Search Java Classes and Packages
#Org.openscience.cdk Classes and Interfaces - 1234 results found.
| Name | Description | Type | Package | Framework |
| ABINITFormat | Class | org.openscience.cdk.io.formats | CDK | |
| AbstractAtomicDescriptor | Abstract atomic descriptor class with helper functions for descriptors that require the whole molecule to calculate the descriptor values, | Class | org.openscience.cdk.qsar | CDK |
| AbstractAWTDrawVisitor | Partial implementation of the IDrawVisitor interface for the AWT widget toolkit, allowing molecules to be rendered with toolkits based on | Class | org.openscience.cdk.renderer.visitor | CDK |
| AbstractBondDescriptor | Abstract bond descriptor class with helper functions for descriptors that require the whole molecule to calculate the descriptor values, | Class | org.openscience.cdk.qsar | CDK |
| AbstractDifference | Class | org.openscience.cdk.tools.diff.tree | CDK | |
| AbstractDifferenceList | Diff between two IChemObjects. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| AbstractGeneratorParameter | Abstract class to provide the base functionality for IGeneratorParameter implementations. | Class | org.openscience.cdk.renderer.generators.parameter | CDK |
| AbstractMCS | Interface for all MCS algorithms. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| AbstractMCSAlgorithm | Interface for MCS search algorithm. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| AbstractReactionLabeller | Class | org.openscience.cdk.smsd.labelling | CDK | |
| AbstractRenderer | 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 | Class | org.openscience.cdk.renderer | CDK |
| AbstractSelection | An abstract selection of IChemObjects. | Class | org.openscience.cdk.renderer.selection | CDK |
| AbstractSubGraph | Interface class for reporting only substructure searches. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| AbstractValidator | Abstract validator that does nothing but provide all the methods that the ValidatorInterface requires. | Class | org.openscience.cdk.validate | CDK |
| Aces2Format | Class | org.openscience.cdk.io.formats | CDK | |
| AcidicGroupCountDescriptor | Returns the number of acidic groups. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AdductFormula | Class defining an adduct object in a MolecularFormula. | Class | org.openscience.cdk.formula | CDK |
| AdductFormula | Class defining an adduct object in a MolecularFormula. | Class | org.openscience.cdk.silent | CDK |
| AdductionLPMechanism | This mechanism adduct together two fragments. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| AdductionPBMechanism | This mechanism adduct together two fragments due to a double bond. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| AdductionProtonLPReaction | IReactionProcess which produces a protonation. | Class | org.openscience.cdk.reaction.type | CDK |
| AdductionProtonPBReaction | IReactionProcess which produces a protonation to double bond. | Class | org.openscience.cdk.reaction.type | CDK |
| AdductionSodiumLPReaction | IReactionProcess which produces an adduction of the Sodium. | Class | org.openscience.cdk.reaction.type | CDK |
| ADFFormat | Class | org.openscience.cdk.io.formats | CDK | |
| AdjacencyMatrix | Calculator for a adjacency matrix representation of this AtomContainer. | Class | org.openscience.cdk.graph.matrix | CDK |
| AlchemyFormat | Class | org.openscience.cdk.io.formats | CDK | |
| Algorithm | This class represents various algorithm type supported by SMSD. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| AliphaticAtom | This matcher any non-aromatic atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| AliphaticSymbolAtom | This smarts atom matches aliphatic atom with element symbol specifiedSee Also:Serialized FormKeywords:SMARTS | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| AllRingsFinder | Finds the Set of all Rings. | Class | org.openscience.cdk.ringsearch | CDK |
| AllRingsFinderMod | Finds the Set of all Rings. | Class | org.openscience.cdk.ringsearch | CDK |
| ALOGPDescriptor | This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity . | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AminoAcid | A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom. | Class | org.openscience.cdk | CDK |
| AminoAcid | A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom. | Class | org.openscience.cdk.silent | CDK |
| AminoAcidCountDescriptor | Class that returns the number of each amino acid in an atom container. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AminoAcidManipulator | Class with convenience methods that provide methods to manipulateAuthor:Egon WillighagenCreated on:2005-08-19 | Class | org.openscience.cdk.tools.manipulator | CDK |
| AminoAcids | Tool that provides templates for the (natural) amino acids. | Class | org.openscience.cdk.templates | CDK |
| AngularMomentum | This class is used to calculate angular momentum states. | Class | org.openscience.cdk.math.qm | CDK |
| AnyAtom | This matcher any Atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| AnyOrderQueryBond | This matches a bond of any orderSee Also:Serialized FormKeywords:SMARTS | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| APolDescriptor | Sum of the atomic polarizabilities (including implicit hydrogens). | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AromaticAtom | This matcher any aromatic atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| AromaticAtomsCountDescriptor | Class that returns the number of aromatic atoms in an atom container. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AromaticBondsCountDescriptor | This Class contains a method that returns the number of aromatic atoms in an AtomContainer. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AromaticityCalculator | Class | org.openscience.cdk.aromaticity | CDK | |
| AromaticOrSingleQueryBond | This matches an aromatic or a single bond, used when no bond is specified between an atomSee Also:Serialized FormKeywords:SMARTS | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| AromaticQueryBond | This matches an aromatic bondSee Also:Serialized FormKeywords:SMARTS | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| AromaticSymbolAtom | This class matches aromatic atom with element symbol specified. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| ArrowElement | IRenderingElement for linear arrows. | Class | org.openscience.cdk.renderer.elements | CDK |
| Association | Base class for storing interactions like hydrogen bonds and ionic interactions. | Class | org.openscience.cdk | CDK |
| ASTAliphatic | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTAnyAtom | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTAromatic | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTAtom | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTAtomicMass | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTAtomicNumber | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTCharge | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTChirality | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTElement | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTExplicitAtom | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTExplicitConnectivity | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTExplicitHighAndBond | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTExplicitHighAndExpression | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTGroup | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTHybrdizationNumber | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTImplicitHCount | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTImplicitHighAndBond | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTImplicitHighAndExpression | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTLowAndBond | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTLowAndExpression | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTNonCHHeavyAtom | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTNotBond | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTNotExpression | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTOrBond | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTOrExpression | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTPeriodicGroupNumber | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTPrimitiveAtomExpression | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTReaction | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTRecursiveSmartsExpression | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTRingConnectivity | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTRingIdentifier | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTRingMembership | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTSimpleBond | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTSmallestRingSize | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTSmarts | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTStart | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTTotalConnectivity | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTTotalHCount | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ASTValence | An AST node. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| Atom | Represents the idea of an chemical atom. | Class | org.openscience.cdk | CDK |
| Atom | Represents the idea of an chemical atom. | Class | org.openscience.cdk.silent | CDK |
| AtomContainer | Base class for all chemical objects that maintain a list of Atoms and ElectronContainers. | Class | org.openscience.cdk | CDK |
| AtomContainer | Base class for all chemical objects that maintain a list of Atoms and ElectronContainers. | Class | org.openscience.cdk.silent | CDK |
| AtomContainerAtomPermutor | This class iterates through all possible permutations of the atom order in a given atom container. | Class | org.openscience.cdk.graph | CDK |
| AtomContainerAtomPermutor | Class | org.openscience.cdk.smsd.labelling | CDK | |
| AtomContainerBondPermutor | This class allows to iterate trough the set of all possible permutations of the bond order in a given atom container. | Class | org.openscience.cdk.graph | CDK |
| AtomContainerBoundsGenerator | IGenerator that draws a rectangular around the IAtomContainer. | Class | org.openscience.cdk.renderer.generators | CDK |
| AtomContainerComparator | Compares two IAtomContainers for order with the following criteria with decreasing priority: Compare molecular weight (heavy atoms only) | Class | org.openscience.cdk.tools.manipulator | CDK |
| AtomContainerComparatorBy2DCenter | Compares two IAtomContainers based on their 2D position. | Class | org.openscience.cdk.tools.manipulator | CDK |
| AtomContainerDiff | Compares two IAtomContainer classes. | Class | org.openscience.cdk.tools.diff | CDK |
| AtomContainerManipulator | Class with convenience methods that provide methods to manipulate AtomContainer's. | Class | org.openscience.cdk.tools.manipulator | CDK |
| AtomContainerPermutor | The permutation code here is based on a pseudo code example on a tutorial site created and maintained by Phillip P. | Class | org.openscience.cdk.graph | CDK |
| AtomContainerPrinter | Class | org.openscience.cdk.smsd.labelling | CDK | |
| AtomContainerRenderer | A general renderer for IAtomContainers. | Class | org.openscience.cdk.renderer | CDK |
| AtomContainerSet | A set of AtomContainers. | Class | org.openscience.cdk | CDK |
| AtomContainerSet | A set of AtomContainers. | Class | org.openscience.cdk.silent | CDK |
| AtomContainerSetManipulator | Class | org.openscience.cdk.tools.manipulator | CDK | |
| AtomCountDescriptor | IDescriptor based on the number of atoms of a certain element type. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AtomDegreeDescriptor | This class returns the number of not-Hs substituents of an atom, also defined as "atom degree". | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| AtomDiff | Compares two IAtom classes. | Class | org.openscience.cdk.tools.diff | CDK |
| AtomHybridizationDescriptor | This class returns the hybridization of an atom. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| AtomHybridizationVSEPRDescriptor | This class returns the hybridization of an atom. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| AtomicNumberAtom | This matches an atom using the atomic number. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| AtomicNumberDifferenceDescriptor | Describes the imbalance in atomic number of the IBond. | Class | org.openscience.cdk.qsar.descriptors.bond | CDK |
| AtomicProperties | Provides atomic property values for descriptor calculations. | Class | org.openscience.cdk.tools | CDK |
| AtomMappingTools | Class | org.openscience.cdk.isomorphism | CDK | |
| AtomMassGenerator | IGenerator that can render mass number information of atoms. | Class | org.openscience.cdk.renderer.generators | CDK |
| AtomMassSymbolElement | Rendering element that shows the IAtom mass number information. | Class | org.openscience.cdk.renderer.elements | CDK |
| AtomMatcher | Interface for the AtomMatcher (atoms) in graph. | Interface | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| AtomNumberGenerator | Class | org.openscience.cdk.renderer.generators | CDK | |
| AtomNumberGenerator .AtomColorer | The color scheme by which to color the atom numbers, if the AtomNumberGenerator. | Class | org.openscience.cdk.renderer.generators | CDK |
| AtomNumberGenerator .AtomNumberTextColor | Color to draw the atom numbers with. | Class | org.openscience.cdk.renderer.generators | CDK |
| AtomNumberGenerator .ColorByType | Boolean to indicate of the AtomNumberGenerator. | Class | org.openscience.cdk.renderer.generators | CDK |
