All Classes

Class	Description
Abbreviations	Utility class for abbreviating (sub)structures.
Abbreviations.Option
ABINITFormat
AbstractAtomicDescriptor	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.
AbstractAtomPairDescriptor	A super class for atom pair descriptors allowing default implementations for interface methods.
AbstractAWTDrawVisitor	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.
AbstractBondDescriptor	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.
AbstractDifference	Difference between two IChemObjects.
AbstractDifferenceList	Diff between two IChemObjects.
AbstractFingerprinter
AbstractFontManager	Implements the common parts of the IFontManager interface.
AbstractGeneratorParameter<T>	Abstract class to provide the base functionality for IGeneratorParameter implementations.
AbstractMCS	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	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AbstractMolecularDescriptor	A super class for molecular descriptors allowing default implementations for interface methods.
AbstractReactionLabeller	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
AbstractRenderer<T extends IChemObject>	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.
AbstractResourceFormat	An abstract class providing AbstractResourceFormat.hashCode() and AbstractResourceFormat.equals(java.lang.Object) for IResourceFormats.
AbstractSelection	An abstract selection of IChemObjects.
AbstractSubGraph	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AbstractValidator	Abstract validator that does nothing but provide all the methods that the ValidatorInterface requires.
Aces2Format
AcidicGroupCountDescriptor	Returns the number of acidic groups.
AdductFormula	Class defining an adduct object in a MolecularFormula.
AdductFormula	Class defining an adduct object in a MolecularFormula.
AdductionLPMechanism	This mechanism adduct together two fragments.
AdductionPBMechanism	This mechanism adduct together two fragments due to a double bond.
AdductionProtonLPReaction	IReactionProcess which produces a protonation.
AdductionProtonPBReaction	IReactionProcess which produces a protonation to double bond.
AdductionSodiumLPReaction	IReactionProcess which produces an adduction of the Sodium.
ADFFormat
AdjacencyMatrix	Calculator for a adjacency matrix representation of this AtomContainer.
AlchemyFormat
Algorithm	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AliphaticAtom	Deprecated.
AliphaticSymbolAtom	Deprecated.
AllCycles	Compute all simple cycles (rings) in a graph.
AllPairsShortestPaths	Utility to determine the shortest paths between all pairs of atoms in a molecule.
AllRingsFinder	Compute the set of all rings in a molecule.
AllRingsFinder.Threshold	The threshold values provide a limit at which the computation stops.
ALOGPDescriptor	This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity [Ghose, A.K. and Crippen, G.M. . Journal of Computational Chemistry. 1986. 7, Ghose, A.K. and Crippen, G.M. . Journal of Chemical Information and Computer Science. 1987. 27].
AminoAcid	A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
AminoAcid	A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
AminoAcidCountDescriptor	Class that returns the number of each amino acid in an atom container.
AminoAcidManipulator	Class with convenience methods that provide methods to manipulate AminoAcid's.
AminoAcids	Tool that provides templates for the (natural) amino acids.
AngularMomentum	This class is used to calculate angular momentum states.
AnyAtom	Deprecated.
AnyOrderQueryBond	Deprecated.
APolDescriptor	Sum of the atomic polarizabilities (including implicit hydrogens).
AromaticAtom	Deprecated.
AromaticAtomsCountDescriptor	Class that returns the number of aromatic atoms in an atom container.
AromaticBondsCountDescriptor	This Class contains a method that returns the number of aromatic atoms in an AtomContainer.
Aromaticity	A configurable model to perceive aromatic systems.
AromaticityCalculator	Deprecated. use Aromaticity
AromaticOrSingleQueryBond	Deprecated.
AromaticQueryBond	Deprecated.
AromaticSymbolAtom	Deprecated.
ArrowElement	IRenderingElement for linear arrows.
Association	Base class for storing interactions like hydrogen bonds and ionic interactions.
Atom	Represents the idea of an chemical atom.
Atom	Represents the idea of an chemical atom.
AtomContainer	Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
AtomContainer	Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
AtomContainerAtomPermutor	An atom container atom permutor that uses ranking and unranking to calculate the next permutation in the series.
AtomContainerAtomPermutor	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
AtomContainerBondPermutor	This class allows the user to iterate through the set of all possible permutations of the bond order in a given atom container.
AtomContainerBoundsGenerator	IGenerator that draws a rectangular around the IAtomContainer.
AtomContainerComparator	Compares two IAtomContainers for order with the following criteria with decreasing priority:
AtomContainerComparatorBy2DCenter	Compares two IAtomContainers based on their 2D position.
AtomContainerDiff	Compares two IAtomContainer classes.
AtomContainerDiscretePartitionRefiner	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 with convenience methods that provide methods to manipulate AtomContainer's.
AtomContainerPermutor	The base class for permutors of atom containers, with a single abstract method containerFromPermutation that should be implemented in concrete derived classes.
AtomContainerPrinter	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
AtomContainerRenderer	A general renderer for IAtomContainers.
AtomContainerSet	A set of AtomContainers.
AtomContainerSet	A set of AtomContainers.
AtomContainerSetManipulator
AtomCountDescriptor	IDescriptor based on the number of atoms of a certain element type.
AtomDegreeDescriptor	This class returns the number of not-Hs substituents of an atom, also defined as "atom degree".
AtomDiff	Compares two IAtom classes.
AtomEncoder	An encoder for invariant atom properties.
AtomHashGenerator	A hash function which generates 64-bit hash codes for the atoms of a molecule.
AtomHybridizationDescriptor	This class returns the hybridization of an atom.
AtomHybridizationVSEPRDescriptor	This class returns the hybridization of an atom.
AtomicNumberAtom	Deprecated.
AtomicNumberDifferenceDescriptor	Describes the imbalance in atomic number of the IBond.
AtomicProperties	Provides atomic property values for descriptor calculations.
AtomMappingTools
AtomMassGenerator	IGenerator that can render mass number information of atoms.
AtomMassSymbolElement	Rendering element that shows the IAtom mass number information.
AtomMatcher	Defines compatibility checking of atoms for (subgraph)-isomorphism mapping.
AtomMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
AtomNumberGenerator	IGenerator for IAtomContainers that will draw atom numbers for the atoms.
AtomNumberGenerator.AtomColorer	The color scheme by which to color the atom numbers, if the AtomNumberGenerator.ColorByType boolean is true.
AtomNumberGenerator.AtomNumberTextColor	Color to draw the atom numbers with.
AtomNumberGenerator.ColorByType	Boolean to indicate of the AtomNumberGenerator.AtomColorer scheme will be used.
AtomNumberGenerator.Offset	Offset vector in screen space coordinates where the atom number label will be placed.
AtomNumberGenerator.WillDrawAtomNumbers	Boolean parameter indicating if atom numbers should be drawn, allowing this feature to be disabled temporarily.
AtomPairs2DFingerprinter	Generates an atom pair 2D fingerprint as implemented in PaDEL given an IAtomContainer, that extends the Fingerprinter.
AtomPlacer	Methods for generating coordinates for atoms in various situations.
AtomPlacer3D	Place aliphatic chains with Z matrix method.
AtomRef	An atom ref, references a CDK IAtom indirectly.
AtomSignature	The signature [Faulon, J. L., Visco, D. P., and Pophale, R. S.. Journal of Chemical Information and Computer Sciences. 2003. 43, Faulon, J. L., Collins, M. J., and Carr, R. D.. Journal of Chemical Information and Computer Sciences. 2004. 44] for a molecule rooted at a particular atom.
AtomSymbolElement	A text element with added information.
AtomTetrahedralLigandPlacer3D	A set of static utility classes for geometric calculations on Atoms.
AtomTools	A set of static utility classes for geometric calculations on Atoms.
AtomType	The base class for atom types.
AtomType	The base class for atom types.
AtomTypeAwareSaturationChecker	This class tries to figure out the bond order of the bonds that has the flag SINGLE_OR_DOUBLE raised (i.e.
AtomTypeCharges	Assigns charges to atom types.
AtomTypeDiff	Compares two IAtomType classes.
AtomTypeFactory	General class for defining AtomTypes.
AtomTypeHandler	SAX Handler for the AtomTypeReader.
AtomTypeHybridizationDifference	IDifference between two IAtomType.Hybridizations.
AtomTypeManipulator	Class with utilities for the IAtomType class.
AtomTypeMapper	An AtomTypeMapper allows the mapping of atom types between atom type schemes.
AtomTypeReader	XML Reader for the CDKBasedAtomTypeConfigurator.
AtomTypeTools	AtomTypeTools is a helper class for assigning atom types to an atom.
AtomValenceDescriptor	This class returns the valence of an atom.
AtomValenceTool	This class returns the valence of an atom.
Atropisomeric	Restricted axial rotation around Aryl-Aryl bonds.
AttachedGroup	Holds data on a specific functional group or substituent.
AutocorrelationDescriptorCharge	This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.
AutocorrelationDescriptorMass	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].
AutocorrelationDescriptorPolarizability	This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.
AverageBondLengthCalculator	Utility class for calculating the average bond length for various IChemObject subtypes : IReaction, IAtomContainerSet, IChemModel, and IReactionSet.
AWTDrawVisitor	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.
AWTFontManager	AWT-specific font manager.
BadMatrixFormatException
BasicAtomEncoder	Enumeration of atom encoders for seeding atomic hash codes.
BasicAtomGenerator	Generates basic IRenderingElements for atoms in an atom container.
BasicAtomGenerator.AtomColor	Class to hold the color by which atom labels are drawn.
BasicAtomGenerator.AtomColorer	IAtomColorer used to draw elements.
BasicAtomGenerator.AtomRadius	Magic number with unknown units that defines the radius around an atom, e.g.
BasicAtomGenerator.ColorByType	Boolean property that triggers atoms to be colored by type when set to true.
BasicAtomGenerator.CompactAtom	Boolean parameters that will cause atoms to be drawn as filled shapes when set to true.
BasicAtomGenerator.CompactShape	Shape to be used when drawing atoms in compact mode, as defined by the BasicAtomGenerator.CompactAtom parameter.
BasicAtomGenerator.KekuleStructure	Determines whether structures should be drawn as Kekule structures, thus giving each carbon element explicitly, instead of not displaying the element symbol.
BasicAtomGenerator.Shape	When atoms are selected or in compact mode, they will be covered by a shape determined by this enumeration.
BasicAtomGenerator.ShowEndCarbons	Boolean parameters that will show carbons with only one (non-hydrogen) neighbor to be drawn with an element symbol.
BasicAtomGenerator.ShowExplicitHydrogens	Boolean property that triggers explicit hydrogens to be drawn if set to true.
BasicBondGenerator	Generator for elements from bonds.
BasicBondGenerator.BondDistance	The gap between double and triple bond lines on the screen.
BasicBondGenerator.BondWidth	The width on screen of a bond.
BasicBondGenerator.DefaultBondColor	The color to draw bonds if not other color is given.
BasicBondGenerator.TowardsRingCenterProportion	The proportion to move in towards the ring center.
BasicBondGenerator.WedgeWidth	The width on screen of the fat end of a wedge bond.
BasicGenerator	Combination generator for basic drawing of molecules.
BasicGroupCountDescriptor	Returns the number of basic groups.
BasicSceneGenerator	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.ArrowHeadWidth	The width of the head of arrows.
BasicSceneGenerator.BackgroundColor	The background color of the drawn image.
BasicSceneGenerator.BondLength	The length on the screen of a typical bond.
BasicSceneGenerator.FitToScreen	If true, the scale is set such that the diagram fills the whole screen.
BasicSceneGenerator.FontName	Font to use for text.
