IAtom.isAromatic()).
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() - Method in class org.openscience.cdk.group.PermutationGroup
Generate the whole group from the compact list of permutations.
all() - Static method in class org.openscience.cdk.renderer.SymbolVisibility
All atom symbols are visible.
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(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_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.
allIs0(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Checks whether all the entries are equal to 0 or not.
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
Create a new all shortest paths utility for an IAtomContainer.
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() - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder
Default constructor using a threshold of AllRingsFinder.Threshold.PubChem_99.
AllRingsFinder(boolean) - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder
Deprecated.
turn logging off by setting the level in the logger implementation
AllRingsFinder.Threshold - Enum Class 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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
ALUMINIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
ALUMINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
ALUMINO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
Am - Static variable in interface org.openscience.cdk.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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
AMERICIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
AMIDE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
AMINE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
AMINO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
AminoAcid - Class in org.openscience.cdk
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
AminoAcid - 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.AminoAcid
Constructs a new AminoAcid.
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.
AND - Enum constant in enum class org.openscience.cdk.isomorphism.matchers.Expr.Type
True if both the subexpressions are true.
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.
ANTI_CLOCKWISE - Enum constant in enum class org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
 
Antimony - Enum constant in enum class org.openscience.cdk.config.Elements
 
ANTIMONY - Static variable in enum class org.openscience.cdk.config.Elements
 
ANTIMONY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
ANY - Enum constant in enum class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type
Deprecated.
 
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(int[]) - Method in class org.openscience.cdk.isomorphism.SmartsStereoMatch
Deprecated.
Backwards compatible method from when we used GUAVA predicates.
apply(PermutationGroup.Backtracker) - Method in class org.openscience.cdk.group.PermutationGroup
Apply the backtracker to all permutations in the larger group.
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.
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
ARGON - Static variable in enum class org.openscience.cdk.config.Elements
 
aromatic() - Method in class org.openscience.cdk.smiles.SmilesGenerator
Deprecated.
configure with SmiFlavor
Aromatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
AROMATIC - Enum constant in enum class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type
Deprecated.
 
AROMATIC_ELEMENT - Enum constant in enum class org.openscience.cdk.isomorphism.matchers.Expr.Type
True if the atomic number (IElement.getAtomicNumber() ()}) of an atom equals the specified 'value' and IAtom.isAromatic() is true.
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
Deprecated.
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.
ArrowBeg - Enum constant in enum class org.openscience.cdk.interfaces.IBond.Display
Display as an arrow (e.g.
ArrowElement - Class in org.openscience.cdk.renderer.elements
IRenderingElement for linear arrows.
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.
ArrowEnd - Enum constant in enum class org.openscience.cdk.interfaces.IBond.Display
Display as an arrow (e.g.
ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
 
ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
 
Arsenic - Enum constant in enum class org.openscience.cdk.config.Elements
 
ARSENIC - Static variable in enum class org.openscience.cdk.config.Elements
 
ARSENIC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
as - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
As - Static variable in interface org.openscience.cdk.interfaces.IElement
 
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() - Constructor for class org.openscience.cdk.Association
Constructs an empty association.
Association(IAtom, IAtom) - Constructor for class org.openscience.cdk.Association
Constructs an association between two Atom's.
Astatine - Enum constant in enum class org.openscience.cdk.config.Elements
 
ASTATINE - Static variable in enum class 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 - Variable in class org.openscience.cdk.LonePair
The atom with which this lone pair is associated.
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 - Class in org.openscience.cdk
Represents the idea of an chemical atom.
Atom - Class in org.openscience.cdk.silent
Represents the idea of an chemical atom.
Atom() - Constructor for class org.openscience.cdk.Atom
Constructs an completely unset Atom.
Atom() - Constructor for class org.openscience.cdk.silent.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) - 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.Atom
Create a new atom with of the specified element and hydrogen count.
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.Atom
Create a new atom with of the specified element, hydrogen count, and formal charge.
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.Atom
Constructs an Atom from a string containing an element symbol and optionally the atomic mass, 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, Point2d) - Constructor for class org.openscience.cdk.Atom
Constructs an Atom from an Element and a Point2d.
Atom(String, Point2d) - Constructor for class org.openscience.cdk.silent.Atom
Constructs an Atom from an Element and a Point2d.
Atom(String, Point3d) - Constructor for class org.openscience.cdk.Atom
Constructs an Atom from an Element and a Point3d.
Atom(String, Point3d) - Constructor for class org.openscience.cdk.silent.Atom
Constructs an Atom from an Element and a Point3d.
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(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 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
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 - 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 - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
The molecular structure on which we work
AtomContainer - Class in org.openscience.cdk
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
AtomContainer - Class in org.openscience.cdk.silent
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
AtomContainer() - Constructor for class org.openscience.cdk.AtomContainer
Constructs an empty AtomContainer.
AtomContainer() - Constructor for class org.openscience.cdk.silent.AtomContainer
Constructs an empty 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(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(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(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).
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 - Class in org.openscience.cdk.smsd.labelling
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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(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
IGenerator that draws a rectangular around the IAtomContainer.
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
Compares two IAtomContainer classes.
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
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AtomContainerPrinter() - Constructor for class org.openscience.cdk.smsd.labelling.AtomContainerPrinter
Deprecated.
 