| AtomNumberGenerator .Offset | Class | org.openscience.cdk.renderer.generators | CDK | |
| AtomNumberGenerator .WillDrawAtomNumbers | Boolean parameter indicating if atom numbers should be drawn, allowing this feature to be disabled temporarily. | Class | org.openscience.cdk.renderer.generators | CDK |
| AtomParity | Represents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms. | Class | org.openscience.cdk | CDK |
| AtomParity | Represents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms. | Class | org.openscience.cdk.silent | CDK |
| AtomPlacer | Methods for generating coordinates for atoms in various situations. | Class | org.openscience.cdk.layout | CDK |
| AtomPlacer3D | Place aliphatic chains with Z matrix method. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| AtomSignature | The signature for a molecule rooted at a particular A signature is a description of the connectivity of a molecule, in the form | Class | org.openscience.cdk.signature | CDK |
| AtomSymbolElement | A text element with added information. | Class | org.openscience.cdk.renderer.elements | CDK |
| AtomTetrahedralLigandPlacer3D | A set of static utility classes for geometric calculations on Atoms. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| AtomTools | A set of static utility classes for geometric calculations on Atoms. | Class | org.openscience.cdk.geometry | CDK |
| AtomType | The base class for atom types. | Class | org.openscience.cdk | CDK |
| AtomType | The base class for atom types. | Class | org.openscience.cdk.silent | CDK |
| AtomTypeCharges | Assigns charges to atom types. | Class | org.openscience.cdk.charges | CDK |
| AtomTypeDiff | Compares two IAtomType classes. | Class | org.openscience.cdk.tools.diff | CDK |
| AtomTypeFactory | General class for defining AtomTypes. | Class | org.openscience.cdk.config | CDK |
| AtomTypeHandler | SAX Handler for the AtomTypeReader. | Class | org.openscience.cdk.config.atomtypes | CDK |
| AtomTypeHybridizationDifference | IDifference between two IAtomType. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| AtomTypeManipulator | Class with utilities for the AtomType class. | Class | org.openscience.cdk.tools.manipulator | CDK |
| AtomTypeMapper | An AtomTypeMapper allows the mapping of atom types between atom type schemes. | Class | org.openscience.cdk.atomtype.mapper | CDK |
| AtomTypeReader | XML Reader for the CDKBasedAtomTypeConfigurator. | Class | org.openscience.cdk.config.atomtypes | CDK |
| AtomTypeTools | AtomTypeTools is a helper class for assigning atom types to an atom. | Class | org.openscience.cdk.tools | CDK |
| AtomValenceDescriptor | This class returns the valence of an atom. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| AtomValenceTool | This class returns the valence of an atom. | Class | org.openscience.cdk.qsar | CDK |
| AttachedGroup | Holds data on a specific functional group or substituent. | Class | org.openscience.cdk.iupac.parser | CDK |
| AutocorrelationDescriptorCharge | This class calculates ATS autocorrelation descriptor, where the weight equalAuthor:FedericoBelongs to the set:qsar-descriptorsCreated on:2007-02-27 | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AutocorrelationDescriptorMass | This class calculates ATS autocorrelation descriptor, where the weight equal to the scaled atomic mass . | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AutocorrelationDescriptorPolarizability | This class calculates ATS autocorrelation descriptor, where the weight equalAuthor:FedericoBelongs to the set:qsar-descriptorsCreated on:2007-03-01 | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| AverageBondLengthCalculator | Utility class for calculating the average bond length for various IChemObject subtypes : IReaction, IMoleculeSet, IChemModel, and IReactionSet. | Class | org.openscience.cdk.renderer | CDK |
| AWTDrawVisitor | widget toolkit, allowing molecules to be rendered with toolkits based on AWT, like the Java reference graphics platform Swing. | Class | org.openscience.cdk.renderer.visitor | CDK |
| AWTFontManager | AWT-specific font manager. | Class | org.openscience.cdk.renderer.font | CDK |
| BadMatrixFormatException | Class | org.openscience.cdk.graph.invariant.exception | CDK | |
| BasicAtomGenerator | Generates basic IRenderingElements for atoms in an atom container. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .AtomColor | This color is overwritten by the IAtomColorer. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .AtomColorer | IAtomColorer used to draw elements. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .AtomRadius | Magic number with unknown units that defines the radius around an atom, e. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .ColorByType | Class | org.openscience.cdk.renderer.generators | CDK | |
| BasicAtomGenerator .CompactAtom | Boolean parameters that will cause atoms to be drawn as filled shapes when set to true. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .CompactShape | Shape to be used when drawing atoms in compact mode, as defined by the BasicAtomGenerator. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .KekuleStructure | Determines whether structures should be drawn as Kekule structures, thus giving each carbon element explicitly, instead of not displaying the | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .Shape | When atoms are selected or in compact mode, they will be covered by a shape determined by this enumeration. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .ShowEndCarbons | Boolean parameters that will show carbons with only one (non-hydrogen) neighbor to be drawn with an element symbol. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicAtomGenerator .ShowExplicitHydrogens | Boolean property that triggers explicit hydrogens to be drawn if set to true. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicBondGenerator | Generator for elements from bonds. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicBondGenerator .BondDistance | The gap between double and triple bond lines on the screen. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicBondGenerator .BondLength | The length on the screen of a typical bond. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicBondGenerator .BondWidth | The width on screen of a bond. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicBondGenerator .DefaultBondColor | The color to draw bonds if not other color is given. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicBondGenerator .TowardsRingCenterProportion | The proportion to move in towards the ring center. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicBondGenerator .WedgeWidth | The width on screen of the fat end of a wedge bond. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicGenerator | Combination generator for basic drawing of molecules. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicGroupCountDescriptor | Returns the number of basic groups. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| 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, | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .ArrowHeadWidth | The width of the head of arrows. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .BackgroundColor | The background color of the drawn image. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .FitToScreen | If true, the scale is set such that the diagram fills the whole screen. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .FontName | Font to use for text. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .ForegroundColor | The foreground color, with which objects are drawn. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .Margin | Area on each of the four margins to keep empty. | Class | org.openscience.cdk.renderer.generators | CDK |
| 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 | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .ShowMoleculeTitle | Determines if the molecule's title is depicted. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .ShowTooltip | Determines if tooltips are to be shown. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .UseAntiAliasing | If set to true, uses anti-aliasing for drawing. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .UsedFontStyle | The font style to use for text. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicSceneGenerator .ZoomFactor | The zoom factor which is a user oriented parameter allowing the user to zoom in on parts of the molecule. | Class | org.openscience.cdk.renderer.generators | CDK |
| BasicValidator | Validator which tests a number of basic chemical semantics. | Class | org.openscience.cdk.validate | CDK |
| BCUTDescriptor | Eigenvalue based descriptor noted for its utility in chemical diversity. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| BFSShortestPath | Utility class that finds the shortest bond path between two atoms using a breadth first search. | Class | org.openscience.cdk.graph | CDK |
| BGFFormat | Class | org.openscience.cdk.io.formats | CDK | |
| BiconnectivityInspector | Finds the biconnected components of a graph. | Class | org.openscience.cdk.graph | CDK |
| BinaryTree | Class to construct a Binary tree for McGregor search. | Class | org.openscience.cdk.smsd.helper | CDK |
| BioPolymer | A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers. | Class | org.openscience.cdk | CDK |
| BioPolymer | A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers. | Class | org.openscience.cdk.silent | CDK |
| BKKCKCF | This class implements Bron-Kerbosch clique detection algorithm as it is described in [F. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| Bond | considered to be a number of electrons connecting two or more of atoms. | Class | org.openscience.cdk | CDK |
| Bond | considered to be a number of electrons connecting two or more of atoms. | Class | org.openscience.cdk.silent | CDK |
| BondCountDescriptor | IDescriptor based on the number of bonds of a certain bond order. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| BondDiff | Compares two IBond classes. | Class | org.openscience.cdk.tools.diff | CDK |
| BondEnergies | Class that stores bond breaking/formation energy between two atoms. | Class | org.openscience.cdk.smsd.tools | CDK |
| BondEnergy | Helper class defining the energy for a bond type. | Class | org.openscience.cdk.smsd.helper | CDK |
| BondManipulator | Class with convenience methods that provide methods to manipulate AtomContainer's. | Class | org.openscience.cdk.tools.manipulator | CDK |
| BondMatcher | Interface for the BondMatcher (bonds) in graph. | Interface | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| BondOrderDifference | IDifference between two IBond. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| BondPartialPiChargeDescriptor | The calculation of bond-pi Partial charge is calculated determining the difference the Partial Pi Charge on atoms | Class | org.openscience.cdk.qsar.descriptors.bond | CDK |
| BondPartialSigmaChargeDescriptor | The calculation of bond-sigma Partial charge is calculated determining the difference the Partial Sigma Charge on atoms | Class | org.openscience.cdk.qsar.descriptors.bond | CDK |
| BondPartialTChargeDescriptor | The calculation of bond total Partial charge is calculated determining the difference the Partial Total Charge on atoms | Class | org.openscience.cdk.qsar.descriptors.bond | CDK |
| BondSigmaElectronegativityDescriptor | The calculation of bond-Polarizability is calculated determining the difference the Sigma electronegativity on atoms A and B of a bond. | Class | org.openscience.cdk.qsar.descriptors.bond | CDK |
| BondsToAtomDescriptor | This class returns the number of bonds on the shortest path between two atoms. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| BondTools | A set of static utility classes for geometric calculations on IBonds. | Class | org.openscience.cdk.geometry | CDK |
| BooleanArrayDifference | Difference between two boolean[]'s. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| BooleanDifference | IDifference between two Booleans. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| BooleanIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
| BooleanResult | Object that provides access to the calculated descriptor value. | Class | org.openscience.cdk.qsar.result | CDK |
| BooleanResultType | IDescriptorResult type for booleans. | Class | org.openscience.cdk.qsar.result | CDK |
| BoundsCalculator | Utility class for calculating the 2D bounding rectangles (bounds) of various IChemObject subtypes - IChemModel, IReactionSet, IReaction, | Class | org.openscience.cdk.renderer | CDK |
| BoundsGenerator | Produce a bounding rectangle for various chem objects. | Class | org.openscience.cdk.renderer.generators | CDK |
| BoundsGenerator .BoundsColor | The color of the box drawn at the bounds of a molecule, molecule set, or reaction. | Class | org.openscience.cdk.renderer.generators | CDK |
| 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 | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| BremserOneSphereHOSECodePredictor | Class | org.openscience.cdk.tools | CDK | |
| BSFormat | Class | org.openscience.cdk.io.formats | CDK | |
| Bspt | BSP-Tree stands for Binary Space Partitioning Tree. | Class | org.openscience.cdk.graph.rebond | CDK |
| Bspt .Tuple | Interface | org.openscience.cdk.graph.rebond | CDK | |
| CacaoCartesianFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CacaoInternalFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CACheFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CanonicalLabeler | Canonically labels an atom container implementing the algorithm published in David Weininger et. | Class | org.openscience.cdk.graph.invariant | CDK |