BasicSceneGenerator.ForegroundColor	The foreground color, with which objects are drawn.
BasicSceneGenerator.Margin	Area on each of the four margins to keep empty.
BasicSceneGenerator.Scale	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	Determines if the molecule's title is depicted.
BasicSceneGenerator.ShowReactionTitle	Determines if the reaction's title is depicted.
BasicSceneGenerator.ShowTooltip	Determines if tooltips are to be shown.
BasicSceneGenerator.UseAntiAliasing	If set to true, uses anti-aliasing for drawing.
BasicSceneGenerator.UsedFontStyle	The font style to use for text.
BasicSceneGenerator.ZoomFactor	The zoom factor which is a user oriented parameter allowing the user to zoom in on parts of the molecule.
BasicValidator	Validator which tests a number of basic chemical semantics.
Bayesian	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.
BCUTDescriptor	Eigenvalue based descriptor noted for its utility in chemical diversity.
BFSShortestPath	Deprecated. Use ShortestPaths
BGFFormat
BiconnectivityInspector	Deprecated. Use RingSearch or Cycles.markRingAtomsAndBonds(IAtomContainer)
BinaryTree	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BioPolymer	A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
BioPolymer	A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
BitSetFingerprint
BKKCKCF	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Bond	Implements the concept of a covalent bond between two or more atoms.
Bond	Implements the concept of a covalent bond between two or more atoms.
BondCountDescriptor	IDescriptor based on the number of bonds of a certain bond order.
BondDiff	Compares two IBond classes.
BondEnergies	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	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BondManipulator	Class with convenience methods that provide methods to manipulate AtomContainer's.
BondMatcher	Defines compatibility checking of bonds for (subgraph)-isomorphism mapping.
BondMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
BondOrderDifference	IDifference between two IBond.Orders.
BondPartialPiChargeDescriptor	The calculation of bond-pi Partial charge is calculated determining the difference the Partial Pi Charge on atoms A and B of a bond.
BondPartialSigmaChargeDescriptor	The calculation of bond-sigma Partial charge is calculated determining the difference the Partial Sigma Charge on atoms A and B of a bond.
BondPartialTChargeDescriptor	The calculation of bond total Partial charge is calculated determining the difference the Partial Total Charge on atoms A and B of a bond.
BondRef	A bond ref, references a CDK IBond indirectly.
BondSigmaElectronegativityDescriptor	The calculation of bond-Polarizability is calculated determining the difference the Sigma electronegativity on atoms A and B of a bond.
BondsToAtomDescriptor	This class returns the number of bonds on the shortest path between two atoms.
BondTools	A set of static utility classes for geometric calculations on IBonds.
BooleanArrayDifference	Difference between two boolean[]'s.
BooleanDifference	IDifference between two Booleans.
BooleanIOSetting	An class for a reader setting which must be of type String.
BooleanResult	Object that provides access to the calculated descriptor value.
BooleanResultType	IDescriptorResult type for boolean.
Bounds	Defines a bounding box element which the renderer can use to determine the true drawing limits.
BoundsCalculator	Utility class for calculating the 2D bounding rectangles (bounds) of various IChemObject subtypes - IChemModel, IReactionSet, IReaction, IAtomContainerSet, and IAtomContainer.
BoundsGenerator	Produce a bounding rectangle for various chem objects.
BoundsGenerator.BoundsColor	The color of the box drawn at the bounds of a molecule, molecule set, or reaction.
BPolDescriptor	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.
BremserOneSphereHOSECodePredictor
BSFormat	See here.
Bspt	BSP-Tree stands for Binary Space Partitioning Tree.
Bspt.Tuple
CacaoCartesianFormat	See here.
CacaoInternalFormat	See here.
CACheFormat
Canon	An implementation based on the canon algorithm [Weininger, David et. al.. Journal of Chemical Information and Computer Sciences. 1989. 29].
CanonicalLabeler	Deprecated. this labeller uses slow data structures and has been replaced - Canon
CanonicalLabellingAdaptor	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
CanonOpts	Basic flavor options to tweak canonical invariants, note these deliberately mirror some fields from the SmiFlavor settings.
CarbonTypesDescriptor	Topological descriptor characterizing the carbon connectivity.
CarbonylEliminationReaction	IReactionProcess which participate mass spectrum process.
CASNumber	Tools to work with CAS registry numbers.
CDK	Helper class to provide general information about this CDK library.
CDK	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.
CDK2DAtomColors	Gives a short table of atom colors for 2D display.
CDKAtomColors	Deprecated. JmolColors provides more comprehensive color pallet for 3D
CDKAtomTypeMatcher	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	AtomType resource that reads the atom type configuration from an XML file.
CDKConstants	An interface providing predefined values for a number of constants used throughout the CDK.
CDKConvention	This is an implementation for the CDK convention.
CDKDictionaryReferences	This class transforms implicit references to dictionary of CDK objects into explicit references.
CDKException	Exception that is thrown by CDK classes when some problem has occurred.
CDKHueckelAromaticityDetector	Deprecated. use Aromaticity with the ElectronDonation.cdk() model
CDKHydrogenAdder	Adds implicit hydrogens based on atom type definitions.
CDKMCS	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
CDKMCSHandler	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
CDKOWLFormat	Serializes a CDK model into the Web Ontology Language using the N3 format.
CDKOWLReader	Reads content from a CDK OWL serialization.
CDKOWLWriter	Serializes the data model into CDK OWL.
CDKRGraph	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
CDKRMap	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
CDKRMapHandler	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
CDKRNode	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
CDKSourceCodeFormat
CDKSourceCodeWriter	Converts a Molecule into CDK source code that would build the same molecule.
CDKSubGraphHandler	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
CDKUtilities	Deprecated. better accomplished with SMARTS patterns or simple REGEX
CDKValencyChecker	Assumes CDK atom types to be detected and adds missing hydrogens based on the atom typing.
CDKValidator	This Validator tests the internal data structures, and tries to detect inconsistencies in it.
ChargeGroup	A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
ChargeRule	This class validate if the charge in the IMolecularFormula correspond with a specific value.
Chem3D_Cartesian_1Format
Chem3D_Cartesian_2Format
ChemDrawFormat
ChemFile	A Object containing a number of ChemSequences.
ChemFile	A Object containing a number of ChemSequences.
ChemFileManipulator	Class with convenience methods that provide methods from methods from ChemObjects within the ChemFile.
ChemGraph
ChemicalFilters	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ChemModel	An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
ChemModel	An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
ChemModelManipulator	Class with convenience methods that provide methods from methods from ChemObjects within the ChemModel.
ChemModelRenderer	A general renderer for IChemModels, IReactions, and IAtomContainers.
ChemObject	The base class for all chemical objects in this cdk.
ChemObject	The base class for all chemical objects in this cdk.
ChemObjectChangeEvent	Event fired by cdk classes to their registered listeners in case something changes within them.
ChemObjectDiff	Compares two IChemObject classes.
ChemObjectDifference	IDifference between two IChemObjects.
ChemObjectIO	Provides some basic functionality for readers and writers.
ChemSequence	A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ChemSequence	A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ChemSequenceManipulator	Class with convenience methods that provide methods from methods from ChemObjects within the ChemSequence.
ChemtoolFormat	See here.
ChiChainDescriptor	Evaluates chi chain descriptors.
ChiClusterDescriptor	Evaluates chi cluster descriptors.
ChiPathClusterDescriptor	Evaluates chi path cluster descriptors.
ChiPathDescriptor	Evaluates chi path descriptors.
ChiralityAtom	Deprecated.
CIFFormat
CIFReader	This is not a reader for the CIF and mmCIF crystallographic formats.
CIPLigandRule	Compares to ILigands based on CIP sequences sub rules.
CIPTool	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.CIP_CHIRALITY	Enumeration with the two tetrahedral chiralities defined by the CIP schema.
CircularFingerprinter	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.FP
Close	Indicates the closing point of the path.
ClosedShellJob	Calculates the orbitals and orbital energies of electron systems with closed shells
CMLCoreModule	Core CML 1.x and 2.x elements are parsed by this class (see [Willighagen, E.L.. Internet Journal of Chemistry. 2001. 4]).
CMLErrorHandler	CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document.
CMLFormat	See here.
CMLHandler	SAX2 implementation for CML XML fragment reading.
CMLModuleStack	Low weight alternative to Sun's Stack class.
CMLReactionModule
CMLReader	Reads a molecule in CML 1.x and 2.0 format.
CMLResolver	This class resolves DOCTYPE declaration for Chemical Markup Language (CML) files and uses a local version for validation.
CMLRSSFormat
CMLWriter	Serializes a IAtomContainerSet or a IAtomContainer object to CML 2 code.
Complex	This class handles complex values.
ConformerContainer	A memory-efficient data structure to store conformers for a single molecule.
ConjugatedPiSystemsDetector
ConnectedComponents	Compute the connected components of an adjacency list.
ConnectionMatrix	Calculator for a connection matrix representation of this AtomContainer.
ConnectivityChecker	Tool class for checking whether the (sub)structure in an AtomContainer is connected.
Convertor
Convertor	Helper class that converts a CDK IChemObject into RDF using a Jena model and the CDK data model ontology.
CovalentRadiusDescriptor	This class returns the covalent radius of a given atom.
CPKAtomColors	Deprecated. JmolColors provides more comprehensive CPK color pallet
CPSADescriptor	Calculates 29 Charged Partial Surface Area (CPSA) descriptors.
CRK2DFormat	See here.
CRK3DFormat	See here.
CrossoverMachine	Modified molecular structures by applying crossover operator on a pair of parent structures and generate a pair of offspring structures.
Crystal	Class representing a molecular crystal.
Crystal	Class representing a molecular crystal.
CrystalGeometryTools	A set of static methods for working with crystal coordinates.
CrystClustFormat
CrystClustReader
CrystClustWriter	Rather stupid file format used for storing crystal information.
CTFileQueryBond	Deprecated. Use Expr.Type.SINGLE_OR_AROMATIC etc.
CTFileQueryBond.Type
CTXFormat
CTXReader	Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files.
CubicTo	A cubic curve in the path.
CustomSerializer	Custom Serializer with the sole purpose and functionality to not output the XML declaration.
CxSmilesGenerator
CycleBasis	Deprecated. internal implemenation detail from SSSRFinder, do not use
CycleFinder	Defines a method to find the cycles of a molecule.
Cycles	A utility class for storing and computing the cycles of a chemical graph.
CyclicVertexSearch	Describes a search to identify vertices which belong to elementary cycles and if those cycles are isolated or are part of a fused system.
DaltonFormat
DataFeatures	Class with constants for possible data features defined in the a Data Feature Ontology.
DataFeaturesTool	Utility that helps determine which data features are present.
DeAromatizationTool	Deprecated. the newer Kekulization provides a faster, more generic and comprehensive algorithm.
DebugAdductFormula	Debugging implementation of IAdductFormula.
DebugAminoAcid	Debugging data class.
DebugAtom	Debugging data class.
DebugAtomContainer	Debugging data class.
DebugAtomContainerSet	Debugging data class.
DebugAtomType	Debugging data class.
DebugBioPolymer	Debugging data class.
DebugBond	Debugging data class.
DebugChemFile	Debugging data class.
DebugChemModel	Debugging data class.
DebugChemObject	Debugging data class.
DebugChemObjectBuilder	A helper class to instantiate a IChemObject for the original CDK implementation.
DebugChemSequence	Debugging data class.
DebugCrystal	Debugging data class.
DebugElectronContainer	Debugging data class.
DebugElement	Debugging data class.