AtomContainerRenderer - Class in org.openscience.cdk.renderer
A general renderer for IAtomContainers.
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 - Variable in class org.openscience.cdk.silent.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() - 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 - Class in org.openscience.cdk.silent
A set of AtomContainers.
AtomContainerSet() - Constructor for class org.openscience.cdk.AtomContainerSet
Constructs an empty AtomContainerSet.
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
Given the current configuration create an AtomHashGenerator.
ATOMIC_NUMBER - Enum constant in enum class org.openscience.cdk.hash.BasicAtomEncoder
Encode the atomic number of an atom.
AtomicMass - Static variable in class org.openscience.cdk.graph.invariant.CanonOpts
Distinguish atoms based on atomic mass.
AtomicMass - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output atomic mass on atoms.
AtomicMass() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
AtomicMassStrict - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Deprecated.
no longer needed, default CDK behaviour is now to pass through mass numbers if non-null
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
The IAtoms mass number.
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 - Interface in org.openscience.cdk.smsd.algorithm.matchers
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AtomMatcher() - Constructor for class org.openscience.cdk.isomorphism.AtomMatcher
 
AtomNumberGenerator - Class in org.openscience.cdk.renderer.generators
IGenerator for IAtomContainers that will draw atom numbers for the atoms.
AtomNumberGenerator() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator
 
AtomNumberGenerator.AtomColorer - Class in org.openscience.cdk.renderer.generators
The color scheme by which to color the atom numbers, if the AtomNumberGenerator.ColorByType boolean is true.
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
Boolean to indicate of the AtomNumberGenerator.AtomColorer scheme will be used.
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
 
atomOccurrence(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Getting the number of atoms' occurrences.
AtomPairs2DFingerprinter - Class in org.openscience.cdk.fingerprint
Generates an atom pair 2D fingerprint as implemented in PaDEL given an IAtomContainer, that extends the Fingerprinter.
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 - Variable in class org.openscience.cdk.Bond
A list of atoms participating in this bond.
atoms - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
 
atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Internal array of atoms.
atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
A list of atoms participating in this query bond.
atoms - Variable in class org.openscience.cdk.silent.AtomContainer
Internal array of atoms.
atoms - Variable in class org.openscience.cdk.silent.Bond
A list of atoms participating in this bond.
atoms() - Method in class org.openscience.cdk.AtomContainer
Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.Bond
Returns the Iterator to atoms making up this bond.
atoms() - Method in class org.openscience.cdk.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() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns an Iterable for looping over all atoms in this container.
atoms() - Method in interface org.openscience.cdk.interfaces.IBond
Returns the Iterable to atoms making up this bond.
atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the Iterator to atoms making up this query bond.
atoms() - Method in class org.openscience.cdk.silent.AtomContainer
Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.silent.Bond
Returns the Iterator to atoms making up this bond.
AtomSignature - Class in org.openscience.cdk.signature
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(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(int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature
Create an atom signature starting at atomIndex.
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(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.
AtomSignature(IAtom, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature
Create an atom signature for the atom atom.
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 - Class in org.openscience.cdk.silent
The base class for atom types.
AtomType(String) - Constructor for class org.openscience.cdk.AtomType
Constructor for the AtomType object.
AtomType(String) - Constructor for class org.openscience.cdk.silent.AtomType
Constructor for the AtomType object.
AtomType(String, String) - Constructor for class org.openscience.cdk.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.AtomType
Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope.
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 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
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
Constructs an AtomTypeAwareSaturationChecker checker.
AtomTypeCharges - Class in org.openscience.cdk.charges
Assigns charges to atom types.
AtomTypeDiff - Class in org.openscience.cdk.tools.diff
Compares two IAtomType classes.
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 - Class in org.openscience.cdk.stereo
Restricted axial rotation around Aryl-Aryl bonds.
Atropisomeric - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
Atropisomeric (e.g.
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>, 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
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
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
This class calculates ATS autocorrelation descriptor, where the weight equal to the scaled atomic mass [Moreau G. and Broto P.. Nouveau Journal de Chimie. 1980. null].
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.
AuxNone - Enum constant in enum class net.sf.jniinchi.INCHI_OPTION
 