| CanonicalLabellingAdaptor | Class | org.openscience.cdk.smsd.labelling | CDK | |
| CarbonTypesDescriptor | Topological descriptor characterizing the carbon connectivity. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| CarbonylEliminationReaction | IReactionProcess which participate mass spectrum process. | Class | org.openscience.cdk.reaction.type | CDK |
| CASNumber | Tools to work with CAS registry numbers. | Class | org.openscience.cdk.index | CDK |
| CDK | Helper class to provide general information about this CDK library. | Class | org.openscience.cdk | CDK |
| 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. | Class | org.openscience.cdk.libio.jena | CDK |
| CDK2DAtomColors | Gives a short table of atom colors for 2D display. | Class | org.openscience.cdk.renderer.color | CDK |
| CDKAtomColors | Gives a short table of atom colors for 3D display. | Class | org.openscience.cdk.renderer.color | CDK |
| CDKAtomTypeMatcher | Atom Type matcher that perceives atom types as defined in the CDK atom type list org/openscience/cdk/dict/data/cdk-atom-types. | Class | org.openscience.cdk.atomtype | CDK |
| CDKBasedAtomTypeConfigurator | AtomType resource that reads the atom type configuration from an XML file. | Class | org.openscience.cdk.config | CDK |
| CDKConstants | An interface providing predefined values for a number of constants used throughout the CDK. | Class | org.openscience.cdk | CDK |
| CDKConvention | This is an implementation for the CDK convention. | Class | org.openscience.cdk.io.cml | CDK |
| CDKDictionaryReferences | This class transforms implicit references to dictionary of CDK objects into explicit references. | Class | org.openscience.cdk.dict | CDK |
| CDKException | Exception that is thrown by CDK classes when some problem has occured. | Class | org.openscience.cdk.exception | CDK |
| CDKHueckelAromaticityDetector | Class | org.openscience.cdk.aromaticity | CDK | |
| CDKHydrogenAdder | Adds implicit hydrogens based on atom type definitions. | Class | org.openscience.cdk.tools | CDK |
| CDKMCSHandler | This class acts as a handler class for CDKMCS algorithm. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKOWLFormat | Serializes a CDK model into the Web Ontology Language using theBelongs to the set:io-formats | Class | org.openscience.cdk.io.formats | CDK |
| CDKOWLReader | Reads content from a CDK OWL serialization. | Class | org.openscience.cdk.io.rdf | CDK |
| CDKOWLWriter | Serializes the data model into CDK OWL. | Class | org.openscience.cdk.io.rdf | CDK |
| CDKPopupMenu | Basically, identical to the JPopupMenu class, except that this menu can also contain the source for which it was popped up. | Class | org.openscience.cdk.controller | CDK |
| CDKRGraph | This class implements the Resolution Graph (CDKRGraph). | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKRMap | An CDKRMap implements the association between an edge (bond) in G1 and an edge (bond) in G2, G1 and G2 being the compared graphs in a RGraph context. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKRMapHandler | This algorithm derives from the algorithm described in [Tonnelier, C. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKRNode | Node of the resolution graphe (RGraph) An CDKRNode represents an association betwwen two edges of the source graphs G1 and G2 that are compared. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKSourceCodeFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CDKSourceCodeWriter | Converts a Molecule into CDK source code that would build the same molecule. | Class | org.openscience.cdk.io | CDK |
| CDKSubGraphHandler | This class acts as a handler class for CDKMCS algorithm. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKUtilities | Utility class written by Todd Martin, for help in his QSAR descriptors and SMILES parser. | Class | org.openscience.cdk.tools | CDK |
| CDKValencyChecker | Class | org.openscience.cdk.tools | CDK | |
| CDKValidator | This Validator tests the internal datastructures, and tries to detect inconsistencies in it. | Class | org.openscience.cdk.validate | CDK |
| ChargeGroup | A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule. | Class | org.openscience.cdk.libio.md | CDK |
| ChargeRule | This class validate if the charge in the IMolecularFormula correspond with a specific value. | Class | org.openscience.cdk.formula.rules | CDK |
| Chem3D_Cartesian_1Format | Class | org.openscience.cdk.io.formats | CDK | |
| Chem3D_Cartesian_2Format | Class | org.openscience.cdk.io.formats | CDK | |
| ChemDrawFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ChemFile | A Object containing a number of ChemSequences. | Class | org.openscience.cdk | CDK |
| ChemFile | A Object containing a number of ChemSequences. | Class | org.openscience.cdk.silent | CDK |
| ChemFileManipulator | Class with convenience methods that provide methods from methods from ChemObjects within the ChemFile. | Class | org.openscience.cdk.tools.manipulator | CDK |
| ChemGraph | Class | org.openscience.cdk.structgen.stochastic.operator | CDK | |
| ChemicalFilters | Class that ranks MCS final solution according to the chemical rules. | Class | org.openscience.cdk.smsd.filters | CDK |
| ChemModel | An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, | Class | org.openscience.cdk | CDK |
| ChemModel | An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, | Class | org.openscience.cdk.silent | CDK |
| ChemModelManipulator | Class with convenience methods that provide methods from methods from ChemObjects within the ChemModel. | Class | org.openscience.cdk.tools.manipulator | CDK |
| ChemModelRenderer | A general renderer for IChemModels, IReactions, and IMolecules. | Class | org.openscience.cdk.renderer | CDK |
| ChemObject | The base class for all chemical objects in this cdk. | Class | org.openscience.cdk | CDK |
| ChemObject | The base class for all chemical objects in this cdk. | Class | org.openscience.cdk.silent | CDK |
| ChemObjectChangeEvent | Event fired by cdk classes to their registered listeners in case something changes within them. | Class | org.openscience.cdk.event | CDK |
| ChemObjectDiff | Compares two IChemObject classes. | Class | org.openscience.cdk.tools.diff | CDK |
| ChemObjectDifference | IDifference between two IChemObjects. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| ChemSequence | A sequence of ChemModels, which can, for example, be used to store the course of a reaction. | Class | org.openscience.cdk | CDK |
| ChemSequence | A sequence of ChemModels, which can, for example, be used to store the course of a reaction. | Class | org.openscience.cdk.silent | CDK |
| ChemSequenceManipulator | Class with convenience methods that provide methods from methods from ChemObjects within the ChemSequence. | Class | org.openscience.cdk.tools.manipulator | CDK |
| ChemtoolFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ChiChainDescriptor | Evaluates chi chain descriptors. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| ChiClusterDescriptor | Evaluates chi cluster descriptors. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| ChiPathClusterDescriptor | Evaluates chi path cluster descriptors. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| ChiPathDescriptor | Evaluates chi path descriptors. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| ChiralityAtom | This matches an atom with chirality property. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| CIFFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CIFReader | This is not a reader for the CIF and mmCIF crystallographic formats. | Class | org.openscience.cdk.io | CDK |
| CIPLigandRule | Compares to ILigands based on CIP sequences sub rules. | Class | org.openscience.cdk.geometry.cip.rules | CDK |
| CIPTool | Tool to help determine the R,S and stereochemistry definitions of a subset of the CIP rules . | Class | org.openscience.cdk.geometry.cip | CDK |
| CIPTool .CIP_CHIRALITY | Class | org.openscience.cdk.geometry.cip | CDK | |
| Close | Indicates the closing point of the path. | Class | org.openscience.cdk.renderer.elements.path | CDK |
| ClosedShellJob | Calculates the orbitals and orbital energies of electron systemsAuthor:Stephan Michels Created on:2001-06-14 | Class | org.openscience.cdk.math.qm | CDK |
| CMLCoreModule | Core CML 1. | Class | org.openscience.cdk.io.cml | CDK |
| CMLErrorHandler | CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document. | Class | org.openscience.cdk.io.cml | CDK |
| CMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CMLHandler | SAX2 implementation for CML XML fragment reading. | Class | org.openscience.cdk.io.cml | CDK |
| CMLReactionModule | Class | org.openscience.cdk.io.cml | CDK | |
| CMLReader | Reads a molecule in CML 1. | Class | org.openscience.cdk.io | CDK |
| CMLResolver | This class resolves DOCTYPE declaration for Chemical Markup Language (CML) files and uses a local version for validation. | Class | org.openscience.cdk.io.cml | CDK |
| CMLRSSFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CMLStack | Low weigth alternative to Sun's Stack class. | Class | org.openscience.cdk.io.cml | CDK |
| CMLWriter | Serializes a IMoleculeSet or a IMolecule object to CML 2 code. | Class | org.openscience.cdk.io | CDK |
| Complex | This class handles complex values. | Class | org.openscience.cdk.math | CDK |
| ConformerContainer | A memory-efficient data structure to store conformers for a single molecule. | Class | org.openscience.cdk | CDK |
| ConjugatedPiSystemsDetector | Class | org.openscience.cdk.graph.invariant | CDK | |
| ConnectionCountAtom | This matcher checks the total valency of the Atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| ConnectionMatrix | Calculator for a connection matrix representation of this AtomContainer. | Class | org.openscience.cdk.graph.matrix | CDK |
| ConnectivityChecker | Tool class for checking whether the (sub)structure in an AtomContainer is connected. | Class | org.openscience.cdk.graph | CDK |
| Convertor | Keywords:CML, class convertorRequires:java1. | Class | org.openscience.cdk.libio.cml | CDK |
| Convertor | Helper class that converts a CDK IChemObject into RDF using a Jena model and the CDK data model ontology. | Class | org.openscience.cdk.libio.jena | CDK |
| CovalentRadiusDescriptor | This class return the covalent radius of a given atom. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| CPKAtomColors | Colors atoms using CPK color scheme . | Class | org.openscience.cdk.renderer.color | CDK |
| CPSADescriptor | Calculates 29 Charged Partial Surface Area (CPSA) descriptors. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| CRK2DFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CRK3DFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CrossoverMachine | Modified molecular structures by applying crossover operator on a pair of parent structures and generate a pair of offspring structures. | Class | org.openscience.cdk.structgen.stochastic.operator | CDK |
| Crystal | Class representing a molecular crystal. | Class | org.openscience.cdk | CDK |
| Crystal | Class representing a molecular crystal. | Class | org.openscience.cdk.silent | CDK |
| CrystalGeometryTools | A set of static methods for working with crystal coordinates. | Class | org.openscience.cdk.geometry | CDK |
| CrystClustFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CrystClustReader | Class | org.openscience.cdk.io | CDK | |
| CrystClustWriter | Rather stupid file format used for storing crystal information. | Class | org.openscience.cdk.io | CDK |
| CTXFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CTXReader | Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files. | Class | org.openscience.cdk.io | CDK |
| CubicTo | A cubic curve in the path. | Class | org.openscience.cdk.renderer.elements.path | CDK |
| CustomSerializer | Custom Serializer with the sole purpose and functionality to not output the XML declaration. | Class | org.openscience.cdk.io.cml | CDK |
| CycleBasis | A minimum basis of all cycles in a graph. | Class | org.openscience.cdk.ringsearch.cyclebasis | CDK |
| DaltonFormat | Class | org.openscience.cdk.io.formats | CDK | |
| DataFeatures | Class with constants for possible data features defined in the a Data Feature Ontology. | Class | org.openscience.cdk.tools | CDK |
| DataFeaturesTool | Utility that helps determine which data features are present. | Class | org.openscience.cdk.tools | CDK |
| DeAromatizationTool | Methods that takes a ring of which all bonds are aromatic, and assigns single and double bonds. | Class | org.openscience.cdk.tools | CDK |
| DebugAdductFormula | Class | org.openscience.cdk.debug | CDK | |
| DebugAminoAcid | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugAtom | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugAtomContainer | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugAtomContainerSet | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugAtomParity | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugAtomType | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugBioPolymer | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugBond | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugChemFile | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugChemModel | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugChemObject | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugChemObjectBuilder | Class | org.openscience.cdk.debug | CDK | |