DebugFragmentAtom	Class to represent an IPseudoAtom which embeds an IAtomContainer.
DebugIsotope	Debugging data class.
DebugLonePair	Debugging data class.
DebugMapping	Debugging data class.
DebugMolecularFormula	Debugging implementation of IMolecularFormula.
DebugMolecularFormulaSet	Debugging implementation of IMolecularFormulaSet.
DebugMonomer	Debugging data class.
DebugPDBAtom	Debugging data class.
DebugPDBMonomer	Debugging data class.
DebugPDBPolymer	Debugging data class.
DebugPDBStructure	Debugging data class.
DebugPolymer	Debugging data class.
DebugPseudoAtom	Debugging data class.
DebugReaction	Debugging data class.
DebugReactionScheme	Debugging data class.
DebugReactionSet	Debugging data class.
DebugRing	Debugging data class.
DebugRingSet	Debugging data class.
DebugSingleElectron	Debugging data class.
DebugStrand	Debugging data class.
DebugSubstance	Debugging data class.
DeduceBondSystemTool	Deprecated. Use the newer Kekulization
DefaultBondMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
DefaultChemObjectBuilder	A factory class to provide implementation independent ICDKObjects.
DefaultChemObjectReader	Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultChemObjectWriter	Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultEventChemObjectReader	Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultIteratingChemObjectReader<T extends IChemObject>	Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
DefaultMCSPlusAtomMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
DefaultRandomAccessChemObjectReader	Abstract class that IRandomAccessChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultRGraphAtomMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
DefaultVFAtomMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
DefaultVFBondMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
Depiction	Base class of a pre-rendered depiction.
DepictionGenerator	A high-level API for depicting molecules and reactions.
DescriptorEngine	A class that provides access to automatic descriptor calculation and more.
DescriptorException	Exception that is thrown by descriptor routines when a problem has occurred.
DescriptorSpecification	Class that is used to distribute descriptor specifications.
DescriptorValue	Class that is used to store descriptor values as IChemObject properties.
DfPattern	The depth-first (DF) backtracking sub-structure matching algorithm so named because it matches the molecule in a depth-first manner (bond by bond).
Dictionary	Dictionary with entries.
DictionaryDatabase	Database of dictionaries listing entries with compounds, fragments and entities.
DictionaryHandler	Class for unmarshalling a dictionary schema file.
DictionaryValidator	Validates the existence of references to dictionaries.
DictRef	Object that can be used as key in IChemObject.setProperty(key, value) to denote that this property is a dictionary reference for this IChemObject.
DiscretePartitionRefiner	A mechanism for refining partitions of graph-like objects.
DisjointSetForest	Implementation of a union-find data structure, largely copied from code due to Derrick Stolee.
DistanceMoment	Fast similarity measure for 3D structures.
DistanceToAtomDescriptor	This class returns the 3D distance between two atoms.
DMol3Format
DOCK5Format	See here.
DoubleArrayResult
DoubleArrayResultType	IDescriptorResult type for doubles.
DoubleBondAcceptingAromaticityDetector	Deprecated. use Aromaticity with the ElectronDonation.cdkAllowingExocyclic() model
DoubleBondElementEncoderFactory	Defines a stereo encoder factory for the hash code.
DoubleBondStereochemistry	Stereochemistry specification for double bonds.
DoubleDifference	IDifference between two Double.
DoubleResult
DoubleResultType	IDescriptorResult type for double.
DynamicFactory	A factory class for constructing ICDKObject and IChemObject implementations.
DynamicFactory.BasicCreator<T>	A simple creator that helps in creating an anonymous classes for a creator.
DynamicFactory.ConstructorKey	A class which encapsulates the information about an interface (of this implementation) and the parameter types of the constructor.
DynamicFactory.CreationModifier<T>	An interface that allows posterior modification of an instance after it has been created.
DynamicFactory.Creator<T>	An interface that wraps object creation via the DynamicFactory.Creator.create(Object[]) method.
DynamicFactory.DefaultInterfaceProvider	A default interface provider implementation that simply returns the classes from Class.getInterfaces().
DynamicFactory.InterfaceProvider	An interface that can provide which interfaces the given class implements.
EccentricConnectivityIndexDescriptor	A topological descriptor combining distance and adjacency information.
EdgeBuilder	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
EffectiveAtomPolarizabilityDescriptor	Effective polarizability of a heavy atom Parameters for this descriptor: Name Default Description no parameters
ElectronContainer	Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
ElectronContainer	Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
ElectronContainerDiff	Compares two IChemObject classes.
ElectronDonation	Defines an electron donation model for perceiving aromatic systems.
Electronegativity	Calculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
ElectronImpactNBEReaction	IReactionProcess which make an electron impact for for Non-Bonding Electron Lost.
ElectronImpactPDBReaction	IReactionProcess which make an electron impact for pi-Bond Dissociation.
ElectronImpactSDBReaction	IReactionProcess which make an electron impact for Sigma Bond Dissociation.
Element	Implements the idea of an element in the periodic table.
Element	Implements the idea of an element in the periodic table.
ElementComparator	Compares elements based on the order commonly used in molecular formula.
ElementDiff	Compares two IElement classes.
ElementGroup	A group of rendering elements, of any type.
ElementRule	This class validate if the occurrence of the IElements in the IMolecularFormula are into a limits.
Elements	Enumeration of chemical elements.
EnsembleHashGenerator	A hash function which generates a single 64-bit hash code for a set of molecules (ensemble).
Entry	Entry in a Dictionary.
EntryReact	Entry in a Dictionary for reactions.
EnzymeResidueLocator	Atom that represents part of an residue in an enzyme, like Arg255.
EquivalentClassPartitioner	An algorithm for topological symmetry.
EssentialCycles	Determine the uniquely defined essential cycles of a graph.
EStateAtomTypeMatcher	Determines the EState atom types.
EStateFingerprinter	This fingerprinter generates 79 bit fingerprints using the E-State fragments.
EStateFragments	A class representing the 79 E-state atom types in terms of SMARTS.
EventCMLHandler	CDO object needed as interface with the JCFL library for reading CML in a event based manner.
EventCMLReader	Reads a molecule in CML 1.x and 2.0 format.
ExactMapping	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ExhaustiveFragmenter	Generate fragments exhaustively.
ExplicitConnectionAtom	Deprecated.
Expr	A expression stores a predicate tree for checking properties of atoms and bonds.
Expr.Type	Types of expression, for use in the Expr tree object.
ExtAtomContainerManipulator	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ExtendedAtomGenerator	A generator for atoms with mass, charge, etc.
ExtendedAtomGenerator.ShowAtomTypeNames	Boolean that indicates if atom type names should be given instead of element symbols.
ExtendedAtomGenerator.ShowImplicitHydrogens	Boolean that indicates if implicit hydrogens should be depicted.
ExtendedCisTrans	Extended Cis/Trans double bond configuration.
ExtendedFingerprinter	Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional (25) bits describing ring features and isotopic masses.
ExtendedTetrahedral	Extended tetrahedral configuration.
FenskeHall_ZMatrixFormat
FiguerasSSSRFinder	Deprecated. Use SSSRFinder instead (exact algorithm).
FinalMappings	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Fingerprinter	Generates a fingerprint for a given AtomContainer.
FingerprinterTool	Tool with helper methods for IFingerprint.
FingerprintFormat
FixBondOrdersTool	Deprecated. use Kekulization
FMFDescriptor	An implementation of the FMF descriptor characterizing complexity of a molecule.
ForceFieldConfigurator	Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable Therefore, it uses the class MM2BasedParameterSetReader.
FormalChargeAtom	Deprecated.
FormatFactory	A factory for recognizing chemical file formats.
FormatStringBuffer	A class for formatting output similar to the C printf command.
FortranFormat	Converts a String representation of a Fortran double to a double.
FourierGridBasis	At this time this class does not work correcly.
FractionalCSP3Descriptor	An implementation of the Fractional CSP3 descriptor described in [Lovering, Frank et. al.. J. Med. Chem.. 2009. 52].
FractionalPSADescriptor	Polar surface area expressed as a ratio to molecular size.
FragmentAtom	Class to represent an IPseudoAtom which embeds an IAtomContainer.
FragmentAtom	Class to represent an IPseudoAtom which embeds an IAtomContainer.
FragmentComplexityDescriptor	Class that returns the complexity of a system.
FragmentUtils	Helper methods for fragmentation algorithms.
GamessFormat	See here.
GamessReader	A reader for GAMESS log file.
GasteigerMarsiliPartialCharges	The calculation of the Gasteiger Marsili (PEOE) partial charges is based on [Gasteiger, J. and Marsili, M.. Tetrahedron. 1980. 36].
GasteigerPEPEPartialCharges	The calculation of the Gasteiger (PEPE) partial charges is based on [Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, ?Institute?].
Gaussian03Format	See here.
Gaussian03Reader	A reader for Gaussian03 output.
Gaussian90Format
Gaussian92Format
Gaussian94Format
Gaussian95Format
Gaussian98Format
Gaussian98Reader	A reader for Gaussian98 output.
GaussianInputFormat	See here.
GaussianInputWriter	File writer thats generates input files for Gaussian calculation jobs.
GaussiansBasis	This class contains the information to use gauss function as a base for calculation of quantum mechanics.
GeneralPath	A path of rendering elements from the elements.path package.
GenerateCompatibilityGraph	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
GeometricCumulativeDoubleBondFactory	Stereo encoder factory for 2D and 3D cumulative double bonds.
GeometricDoubleBondEncoderFactory	A stereo encoder factory encoding double bond configurations by 2D and 3D coordinates.
GeometricTetrahedralEncoderFactory	A stereo encoder factory for tetrahedral centres.
Geometry3DValidator	Validates the 3D geometry of the model.
GeometryTools	Deprecated. use GeometryUtil moved for dependency reorganisation
GeometryTools.CoordinateCoverage	Provides the coverage of coordinates for this molecule.
GeometryUtil	A set of static utility classes for geometric calculations and operations.
GeometryUtil.CoordinateCoverage	Provides the coverage of coordinates for this molecule.
GhemicalMMFormat	See here.
GhemicalMMReader	Reads Ghemical ( http://www.uku.fi/~thassine/ghemical/) molecular mechanics (*.mm1gp) files.
GhemicalSPMFormat
GIMatrix	This class is intended to provide the user an efficient way of implementing matrix of double number and using normal operations (linear operations, addition, subtraction, multiplication, inversion, concatenation) on them.
GraphOnlyFingerprinter	Specialized version of the Fingerprinter which does not take bond orders into account.
GraphRendererModel	This class handles a set of function for the GraphRenderer
GraphUtil	Collection of static utilities for manipulating adjacency list representations stored as a int[][].
GraphUtil.EdgeToBondMap	Utility for storing IBonds indexed by vertex end points.
GravitationalIndexDescriptor	IDescriptor characterizing the mass distribution of the molecule.
GridGenerator	Generates a grid of points in 3D space within given boundaries.
GROMOS96Format	See here.
HanserRingFinder	Deprecated. Use CDK AllRingsFinder.
HashGeneratorMaker	Fluent API for creating hash generators.
HBondAcceptorCountDescriptor	This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types.
HBondDonorCountDescriptor	This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the PHACIR atom types.
HeterolyticCleavageMechanism	This mechanism displaces the chemical bond to an Atom.
HeterolyticCleavagePBReaction	IReactionProcess which a bond is broken displacing the electron to one of the atoms.
HeterolyticCleavageSBReaction	IReactionProcess which a bond is broken displacing the electron to one of the atoms.
HighlightGenerator	Generate an under/overlaid highlight in structure depictions.