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

b - Variable in class org.openscience.cdk.io.random.RandomAccessReader
 
B - Static variable in interface org.openscience.cdk.interfaces.IElement
 
B - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
B - Static variable in class org.openscience.cdk.stereo.Octahedral
 
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.
backward(int[][], int[], int[], int[], boolean[], int[], int[][][], int[][][], int[][][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Backward step in the algorithm.
BACKWARD - Enum constant in enum class org.openscience.cdk.interfaces.IReaction.Direction
Reaction equilibrium which is (almost) fully on the reactant side.
backwardCriteria(int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
The criteria to decide which function is needed: forward or backward.
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
BARIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
BARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
BasicAtomEncoder - Enum Class in org.openscience.cdk.hash
Enumeration of atom encoders for seeding atomic hash codes.
BasicAtomGenerator - Class in org.openscience.cdk.renderer.generators
Generates basic IRenderingElements for atoms in an atom container.
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
IAtomColorer used to draw elements.
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
Shape to be used when drawing atoms in compact mode, as defined by the BasicAtomGenerator.CompactAtom parameter.
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 Class 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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
BERKELIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
BERKELIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
Beryllium - Enum constant in enum class org.openscience.cdk.config.Elements
 
BERYLLIUM - Static variable in enum class 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
Deprecated.
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 Sets, 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.
Bicoordinate - Enum constant in enum class org.openscience.cdk.stereo.Stereocenters.Type
An atom within a cumulated system.
BIDIRECTIONAL - Enum constant in enum class org.openscience.cdk.interfaces.IReaction.Direction
Reaction equilibrium state.
biggerCheck(int, int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Checks two arrays in descending order.
BinaryTree - Class in org.openscience.cdk.smsd.helper
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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 - 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.BioPolymer
Constructs a new Polymer to store the Strands.
BioPolymer() - Constructor for class org.openscience.cdk.silent.BioPolymer
Constructs a new Polymer to store the Strands.
Bismuth - Enum constant in enum class org.openscience.cdk.config.Elements
 
BISMUTH - Static variable in enum class 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() - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
 
BitSetFingerprint(int) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
 
BitSetFingerprint(BitSet) - 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
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
BOHRIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
BOHRIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
Bold - Enum constant in enum class org.openscience.cdk.interfaces.IBond.Display
A bold line.
BOLD - Enum constant in enum class org.openscience.cdk.renderer.font.IFontManager.FontStyle
Bold font style.
Bond - Class in org.openscience.cdk
Implements the concept of a covalent bond between two or more atoms.
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.Bond
Constructs an empty bond.
Bond() - Constructor for class org.openscience.cdk.silent.Bond
Constructs an empty bond.
Bond(IAtom[]) - Constructor for class org.openscience.cdk.Bond
Constructs a multi-center bond, with undefined order and no stereo information.
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.Bond
Constructs a multi-center bond, with a specified 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) - Constructor for class org.openscience.cdk.Bond
Constructs a bond with a single bond order..
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.Bond
Constructs a bond with a given order.
Bond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.silent.Bond
Constructs a bond with a given order.
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(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.
BOND - Static variable in class org.openscience.cdk.libio.jena.CDK
 
BOND_ORDER_SUM - Enum constant in enum class org.openscience.cdk.hash.BasicAtomEncoder
Encode the explicit bond order sum of an atom.
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
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BondEnergies() - Constructor for class org.openscience.cdk.smsd.tools.BondEnergies
Deprecated.
 