| DebugChemSequence | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugCrystal | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugElectronContainer | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugElement | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugFragmentAtom | Class to represent an IPseudoAtom which embeds an IAtomContainer. | Class | org.openscience.cdk.debug | CDK |
| DebugIsotope | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugLonePair | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugMapping | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugMolecularFormula | Class | org.openscience.cdk.debug | CDK | |
| DebugMolecularFormulaSet | Class | org.openscience.cdk.debug | CDK | |
| DebugMolecule | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugMoleculeSet | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugMonomer | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugPDBAtom | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugPDBMonomer | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugPDBPolymer | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugPDBStructure | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugPolymer | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugPseudoAtom | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugReaction | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugReactionScheme | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugReactionSet | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugRing | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugRingSet | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugSingleElectron | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DebugStrand | Debugging data class. | Class | org.openscience.cdk.debug | CDK |
| DeduceBondSystemTool | Tool that tries to deduce bond orders based on connectivity and hybridization for a number of common ring systems of up to seven-membered rings. | Class | org.openscience.cdk.smiles | CDK |
| DefaultBondMatcher | Checks if a bond is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultChemObjectBuilder | Class | org.openscience.cdk | CDK | |
| DefaultChemObjectReader | Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io | CDK |
| DefaultChemObjectWriter | Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io | CDK |
| DefaultEventChemObjectReader | Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.iterator.event | CDK |
| DefaultIteratingChemObjectReader | Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.iterator | CDK |
| DefaultMatcher | Checks if atom is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultMCSPlusAtomMatcher | Checks if atom is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultRandomAccessChemObjectReader | Abstract class that IRandomAccessChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.random | CDK |
| DefaultRGraphAtomMatcher | Checks if atom is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultVFAtomMatcher | Checks if atom is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultVFBondMatcher | Checks if a bond is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DegreeAtom | This matcher checks the number of connections of the checked Atom with other Atom's. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| DescriptorEngine | A class that provides access to automatic descriptor calculation and more. | Class | org.openscience.cdk.qsar | CDK |
| DescriptorException | Exception that is thrown by descriptor routines when a problem has occured. | Class | org.openscience.cdk.qsar | CDK |
| DescriptorSpecification | Class that is used to distribute descriptor specifications. | Class | org.openscience.cdk.qsar | CDK |
| DescriptorValue | Class that is used to store descriptor values as IChemObject properties. | Class | org.openscience.cdk.qsar | CDK |
| Dictionary | Dictionary with entries. | Class | org.openscience.cdk.dict | CDK |
| DictionaryDatabase | Database of dictionaries listing entries with compounds, fragmentsAuthor:Egon WillighagenKeywords:dictionaryCreated on:2003-04-06Required library to be able to run this class:xom. | Class | org.openscience.cdk.dict | CDK |
| DictionaryHandler | Class for unmarshalling a dictionary schema file. | Class | org.openscience.cdk.dict | CDK |
| DictionaryValidator | Validates the existence of references to dictionaries. | Class | org.openscience.cdk.validate | CDK |
| DictRef | Object that can be used as key in IChemObject. | Class | org.openscience.cdk.dict | CDK |
| DistanceMoment | Fast similarity measure for 3D structures. | Class | org.openscience.cdk.similarity | CDK |
| DistanceToAtomDescriptor | This class returns the 3D distance between two atoms. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| DMol3Format | Class | org.openscience.cdk.io.formats | CDK | |
| DOCK5Format | Class | org.openscience.cdk.io.formats | CDK | |
| DoubleArrayResult | Class | org.openscience.cdk.qsar.result | CDK | |
| DoubleArrayResultType | IDescriptorResult type for booleans. | Class | org.openscience.cdk.qsar.result | CDK |
| DoubleBondAcceptingAromaticityDetector | Class | org.openscience.cdk.aromaticity | CDK | |
| DoubleBondStereochemistry | Stereochemistry specification for double bonds. | Class | org.openscience.cdk.stereo | CDK |
| DoubleDifference | IDifference between two Double. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| DoubleResult | Class | org.openscience.cdk.qsar.result | CDK | |
| DoubleResultType | IDescriptorResult type for booleans. | Class | org.openscience.cdk.qsar.result | CDK |
| EccentricConnectivityIndexDescriptor | A topological descriptor combining distance and adjacency information. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| EdgeBuilder | Class for building/storing edges (bonds) in the graph with bond query capabilities. | Class | org.openscience.cdk.smsd.algorithm.vflib.builder | CDK |
| EffectiveAtomPolarizabilityDescriptor | Effective polarizability of an heavy atom This descriptor uses these parameters: | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| ElectronContainer | Base class for entities containing electrons, like bonds, orbitals, lone-pairs. | Class | org.openscience.cdk | CDK |
| ElectronContainer | Base class for entities containing electrons, like bonds, orbitals, lone-pairs. | Class | org.openscience.cdk.silent | CDK |
| ElectronContainerDiff | Compares two IChemObject classes. | Class | org.openscience.cdk.tools.diff | CDK |
| 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). | Class | org.openscience.cdk.charges | CDK |
| ElectronImpactNBEReaction | IReactionProcess which make an electron impact for for Non-Bonding Electron Lost. | Class | org.openscience.cdk.reaction.type | CDK |
| ElectronImpactPDBReaction | IReactionProcess which make an electron impact for pi-Bond Dissociation. | Class | org.openscience.cdk.reaction.type | CDK |
| ElectronImpactSDBReaction | IReactionProcess which make an electron impact for Sigma Bond Dissociation. | Class | org.openscience.cdk.reaction.type | CDK |
| Element | Use the IsotopeFactory to get a ready-to-use elements by symbol or atomic number: | Class | org.openscience.cdk | CDK |
| Element | Use the IsotopeFactory to get a ready-to-use elements by symbol or atomic number: | Class | org.openscience.cdk.silent | CDK |
| ElementComparator | Compares elements based on the order commonly used in molecular formula. | Class | org.openscience.cdk.tools | CDK |
| ElementDiff | Compares two IElement classes. | Class | org.openscience.cdk.tools.diff | CDK |
| ElementGroup | A group of rendering elements, of any type. | Class | org.openscience.cdk.renderer.elements | CDK |
| ElementRule | This class validate if the occurrence of the IElements in the IMolecularFormula are into a limits. | Class | org.openscience.cdk.formula.rules | CDK |
| Elements | List of elements. | Class | org.openscience.cdk.config | CDK |
| Entry | Entry in a Dictionary. | Class | org.openscience.cdk.dict | CDK |
| EntryReact | Entry in a Dictionary for reactions. | Class | org.openscience.cdk.dict | CDK |
| EnzymeResidueLocator | Atom that represents part of an residue in an enzyme, like Arg255. | Class | org.openscience.cdk | CDK |
| EquivalentClassPartitioner | An algorithm for topological symmetry. | Class | org.openscience.cdk.graph.invariant | CDK |
| EStateAtomTypeMatcher | Determines the EState atom types. | Class | org.openscience.cdk.atomtype | CDK |
| EStateFingerprinter | This fingerprinter generates 79 bit fingerprints using the E-State The E-State fragments are those described in and | Class | org.openscience.cdk.fingerprint | CDK |
| EStateFragments | A class representing the 79 E-state atom types in terms of SMARTS. | Class | org.openscience.cdk.config.fragments | CDK |
| EventCMLHandler | CDO object needed as interface with the JCFL library for reading CML in a event based manner. | Class | org.openscience.cdk.io.iterator.event | CDK |
| EventCMLReader | Reads a molecule in CML 1. | Class | org.openscience.cdk.io.iterator.event | CDK |
| ExactMapping | This class handles MCS between two identical molecules. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| ExhaustiveFragmenter | Generate fragments exhaustively. | Class | org.openscience.cdk.fragment | CDK |
| ExplicitConnectionAtom | This smarts atom matches any atom with a certain number of explicitSee Also:Serialized FormKeywords:SMARTS | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| ExtAtomContainerManipulator | Class that handles some customised features for SMSD atom containers. | Class | org.openscience.cdk.smsd.tools | CDK |
| ExtendedAtomGenerator | A generator for atoms with mass, charge, etc. | Class | org.openscience.cdk.renderer.generators | CDK |
| ExtendedAtomGenerator .ShowAtomTypeNames | Boolean that indicates if atom type names should be given instead of element symbols. | Class | org.openscience.cdk.renderer.generators | CDK |
| ExtendedAtomGenerator .ShowImplicitHydrogens | Boolean that indicates if implicit hydrogens should be depicted. | Class | org.openscience.cdk.renderer.generators | CDK |
| ExtendedFingerprinter | Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional bits describing ring | Class | org.openscience.cdk.fingerprint | CDK |
| FenskeHall_ZMatrixFormat | Class | org.openscience.cdk.io.formats | CDK | |
| FiguerasSSSRFinder | Finds the Smallest Set of Smallest Rings. | Class | org.openscience.cdk.ringsearch | CDK |
| FinalMappings | Class that stores raw mapping(s) after each algorithm is executed. | Class | org.openscience.cdk.smsd.helper | CDK |
| Fingerprinter | Generates a fingerprint for a given AtomContainer. | Class | org.openscience.cdk.fingerprint | CDK |
| FingerprinterTool | Tool with helper methods for IFingerprint. | Class | org.openscience.cdk.fingerprint | CDK |
| FingerprintFormat | Class | org.openscience.cdk.io.formats | CDK | |
| FixBondOrdersTool | Class to Fix bond orders at present for Aromatic Rings only. | Class | org.openscience.cdk.smiles | CDK |
| FixedSizeStack | A LIFO queue for result structures. | Class | org.openscience.cdk.tools | CDK |
| FMFDescriptor | An implementation of the FMF descriptor characterizing complexity of a molecule. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| 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. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| FormalChargeAtom | This matcher checks the formal charge of the Atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| FormatFactory | A factory for recognizing chemical file formats. | Class | org.openscience.cdk.io | CDK |
| FormatStringBuffer | A class for formatting output similar to the C printf command. | Class | org.openscience.cdk.tools | CDK |
| FortranFormat | Converts a String representation of a Fortran double to a double. | Class | org.openscience.cdk.math | CDK |
| FragmentAtom | Class to represent an IPseudoAtom which embeds an IAtomContainer. | Class | org.openscience.cdk | CDK |
| FragmentAtom | Class to represent an IPseudoAtom which embeds an IAtomContainer. | Class | org.openscience.cdk.silent | CDK |
| FragmentComplexityDescriptor | Class that returns the complexity of a system. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| FragmentUtils | Helper methods for fragmentation algorithms. | Class | org.openscience.cdk.fragment | CDK |
| GamessFormat | Class | org.openscience.cdk.io.formats | CDK | |
| GamessReader | A reader for GAMESS log file. | Class | org.openscience.cdk.io | CDK |
| GasteigerMarsiliPartialCharges | The calculation of the Gasteiger Marsili (PEOE) partial charges is based on . | Class | org.openscience.cdk.charges | CDK |
| GasteigerPEPEPartialCharges | The calculation of the Gasteiger (PEPE) partial charges is based on . | Class | org.openscience.cdk.charges | CDK |
| Gaussian03Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian03Reader | A reader for Gaussian03 output. | Class | org.openscience.cdk.io | CDK |
| Gaussian90Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian92Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian94Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian95Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian98Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian98Reader | A reader for Gaussian98 output. | Class | org.openscience.cdk.io | CDK |
| GaussianInputFormat | Class | org.openscience.cdk.io.formats | CDK | |
| GaussianInputWriter | File writer thats generates input files for Gaussian calculation jobs. | Class | org.openscience.cdk.io.program | CDK |
| GeneralPath | A path of rendering elements from the elements. | Class | org.openscience.cdk.renderer.elements | CDK |
| GenerateCompatibilityGraph | This class generates compatibility graph between query and target molecule. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| Geometry3DValidator | Validates the 3D geometry of the model. | Class | org.openscience.cdk.validate | CDK |