HighlightGenerator.HighlightPalette	Defines the color palette used to provide the highlight colors.
HighlightGenerator.HighlightRadius	Magic number with unknown units that defines the radius around an atom, e.g.
HighlightGenerator.Palette	Defines a color palette, the palette should provide a color the specified identifier (id).
HINFormat	See here.
HINReader	Reads an object from HIN formated input.
HINWriter	Writer that outputs in the HIN format.
HomolyticCleavageMechanism	This mechanism breaks the chemical bond between atoms.
HomolyticCleavageReaction	IReactionProcess which breaks the bond homogeneously leading to radical ions.
HOSECodeAnalyser	Analyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula.
HOSECodeGenerator	Generates HOSE codes [Bremser, W.. Analytica Chimica Acta. 1978. 103].
HuLuIndexTool	Collection of methods for the calculation of topological indices of a molecular graph as described in [Chang-Yu Hu and Lu Xu. J. Chem. Inf. Comput. Sci.. 1996. 36].
HybridizationFingerprinter	Generates a fingerprint for a given IAtomContainer.
HybridizationNumberAtom	Deprecated.
HybridizationRatioDescriptor	IMolecularDescriptor that reports the fraction of sp3 carbons to sp2 carbons.
HydrogenAtom	Deprecated.
HydrogenPlacer	This is a wrapper class for some existing methods in AtomPlacer.
HyperconjugationReaction	HyperconjugationReaction is the stabilizing interaction that results from the interaction of the electrons in a s-bond (for our case only C-H) with an adjacent empty (or partially filled) p-orbital.
IAdductFormula	Class defining an adduct object in a MolecularFormula.
IAminoAcid	A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
IAtom	Represents the idea of an chemical atom.
IAtomColorer	Interface to a class for coloring atoms.
IAtomContainer	Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
IAtomContainerSet	A set of AtomContainers.
IAtomicDescriptor	Classes that implement this interface are QSAR descriptor calculators.
IAtomPairDescriptor	Classes that implement this interface are QSAR descriptor calculators.
IAtomType	The base class for atom types.
IAtomType.Hybridization	An enum for the different hybridization states.
IAtomTypeConfigurator	Interface that allows reading atom type configuration data from some source.
IAtomTypeGuesser	Classes that implement this interface are atom type guessers.
IAtomTypeMatcher	Classes that implement this interface are atom type matchers.
IBasis	A basis set must implement this class.
IBioPolymer	A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
IBitFingerprint	Interface for bit fingerprint representations.
IBond	Implements the concept of a covalent bond between two or more atoms.
IBond.Display	Bond display style, controlling how bonds appear in a 2D depiction.
IBond.Order	A list of permissible bond orders.
IBond.Stereo	Enumeration of possible stereo types of two-atom bonds.
IBondDescriptor	Classes that implement this interface are QSAR descriptor calculators.
ICanonicalMoleculeLabeller	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
ICanonicalReactionLabeller	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
ICDKChangeListener	A ChangeListener for the CDK, to be independent from the Swing package.
ICDKObject	The base class for all data objects in this CDK.
ICDKSelectionChangeListener	A ChangeListener for the CDK, to be independent from the Swing package.
IChargeCalculator	Interface for classes that calculate (partial) charges centered on atom nuclei.
IChemFile	An IChemObject containing a number of ChemSequences.
IChemFormat	This class is the interface that all ChemFormat's should implement.
IChemFormatMatcher	This interface is used for classes that are able to match a certain chemical file format.
IChemFormatMatcher.MatchResult	Simple class holds whether a format matcher matched, when it matched and what the format was.
IChemModel	An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
IChemObject	The base class for all chemical objects in this cdk.
IChemObjectBuilder	A helper class to instantiate a ICDKObject instance for a specific implementation.
IChemObjectChangeEvent	Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.
IChemObjectIO	This class is the interface that all IO readers should implement.
IChemObjectIOListener	Allows monitoring of progress of file reader activities.
IChemObjectListener	Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.
IChemObjectReader	This interface specifies the common functionality all IO readers should provide.
IChemObjectReader.Mode
IChemObjectReaderErrorHandler	Interface for classes aimed to handle IChemObjectReader errors.
IChemObjectSelection	A selection of some atoms and bonds from an IAtomContainer or IChemModel.
IChemObjectWriter	This class is the interface that all IO writers should implement.
IChemSequence	A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ICMLConvention	This interface describes the procedures classes must implement to be plugable into the CMLHandler.
ICMLCustomizer	Interface for classes that allow the Convertor to be customized for certain features.
ICMLModule	This interface describes the procedures classes must implement to be plugable into the CMLHandler.
ICountFingerprint	Interface for count fingerprint representations.
ICrystal	Class representing a molecular crystal.
IDCreator	Class that provides methods to give unique IDs to ChemObjects.
IDeduceBondOrderTool	A common interface for tools that deduce bond orders from connectivity and optionally additional information, like number of implicit or explicit hydrogens, or hybridization states.
IDescriptor	Classes that implement this interface are QSAR descriptor calculators.
IDescriptorResult	Object that provides access to the calculated descriptor value.
IDifference	Object that describes the difference between two Objects.
IDifferenceList	IDifference between two Objects which contains one or more child IDifference objects.
IDoubleBondStereochemistry	Stereochemistry specification for double bond stereochemistry.
IDoubleBondStereochemistry.Conformation	Enumeration that defines the two possible values for this stereochemistry type.
IDrawVisitor	An IDrawVisitor is an IRenderingVisitor that can be customized and knows about fonts and other rendering parameters.
IEdge	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IElectronContainer	Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
IElectronicPropertyCalculator	Interface for classes that calculate (partial) charges centered on atom nuclei.
IElement	Implements the idea of an element in the periodic table.
IEventChemObjectReader	Interface for an iterating molecule reader.
IFinalMapping	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IFingerprinter	Interface for fingerprint calculators.
IFontManager	An interface for managing the drawing of fonts at different zoom levels.
IFontManager.FontStyle	Style of the font to use to draw text.
IFragmentAtom	Class to represent an IPseudoAtom which embeds an IAtomContainer.
IFragmenter	An interface for classes implementing fragmentation algorithms.
IFunction	A class, which has a function value should implement this interface.
IGenerator<T extends IChemObject>	An IGenerator converts chemical entities into parts of the chemical drawing expressed as IRenderingElements.
IGeneratorParameter<T>	Parameter from some rendering of the 2D diagram.
IGraphMatrix	Interface describing a molecular graph matrix calculator.
IImplementationSpecification	Interface that is used to describe the specification of a certain implementation of an algorithm.
IIsotope	Used to store and retrieve data of a particular isotope.
IIteratingChemObjectReader<T extends IChemObject>	Interface for an iterating molecule reader.
ILigand	Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.
ILoggingTool	Useful for logging messages.
ILonePair	A LonePair is an orbital primarily located with one Atom, containing two electrons.
IMapper	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IMapping	Represents a mapping of two atoms.
IMatrix	This class contains a complex matrix.
IMCSBase	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IMolecularDescriptor	Classes that implement this interface are QSAR descriptor calculators for IAtomContainer objects.
IMolecularFormula	Class defining a molecular formula object.
IMolecularFormulaSet	Class defining a molecular formula object.
IMonomer	A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
IMouseEventRelay	Widget toolkit-independent interface to relay for mouse events.
ImplicitHCountAtom	Deprecated.
ImplicitHydrogenLigand	Subclass of Ligand to which no further recursion must be applied.
INCHI_OPTION	This class provides backwards compatibility of JNA-INCHI with JNI-INCHI, this enum was exposed in the CDK API.
INCHI_RET	This class provides backwards compatibility of JNA-INCHI with JNI-INCHI, this enum was exposed in the CDK API.
INChIContentProcessorTool	Deprecated.
INChIFormat	See here.
InChIGenerator	This class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer.
InChIGeneratorFactory	Factory providing access to InChIGenerator and InChIToStructure.
INChIHandler	Deprecated.
InChINumbersTools	Tool for calculating atom numbers using the InChI algorithm.
INChIPlainTextFormat
INChIPlainTextReader	Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document.
INChIReader	Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document.
InChITautomerGenerator	Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI.
InChIToStructure	This class generates a CDK IAtomContainer from an InChI string.
IncorrectUseOfCDKCoreClassError	Error that is thrown by debug implementations of the core CDK classes.
IndexOutOfBoundsException
InductiveAtomicHardnessDescriptor	Inductive atomic hardness of an atom in a polyatomic system can be defined as the "resistance" to a change of the atomic charge.
InductiveAtomicSoftnessDescriptor	Inductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability.
InductivePartialCharges	The calculation of the inductive partial atomic charges and equalization of effective electronegativities is based on [Cherkasov, A.. J. Chem. Inf. Comput. Sci.. 2003. 43].
INode	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IntArrayCountFingerprint
IntArrayFingerprint
IntegerArrayResult
IntegerArrayResultType	IDescriptorResult type for integers.
IntegerDifference	IDifference between two Integer.
IntegerIOSetting	An class for a reader setting which must be of type String.
IntegerResult	Object that provides access to the calculated descriptor value.
IntegerResultType	IDescriptorResult type for integer.
Intractable	Indicates a computation did not complete within some predefined bound.
InvalidSmilesException	Exception thrown when an error is occurred during SMILES parsing.
Invariant	Marker interface for invariants.
InverseSymbolSetQueryAtom	Deprecated.
InvPair	This is used to hold the invariance numbers for the canonical labeling of IAtomContainers.
IonizationPotentialTool	Deprecated. Results depend on the order of atoms in bonds, resolving this would require retraining the models which are not available.
IOSetting	An interface for reader settings.
IOSetting.Importance
IParameterReact	Interface for classes that generate parameters used in reactions.
IPAtomicHOSEDescriptor	This class returns the ionization potential of an atom containing lone pair electrons.
IPAtomicLearningDescriptor	Deprecated.
IPBondLearningDescriptor	Deprecated.
IPDBAtom	A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
IPDBMonomer	Represents the idea of an protein monomer as found in PDB files.
IPDBPolymer	A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.
IPDBStructure	Represents the idea of an chemical structure.
IPMolecularLearningDescriptor	Deprecated.
IPolymer	Subclass of Molecule to store Polymer specific attributes that a Polymer has.
IPseudoAtom	Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
IQuery	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IQueryAtom	Defines the ability to be matched against IAtom's.
IQueryAtomContainer	General concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester.
IQueryBond	Defines the abililty to be matched against IBond's.
IQueryCompiler	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IRandomAccessChemObjectReader<T>	Extension of ListIterator.
IRDFWeightFunction	Weight function used in the RDFCalculator.
IReaction	Represents the idea of a chemical reaction.
IReaction.Direction	Permissible reaction directions.
IReactionMechanism	Classes that implement this interface are reaction mechanisms.
IReactionProcess	Classes that implement this interface are Reactions types.
IReactionScheme	Classes that implement this interface of a scheme.
IReactionSet	A set of reactions, for example those taking part in a reaction.
IReaderListener	Allows monitoring of progress of file reader activities.
IRenderer<T extends IChemObject>	Interface that all 2D renderers implement.
IRenderingElement	Widget toolkit-independent, abstract definition of something to be drawn.
IRenderingVisitor	An IRenderingVisitor is responsible of converting an abstract chemical drawing into a widget set specific drawing.
IResourceFormat	This class is the interface that all ResourceFormat's should implement.
IRGroup	Represents a single substitute structure in an IRGroupList.
IRGroupList	Represents a list of Rgroup substitutes to be associated with some key in an IRGroupQuery.