BondEnergy - Class in org.openscience.cdk.smsd.helper
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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 - Interface in org.openscience.cdk.smsd.algorithm.matchers
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BondMatcher() - Constructor for class org.openscience.cdk.isomorphism.BondMatcher
 
BONDORDER_DOUBLE - Static variable in class org.openscience.cdk.CDKConstants
Deprecated.
Use IBond.Order DOUBLE directly.
BONDORDER_QUADRUPLE - Static variable in class org.openscience.cdk.CDKConstants
Deprecated.
Use IBond.Order QUADRUPLE directly.
BONDORDER_SINGLE - Static variable in class org.openscience.cdk.CDKConstants
Deprecated.
Use IBond.Order SINGLE directly.
BONDORDER_TRIPLE - Static variable in class org.openscience.cdk.CDKConstants
Deprecated.
Use IBond.Order TRIPLE directly.
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
IDifference between two IBond.Orders.
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 - Variable in class org.openscience.cdk.AtomContainer
Internal array of bonds.
bonds - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Internal array of bonds.
bonds - Variable in class org.openscience.cdk.silent.AtomContainer
Internal array of bonds.
bonds() - Method in class org.openscience.cdk.Atom
Returns the bonds connected to this atom.
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() - 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() - 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 IBonds.
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
IDifference between two Booleans.
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
BORON - Static variable in enum class 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() - Constructor for class org.openscience.cdk.renderer.elements.Bounds
An empty bounding box.
Bounds(double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.Bounds
Specify the min/max coordinates of the 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[]) - 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.
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.
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
BROMINE - Static variable in enum class 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
See here.
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.
buildArray(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Building the copy of the partition array
buildAtomContainerFromMatrix(int[][], IAtomContainer) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Building an atom container for an adjacency matrix.
buildBondMatrix() - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
Build bond matrix.
buildContainer4SDF(int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Building an atom container for an adjacency matrix.
buildContainer4SDF(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Building an atom container for SDF output from its symbols
buildContainer4SDF(IAtomContainer, int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Building an atom container for an adjacency 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.
buildSymbolArray() - Method in class org.openscience.cdk.structgen.maygen.Maygen
 
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
 
BUSY - Enum constant in enum class net.sf.jniinchi.INCHI_RET
 
BUT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.

C

c - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
C - Static variable in interface org.openscience.cdk.interfaces.IElement
Carbon atomic number
C - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
C - Static variable in class org.openscience.cdk.stereo.Octahedral
 
C_TERMINAL_AMINO_ACID - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
 
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
See here.
CacaoCartesianFormat() - Constructor for class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
CacaoInternalFormat - Class in org.openscience.cdk.io.formats
See here.
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
CADMIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
CADMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
Caesium - Enum constant in enum class org.openscience.cdk.config.Elements
 
CAESIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
calcD(double, double, double, double, Vector, Vector) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
 
calcG(int, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Transfer equation for the calculation of core potentials
calcG(int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Transfer equation for a four center integral.
calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
calcI(int, int, int, int) - 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 >.
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.
calcInvertedAxes(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
Inverts three cell axes.
Calcium - Enum constant in enum class org.openscience.cdk.config.Elements
 
CALCIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
CALCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
calcJ(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
calcJ(int, int) - 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>.
calcJ(int, int, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Transfer equation the the calculation of the impulse
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() - Method in class org.openscience.cdk.math.qm.ClosedShellJob
 
calculate() - Method in class org.openscience.cdk.math.qm.OneElectronJob
 
calculate(double[], double[]) - Static method in class org.openscience.cdk.similarity.Tanimoto
Evaluates the continuous Tanimoto coefficient for two real valued vectors.
calculate(BitSet, BitSet) - Static method in class org.openscience.cdk.similarity.Tanimoto
Evaluates Tanimoto coefficient for two bit sets.
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(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(IBitFingerprint, IBitFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto
Evaluates Tanimoto coefficient for two IBitFingerprint.
calculate(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto
Evaluate continuous Tanimoto coefficient for two feature, count fingerprint representations.
calculate(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
Calculates the fingerprints for the given IAtomContainer, and stores them for subsequent retrieval.
calculate(IAtomContainer) - Static method in class org.openscience.cdk.geometry.volume.VABCVolume
Calculates the volume for the given IAtomContainer.
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 the sum of atomic polarizabilities in an IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
Calculate the count of aromatic atoms in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
Calculate the count of aromatic atoms in the supplied IAtomContainer.
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
Calculates the FMF descriptor value for the given IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor
Calculates the Fsp3 descriptor value for the given IAtomContainer.
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 the complexity in the supplied IAtomContainer.
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 sp3/sp2 hybridization ratio in the supplied IAtomContainer.
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(IAtomContainer) - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor
Calculates the descriptor value for the given IAtomContainer.
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, IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment
Evaluate the 3D similarity between two molecules.
calculate(IAtom, IAtom) - Method in interface org.openscience.cdk.geometry.IRDFWeightFunction
Calculates the weight for the interaction between the two atoms.
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) - 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_topol
 