| GeometryTools | A set of static utility classes for geometric calculations and operations. | Class | org.openscience.cdk.geometry | CDK |
| GhemicalMMFormat | Class | org.openscience.cdk.io.formats | CDK | |
| GhemicalMMReader | http://www. | Class | org.openscience.cdk.io | CDK |
| GhemicalSPMFormat | Class | org.openscience.cdk.io.formats | CDK | |
| 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, substraction, multiplication, inversion, concatenation) | Class | org.openscience.cdk.graph.invariant | CDK |
| GraphOnlyFingerprinter | Specialized version of the Fingerprinter which does not take bond ordersAuthor:egonwSee Also:FingerprinterKeywords:fingerprint, similarityCreated on:2007-01-11 | Class | org.openscience.cdk.fingerprint | CDK |
| GraphRendererModel | This class handles a set of function for the GraphRendererAuthor:Stephan Michels Created on:2001-07-02 | Class | org.openscience.cdk.renderer | CDK |
| GravitationalIndexDescriptor | IDescriptor characterizing the mass distribution of the molecule. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| GridGenerator | Generates a grid of points in 3D space within given boundaries. | Class | org.openscience.cdk.tools | CDK |
| GROMOS96Format | Class | org.openscience.cdk.io.formats | CDK | |
| HanserRingFinder | Finds the Set of all Rings. | Class | org.openscience.cdk.smsd.ring | CDK |
| HBondAcceptorCountDescriptor | This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the The following groups are counted as hydrogen bond acceptors: | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| HBondDonorCountDescriptor | This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the The following groups are counted as hydrogen bond donors: | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| HeterolyticCleavageMechanism | This mechanism displaces the chemical bond to an Atom. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| HeterolyticCleavagePBReaction | IReactionProcess which a bond is broken displacing the electron to one of the atoms. | Class | org.openscience.cdk.reaction.type | CDK |
| HeterolyticCleavageSBReaction | IReactionProcess which a bond is broken displacing the electron to one of the atoms. | Class | org.openscience.cdk.reaction.type | CDK |
| HINFormat | Class | org.openscience.cdk.io.formats | CDK | |
| HINReader | Reads an object from HIN formated input. | Class | org.openscience.cdk.io | CDK |
| HINWriter | Writer that outputs in the HIN format. | Class | org.openscience.cdk.io | CDK |
| HomolyticCleavageMechanism | This mechanism breaks the chemical bond between atoms. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| HomolyticCleavageReaction | IReactionProcess which breaks the bond homogeneously leading to radical ions. | Class | org.openscience.cdk.reaction.type | CDK |
| HOSECodeAnalyser | Analyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula. | Class | org.openscience.cdk.tools | CDK |
| HOSECodeGenerator | Generates HOSE codes . | Class | org.openscience.cdk.tools | CDK |
| HuLuIndexTool | Class | org.openscience.cdk.graph.invariant | CDK | |
| HybridizationFingerprinter | Generates a fingerprint for a given IAtomContainer. | Class | org.openscience.cdk.fingerprint | CDK |
| HybridizationNumberAtom | This matcher checks the hybridization state of an atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| HybridizationRatioDescriptor | IMolecularDescriptor that reports the fraction of sp3 carbons to sp2 carbons. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| HydrogenAtom | This matches Hydrogen atoms. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| HydrogenPlacer | This is a wrapper class for some existing methods in AtomPlacer. | Class | org.openscience.cdk.layout | CDK |
| HyperconjugationReaction | HyperconjugationReaction is the stabilizing interaction that results from the interaction of the electrons in a s-bond (for our case only C-H) | Class | org.openscience.cdk.reaction.type | CDK |
| IAdductFormula | Class defining an adduct object in a MolecularFormula. | Interface | org.openscience.cdk.interfaces | CDK |
| IAminoAcid | A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom. | Interface | org.openscience.cdk.interfaces | CDK |
| IAtom | Represents the idea of an chemical atom. | Interface | org.openscience.cdk.interfaces | CDK |
| IAtomColorer | Interface to a class for coloring atoms. | Interface | org.openscience.cdk.renderer.color | CDK |
| IAtomContainer | Base class for all chemical objects that maintain a list of Atoms and ElectronContainers. | Interface | org.openscience.cdk.interfaces | CDK |
| IAtomContainerSet | A set of AtomContainers. | Interface | org.openscience.cdk.interfaces | CDK |
| IAtomicDescriptor | Classes that implement this interface are QSAR descriptor calculators. | Interface | org.openscience.cdk.qsar | CDK |
| IAtomPairDescriptor | Classes that implement this interface are QSAR descriptor calculators. | Interface | org.openscience.cdk.qsar | CDK |
| IAtomParity | Represents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms. | Interface | org.openscience.cdk.interfaces | CDK |
| IAtomType | The base class for atom types. | Interface | org.openscience.cdk.interfaces | CDK |
| IAtomType .Hybridization | An enum for the different hybridization states. | Interface | org.openscience.cdk.interfaces | CDK |
| IAtomTypeConfigurator | Interface | org.openscience.cdk.config | CDK | |
| IAtomTypeGuesser | Classes that implement this interface are atom type guessers. | Interface | org.openscience.cdk.atomtype | CDK |
| IAtomTypeMatcher | Classes that implement this interface are atom type matchers. | Interface | org.openscience.cdk.atomtype | CDK |
| IBioPolymer | A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers. | Interface | org.openscience.cdk.interfaces | CDK |
| IBond | considered to be a number of electrons connecting two ore more atoms. | Interface | org.openscience.cdk.interfaces | CDK |
| IBond .Order | A list of permissible bond orders. | Interface | org.openscience.cdk.interfaces | CDK |
| IBond .Stereo | Stereo type defines not just define the stereochemistry, but also the which atom is the stereo center for which the Stereo is defined. | Interface | org.openscience.cdk.interfaces | CDK |
| IBondDescriptor | Classes that implement this interface are QSAR descriptor calculators. | Interface | org.openscience.cdk.qsar | CDK |
| ICanonicalMoleculeLabeller | Interface | org.openscience.cdk.smsd.labelling | CDK | |
| ICanonicalReactionLabeller | Interface | org.openscience.cdk.smsd.labelling | CDK | |
| ICDKChangeListener | A ChangeListener for the CDK, to be independent from the Swing package. | Interface | org.openscience.cdk.event | CDK |
| ICDKObject | The base class for all data objects in this CDK. | Interface | org.openscience.cdk.interfaces | CDK |
| ICDKSelectionChangeListener | A ChangeListener for the CDK, to be independent from the Swing package. | Interface | org.openscience.cdk.event | CDK |
| IChargeCalculator | Interface | org.openscience.cdk.charges | CDK | |
| IChemFile | An IChemObject containing a number of ChemSequences. | Interface | org.openscience.cdk.interfaces | CDK |
| IChemFormat | This class is the interface that all ChemFormat's should implement. | Interface | org.openscience.cdk.io.formats | CDK |
| IChemFormatMatcher | This interface is used for classes that are able to match a certain chemical file format. | Interface | org.openscience.cdk.io.formats | CDK |
| IChemModel | An object containig multiple MoleculeSet and the other lower level concepts like rings, sequences, | Interface | org.openscience.cdk.interfaces | CDK |
| IChemObject | The base class for all chemical objects in this cdk. | Interface | org.openscience.cdk.interfaces | CDK |
| IChemObjectBuilder | Interface | org.openscience.cdk.interfaces | CDK | |
| IChemObjectChangeEvent | Event fired by CDK IChemObject classes to their registered listeners in case something changed within them. | Interface | org.openscience.cdk.interfaces | CDK |
| IChemObjectIO | This class is the interface that all IO readers should implement. | Interface | org.openscience.cdk.io | CDK |
| IChemObjectIOListener | Allows monitoring of progress of file reader activities. | Interface | org.openscience.cdk.io.listener | CDK |
| IChemObjectListener | Classes implementing this interface must implement this method such that they react appropriately to changes in the object they | Interface | org.openscience.cdk.interfaces | CDK |
| IChemObjectReader | This interface specifies the common functionality all IO readers should provide. | Interface | org.openscience.cdk.io | CDK |
| IChemObjectReader .Mode | Only fail on serious format problemsFail on any format problem | Class | org.openscience.cdk.io | CDK |
| IChemObjectReaderErrorHandler | Interface for classes aimed to handle IChemObjectReader errors. | Interface | org.openscience.cdk.io | CDK |
| IChemObjectSelection | Interface | org.openscience.cdk.renderer.selection | CDK | |
| IChemObjectWriter | This class is the interface that all IO writers should implement. | Interface | org.openscience.cdk.io | CDK |
| IChemSequence | A sequence of ChemModels, which can, for example, be used to store the course of a reaction. | Interface | org.openscience.cdk.interfaces | CDK |
| ICMLConvention | This interface describes the procedures classes must implement to be plugable into the CMLHandler. | Interface | org.openscience.cdk.io.cml | CDK |
| ICMLCustomizer | Interface for classes that allow the Convertor to be customized for certain features. | Interface | org.openscience.cdk.libio.cml | CDK |
| ICMLModule | This interface describes the procedures classes must implement to be plugable into the CMLHandler. | Interface | org.openscience.cdk.io.cml | CDK |
| ICrystal | Class representing a molecular crystal. | Interface | org.openscience.cdk.interfaces | CDK |
| IDCreator | Class that provides methods to give unique IDs to ChemObjects. | Class | org.openscience.cdk.tools | CDK |
| IDeduceBondOrderTool | A common interface for tools that deduce bond orders from connectivity and optionally additional information, like number of implicit or | Interface | org.openscience.cdk.tools | CDK |
| IDescriptor | Classes that implement this interface are QSAR descriptor calculators. | Interface | org.openscience.cdk.qsar | CDK |
| IDescriptorResult | Object that provides access to the calculated descriptor value. | Interface | org.openscience.cdk.qsar.result | CDK |
| IDifference | Interface | org.openscience.cdk.tools.diff.tree | CDK | |
| IDifferenceList | IDifference between two Objects which contains one or more child IDifference objects. | Interface | org.openscience.cdk.tools.diff.tree | CDK |
| IDoubleBondStereochemistry | Stereochemistry specification for double bond stereochemistry. | Interface | org.openscience.cdk.interfaces | CDK |
| IDoubleBondStereochemistry .Conformation | Interface | org.openscience.cdk.interfaces | CDK | |
| IDrawVisitor | An IDrawVisitor is an IRenderingVisitor that can be customized and knows about fonts and other rendering parameters. | Interface | org.openscience.cdk.renderer.visitor | CDK |
| IEdge | Interface for the Edges (bonds) in graph. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IElectronContainer | Base class for entities containing electrons, like bonds, orbitals, lone-pairs. | Interface | org.openscience.cdk.interfaces | CDK |
| IElectronicPropertyCalculator | Interface | org.openscience.cdk.charges | CDK | |
| IElement | Interface | org.openscience.cdk.interfaces | CDK | |
| IEventChemObjectReader | Interface for an iterating molecule reader. | Interface | org.openscience.cdk.io.iterator.event | CDK |
| IFinalMapping | Interface for mappings. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| IFingerprinter | Interface for fingerprint calculators. | Interface | org.openscience.cdk.fingerprint | CDK |
| IFontManager | An interface for managing the drawing of fonts at different zoom levels. | Interface | org.openscience.cdk.renderer.font | CDK |
| IFontManager .FontStyle | Style of the font to use to draw text. | Class | org.openscience.cdk.renderer.font | CDK |
| IFragmentAtom | Class to represent an IPseudoAtom which embeds an IAtomContainer. | Interface | org.openscience.cdk.interfaces | CDK |
| IFragmenter | An interface for classes implementing fragmentation algorithms. | Interface | org.openscience.cdk.fragment | CDK |
| IFunction | A class, which has a function value should implement this interface. | Interface | org.openscience.cdk.math | CDK |
| IGenerator | An IGenerator converts chemical entities into parts of the chemical drawing expressed as IRenderingElements. | Interface | org.openscience.cdk.renderer.generators | CDK |
| IGeneratorParameter | Parameter from some rendering of the 2D diagram. | Interface | org.openscience.cdk.renderer.generators | CDK |
| IGraphMatrix | Interface | org.openscience.cdk.graph.matrix | CDK | |
| IImplementationSpecification | Interface that is used to describe the specification of a certain implementation of an algorithm. | Interface | org.openscience.cdk | CDK |
| IIsotope | Used to store and retrieve data of a particular isotope. | Interface | org.openscience.cdk.interfaces | CDK |
| IIteratingChemObjectReader | Interface for an iterating molecule reader. | Interface | org.openscience.cdk.io.iterator | CDK |
| ILigand | Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another. | Interface | org.openscience.cdk.geometry.cip | CDK |
| ILoggingTool | Useful for logging messages. | Interface | org.openscience.cdk.tools | CDK |