IRGroupQuery	Interface definition for Rgroup query classes.
IRing	Class representing a ring structure in a molecule.
IRingSet	Maintains a set of Ring objects.
IRule	Interface which groups all method that validate a IMolecularFormula.
ISequenceSubRule<ILigand>	Sequence sub rule used in the CIP method to decide which of the two ligands takes precedence [Cahn, R.S. et. al.. Angew. Chem. Int. Ed.. 1966. 5].
ISetting	A simple setting that can be managed by the SettingManager.
ISimpleChemObjectReader	This class is the interface that all IO readers should implement.
ISingleElectron	A Single Electron is an orbital which is occupied by only one electron.
IsoAlkanes	This class contains methods for generating simple organic alkanes.
Isomorphism	Deprecated. A more recent version of SMSD is available at http://github.com/asad/smsd
IsomorphismTester	A too simplistic implementation of an isomorphism test for chemical graphs.
Isotope	Used to store and retrieve data of a particular isotope.
Isotope	Used to store and retrieve data of a particular isotope.
IsotopeContainer	This class defines a isotope container.
IsotopeDiff	Compares two IIsotope classes.
IsotopeFactory	Used to store and return data of a particular isotope.
IsotopeHandler	Reads an isotope list in CML2 format.
IsotopePattern	This class defines the properties of a deisotoped pattern distribution.
IsotopePatternGenerator	Generates all Combinatorial chemical isotopes given a structure.
IsotopePatternManipulator	Class to manipulate IsotopePattern objects.
IsotopePatternRule	This class validate if the Isotope Pattern from a given IMolecularFormula correspond with other to compare.
IsotopePatternSimilarity	This class gives a score hit of similarity between two different isotope abundance pattern.
IsotopeReader	Reader that instantiates an XML parser and customized handler to process the isotope information in the CML2 isotope data file.
Isotopes	List of isotopes.
IsProtonInAromaticSystemDescriptor	This descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions.
IsProtonInConjugatedPiSystemDescriptor	This class evaluates if a proton is joined to a conjugated system.
IState	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IStereoElement<F extends IChemObject,C extends IChemObject>	Representation of stereochemical configuration.
IStrand	A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
IStructureGenerationListener
ISubstance	A chemical substance that consists of one or more chemical structures.
ISubstanceDescriptor	Classes that implement this interface are QSAR substance calculators.
IteratingMDLConformerReader	Iterate over conformers of a collection of molecules stored in SDF format.
IteratingPCCompoundASNReader	Iterating PubChem PCCompound ASN reader.
IteratingPCCompoundXMLReader	Iterating PubChem PCCompound ASN.1 XML reader.
IteratingPCSubstancesXMLReader	Iterating PubChem PC-Substances ASN.1 XML reader.
IteratingSDFReader	Iterating MDL SDF reader.
IteratingSMILESReader	Iterating SMILES file reader.
ITetrahedralChirality	Stereochemistry specification for quadrivalent atoms.
ITetrahedralChirality.Stereo	Enumeration that defines the two possible chiralities for this stereochemistry type.
IValencyChecker	A common interface for SaturationChecker and ValencyChecker.
IValidator	Interface that Validators need to implement to be used in validation.
IVector
IViewEventRelay
IWriterListener	Allows monitoring of progress of writing activities.
JaguarFormat	See here.
JJTSMARTSParserState
JMEFormat
JMOLANIMATIONConvention
JmolColors	Default Jmol colors.
JPlogPDescriptor	A logP model donated by Lhasa Limited.
KabschAlignment	Aligns two structures to minimize the RMSD using the Kabsch algorithm.
KappaShapeIndicesDescriptor	Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH : "they are intended to capture different aspects of molecular shape.
Kekulization	Assign a Kekulé representation to the aromatic systems of a compound.
KierHallSmartsDescriptor	A fragment count descriptor that uses e-state fragments.
KlekotaRothFingerprinter	SMARTS based substructure fingerprint based on Chemical substructures that enrich for biological activity [Klekota, Justin and Roth, Frederick P.. Bioinformatics. 2008. 24].
LabelContainer	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
LargestChainDescriptor	Class that returns the number of atoms in the largest chain.
LargestPiSystemDescriptor	Class that returns the number of atoms in the largest pi system.
LengthOverBreadthDescriptor	Evaluates length over breadth descriptors.
Ligand	Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.
LineElement	A line between two points.
LineElement.LineType	The type of the line.
LineTo	A line element in the path.
LingoFingerprinter	An implementation of the LINGO fingerprint [Vidal, D. et. al.. J. Chem. Inf. Model.. 2005. 45].
LingoSimilarity	A class to evaluate the similarity between two LINGO's as described in [Vidal, D. et. al.. J. Chem. Inf. Model.. 2005. 45].
LoggingToolFactory	Factory used to instantiate a ILoggingTool.
LogicalOperatorAtom	Deprecated.
LogicalOperatorBond	Deprecated.
LonePair	A LonePair is an orbital primarily located with one Atom, containing two electrons.
LonePair	A LonePair is an orbital primarily located with one Atom, containing two electrons.
LonePairDiff	Compares two ILonePair classes.
LonePairElectronChecker	Provides methods for checking whether an atoms lone pair electrons are saturated with respect to a particular atom type.
LonePairGenerator	Generate the symbols for lone pairs.
LongestAliphaticChainDescriptor	Counts the number of atoms in the longest aliphatic chain.
MACCSFingerprinter	This fingerprinter generates 166 bit MACCS keys.
MacroModelFormat
MannholdLogPDescriptor	Prediction of logP based on the number of carbon and hetero atoms.
Mapping	A Mapping is an relation between two ChemObjects in a non-chemical entity.
Mapping	A Mapping is an relation between two ChemObjects in a non-chemical entity.
MappingGenerator	IGenerator that will show how atoms map between the reactant and product side.
MappingGenerator.AtomAtomMappingLineColor	The width on screen of an atom-atom mapping line.
MappingGenerator.MappingLineWidth	The width on screen of an atom-atom mapping line.
MappingGenerator.ShowAtomAtomMapping	Boolean by which atom-atom mapping depiction can be temporarily disabled.
Mappings	A fluent interface for handling (sub)-graph mappings from a query to a target structure.
MarkedElement	A marked element adds meta-data (id and tags) to a CDK rendering element (or group of elements).
MassAtom	Deprecated.
MassToFormulaTool	Deprecated. Please use MolecularFormulaGenerator
Match	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Matching	A matching is an independent edge set of a graph.
Matrix	This class contains a matrix.
MatrixNotInvertibleException
Maygen	The main class of the MAYGEN package.
Maygen.Consumer
McGregor	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
McGregorChecks	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
McgregorHelper	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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.
MCSPlusHandler	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
MDEDescriptor	Calculates the Molecular Distance Edge descriptor described in [Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38].
MDLFormat	See here.
MDLMolConvention	Implementation of the MDLMol Covention for CML.
MDLReader	Deprecated. This reader is only for molfiles without a version tag, typically the most common molfile now encountered is V2000 and the MDLV2000Reader should be used instead.
MDLRXNFormat	See here.
MDLRXNReader	Deprecated. Use V2000 or V3000
MDLRXNV2000Format	See here.
MDLRXNV2000Reader	Reads a molecule from an MDL RXN file [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32].
MDLRXNV3000Format	See here.
MDLRXNV3000Reader	Class that implements the new MDL mol format introduced in August 2002.
MDLRXNWriter	Writes a reaction to a MDL rxn or SDF file.
MDLV2000Format
MDLV2000Reader	Reads content from MDL molfiles and SD files.
MDLV2000Writer	Writes MDL molfiles, which contains a single molecule (see [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]).
MDLV2000Writer.SPIN_MULTIPLICITY	Enumeration of all valid radical values.
MDLV3000Format
MDLV3000Reader	Class that implements the MDL mol V3000 format.
MDLV3000Writer	Ctab V3000 format output.
MDMolecule
MDMoleculeConvention	Implements a Convention for parsing an MDMolecule from CML.
MDMoleculeCustomizer	Customize persistence of MDMolecule by adding support for residues and charge groups.
MinimalPathIterator	Deprecated. use ShortestPaths
MinimumCycleBasis	Compute the minimum cycle basis (MCB) of a graph.
MM2AtomTypeMatcher	Deprecated. Incomplete and error prone - use at your own risk.
MM2BasedAtomTypePattern	Class stores hose code patterns to identify mm2 force field atom types.
MM2BasedParameterSetReader	AtomType list configurator that uses the ParameterSet originally defined in mm2.prm from tinker.
MMElementRule	This class validate if the occurrence of the IElements in the IMolecularFormula, for metabolites, are into a maximal limit according paper: .
MMElementRule.Database	A enumeration of the possible databases according the rules.
MMElementRule.RangeMass	A enumeration of the possible mass range according the rules.
Mmff	Facade to access Merck Molecular Force Field (MMFF) functions.
MMFF94AtomTypeMatcher	Deprecated. use the newer Mmff.assignAtomTypes()
MMFF94BasedAtomTypePattern	Deprecated. Mmff is faster more robust and fully validated
MMFF94BasedParameterSetReader	AtomType list configurator that uses the ParameterSet originally defined in mmff94.prm from moe.
MMFF94ParametersCall	Set the right atoms order to get the parameters.
MMFF94PartialCharges	The calculation of the MMFF94 partial charges.
MMODFormat	See here.
ModelBuilder3D	The main class to generate the 3D coordinates of a molecule ModelBuilder3D.
Mol2Format	See here.
Mol2Reader	Reads a molecule from an Mol2 file, such as written by Sybyl.
Mol2Writer	An output Writer that writes molecular data into the Tripos Mol2 format.
MolecularFormula	Class defining a molecular formula object.
MolecularFormula	Class defining a molecular formula object.
MolecularFormulaChecker	Validate a molecular formula given in IMolecularformula object.
MolecularFormulaGenerator	This class generates molecular formulas within given mass range and elemental composition.
MolecularFormulaManipulator	Class with convenience methods that provide methods to manipulate IMolecularFormula's.
MolecularFormulaRange	Class defining a expanded molecular formula object.
MolecularFormulaRangeManipulator	Class with convenience methods that provide methods to manipulate MolecularFormulaRange's.
MolecularFormulaSet	Class defining an set object of MolecularFormulas.
MolecularFormulaSet	Class defining an set object of MolecularFormulas.
MolecularFormulaSetManipulator	Class with convenience methods that provide methods to manipulate MolecularFormulaSet's.
MoleculeBuilder	Takes in parsed Tokens from NomParser and contains rules to convert those tokens to a Molecule.
MoleculeFactory	Deprecated. Old CDK class primarily for testing, for CDK Tests please use TestMoleculeFactory in cdk-data (testjar).
MoleculeFeaturesTool	Utility that helps determine which data features are present.
MoleculeFromSignatureBuilder	Builds a molecule from a signature.
MoleculeGraphs	Deprecated.
MoleculeHashGenerator	A hash function which generates a single 64-bit hash code for a molecule.
MoleculeSanityCheck	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
MoleculeSetManipulator
MoleculeSetRenderer	A general renderer for IChemModels, IReactions, and IAtomContainers.
MoleculeSignature	A molecule signature is a way to produce AtomSignatures and to get the canonical [Faulon, J. L., Collins, M. J., and Carr, R. D.. Journal of Chemical Information and Computer Sciences. 2004. 44] signature string for a molecule.
MoleculeSignatureLabellingAdaptor	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
MolHandler	Deprecated. A more recent version of SMSD is available at http://github.com/asad/smsd
MomentOfInertiaDescriptor	A descriptor that calculates the moment of inertia and radius of gyration.