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
 
calculate(IAtom, IAtomContainer) - 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, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IAtomicDescriptor
Calculates the descriptor value for the given IAtom.
calculate(IAtom, IAtomContainer, IRingSet) - 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_GDR
 
calculate(IAtom, IAtomContainer, IRingSet) - 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
 
calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
 
calculate(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
The method returns if two atoms have pi-contact.
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 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(IBond, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IBondDescriptor
Calculates the descriptor value for the given IBond.
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.
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(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(IReaction) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
Calculate the average bond length for the bonds in a reaction.
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(IAtomContainer) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
Calculate the bounding rectangle for an atom container.
calculateBounds(IAtomContainerSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
Calculate the bounding rectangle for a molecule set.
calculateBounds(IChemModel) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
Calculate the bounding rectangle for a chem model.
calculateBounds(IReaction) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
Calculate the bounding rectangle for a reaction.
calculateBounds(IReactionSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
Calculate the bounding rectangle for a reaction set.
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(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
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(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.
calculateDiagramBounds(T) - Method in interface org.openscience.cdk.renderer.IRenderer
Given a IChemObject, calculates the bounding rectangle in screen space.
calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, boolean, int[][]) - Method in class org.openscience.cdk.charges.Polarizability
calculate effective atom polarizability.
calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, int, boolean) - 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) - 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.SaturationChecker
Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.
calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
 
calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker
 
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) - 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>.
calcV(int, int, Vector, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Calculates the core potential.
Californium - Enum constant in enum class org.openscience.cdk.config.Elements
 
CALIFORNIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
CALIFORNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
canBuildIsomer(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Checking whether a molecular formula can represent a graph or not.
canBuildIsomerSingle(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Checking whether a molecular formula can represent a graph or not.
cancel() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
Cancel the current search.
candidatePermutations(int, List<Permutation>, List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Calculating all candidate permutations for row canonical test.
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
Deprecated.
this labeller uses slow data structures and has been replaced - Canon
CanonicalLabeler() - Constructor for class org.openscience.cdk.graph.invariant.CanonicalLabeler
Deprecated.
 
CanonicalLabellingAdaptor - Class in org.openscience.cdk.smsd.labelling
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CanonicalLabellingAdaptor() - Constructor for class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
Deprecated.
 
canonicalPartition(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
To get the canonical partition.
canonicalTest(int[][], int[], int[][], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
 
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
CARBON - Static variable in enum class org.openscience.cdk.config.Elements
 
CarbonTypesDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
Topological descriptor characterizing the carbon connectivity.
CarbonTypesDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
 
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 - 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.CDK
 
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
Deprecated.
JmolColors provides more comprehensive color pallet for 3D
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
Deprecated.
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
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKMCS - Enum constant in enum class org.openscience.cdk.smsd.interfaces.Algorithm
Deprecated.
CDK UIT MCS.
CDKMCS() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
 
CDKMCSHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader
Creates a new CDKOWLReader with an undefined input.
CDKOWLReader(Reader) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader
Creates a new CDKOWLReader sending output to the given Writer.
CDKOWLWriter - Class in org.openscience.cdk.io.rdf
Serializes the data model into CDK OWL.
CDKOWLWriter() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter
Creates a new CDKOWLWriter with an undefined output.
CDKOWLWriter(Writer) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter
Creates a new CDKOWLWriter sending output to the given Writer.
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
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKRMapHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
Deprecated.
 
CDKRNode - Class in org.openscience.cdk.smsd.algorithm.rgraph
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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() - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
 
CDKSourceCodeWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
 
CDKSourceCodeWriter(Writer) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
Constructs a new CDKSourceCodeWriter.
CDKStyleAromaticity() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity
 
CDKSubGraphHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKSubGraphHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
Deprecated.
 