| ILonePair | A LonePair is an orbital primarily located with one Atom, containingKeywords:orbital, lone-pair | Interface | org.openscience.cdk.interfaces | CDK |
| IMapper | Interface for the mappings (mapped objects). | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IMapping | Represents a mapping of two atoms. | Interface | org.openscience.cdk.interfaces | CDK |
| IMatrix | This class contains a complex matrix. | Class | org.openscience.cdk.math | CDK |
| IMCSBase | Interface that holds basic core interface for all MCS algorithm. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| IMolecularDescriptor | Classes that implement this interface are QSAR descriptor calculators for IMolecule objects. | Interface | org.openscience.cdk.qsar | CDK |
| IMolecularFormula | Class defining a molecular formula object. | Interface | org.openscience.cdk.interfaces | CDK |
| IMolecularFormulaSet | Class defining a molecular formula object. | Interface | org.openscience.cdk.interfaces | CDK |
| IMolecule | Represents a set of Molecules. | Interface | org.openscience.cdk.interfaces | CDK |
| IMoleculeSet | Represents a set of Molecules. | Interface | org.openscience.cdk.interfaces | CDK |
| IMonomer | A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms. | Interface | org.openscience.cdk.interfaces | CDK |
| IMouseEventRelay | Widget toolkit-independent interface to relay for mouse events. | Interface | org.openscience.cdk.controller | CDK |
| ImplicitHCountAtom | This matcher checks the number of implicit hydrogens of the Atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| ImplicitHydrogenLigand | Subclass of Ligand to which no further recursion must be applied. | Class | org.openscience.cdk.geometry.cip | CDK |
| INChIContentProcessorTool | Tool to help process INChI 1. | Class | org.openscience.cdk.io.inchi | CDK |
| INChIFormat | Class | org.openscience.cdk.io.formats | CDK | |
| InChIGenerator | This class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer. | Class | org.openscience.cdk.inchi | CDK |
| InChIGeneratorFactory | Factory providing access to InChIGenerator and InChIToStructure. | Class | org.openscience.cdk.inchi | CDK |
| INChIHandler | SAX2 implementation for INChI XML fragment parsing. | Class | org.openscience.cdk.io.inchi | CDK |
| InChINumbersTools | Tool for calculating atom numbers using the InChI algorithm. | Class | org.openscience.cdk.graph.invariant | CDK |
| INChIPlainTextFormat | Class | org.openscience.cdk.io.formats | CDK | |
| INChIPlainTextReader | Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document. | Class | org.openscience.cdk.io | CDK |
| INChIReader | Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document. | Class | org.openscience.cdk.io | CDK |
| InChITautomerGenerator | Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI. | Class | org.openscience.cdk.tautomers | CDK |
| InChIToStructure | This class generates a CDK IAtomContainer from an InChI string. | Class | org.openscience.cdk.inchi | CDK |
| IncorrectUseOfCDKCoreClassError | Error that is thrown by debug implementations of the core CDK classes. | Class | org.openscience.cdk.exception | CDK |
| IndexOutOfBoundsException | Class | org.openscience.cdk.graph.invariant.exception | CDK | |
| InductiveAtomicHardnessDescriptor | Inductive atomic hardness of an atom in a polyatomic system can be defined as the "resistance" to a change of the atomic charge. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| InductiveAtomicSoftnessDescriptor | Inductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| InductivePartialCharges | The calculation of the inductive partial atomic charges and equalization of effective electronegativities is based on . | Class | org.openscience.cdk.charges | CDK |
| INode | Interface for the Node (atomss) in graph. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IntegerArrayResult | Class | org.openscience.cdk.qsar.result | CDK | |
| IntegerArrayResultType | IDescriptorResult type for booleans. | Class | org.openscience.cdk.qsar.result | CDK |
| IntegerDifference | IDifference between two Integer. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| IntegerIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
| IntegerResult | Object that provides access to the calculated descriptor value. | Class | org.openscience.cdk.qsar.result | CDK |
| IntegerResultType | IDescriptorResult type for booleans. | Class | org.openscience.cdk.qsar.result | CDK |
| InvalidSmilesException | Class | org.openscience.cdk.exception | CDK | |
| InverseSymbolSetQueryAtom | A QueryAtom that matches all symbols but those in this container. | Class | org.openscience.cdk.isomorphism.matchers | CDK |
| InvPair | This is used to hold the invariance numbers for the canonical labeling ofSee Also:Serialized Form | Class | org.openscience.cdk.smiles | CDK |
| IonizationPotentialTool | This class contains the necessary information to predict ionization potential energy. | Class | org.openscience.cdk.tools | CDK |
| IOSetting | An interface for reader settings. | Class | org.openscience.cdk.io.setting | CDK |
| IParameterReact | Interface for classes that generate parameters used in reactions. | Interface | org.openscience.cdk.reaction.type.parameters | CDK |
| IPAtomicHOSEDescriptor | This class returns the ionization potential of an atom containg lone pair electrons. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| IPAtomicLearningDescriptor | This class returns the ionization potential of an atom containing lone pair electrons. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| IPBondLearningDescriptor | This class returns the ionization potential of a Bond. | Class | org.openscience.cdk.qsar.descriptors.bond | CDK |
| IPDBAtom | A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom. | Interface | org.openscience.cdk.interfaces | CDK |
| IPDBMonomer | Represents the idea of an protein monomer as found in PDB files. | Interface | org.openscience.cdk.interfaces | CDK |
| IPDBPolymer | A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers. | Interface | org.openscience.cdk.interfaces | CDK |
| IPDBStructure | Represents the idea of an chemical structure. | Interface | org.openscience.cdk.interfaces | CDK |
| IPMolecularLearningDescriptor | This class returns the ionization potential of a molecule. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| IPolymer | Subclass of Molecule to store Polymer specific attributes that a Polymer has. | Interface | org.openscience.cdk.interfaces | CDK |
| IPseudoAtom | Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc. | Interface | org.openscience.cdk.interfaces | CDK |
| IQuery | Interface for the query molecule/graph. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IQueryAtom | Defines the ability to be matched against IAtom's. | Interface | org.openscience.cdk.isomorphism.matchers | CDK |
| IQueryAtomContainer | General concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester. | Interface | org.openscience.cdk.isomorphism.matchers | CDK |
| IQueryBond | Defines the abililty to be matched against IBond's. | Interface | org.openscience.cdk.isomorphism.matchers | CDK |
| IQueryCompiler | Interface for the query graph generator. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IRandomAccessChemObjectReader | Extension of ListIterator. | Interface | org.openscience.cdk.io.random | CDK |
| IRDFWeightFunction | Weight function used in the RDFCalculator. | Interface | org.openscience.cdk.geometry | CDK |
| IReaction | Represents the idea of a chemical reaction. | Interface | org.openscience.cdk.interfaces | CDK |
| IReaction .Direction | Permissible reaction directions. | Interface | org.openscience.cdk.interfaces | CDK |
| IReactionMechanism | Classes that implement this interface are reaction mechanisms. | Interface | org.openscience.cdk.reaction | CDK |
| IReactionProcess | Classes that implement this interface are Reactions types. | Interface | org.openscience.cdk.reaction | CDK |
| IReactionScheme | Classes that implement this interface of a scheme. | Interface | org.openscience.cdk.interfaces | CDK |
| IReactionSet | A set of reactions, for example those taking part in a reaction. | Interface | org.openscience.cdk.interfaces | CDK |
| IReaderListener | Allows monitoring of progress of file reader activities. | Interface | org.openscience.cdk.io.listener | CDK |
| IRenderer | Interface that all 2D renderers implement. | Interface | org.openscience.cdk.renderer | CDK |
| IRenderingElement | Widget toolkit-independent, abstract definition of something to be drawn. | Interface | org.openscience.cdk.renderer.elements | CDK |
| IRenderingVisitor | An IRenderingVisitor is responsible of converting an abstract chemical drawing into a widget set specific drawing. | Interface | org.openscience.cdk.renderer.elements | CDK |
| IResourceFormat | This class is the interface that all ResourceFormat's should implement. | Interface | org.openscience.cdk.io.formats | CDK |
| IRGroupQuery | Interface definition for Rgroup query classes. | Interface | org.openscience.cdk.isomorphism.matchers | CDK |
| IRing | Class representing a ring structure in a molecule. | Interface | org.openscience.cdk.interfaces | CDK |
| IRingSet | Maintains a set of Ring objects. | Interface | org.openscience.cdk.interfaces | CDK |
| IRule | Interface which groups all method that validate a IMolecularFormula. | Interface | org.openscience.cdk.formula.rules | CDK |
| ISequenceSubRule | Sequence sub rule used in the CIP method to decide which of the two ligands takes precedence . | Interface | org.openscience.cdk.geometry.cip.rules | CDK |
| ISimpleChemObjectReader | This class is the interface that all IO readers should implement. | Interface | org.openscience.cdk.io | CDK |
| ISingleElectron | A Single Electron is an orbital which is occupied by only one electron. | Interface | org.openscience.cdk.interfaces | CDK |
| IsoAlkanes | This class contains methods for generating simple organic alkanes. | Class | org.openscience.cdk.templates.saturatedhydrocarbons | CDK |
| Isomorphism | This class implements the Isomorphism- a multipurpose structure comparison tool. | Class | org.openscience.cdk.smsd | CDK |
| IsomorphismTester | A too simplistic implementation of an isomorphism test for chemical graphs. | Class | org.openscience.cdk.isomorphism | CDK |
| Isotope | Used to store and retrieve data of a particular isotope. | Class | org.openscience.cdk | CDK |
| Isotope | Used to store and retrieve data of a particular isotope. | Class | org.openscience.cdk.silent | CDK |
| IsotopeContainer | This class defines a isotope container. | Class | org.openscience.cdk.formula | CDK |
| IsotopeDiff | Compares two IIsotope classes. | Class | org.openscience.cdk.tools.diff | CDK |
| IsotopeFactory | Used to store and return data of a particular isotope. | Class | org.openscience.cdk.config | CDK |
| IsotopeHandler | Reads an isotope list in CML2 format. | Class | org.openscience.cdk.config.isotopes | CDK |
| IsotopePattern | This class defines the properties of a deisotoped pattern distribution. | Class | org.openscience.cdk.formula | CDK |
| IsotopePatternGenerator | Generates all Combinatorial chemical isotopes given a structure. | Class | org.openscience.cdk.formula | CDK |
| IsotopePatternManipulator | Class to manipulate IsotopePattern objects. | Class | org.openscience.cdk.formula | CDK |
| IsotopePatternRule | This class validate if the Isotope Pattern from a given IMolecularFormula correspond with other to compare. | Class | org.openscience.cdk.formula.rules | CDK |
| IsotopePatternSimilarity | This class gives a score hit of similarity between two different isotope abundance pattern. | Class | org.openscience.cdk.formula | CDK |
| IsotopeReader | Reader that instantiates an XML parser and customized handler to process the isotope information in the CML2 isotope data file. | Class | org.openscience.cdk.config.isotopes | CDK |
| 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, | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| IsProtonInConjugatedPiSystemDescriptor | This class evaluates if a proton is joined to a conjugated system. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| IState | Interface for the storing the states of the mapping in the VF algorithm. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IStereoElement | Represents the concept of a stereo element in the molecule. | Interface | org.openscience.cdk.interfaces | CDK |
| IStrand | A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms. | Interface | org.openscience.cdk.interfaces | CDK |
| IStructureGenerationListener | Interface | org.openscience.cdk.structgen | CDK | |
| IteratingMDLConformerReader | Iterate over conformers of a collection of molecules stored in SDF format. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingMDLReader | Iterating MDL SDF reader. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingPCCompoundASNReader | Iterating PubChem PCCompound ASN reader. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingPCCompoundXMLReader | Iterating PubChem PCCompound ASN. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingPCSubstancesXMLReader | Iterating PubChem PC-Substances ASN. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingSMILESReader | Iterating SMILES file reader. | Class | org.openscience.cdk.io.iterator | CDK |
| ITetrahedralChirality | Stereochemistry specification for quadrivalent atoms. | Interface | org.openscience.cdk.interfaces | CDK |
| ITetrahedralChirality .Stereo | Interface | org.openscience.cdk.interfaces | CDK | |
| IValencyChecker | A common interface for SaturationChecker and ValencyChecker. | Interface | org.openscience.cdk.tools | CDK |