Monomer	A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
Monomer	A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
MOPAC2002Format
MOPAC2007Format
MOPAC2009Format
MOPAC2012Format
MOPAC7Format
MOPAC7InputFormat
Mopac7Reader	Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule properties.
Mopac7Writer	Prepares input file for running MOPAC.
MOPAC93Format
MOPAC97Format
MorganNumbersTools	Compute the extended connectivity values (Morgan Numbers) [Morgan, H.L.. J.Chem.Doc.. 1965. 5].
MoSSOutputFormat
MoSSOutputReader	Reader for MoSS output files [Unknown BibTeXML type: BOR2002] which present the results of a substructure mining study.
MoveTo	A MoveTo path element moves the drawing 'pen' without making any lines or curves and is commonly used to start a path or make gaps in the path.
MPQCFormat	See here.
MurckoFragmenter	An implementation of the Murcko fragmenation method [Bemis, G.W. and Murcko, M.A. . Journal of Medicinal Chemistry. 1996. 39].
NeighborList	Creates a list of atoms neighboring each atom in the molecule.
NitrogenRule	This class validate if the rule of nitrogen is kept.
Node	Deprecated.
NodeBuilder	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
NomParser	Deprecated. The OPSIN (http://opsin.ch.cam.ac.uk/) tool offers a more comprehensive alternative to this parsers functionality.
NomParserConstants	Token literal values and constants.
NomParserTokenManager	Token Manager.
NonCHHeavyAtom	Deprecated.
Normalizer	Deprecated. The functionality provided by with class is better suited to SMIRKS
NoSuchAtomException	Exception that is thrown when an Atom is requested or required that does not exist in the relevant environment.
NoSuchAtomTypeException	Exception that may be thrown when an atom type is looked up or perceived but no such atom type was found.
NoSuchBondException	Exception that is thrown when a Bond is requested or required that does not exist in the relevant environment.
NumericalSurface	A class representing the solvent accessible surface area surface of a molecule.
NWChemFormat	See here.
Octahedral	Represents an octahedral configuration of an atom six neighbors.
OneElectronJob	Calculates the orbitals and orbital energies of electron systems without electron electron interactions
OptionIOSetting	An class for a reader setting which must be found in the list of possible settings.
Orbit	A list of atom indices, and the label of the orbit.
Orbitals	This class represents a set of orbitals
OrderQueryBond	Deprecated.
OrderQueryBond	Deprecated.
OrderQueryBondOrderOnly	Deprecated. Use new QueryBond(beg, end, ORDER, bord)
OvalElement	An oval element (should) have both a width and a height.
OverlapResolver	Deprecated. does not resolve overlaps correctly
OWLAtomTypeHandler	SAX Handler for the OWLAtomTypeReader.
OWLAtomTypeMappingHandler	SAX Handler for the OWLAtomTypeMappingReader.
OWLAtomTypeMappingReader	XML Reader for the OWLBasedAtomTypeConfigurator.
OWLAtomTypeReader	XML Reader for the OWLBasedAtomTypeConfigurator.
OWLBasedAtomTypeConfigurator	AtomType resource that reads the atom type configuration from an OWL file.
OWLFile	Dictionary with entries build from an OWL file.
OWLReact	Dictionary with entries build from an OWL React.
OxygenAtomCountDescriptor	Descriptor that returns the number of oxygens in the chemical formula.
ParameterReact	Class which defines the allowed parameters of a reaction.
ParseException	This exception is thrown when parse errors are encountered.
ParseException	This exception is thrown when parse errors are encountered.
PartialAtomicChargeColors	Class defining the color which with atoms are colored.
PartialFilledStructureMerger	Randomly generates a single, connected, correctly bonded structure from a number of fragments.
PartialPiChargeDescriptor	The calculation of pi partial charges in pi-bonded systems of an heavy atom was made by Saller-Gasteiger.
PartialSigmaChargeDescriptor	The calculation of sigma partial charges in sigma-bonded systems of an heavy atom was made by Marsilli-Gasteiger.
PartialTChargeMMFF94Descriptor	The calculation of total partial charges of an heavy atom is based on MMFF94 model.
PartialTChargePEOEDescriptor	The calculation of total partial charges of an heavy atom is based on Partial Equalization of Electronegativity method (PEOE-PEPE) from Gasteiger.
Partition	A partition of a set of integers, such as the discrete partition {{1}, {2}, {3}, {4}} or the unit partition {{1, 2, 3, 4}} or an intermediate like {{1, 2}, {3, 4}}.
PartitionRefinement	Factory for partition refiners.
PartitionRefinement.AtomRefinerBuilder
PartitionRefinement.BondRefinerBuilder
PathBuilder	Builder class for paths.
PathEdge	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
PathElement	A path element.
PathElement	A path composed of points.
PathGraph	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
PathTools	Tools class with methods for handling molecular graphs.
Pattern	A structural pattern for finding an exact matching in a target compound.
PCCompoundASNReader	Reads an object from ASN formated input for PubChem Compound entries.
PCCompoundXMLReader	Reads an object from ASN.1 XML formated input for PubChem Compound entries.
PCModelFormat	See here.
PCSubstanceXMLReader	Reads an object from ASN formated input for PubChem Compound entries.
PDBAtom	Represents the idea of an atom as used in PDB files.
PDBAtom	Represents the idea of an atom as used in PDB files.
PDBAtomCustomizer	ICMLCustomizer for the libio-cml Convertor to be able to export details for IPDBAtom's.
PDBConvention	Implements the PDB convention used by PDB2CML.
PDBFormat	See here.
PDBMLFormat	XML version of the PDB format.
PDBMonomer	Represents the idea of an monomer as used in PDB files.
PDBMonomer	Represents the idea of an monomer as used in PDB files.
PDBPolymer	An entry in the PDB database.
PDBPolymer	An entry in the PDB database.
PDBReader	Reads the contents of a PDBFile.
PDBStrand	An entry in the PDB database.
PDBStructure	Holder for secundary protein structure elements.
PDBStructure	Holder for secundary protein structure elements.
PDBWriter	Saves small molecules in a rudimentary PDB format.
PeriodicGroupNumberAtom	Deprecated.
PeriodicTable	Represents elements of the Periodic Table.
PeriodicTablePositionDescriptor	This class returns the period in the periodic table of an atom belonging to an atom container Parameters for this descriptor: Name Default Description no parameters
Permutation	A permutation with some associated methods to multiply, invert, and convert to cycle strings.
PermutationGroup	A permutation group with a Schreier-Sims representation.
PermutationGroup.Backtracker	An interface for use with the apply method, which runs through all the permutations in this group.
Permutor	General permutation generator, that uses orderly generation by ranking and unranking.
Permutor	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
PetitjeanNumberDescriptor	According to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph.
PetitjeanShapeIndexDescriptor	Evaluates the Petitjean shape indices, These original Petitjean number was described by Petitjean ([ Petitjean, M. . Journal of Chemical Information and Computer Science. 1992. 32]) and considered the molecular graph.
PharmacophoreAngleBond	Represents an angle relationship between three pharmacophore groups.
PharmacophoreAtom	A representation of a pharmacophore group.
PharmacophoreBond	Represents a distance relationship between two pharmacophore groups.
PharmacophoreMatcher	Identifies atoms whose 3D arrangement matches a specified pharmacophore query.
PharmacophoreQuery	Represents a colleciton of pharmacophore groups and constraints.
PharmacophoreQueryAngleBond	Represents a pharmacophore query angle constraint.
PharmacophoreQueryAtom	Represents a query pharmacophore group.
PharmacophoreQueryBond	Represents a pharmacophore query distance constraint.
PharmacophoreUtils	Provides some utility methods for pharmacophore handling.
PhysicalConstants	An class providing predefined properties of physical constants.
PiBondingMovementReaction	IReactionProcess which tries to reproduce the delocalization of electrons which are unsaturated bonds from conjugated rings.
PiContactDetectionDescriptor	This class checks if two atoms have pi-contact (this is true when there is one and the same conjugated pi-system which contains both atoms, or directly linked neighbours of the atoms).
PiElectronegativity	Calculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
PiElectronegativityDescriptor	Pi electronegativity is given by X = a + bq + c(q*q) Parameters for this descriptor: Name Default Description maxIterations 0 Number of maximum iterations
PMPConvention	Implementation of the PMPMol Covention for CML.
PMPFormat
PMPReader	Reads an frames from a PMP formated input.
Point
Point2dDifference	Difference between two boolean[]'s.
Point3dDifference	Difference between two boolean[]'s.
Polarizability	Calculation of the polarizability of a molecule by the method of Kang and Jhon and Gasteiger based on [Kang, Y.K. and Jhon, M.S.. Theoretica Chimica Acta. 1982. 61] and [Gasteiger, J. and Hutchings, M.G.. J. Amer. Chem. Soc.. 1984. 106] Limitations in parameterization of atoms: H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3, P, Osp3 and Osp2.
Polymer	Subclass of Molecule to store Polymer specific attributes that a Polymer has.
Polymer	Subclass of Molecule to store Polymer specific attributes that a Polymer has.
PostFilter	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
POVRayFormat	See here.
PQSChemFormat	See here.
Primes	Deprecated.
ProblemMarker	Tool to mark IChemObject's as having a problem.
ProductsBoxGenerator	Generate the symbols for radicals.
Projection	Stereochemistry projection types.
Projector	Tool to make projections from 3D to 2D.
PropertiesListener	Answers the questions by looking up the values in a Properties object.
ProteinBuilderTool	Class that facilitates building protein structures.
ProteinPocketFinder	The detection of pocket and cavities in a bioPolymer is done similar to the program LIGSITE [Hendlich, M. et. al.. Journal of Molecular Graphics and Modelling. 1997. 15].
ProtonAffinityHOSEDescriptor	This class returns the proton affinity of an atom containing.
ProtonTotalPartialChargeDescriptor	The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE).
PseudoAtom	Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
PseudoAtom	Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
PubChemASNFormat
PubChemCompoundsXMLFormat
PubChemCompoundXMLFormat
PubchemFingerprinter	Generates a Pubchem fingerprint for a molecule.
PubChemFormat	See here.
PubChemSubstancesASNFormat
PubChemSubstancesXMLFormat
PubChemSubstanceXMLFormat
PubChemXMLHelper	Helper class to parse PubChem XML documents.
QChemFormat	See here.
QSARConvention	This is an implementation for the CDK convention.
QSARCustomizer	Customizer for the libio-cml Convertor to be able to export details for QSAR descriptors calculated for Molecules.
QuadTo	Make a quadratic curve in the path.
Quaternion	This class handles quaternions.
QueryAtom
QueryAtomContainer
QueryAtomContainerCreator	Utilities for creating queries from 'real' molecules.
QueryBond	Implements the concept of a "query bond" between two or more atoms.
QueryChemObject
QueryCompiler	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
QueryProcessor	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Queue	Deprecated. internal implemenation detail from SSSRFinder, do not use
RadicalChargeSiteInitiationHReaction	IReactionProcess which participate mass spectrum process.
RadicalChargeSiteInitiationReaction	IReactionProcess which participate mass spectrum process.
RadicalGenerator	Generate the symbols for radicals.
RadicalSiteHrAlphaReaction	This reaction could be represented as [A*]-(C)_2-C3[H] => A([H])-(C_2)-[C3*].
RadicalSiteHrBetaReaction	This reaction could be represented as [A*]-(C)_3-C4[H] => A([H])-(C_3)-[C4*].
RadicalSiteHrDeltaReaction	This reaction could be represented as [A*]-(C)_4-C5[H] => A([H])-(C_4)-[C5*].