CDKUtilities - Class in org.openscience.cdk.tools
Deprecated.
better accomplished with SMARTS patterns or simple REGEX
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, double[]) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Centers the molecule in the given area.
center(IAtomContainer, Dimension) - Static method in class org.openscience.cdk.geometry.GeometryTools
Deprecated.
Centers the molecule in the given area.
centerCode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
 
Cerium - Enum constant in enum class org.openscience.cdk.config.Elements
 
CERIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
CERIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
CESIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
Cf - Static variable in interface org.openscience.cdk.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.
Chair - Enum constant in enum class org.openscience.cdk.stereo.Projection
Projection of the low energy conformation (chair) of a cyclohexane.
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, List<Integer>, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
Deprecated.
 
changeCharBonds(int, String, int, IAtomContainer, 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 - Variable in class org.openscience.cdk.stereo.StereoElementFactory
Verify if created stereochemistry are actually stereo-centres.
check(int, int, int[][], int[], List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
 
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
Checks if each next ILigand is different from the previous one according to the CIPLigandRule.
checkInputParameters(IChemObjectBuilder, double, double, MolecularFormulaRange) - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
Checks if input parameters are valid and throws an IllegalArgumentException otherwise.
checkJustH(int[][][], int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
 
checkLengthTwoFormula(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
checking whether a molecular formula is length 2 or not.
checkOxygenSulfur(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
 
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
Deprecated.
timeout not used
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 - Class in org.openscience.cdk.silent
A Object containing a number of ChemSequences.
ChemFile() - Constructor for class org.openscience.cdk.ChemFile
Constructs an empty ChemFile.
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
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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 - 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.ChemModel
Constructs an new ChemModel with a null setOfMolecules.
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
A general renderer for IChemModels, IReactions, and IAtomContainers.
ChemModelRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer
 
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.
chemModels - Variable in class org.openscience.cdk.ChemSequence
Array of ChemModels.
chemModels - Variable in class org.openscience.cdk.silent.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() - 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 - Class in org.openscience.cdk.silent
The base class for all chemical objects in this cdk.
ChemObject() - Constructor for class org.openscience.cdk.ChemObject
Constructs a new IChemObject.
ChemObject() - Constructor for class org.openscience.cdk.silent.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(IChemObject) - Constructor for class org.openscience.cdk.silent.ChemObject
Constructs a new IChemObject by copying the flags, and the identifier.
CHEMOBJECT - Static variable in class org.openscience.cdk.libio.jena.CDK
 
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
Compares two IChemObject classes.
ChemObjectDifference - Class in org.openscience.cdk.tools.diff.tree
IDifference between two IChemObjects.
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 - 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.ChemSequence
Constructs an empty ChemSequence.
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 - Variable in class org.openscience.cdk.silent.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() - Method in class org.openscience.cdk.silent.ChemFile
Returns the Iterable to ChemSequences of this container.
ChemtoolFormat - Class in org.openscience.cdk.io.formats
See here.
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, String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child
Make a child element with the specified text, subscript, and position.
Child(String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child
Make a child element with the specified text and position.
childCount() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
Returns the number of children of this IDifference.
childCount() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
Returns the number of children of this IDifference.
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.
ChiralFlagOFF - Enum constant in enum class net.sf.jniinchi.INCHI_OPTION
 
ChiralFlagON - Enum constant in enum class net.sf.jniinchi.INCHI_OPTION
 
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
CHLORINE - Static variable in enum class org.openscience.cdk.config.Elements
 
CHLORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
Chromium - Enum constant in enum class org.openscience.cdk.config.Elements
 
CHROMIUM - Static variable in enum class org.openscience.cdk.config.Elements
 
CHROMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
CIFFormat - Class in org.openscience.cdk.io.formats
 
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() - Constructor for class org.openscience.cdk.io.CIFReader
 
CIFReader(InputStream) - Constructor for class org.openscience.cdk.io.CIFReader
 
CIFReader(Reader) - Constructor for class org.openscience.cdk.io.CIFReader
Create an CIF like file reader.
cInverse(int, int, int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Calculating the sum of the entries in the jth column until the ith row.
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 ILigands based on CIP sequences sub rules.
CIPLigandRule() - Constructor for class org.openscience.cdk.geometry.cip.rules.CIPLigandRule
 
CIPTool - Class in org.openscience.cdk.geometry.cip
Tool to help determine the R,S and stereochemistry definitions of a subset of the CIP rules [Cahn, R.S. et. al.. Angew. Chem. Int. Ed.. 1966. 5].
CIPTool() - Constructor for class org.openscience.cdk.geometry.cip.CIPTool
 
CIPTool.CIP_CHIRALITY - Enum Class 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.
clearAtomConfigurations(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
This method will reset all atom properties related to atom configuration to the value CDKConstants.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.
 