| IValidator | Interface that Validators need to implement to be used in validation. | Interface | org.openscience.cdk.validate | CDK |
| IVector | Class | org.openscience.cdk.math | CDK | |
| IViewEventRelay | Interface | org.openscience.cdk.controller | CDK | |
| IWriterListener | Interface | org.openscience.cdk.io.listener | CDK | |
| JaguarFormat | Class | org.openscience.cdk.io.formats | CDK | |
| JCPAction2D | Superclass of all JChemPaint GUI actionsAuthor:steinbeckSee Also:Serialized Form | Class | org.openscience.cdk.renderer | CDK |
| JJTSMARTSParserState | Class | org.openscience.cdk.smiles.smarts.parser | CDK | |
| JMEFormat | Class | org.openscience.cdk.io.formats | CDK | |
| JMOLANIMATIONConvention | Class | org.openscience.cdk.io.cml | CDK | |
| KabschAlignment | Aligns two structures to minimize the RMSD using the Kabsch algorithm. | Class | org.openscience.cdk.geometry.alignment | CDK |
| 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. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| KierHallSmartsDescriptor | A fragment count descriptor that uses e-state fragments. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| KlekotaRothFingerprinter | SMARTS based substructure fingerprint based on Chemical substructures that enrich for biological activity . | Class | org.openscience.cdk.fingerprint | CDK |
| LabelContainer | Class that handles atoms and assignes an integer lable to them. | Class | org.openscience.cdk.smsd.helper | CDK |
| LargestChainDescriptor | Class that returns the number of atoms in the largest chain. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| LargestPiSystemDescriptor | Class that returns the number of atoms in the largest pi system. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| LengthOverBreadthDescriptor | Evaluates length over breadth descriptors. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| Ligand | Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another. | Class | org.openscience.cdk.geometry.cip | CDK |
| LineElement | A line between two points. | Class | org.openscience.cdk.renderer.elements | CDK |
| LineElement .LineType | The type of the line. | Class | org.openscience.cdk.renderer.elements | CDK |
| LineTo | A line element in the path. | Class | org.openscience.cdk.renderer.elements.path | CDK |
| LoggingTool | Useful for logging messages. | Class | org.openscience.cdk.tools | CDK |
| LoggingToolFactory | Factory used to instantiate a ILoggingTool. | Class | org.openscience.cdk.tools | CDK |
| LogicalOperatorAtom | This class matches a logical operator that connects two query atomsSee Also:Serialized FormKeywords:SMARTS | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| LogicalOperatorBond | This class matches a logical operator that connects two query bonds. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| LonePair | A LonePair is an orbital primarily located with one Atom, containingSee Also:Serialized FormKeywords:orbital, lone-pair | Class | org.openscience.cdk | CDK |
| LonePair | A LonePair is an orbital primarily located with one Atom, containingSee Also:Serialized FormKeywords:orbital, lone-pair | Class | org.openscience.cdk.silent | CDK |
| LonePairDiff | Compares two ILonePair classes. | Class | org.openscience.cdk.tools.diff | CDK |
| LonePairElectronChecker | Provides methods for checking whether an atoms lone pair electrons are saturated with respect to a particular atom type. | Class | org.openscience.cdk.tools | CDK |
| LonePairGenerator | Generate the symbols for lone pairs. | Class | org.openscience.cdk.renderer.generators | CDK |
| LongestAliphaticChainDescriptor | Class that returns the number of atoms in the longest aliphatic chain. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| MACCSFingerprinter | This fingerprinter generates 166 bit MACCS keys. | Class | org.openscience.cdk.fingerprint | CDK |
| MacroModelFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MannholdLogPDescriptor | Prediction of logP based on the number of carbon and hetero atoms. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| Mapping | A Mapping is an relation between two ChemObjects in a non-chemical entity. | Class | org.openscience.cdk | CDK |
| Mapping | A Mapping is an relation between two ChemObjects in a non-chemical entity. | Class | org.openscience.cdk.silent | CDK |
| MappingGenerator | Class | org.openscience.cdk.renderer.generators | CDK | |
| MappingGenerator .AtomAtomMappingLineColor | The width on screen of an atom-atom mapping line. | Class | org.openscience.cdk.renderer.generators | CDK |
| MappingGenerator .MappingLineWidth | The width on screen of an atom-atom mapping line. | Class | org.openscience.cdk.renderer.generators | CDK |
| MappingGenerator .ShowAtomAtomMapping | Boolean by which atom-atom mapping depiction can be temporarily disabled. | Class | org.openscience.cdk.renderer.generators | CDK |
| MassAtom | This class matches an atom based on the atomic mass. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| MassToFormulaTool | Tool to determine molecular formula consistent with a given accurate mass. | Class | org.openscience.cdk.formula | CDK |
| Match | Holds matching query and target nodes. | Class | org.openscience.cdk.smsd.algorithm.vflib.map | CDK |
| MathTools | Class providing convenience methods for simple mathematical operations. | Class | org.openscience.cdk.math | CDK |
| Matrix | This class contains a matrix. | Class | org.openscience.cdk.math | CDK |
| MatrixNotInvertibleException | Class | org.openscience.cdk.graph.invariant.exception | CDK | |
| McGregor | Class which reports MCS solutions based on the McGregor algorithm The SMSD algorithm is described in this paper. | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK |
| McGregorChecks | Class to perform check/methods for McGregor class. | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK |
| McgregorHelper | Helper Class for McGregor algorithm. | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK |
| MCSPlus | This class handles MCS plus algorithm which is a combination of c-clique algorithm and McGregor algorithm. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| MCSPlusHandler | This class acts as a handler class for MCSPlus algorithm. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| MDEDescriptor | Calculates the Molecular Distance Edge descriptor described in . | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| MDLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MDLMolConvention | Class | org.openscience.cdk.io.cml | CDK | |
| MDLReader | Reads a molecule from the original MDL MOL or SDF file . | Class | org.openscience.cdk.io | CDK |
| MDLRXNFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MDLRXNReader | Reads a molecule from an MDL RXN file . | Class | org.openscience.cdk.io | CDK |
| MDLRXNV2000Reader | Reads a molecule from an MDL RXN file . | Class | org.openscience.cdk.io | CDK |
| MDLRXNV3000Format | Class | org.openscience.cdk.io.formats | CDK | |
| MDLRXNV3000Reader | Class that implements the new MDL mol format introduced in August 2002. | Class | org.openscience.cdk.io | CDK |
| MDLRXNWriter | Writes a reaction to a MDL rxn or SDF file. | Class | org.openscience.cdk.io | CDK |
| MDLV2000Format | Class | org.openscience.cdk.io.formats | CDK | |
| MDLV2000Reader | Reads content from MDL molfiles and SD files. | Class | org.openscience.cdk.io | CDK |
| MDLV2000Writer | Writes MDL molfiles, which contains a single molecule (see ). | Class | org.openscience.cdk.io | CDK |
| MDLV3000Format | Class | org.openscience.cdk.io.formats | CDK | |
| MDLV3000Reader | Class that implements the MDL mol V3000 format. | Class | org.openscience.cdk.io | CDK |
| MDMolecule | Class | org.openscience.cdk.libio.md | CDK | |
| MDMoleculeConvention | Class | org.openscience.cdk.io.cml | CDK | |
| MDMoleculeCustomizer | Customize persistence of MDMolecule by adding support for residues and charge groups. | Class | org.openscience.cdk.libio.cml | CDK |
| MinimalPathIterator | Iterates over all shortest paths between two vertices in an undirected, unweighted graph. | Class | org.openscience.cdk.graph | CDK |
| MM2AtomTypeMatcher | Class implements methods to assign mmff94 atom types for a specific atom in an molecule. | Class | org.openscience.cdk.atomtype | CDK |
| MM2BasedAtomTypePattern | Class stores hose code patterns to identify mm2 force field atom types. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| MM2BasedParameterSetReader | AtomType list configurator that uses the ParameterSet originally defined in mm2. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| MMElementRule | This class validate if the occurrence of the IElements in the IMolecularFormula, for metabolites, are into a maximal limit according paper: . | Class | org.openscience.cdk.formula.rules | CDK |
| MMElementRule .Database | A enumeration of the possible databases according the rules | Class | org.openscience.cdk.formula.rules | CDK |
| MMElementRule .RangeMass | A enumeration of the possible mass range according the rules | Class | org.openscience.cdk.formula.rules | CDK |
| MMFF94AtomTypeMatcher | Class implements methods to assign mmff94 atom types for a specific atom in an molecule. | Class | org.openscience.cdk.atomtype | CDK |
| MMFF94BasedAtomTypePattern | Class stores hose code patterns to identify mm2 force field atom typesAuthor:chhoppeCreated on:2004-09-07 | Class | org.openscience.cdk.modeling.builder3d | CDK |
| MMFF94BasedParameterSetReader | AtomType list configurator that uses the ParameterSet originally defined in mmff94. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| MMFF94ParametersCall | Set the right atoms order to get the parameters. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| MMFF94PartialCharges | The calculation of the MMFF94 partial charges. | Class | org.openscience.cdk.charges | CDK |
| MMODFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ModelBuilder3D | The main class to generate the 3D coordinates of a molecule ModelBuilder3D. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| Mol2Format | Class | org.openscience.cdk.io.formats | CDK | |
| Mol2Reader | Reads a molecule from an Mol2 file, such as written by Sybyl. | Class | org.openscience.cdk.io | CDK |
| Mol2Writer | An output Writer that writes molecular data into the Tripos Mol2 format. | Class | org.openscience.cdk.io | CDK |
| MolecularFormula | Class defining a molecular formula object. | Class | org.openscience.cdk.formula | CDK |
| MolecularFormula | Class defining a molecular formula object. | Class | org.openscience.cdk.silent | CDK |
| MolecularFormulaChecker | Validate a molecular formula given in IMolecularformula object. | Class | org.openscience.cdk.formula | CDK |
| MolecularFormulaManipulator | Class with convenience methods that provide methods to manipulate IMolecularFormula's. | Class | org.openscience.cdk.tools.manipulator | CDK |
| MolecularFormulaRange | Class defining a expanded molecular formula object. | Class | org.openscience.cdk.formula | CDK |
| MolecularFormulaRangeManipulator | Class with convenience methods that provide methods to manipulate MolecularFormulaRange's. | Class | org.openscience.cdk.tools.manipulator | CDK |
| MolecularFormulaSet | Class defining an set object of MolecularFormulas. | Class | org.openscience.cdk.formula | CDK |
| MolecularFormulaSet | Class defining an set object of MolecularFormulas. | Class | org.openscience.cdk.silent | CDK |
| MolecularFormulaSetManipulator | Class with convenience methods that provide methods to manipulate MolecularFormulaSet's. | Class | org.openscience.cdk.tools.manipulator | CDK |
| Molecule | Represents the concept of a chemical molecule, an object composed of atoms connected by bonds. | Class | org.openscience.cdk | CDK |
| Molecule | Represents the concept of a chemical molecule, an object composed of atoms connected by bonds. | Class | org.openscience.cdk.silent | CDK |
| MoleculeBuilder | Takes in parsed Tokens from NomParser and contains rules to convert those tokens to a Molecule. | Class | org.openscience.cdk.iupac.parser | CDK |
| MoleculeFactory | This class contains methods for generating simple organic molecules. | Class | org.openscience.cdk.templates | CDK |
| MoleculeFeaturesTool | Utility that helps determine which data features are present. | Class | org.openscience.cdk.tools.features | CDK |
| MoleculeFromSignatureBuilder | Builds a molecule from a signature. | Class | org.openscience.cdk.signature | CDK |
| MoleculeGraphs | Utility class to create a molecule graph for use with JGraphT. | Class | org.openscience.cdk.graph | CDK |
| MoleculeSanityCheck | Class that cleans a molecule before MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |
| MoleculeSet | A set of molecules, for example those taking part in a reaction. | Class | org.openscience.cdk | CDK |
| MoleculeSet | A set of molecules, for example those taking part in a reaction. | Class | org.openscience.cdk.silent | CDK |
| MoleculeSetManipulator | Class | org.openscience.cdk.tools.manipulator | CDK | |
| MoleculeSetRenderer | A general renderer for IChemModels, IReactions, and IMolecules. | Class | org.openscience.cdk.renderer | CDK |
| MoleculeSignature | A molecule signature is a way to produce AtomSignatures and to get the canonical signature string for a molecule. | Class | org.openscience.cdk.signature | CDK |
| MoleculeSignatureLabellingAdaptor | Class | org.openscience.cdk.smsd.labelling | CDK | |
| MolHandler | Class that handles molecules for MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |
| MomentOfInertiaDescriptor | A descriptor that calculates the moment of inertia and radius of gyration. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| Monomer | A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms. | Class | org.openscience.cdk | CDK |