RadicalSiteHrGammaReaction	This reaction could be represented as [A*]-C1-C2-C3[H] => A([H])-C1-C2-[C3*].
RadicalSiteInitiationHReaction	IReactionProcess which participate mass spectrum process.
RadicalSiteInitiationReaction	IReactionProcess which participate mass spectrum process.
RadicalSiteIonizationMechanism	This mechanism extracts an atom because of the stabilization of a radical.
RadicalSiteRearrangementMechanism	This mechanism displaces an Atom or substructure (R) from one position to an other.
RadicalSiteRrAlphaReaction	This reaction could be represented as [A*]-(C)_2-C3[R] => A([RH])-(C_2)-[C3*].
RadicalSiteRrBetaReaction	This reaction could be represented as [A*]-(C)_3-C4[R] => A([R])-(C_3)-[C4*].
RadicalSiteRrDeltaReaction	This reaction could be represented as [A*]-(C)_5-C6[R] => A([R])-(C_5)-[C6*].
RadicalSiteRrGammaReaction	This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*].
RandomAccessReader	Random access to text files of compounds.
RandomAccessSDFReader	Random access of SDF file.
RandomGenerator	RandomGenerator is a generator of constitutional isomers.
RandomNumbersTool	Class supplying useful methods to generate random numbers.
RasmolColors	Atom coloring following RasMol/Chime Color scheme http://www.umass.edu/microbio/rasmol/rascolor.htm.
RawCopyFormat	See here.
RDBERule	Ring Double Bond Equivalents (RDBE) or Double Bond Equivalents (DBE) are calculated from valence values of elements contained in a formula and should tell the number of bonds - or rings.
RDFCalculator	Calculator of radial distribution functions.
RDFProtonDescriptor_G3R	This class calculates G3R proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_GDR	This class calculates GDR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_GHR	This class calculates GHR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_GHR_topol	This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_GSR	This class calculates GDR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
ReactantsBoxGenerator	Generate the symbols for radicals.
Reaction	Represents the idea of a chemical reaction.
Reaction	Represents the idea of a chemical reaction.
ReactionArrowGenerator	Generate the arrow for a reaction.
ReactionBoxGenerator	Generate the symbols for radicals.
ReactionChain	Classes that extends the definition of reaction to a chain reaction.
ReactionEngine	The base class for all chemical reactions objects in this cdk.
ReactionManipulator	Provides a variety of methods to manipulate and convert from/to IReaction.
ReactionPlusGenerator	Generate the arrow for a reaction.
ReactionRenderer	A general renderer for IChemModels, IReactions, and IAtomContainers.
ReactionRole
ReactionRoleQueryAtom	Deprecated.
ReactionSceneGenerator	Generator for general reaction scene components.
ReactionSceneGenerator.ArrowHeadWidth	Double which indicates how wide the arrow head is in screen pixels.
ReactionSceneGenerator.ShowReactionBoxes	Boolean that indicates if boxes are drawn around the reaction.
ReactionScheme	Classes that extends the definition of reaction to a scheme.
ReactionScheme	Classes that extends the definition of reaction to a scheme.
ReactionSchemeManipulator
ReactionSet	A set of reactions, for example those taking part in a reaction.
ReactionSet	A set of reactions, for example those taking part in a reaction.
ReactionSetManipulator
ReactionSetRenderer	A general renderer for IChemModels, IReactions, and IAtomContainers.
ReactionSpecification	Class that is used to distribute reactions specifications.
ReaderEvent	Signals that something has happened in a file reader.
ReaderFactory	A factory for creating ChemObjectReaders.
RearrangementAnionReaction	IReactionProcess which participate in movement resonance.
RearrangementCationReaction	IReactionProcess which participate in movement resonance.
RearrangementChargeMechanism	This mechanism displaces the charge(radical, charge + or charge -) because of a double bond which is associated.
RearrangementLonePairReaction	IReactionProcess which participate in movement resonance.
RearrangementRadicalReaction	IReactionProcess which participate in movement resonance.
RebondTool	Provides tools to rebond a molecule from 3D coordinates only.
RectangleElement	A rectangle, with width and height.
RecursiveSmartsAtom	Deprecated.
Refinable	Implementors are graph-like objects that are refinable by the equitable and discrete partition refiners.
RelevantCycles	Compute the relevant cycles (CR) of a graph.
RemovingSEofBMechanism	This mechanism extracts a single electron from a bonding orbital which located in an bond.
RemovingSEofNBMechanism	This mechanism extracts a single electron from a non-bonding orbital which located in a ILonePair container.
RendererModel	Model for IRenderer that contains settings for drawing objects.
RendererModel.ColorHash	The color hash is used to color substructures.
RendererModel.ExternalHighlightColor	The color used to highlight external selections.
RendererModel.MarkedOutput	If format supports it (e.g.
RendererModel.Padding	Padding between molecules in a grid or row.
RendererModel.SelectionColor	Color of a selection.
RendererModel.TitleColor	Color of title text.
RendererModel.TitleFontScale	Size of title font relative compared to atom symbols
Residue	A residue is a named, numbered collection of atoms in an MDMolecule.
RGraph	This class implements the Resolution Graph (RGraph).
RGroup	Represents a single substitute structure in an RGroupList.
RGroupList	Represents a list of Rgroup substitutes to be associated with some RGroupQuery.
RGroupQuery	Represents information contained in a Symyx RGfile (R-group query file). It contains a root structure (the scaffold if you like), a map with R-group definitions (each of which can contain multiple substitutes) and a map with attachment points.
RGroupQueryFormat	Format for Symyx RGfiles (Rgroup query files).
RGroupQueryReader	A reader for Symyx' Rgroup files (RGFiles).
RGroupQueryWriter	A writer for Symyx' Rgroup files (RGFiles). An RGfile describes a single molecular query with Rgroups.
Ring	Class representing a ring structure in a molecule.
Ring	Class representing a ring structure in a molecule.
RingBond	Deprecated.
RingElement	A ring is just a circle - in other words, an oval whose width and height are the same.
RingFilter	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
RingFinder	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
RingGenerator	Generates just the aromatic indicators for rings : circles, or light-gray inner bonds, depending on the value of CDKStyleAromaticity.
RingGenerator.CDKStyleAromaticity	Depicts aromaticity of rings in the original CDK style.
RingGenerator.MaxDrawableAromaticRing	The maximum ring size for which an aromatic ring should be drawn.
RingGenerator.RingProportion	The proportion of a ring bounds to use to draw the ring.
RingGenerator.ShowAromaticity	Determines whether rings should be drawn with a circle if they are aromatic.
RingIdentifierAtom	Deprecated.
RingManipulator
RingMembershipAtom	Deprecated.
RingPartitioner	Partitions a RingSet into RingSets of connected rings.
RingPlacer	Class providing methods for generating coordinates for ring atoms.
RingSearch	Efficiently search for atoms that are members of a ring.
RingSet	Maintains a set of Ring objects.
RingSet	Maintains a set of Ring objects.
RingSetManipulator
RingSizeComparator
RMap	An RMap implements the association between an edge (bond) in G1 and an edge (bond) in G2, G1 and G2 being the compared graphs in a RGraph context.
RNode	Node of the resolution graph (RGraph) An RNode represents an association between two edges of the source graphs G1 and G2 that are compared.
RotatableBondsCountDescriptor	The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial
RssWriter	Generates an RSS feed.
RuleOfFiveDescriptor	This Class contains a method that returns the number failures of the Lipinski's Rule Of 5.
SaturationChecker	Provides methods for checking whether an atoms valences are saturated with respect to a particular atom type.
SDFFormat	See here.
SDFWriter	Writes MDL SD files ([Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]).
SelectionVisibility	Extended existing symbol visibility options to account for selection of atoms in the standard generator.
SetReactionCenter	Class extension of ParameterReact class which defines if a reaction is set already the reaction center in the reactants.
SettingManager<T extends ISetting>	Provides dynamic management of settings.
Sgroup	Generic CTab Sgroup (substructure group) that stores all other types of group.
SgroupBracket	Representation of an Sgroup bracket.
SgroupKey	Keys for indexing common Sgroup attributes.
SgroupManipulator	Utilities related to Ctab Sgroups.
SgroupType	Enumeration of Ctab Sgroup types.
SharingAnionReaction	IReactionProcess which participate in movement resonance.
SharingChargeDBReaction	IReactionProcess which participate in movement resonance.
SharingChargeSBReaction	IReactionProcess which participate in movement resonance.
SharingElectronMechanism	This mechanism displaces the charge (lonePair) because of deficiency of charge.
SharingLonePairReaction	IReactionProcess which participate in movement resonance.
ShelXFormat	See here.
ShelXReader	A reader for ShelX output (RES) files.
ShelXWriter	Serializes a MoleculeSet or a Molecule object to ShelX code.
ShortestPathFingerprinter	Generates a fingerprint for a given IAtomContainer.
ShortestPaths	Find and reconstruct the shortest paths from a given start atom to any other connected atom.
ShortestPathWalker
SigmaElectronegativityDescriptor	Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity.
SignatureFingerprinter	An implementation of a AtomSignature-based fingerprint.
SignatureQuotientGraph	A signature quotient graph has a vertex for every signature symmetry class and an edge for each bond in the molecule between atoms in their class.
SignatureReactionCanoniser	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
SilentChemObjectBuilder	A factory class to provide implementation independent ICDKObjects.
SimpleAtomCanonicalizer	This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
SimpleAtomComparator	This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
SimpleBasisSet	This class will generate a simple base set for a atom container.
SimpleCharStream	An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream	An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCycle	Deprecated. internal implemenation detail from SSSRFinder, do not use
SimpleCycleBasis	Deprecated. internal implemenation detail from SSSRFinder, do not use
SingleElectron	A Single Electron is an orbital which is occupied by only one electron.
SingleElectron	A Single Electron is an orbital which is occupied by only one electron.
SingleElectronDiff	Compares two ISingleElectron classes.
SingleMapping	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
SingleMappingHandler	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
SingleStructureRandomGenerator	Randomly generates a single, connected, correctly bonded structure for a given molecular formula.
SmallestRingAtom	Deprecated.
SmallRingDescriptor	Small ring descriptors: these are based on enumeration of all the small rings (sizes 3 to 9) in a molecule, which can be obtained quickly and deterministically.
Smarts	Parse and generate the SMARTS query language.
Smarts2MQLVisitor	Deprecated.
SMARTSAtom	Deprecated.
SMARTSBond	Deprecated.
SmartsDumpVisitor	Deprecated.
SMARTSFormat	See here.
SmartsFragmentExtractor	Utility class to create SMARTS that match part (substructure) of a molecule.
SmartsMatchers	Deprecated.
SMARTSParser	This parser implements a nearly complete subset of the SMARTS syntax as defined on the Daylight website.
SMARTSParserConstants	Token literal values and constants.
SMARTSParserDefaultVisitor
SMARTSParserTokenManager	Token Manager.
SMARTSParserTreeConstants
SMARTSParserVisitor
SmartsPattern	A Pattern for matching a single SMARTS query against multiple target compounds.
SmartsPattern	Deprecated.
SMARTSQueryTool	Deprecated. use SmartsPattern
SmartsQueryVisitor	Deprecated.
SmartsResult	The result of parsing a SMARTS.
SmartsStereoMatch	Deprecated. use QueryStereoFilter
SmiFlavor	Flags for customising SMILES generation.
SMILESFIXFormat
SMILESFormat	See here.