clearFormers(boolean, int, int[][], List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
When an adjacency matrix is non-canonical, cleaning the formerPermutations and partitionList from the first row of the tested block.
clearGlobals() - Method in class org.openscience.cdk.structgen.maygen.Maygen
For several calls of the run function, setting the global variables.
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.
CLOCKWISE - Enum constant in enum class org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
 
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 IChemObjects.
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 Reactions 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 IChemObjects.
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() - 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 Reactions 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 IChemObjects.
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 Reactions 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
 
clone(IAtomContainer) - Static method in class org.openscience.cdk.qsar.AbstractMolecularDescriptor
 
cloneArray(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Cloning int array
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() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
Close the path.
close() - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
 
Close - Class in org.openscience.cdk.renderer.elements.path
Indicates the closing point of the path.
Close - Enum constant in enum class org.openscience.cdk.renderer.elements.path.Type
 
Close() - Constructor for class org.openscience.cdk.renderer.elements.path.Close
Make a Close PathElement.
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.
closeFilesAndDisplayStatistic(long) - Method in class org.openscience.cdk.structgen.maygen.Maygen
 
closeNodeScope(Node, boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
 
closeNodeScope(Node, int) - 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
Core CML 1.x and 2.x elements are parsed by this class (see [Willighagen, E.L.. Internet Journal of Chemistry. 2001. 4]).
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
See here.
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() - Constructor for class org.openscience.cdk.io.CMLReader
 
CMLReader(InputStream) - Constructor for class org.openscience.cdk.io.CMLReader
Reads CML from an java.io.InputStream, for example the FileInputStream.
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
Serializes a IAtomContainerSet or a IAtomContainer object to CML 2 code.
CMLWriter() - Constructor for class org.openscience.cdk.io.CMLWriter
 
CMLWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CMLWriter
 
CMLWriter(Writer) - Constructor for class org.openscience.cdk.io.CMLWriter
Constructs a new CMLWriter class.
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 - Enum constant in enum class org.openscience.cdk.config.Elements
 
COBALT - Static variable in enum class org.openscience.cdk.config.Elements
 
COBALT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
color - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
Color 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 - 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.
color(Color) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
Sets the color if this path.
ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
 
ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
 
Colored - Enum constant in enum class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle
Displayed atom symbols and bonds are coloured.
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(int[], int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Comparing two arrays for specific range of entries, whether the first array is bigger than the second one or not.
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 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(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(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(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(IAtom, IAtom) - Method in class org.openscience.cdk.fingerprint.SimpleAtomComparator
 
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
 
compareIndexwise(int[], int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Comparing two int arrays are equal or not for given range of entries.
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.
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.
Compress - Enum constant in enum class net.sf.jniinchi.INCHI_OPTION
 
computeFloydAPSP(double[][]) - Static method in class org.openscience.cdk.graph.PathTools
All-Pairs-Shortest-Path computation based on Floyd's algorithm [Floyd, R.W.. Commun. ACM. 1962. 5].
computeFloydAPSP(int[][]) - Static method in class org.openscience.cdk.graph.PathTools
All-Pairs-Shortest-Path computation based on Floyd's algorithm [Floyd, R.W.. Commun. ACM. 1962. 5].
configure(String) - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
 
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(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.
configure(IAtom, IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory
Configures an atom to have all the data of the given isotope.
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.
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
 
connectivityTest(int[][], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Test whether an adjacency matrix is connected or disconnected.
CONSTANT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
construct(String, boolean[], boolean[]) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanArrayDifference
Constructs a new IDifference object.
construct(String, Boolean, Boolean) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanDifference
Constructs a new IDifference object.
construct(String, Double, Double) - Static method in class org.openscience.cdk.tools.diff.tree.DoubleDifference
Constructs a new IDifference object.
construct(String, Integer, Integer) - Static method in class org.openscience.cdk.tools.diff.tree.IntegerDifference
Constructs a new IDifference object.
construct(String, String, String) - Static method in class org.openscience.cdk.tools.diff.tree.StringDifference
Constructs a new IDifference object.
construct(String, Point2d, Point2d) - Static method in class org.openscience.cdk.tools.diff.tree.Point2dDifference
Constructs a new IDifference object.
construct(String, Point3d, Point3d) - Static method in class org.openscience.cdk.tools.diff.tree.Point3dDifference
Constructs a new IDifference object.
construct(String, IAtomType.Hybridization, IAtomType.Hybridization) - Static method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference
Constructs a new IDifference object.
construct(String, IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.diff.tree.BondOrderDifference
Constructs a new IDifference object.
ConstructorKey() - Constructor for class org.openscience.cdk.DynamicFactory.ConstructorKey
 