SmilesGenerator	SMILES [Weininger, David. Journal of Chemical Information and Computer Sciences. 1988. 28, Weininger, David et. al.. Journal of Chemical Information and Computer Sciences. 1989. 29] provides a compact representation of chemical structures and reactions.
SmilesParser	Read molecules and reactions from a SMILES [?Authors?, SMILES Tutorial] string.
SmilesReactionCanoniser	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
SMILESReader	This Reader reads files which has one SMILES string on each line, where the format is given as below:
SmilesValencyChecker	Small customization of ValencyHybridChecker suggested by Todd Martin specially tuned for SMILES parsing.
SMILESWriter	Writes the SMILES strings to a plain text file.
SMSDNormalizer	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
SpanningTree	Spanning tree of a molecule.
SpartanFormat
SpiroAtomCountDescriptor	Returns the number of spiro atoms.
SquarePlanar	Describes square planar configuration.
SSSRFinder	Deprecated. Use the Cycles API Cycles.sssr(IAtomContainer)
StabilizationCharges	The stabilization of the positive and the negative charge obtained (e.g in the polar breaking of a bond) is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges.
StabilizationPlusChargeDescriptor	The stabilization of the positive charge (e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges.
StandardGenerator	The standard generator creates IRenderingElements for the atoms and bonds of a structure diagram.
StandardGenerator.AnnotationColor	The color of the atom numbers.
StandardGenerator.AnnotationDistance	The distance of atom numbers from their parent atom as a percentage of bond length, default value is 0.25 (25%)
StandardGenerator.AnnotationFontScale	Annotation font size relative to element symbols, default = 0.4 (40%).
StandardGenerator.AtomColor	Defines the color of unselected atoms (and bonds).
StandardGenerator.BondSeparation	Defines the ratio of the separation between lines in double bonds as a percentage of length (BasicSceneGenerator.BondLength).
StandardGenerator.DashSection	The number of sections to render in a dashed 'unknown' bond, default = 4;
StandardGenerator.DelocalisedDonutsBondDisplay	Render small delocalised rings as bonds/life buoys? This can sometimes be misleading for fused rings but is commonly used.
StandardGenerator.DeuteriumSymbol	Display deuterium [2H] as 'D'.
StandardGenerator.FancyBoldWedges	Modify bold wedges to be flush with adjacent bonds, default = true.
StandardGenerator.FancyHashedWedges	Modify hashed wedges to be flush when there is a single adjacent bond, default = true.
StandardGenerator.ForceDelocalisedBondDisplay	Indicate delocalised/aromatic bonds should always be rendered, even when there is a valid Kekule structure.
StandardGenerator.HashSpacing	The preferred spacing between lines in hashed bonds.
StandardGenerator.Highlighting	Parameter defines the style of highlight used to emphasis atoms and bonds.
StandardGenerator.HighlightStyle	Enumeration of highlight style.
StandardGenerator.OmitMajorIsotopes	Whether Major Isotopes e.g.
StandardGenerator.OuterGlowWidth	The width of outer glow as a percentage of stroke width.
StandardGenerator.PseudoFontStyle	The default font style for pseudo-atoms, is Bold and Italic.
StandardGenerator.SgroupBracketDepth	How "deep" are brackets drawn.
StandardGenerator.SgroupFontScale	Scale Sgroup annotations relative to the normal font size (atom symbol).
StandardGenerator.StrokeRatio	Defines the ratio of the stroke to the width of the stroke of the font used to depict atom symbols.
StandardGenerator.SymbolMarginRatio	Defines the margin between an atom symbol and a connected bond based on the stroke width.
StandardGenerator.Visibility	Defines which atoms have their symbol displayed.
StandardGenerator.WaveSpacing	The spacing of waves (semi circles) drawn in wavy bonds with.
StandardGenerator.WedgeRatio	Ratio of the wide end of wedge compared to the narrow end (stroke width).
StandardSubstructureSets	Default sets of atom containers aimed for use with the substructure.
StereoBond	Deprecated.
StereoBond.Direction
Stereocenters	Find atoms which can support stereo chemistry based on the connectivity.
Stereocenters.Stereocenter	Defines the type of a stereocenter.
Stereocenters.Type
StereoElementFactory	Create stereo elements for a structure with 2D and 3D coordinates.
StereoEncoder	An encoder for stereo chemistry.
StereoEncoderFactory	Describes a factory for stereo elements.
StereoTool	Methods to determine or check the stereo class of a set of atoms.
StereoTool.SquarePlanarShape	The shape that four atoms take in a plane.
StereoTool.StereoClass	Currently unused, but intended for the StereoTool to indicate what it 'means' by an assignment of some atoms to a class.
StereoTool.TetrahedralSign	The handedness of a tetrahedron, in terms of the point-plane distance of three of the corners, compared to the fourth.
Strand	A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
Strand	A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
StringDifference	IDifference between two String.
StringIOSetting	An class for a reader setting which must be of type String.
StructGenAtomTypeGuesser	AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
StructGenMatcher	AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
StructureDiagramGenerator	Generates 2D coordinates for a molecule.
StructureResonanceGenerator	This class try to generate resonance structure for a determinate molecule.
Substance	An implementation of the ISubstance interface.
Substance	An implementation of the ISubstance interface.
SubstructureFingerprinter	IFingerprinter that gives a bit set which has a size equal to the number of substructures it was constructed from.
SVGFormat
SwingEventRelay
SwingGUIListener	Allows processing of IOSetting quesions which are passed to the user by using Swing dialogs.
SwingMouseEventRelay
SwissArmyKnife	Deprecated.
SybylAtomTypeMatcher	Atom Type matcher for Sybyl atom types.
SybylDescriptorFormat	See here.
SymbolAndChargeQueryAtom	Deprecated.
SymbolChargeIDQueryAtom
SymbolQueryAtom	Deprecated.
SymbolSetQueryAtom	Deprecated. Use new Expr(Element, 6).and(new Expr(Element, 8)) etc
SymbolVisibility	Predicate that defines whether an atom symbol is displayed in a structure diagram.
SystemOutLoggingTool	Deprecated. should not be used directly
TaeAminoAcidDescriptor	An implementation of the TAE descriptors for amino acids.
Tanimoto	Calculates the Tanimoto coefficient for a given pair of two fingerprint bitsets or real valued feature vectors.
TargetProcessor	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
TargetProperties	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
TautomerizationMechanism	This mechanism produces the tautomerization chemical reaction between two tautomers.
TautomerizationReaction	IReactionProcess which produces a tautomerization chemical reaction.
TemplateExtractor	Helper class that help setup a template library of CDK's Builder3D.
TemplateHandler	Helper class for Structure Diagram Generation.
TemplateHandler3D	Helper class for ModelBuilder3D.
Tessellate	Performs a tessellation of the unit sphere.
TestMoleculeFactory	This class contains methods for generating simple organic molecules and is copy of MoleculeFactory for use in tests.
TetrahedralChirality	Stereochemistry specification for tetravalent atoms.
TetrahedralElementEncoderFactory	Defines a stereo encoder factory for the hash code.
TextElement	Text element as used in the chemical drawing.
TextGroupElement	A group of text elements, particularly the element symbol (eg: "C") surrounded by other annotations such as mass number, charge, etc.
TextGroupElement.Position	Compass-point positions for text element annotation children.
TextGUIListener	Allows processing of IOSetting quesions which are passed to the user by using the System.out and System.in by default.
TimeManager	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
TimeOut	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
TinkerMM2Format	See here.
TinkerXYZFormat	See here.
Token	Describes the input token stream.
Token	Describes the input token stream.
TokenMgrError	Token Manager Error.
TokenMgrError	Token Manager Error.
ToleranceRangeRule	This class validate if the mass from an IMolecularFormula is between the tolerance range give a experimental mass.
TopologicalMatrix	Calculator for a topological matrix representation of this AtomContainer.
TotalConnectionAtom	Deprecated.
TotalHCountAtom	Deprecated.
TotalRingConnectionAtom	Deprecated.
TotalValencyAtom	Deprecated.
TPSADescriptor	Calculation of topological polar surface area based on fragment contributions (TPSA) [Ertl, P. et. al.. J. Med. Chem.. 2000. 43].
Triangle	Representation of a triangle in 3D.
TrigonalBipyramidal	Describes a trigonal-bipyramidal configuration.
TripletShortCycles	Compute the shortest cycles through each vertex triple.
TurboMoleFormat	See here.
TXTBasedAtomTypeConfigurator	AtomType list configurator that uses the AtomTypes originally defined in Jmol v5.
Type	The type of the path elements.
Ullmann	A structure pattern which utilises the Ullmann algorithm [Ullmann J R. Journal of the Association for Computing Machinery. 1976. 23].
UndoAdapter	An undo adapter for updating the state of the undo components according to the new state of the undo history list.
UniChemXYZFormat
UniColor	Defines an atom color that draws as a single uniform color.
UniversalIsomorphismTester	This class implements a multipurpose structure comparison tool.
UnsupportedChemObjectException
VABCDescriptor	Volume descriptor using the method implemented in the VABCVolume class.
VABCVolume	Calculates the Van der Waals volume using the method proposed in [Zhao, Yuan H. et. al.. The Journal of Organic Chemistry. 2003. 68].
VAdjMaDescriptor	Vertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds.
ValidationReport	A report on validation of chemical semantics.
ValidationTest	Error found during sematical validation of a IChemObject.
ValidatorEngine	Engine that performs the validation by traversing the IChemObject hierarchy.
VASPFormat
VASPReader	Read output files generated with the VASP software.
VdWRadiusDescriptor	This class return the VdW radius of a given atom.
Vector	This class handles vectors.
VentoFoggia	A structure pattern which utilises the Vento-Foggia (VF) algorithm [Cordella Luigi P et. al.. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. 2004. 26].
VFAtomMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
VFBondMatcher	Deprecated. This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details.
VFlibMCSHandler	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFlibSubStructureHandler	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFlibTurboHandler	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFMapper	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFMCSMapper	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFQueryBuilder	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFState	Deprecated. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Vibration	A molecular vibration composed of a set of atom vectors.
VicinitySampler	The VicinitySampler is a generator of constitutional isomers.
ViewmolFormat	See here.
VisitedAtoms	Helper class for the CIPTool to keep track of which atoms have already been visited.
WedgeLineElement	A 'wedge' is a triangle aligned along a bond that indicates stereochemistry.
WedgeLineElement.Direction	'toFirst' means that the wedge gets thicker in the direction of the first point in the line.
WedgeLineElement.TYPE	If the bond is dashed ,wedged, or "up_or_down", i.e., not defined.
WeightDescriptor	IDescriptor based on the weight of atoms of a certain element type.
WeightedPathDescriptor	Evaluates the weighted path descriptors.
WHIMDescriptor	Holistic descriptors described by Todeschini et al [Todeschini, R. and Gramatica, P.. Persepectives in Drug Discovery and Design. 1998. null].
WienerNumbersDescriptor	This descriptor calculates the Wiener numbers.
WriterFactory	Helper tool to create IChemObjectWriters.
XEDFormat
XLogPDescriptor	Prediction of logP based on the atom-type method called XLogP.
XMLIsotopeFactory	Used to store and return data of a particular isotope.
XYZFormat
XYZReader	Reads an object from XYZ formated input.
XYZWriter
YasaraFormat	See here.
ZagrebIndexDescriptor	Zagreb index: the sum of the squares of atom degree over all heavy atoms i.
ZindoFormat	See here.
ZMatrixFormat
ZMatrixReader	It reads Z matrices like in Gaussian input files.
ZMatrixTools	A set of static utility classes for dealing with Z matrices.