consume(IAtomContainer) - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
 
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(int) - Method in class org.openscience.cdk.signature.Orbit
Checks to see if the orbit contains this atom index.
contains(Object) - Method in class org.openscience.cdk.ConformerContainer
Checks to see whether the specified conformer is currently stored.
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(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(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
True, if the AtomContainer contains the given atom 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(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair
Returns true if the given atom participates in this lone pair.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
True, if the AtomContainer contains the given atom 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(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
True, if the AtomContainer contains the given atom 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(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(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(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(IAtom) - Method in class org.openscience.cdk.RingSet
True, if at least one of the rings in the ringset contains the given atom.
contains(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
True, if the AtomContainer contains the given atom 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(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(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(IAtom) - Method in class org.openscience.cdk.stereo.Octahedral
Does the stereo element contain the provided atom.
contains(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IRingSet
True, if this set contains the IAtomContainer.
contains(IAtomContainer) - Method in class org.openscience.cdk.RingSet
Checks for presence of a ring in this RingSet.
contains(IAtomContainer) - Method in class org.openscience.cdk.silent.RingSet
Checks for presence of a ring in this RingSet.
contains(IBond) - Method in class org.openscience.cdk.AtomContainer
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugRing
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
True, if the AtomContainer contains the given bond object.
contains(IChemObject) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
Determines if the IChemObject is part of the current selection.
contains(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
True, if the AtomContainer contains the given ElectronContainer object.
contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula
True, if the AdductFormula contains the given IIsotope object and not the instance.
contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
True, if the MolecularFormula contains the given IIsotope object and not the instance.
contains(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula
True, if the AdductFormula contains the given IIsotope object and not the instance.
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(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula
True, if the AdductFormula contains the given IIsotope object.
contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
True, if the MolecularFormula contains the given IIsotope object.
contains(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula
True, if the AdductFormula contains the given IIsotope object and not the instance.
contains(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
True, if the MolecularFormula contains the given IIsotope object and not the instance.
contains(ILonePair) - Method in class org.openscience.cdk.AtomContainer
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
True, if the AtomContainer contains the given LonePair object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula
True, if the AdductFormula contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula
True, if the AdductFormula contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
True, if the IMolecularFormulaSet contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula
True, if the AdductFormula contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
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.
contains(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
True, if the AtomContainer contains the given SingleElectron 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 - 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
 
Convertor(boolean, String) - Constructor for class org.openscience.cdk.libio.cml.Convertor
Constructs a CML convertor.
convertOrder(double) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
Deprecated.
Get bond order value as IBond.Order.
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.
Copernicium - Enum constant in enum class org.openscience.cdk.config.Elements
 
Copper - Enum constant in enum class org.openscience.cdk.config.Elements
 
COPPER - Static variable in enum class 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.
copy(IAtomContainer, IAtomContainer, Collection<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Copy atoms in the collection from a 'source' molecule to the provided destination.
copy(IAtomContainer, IAtomContainer, Predicate<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Copy selected atoms from a 'source' molecule to the provided destination.
copy(IAtomContainer, IAtomContainer, Predicate<IAtom>, Predicate<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Copy selected atoms/bonds from a 'source' molecule to the provided destination.
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(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
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.
count() - Method in class org.openscience.cdk.isomorphism.Mappings
Convenience method to count the number mappings.
count() - Method in enum class 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(IAtomContainer) - 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 interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
Deprecated.
Returns solution map count.
countMaps(TargetProperties) - 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.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() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
Deprecated.
Returns Neighbors count.
countNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
Deprecated.
 
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 class 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
Deprecated.
JmolColors provides more comprehensive CPK color pallet
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() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
 
create() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
 
create(Class<?>) - Static method in class org.openscience.cdk.tools.SystemOutLoggingTool
Deprecated.
Creates a new SystemOutLoggingTool for the given class.
create(Object[]) - Method in interface org.openscience.cdk.DynamicFactory.Creator
Create a new instance with the provided object parameters.
create(String) - Static method in class org.openscience.cdk.smarts.SmartsPattern
Default SMARTS pattern constructor, passes in a null chem object builder.
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(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smarts.SmartsPattern
Create a Pattern that will match the given smarts query.
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(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[][]) - 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, 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(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(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(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(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.
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
Deprecated.
not all attributes are removed producing unexpected results, use AtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)
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(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(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.
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.Prot