| Monomer | A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms. | Class | org.openscience.cdk.silent | CDK |
| MOPAC2002Format | Class | org.openscience.cdk.io.formats | CDK | |
| MOPAC7Format | Class | org.openscience.cdk.io.formats | CDK | |
| MOPAC93Format | Class | org.openscience.cdk.io.formats | CDK | |
| MOPAC97Format | Class | org.openscience.cdk.io.formats | CDK | |
| MorganNumbersTools | Tool for calculating Morgan numbers . | Class | org.openscience.cdk.graph.invariant | CDK |
| MoSSOutputFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MoSSOutputReader | Reader for MoSS output files which present the results of a substructure mining study. | Class | org.openscience.cdk.io | CDK |
| 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. | Class | org.openscience.cdk.renderer.elements.path | CDK |
| MPQCFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MurckoFragmenter | An implementation of the Murcko fragmenation method . | Class | org.openscience.cdk.fragment | CDK |
| NeighborList | Creates a list of atoms neighboring each atom in the molecule. | Class | org.openscience.cdk.geometry.surface | CDK |
| NitrogenRule | This class validate if the rule of nitrogen is kept. | Class | org.openscience.cdk.formula.rules | CDK |
| NNAdductFormula | Class | org.openscience.cdk.nonotify | CDK | |
| NNAminoAcid | Class | org.openscience.cdk.nonotify | CDK | |
| NNAtom | Class | org.openscience.cdk.nonotify | CDK | |
| NNAtomContainer | Class | org.openscience.cdk.nonotify | CDK | |
| NNAtomContainerSet | Class | org.openscience.cdk.nonotify | CDK | |
| NNAtomParity | Class | org.openscience.cdk.nonotify | CDK | |
| NNAtomType | Class | org.openscience.cdk.nonotify | CDK | |
| NNBioPolymer | Class | org.openscience.cdk.nonotify | CDK | |
| NNBond | Class | org.openscience.cdk.nonotify | CDK | |
| NNChemFile | Class | org.openscience.cdk.nonotify | CDK | |
| NNChemModel | Class | org.openscience.cdk.nonotify | CDK | |
| NNChemObject | Class | org.openscience.cdk.nonotify | CDK | |
| NNChemSequence | Class | org.openscience.cdk.nonotify | CDK | |
| NNCrystal | Class | org.openscience.cdk.nonotify | CDK | |
| NNElectronContainer | Class | org.openscience.cdk.nonotify | CDK | |
| NNElement | Class | org.openscience.cdk.nonotify | CDK | |
| NNFragmentAtom | Class to represent an IPseudoAtom which embeds an IAtomContainer. | Class | org.openscience.cdk.nonotify | CDK |
| NNIsotope | Class | org.openscience.cdk.nonotify | CDK | |
| NNLonePair | Class | org.openscience.cdk.nonotify | CDK | |
| NNMapping | Class | org.openscience.cdk.nonotify | CDK | |
| NNMolecularFormula | Class | org.openscience.cdk.nonotify | CDK | |
| NNMolecularFormulaSet | Class | org.openscience.cdk.nonotify | CDK | |
| NNMolecule | Class | org.openscience.cdk.nonotify | CDK | |
| NNMoleculeSet | Class | org.openscience.cdk.nonotify | CDK | |
| NNMonomer | Class | org.openscience.cdk.nonotify | CDK | |
| NNPDBAtom | Class | org.openscience.cdk.nonotify | CDK | |
| NNPDBMonomer | Class | org.openscience.cdk.nonotify | CDK | |
| NNPDBPolymer | Class | org.openscience.cdk.nonotify | CDK | |
| NNPDBStructure | Class | org.openscience.cdk.nonotify | CDK | |
| NNPolymer | Class | org.openscience.cdk.nonotify | CDK | |
| NNPseudoAtom | Class | org.openscience.cdk.nonotify | CDK | |
| NNReaction | Class | org.openscience.cdk.nonotify | CDK | |
| NNReactionScheme | Class | org.openscience.cdk.nonotify | CDK | |
| NNReactionSet | Class | org.openscience.cdk.nonotify | CDK | |
| NNRing | Class | org.openscience.cdk.nonotify | CDK | |
| NNRingSet | Class | org.openscience.cdk.nonotify | CDK | |
| NNSingleElectron | Class | org.openscience.cdk.nonotify | CDK | |
| NNStrand | Class | org.openscience.cdk.nonotify | CDK | |
| Node | All AST nodes must implement this interface. | Interface | org.openscience.cdk.smiles.smarts.parser | CDK |
| NodeBuilder | Class for building/storing nodes (atoms) in the graph with atom query capabilities. | Class | org.openscience.cdk.smsd.algorithm.vflib.builder | CDK |
| NomParser | A class partly generated by JavaCC which breaks down the chemical name into computable subparts and passes these parts to the MoleculeBuilder. | Class | org.openscience.cdk.iupac.parser | CDK |
| NomParserConstants | Token literal values and constants. | Interface | org.openscience.cdk.iupac.parser | CDK |
| NomParserTokenManager | Class | org.openscience.cdk.iupac.parser | CDK | |
| NonCHHeavyAtom | This matcher any heavy atom that is not C or H. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| NoNotificationChemObjectBuilder | Class | org.openscience.cdk.nonotify | CDK | |
| Normalizer | Adjusts parts of an AtomContainer to the congiguratin of a fragment. | Class | org.openscience.cdk.normalize | CDK |
| NoSuchAtomException | Exception that is thrown when an Atom is requested or required that does not exist in the relevant environment. | Class | org.openscience.cdk.exception | CDK |
| NoSuchAtomTypeException | Exception that may be thrown when an atom type is looked up or perceived but no such atom type was found. | Class | org.openscience.cdk.exception | CDK |
| NumericalSurface | A class representing the solvent acessible surface area surface of a molecule. | Class | org.openscience.cdk.geometry.surface | CDK |
| NWChemFormat | Class | org.openscience.cdk.io.formats | CDK | |
| OneElectronJob | Calculates the orbitals and orbital energies of electron systems without electron electron interactions | Class | org.openscience.cdk.math.qm | CDK |
| OptionIOSetting | An class for a reader setting which must be found in the list of possible settings. | Class | org.openscience.cdk.io.setting | CDK |
| Orbit | A list of atom indices, and the label of the orbit. | Class | org.openscience.cdk.signature | CDK |
| Orbitals | This class represents a set of orbitalsAuthor:Stephan Michels Created on:2001-06-14 | Class | org.openscience.cdk.math.qm | CDK |
| OrderQueryBond | Class | org.openscience.cdk.isomorphism.matchers | CDK | |
| OrderQueryBond | This matches a bond with a certain bond order. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| OrderQueryBondOrderOnly | IQueryBond that matches IBond object only based on bond order, and disregarding any aromaticity flag. | Class | org.openscience.cdk.isomorphism.matchers | CDK |
| OvalElement | An oval element (should) have both a width and a height. | Class | org.openscience.cdk.renderer.elements | CDK |
| OverlapResolver | Helper class for Structure Diagram Generation. | Class | org.openscience.cdk.layout | CDK |
| OWLAtomTypeHandler | SAX Handler for the OWLAtomTypeReader. | Class | org.openscience.cdk.config.atomtypes | CDK |
| OWLAtomTypeMappingHandler | SAX Handler for the OWLAtomTypeMappingReader. | Class | org.openscience.cdk.config.atomtypes | CDK |
| OWLAtomTypeMappingReader | XML Reader for the OWLBasedAtomTypeConfigurator. | Class | org.openscience.cdk.config.atomtypes | CDK |
| OWLAtomTypeReader | XML Reader for the OWLBasedAtomTypeConfigurator. | Class | org.openscience.cdk.config.atomtypes | CDK |
| OWLBasedAtomTypeConfigurator | AtomType resource that reads the atom type configuration from an OWL file. | Class | org.openscience.cdk.config | CDK |
| OWLFile | Dictionary with entries build from an OWL file. | Class | org.openscience.cdk.dict | CDK |
| OWLReact | Dictionary with entries build from an OWL React. | Class | org.openscience.cdk.dict | CDK |
| ParameterReact | Class which defines the allowed parameters of a reaction. | Class | org.openscience.cdk.reaction.type.parameters | CDK |
| ParseException | This exception is thrown when parse errors are encountered. | Class | org.openscience.cdk.iupac.parser | CDK |
| ParseException | This exception is thrown when parse errors are encountered. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| PartialAtomicChargeColors | Class defining the color which with atoms are colored. | Class | org.openscience.cdk.renderer.color | CDK |
| PartialFilledStructureMerger | Randomly generates a single, connected, correctly bonded structure from a number of fragments. | Class | org.openscience.cdk.structgen.stochastic | CDK |
| PartialPiChargeDescriptor | The calculation of pi partial charges in pi-bonded systems of an heavy atom was made by Saller-Gasteiger. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| PartialSigmaChargeDescriptor | The calculation of sigma partial charges in sigma-bonded systems of an heavy atom was made by Marsilli-Gasteiger. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| PartialTChargeMMFF94Descriptor | The calculation of total partial charges of an heavy atom is based on MMFF94 model. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| PartialTChargePEOEDescriptor | The calculation of total partial charges of an heavy atom is based on Partial Equalization of Electronegativity method (PEOE-PEPE) from Gasteiger. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| Path | Class | org.openscience.cdk.ringsearch | CDK | |
| PathBuilder | Builder class for paths. | Class | org.openscience.cdk.renderer.elements.path | CDK |
| PathEdge | Class | org.openscience.cdk.smsd.ring | CDK | |
| PathElement | Class | org.openscience.cdk.renderer.elements.path | CDK | |
| PathElement | A path composed of points. | Class | org.openscience.cdk.renderer.elements | CDK |
| PathGraph | Class | org.openscience.cdk.smsd.ring | CDK | |
| PathTools | Tools class with methods for handling molecular graphs. | Class | org.openscience.cdk.graph | CDK |
| PCCompoundASNReader | Reads an object from ASN formated input for PubChem Compound entries. | Class | org.openscience.cdk.io | CDK |
| PCCompoundXMLReader | Reads an object from ASN. | Class | org.openscience.cdk.io | CDK |
| PCModelFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PCSubstanceXMLReader | Reads an object from ASN formated input for PubChem Compound entries. | Class | org.openscience.cdk.io | CDK |
| PDBAtom | Represents the idea of an atom as used in PDB files. | Class | org.openscience.cdk.protein.data | CDK |
| PDBAtom | Represents the idea of an atom as used in PDB files. | Class | org.openscience.cdk.silent | CDK |
| PDBAtomCustomizer | Customizer for the libio-cml Convertor to be able to export details forAuthor:egonwBelongs to the set:libio-cml-customizersCreated on:2005-05-04Requires:java1. | Class | org.openscience.cdk.libio.cml | CDK |
| PDBConvention | This is a lousy implementation, though. | Class | org.openscience.cdk.io.cml | CDK |
| PDBFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PDBMLFormat | XML version of the PDB format. | Class | org.openscience.cdk.io.formats | CDK |
| PDBMonomer | Represents the idea of an monomer as used in PDB files. | Class | org.openscience.cdk.protein.data | CDK |
| PDBMonomer | Represents the idea of an monomer as used in PDB files. | Class | org.openscience.cdk.silent | CDK |
| PDBPolymer | An entry in the PDB database. | Class | org.openscience.cdk.protein.data | CDK |
| PDBPolymer | An entry in the PDB database. | Class | org.openscience.cdk.silent | CDK |
| PDBReader | Reads the contents of a PDBFile. | Class | org.openscience.cdk.io | CDK |
| PDBStrand | An entry in the PDB database. | Class | org.openscience.cdk.protein.data | CDK |
| PDBStructure | Holder for secundary protein structure elements. | Class | org.openscience.cdk.protein.data | CDK |
| PDBStructure | Holder for secundary protein structure elements. | Class | org.openscience.cdk.silent | CDK |
| PDBWriter | Saves small molecules in a rudimentary PDB format. | Class | org.openscience.cdk.io | CDK |
| PeriodicGroupNumberAtom | This matcher checks the periodic group number of an atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| PeriodicTable | Represents elements of the Periodic Table. | Class | org.openscience.cdk.tools.periodictable | CDK |
| PeriodicTablePositionDescriptor | This class returns the period in the periodic table of an atom belonging to an atom container This descriptor uses these parameters: | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| Permutor | General permutation generator, that uses orderly generation by ranking and unranking. | Class | org.openscience.cdk.smsd.labelling | CDK |
| 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. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| PetitjeanShapeIndexDescriptor | Evaluates the Petitjean shape indices, These original Petitjean number was described by Petitjean () | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| PharmacophoreAngleBond | Represents an angle relationship between three pharmacophore groups. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreAtom | A representation of a pharmacophore group. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreBond | Represents a distance relationship between two pharmacophore groups. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreMatcher | Identifies atoms whose 3D arrangement matches a specified pharmacophore query. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreQuery | Represents a colleciton of pharmacophore groups and constraints. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreQueryAngleBond | Represents a pharmacophore query angle constraint. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreQueryAtom | Represents a query pharmacophore group. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreQueryBond | Represents a pharmacophore query distance constraint. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreUtils | Provides some utility methods for pharmacophore handling. | Class | org.openscience.cdk.pharmacophore | CDK |
| PhysicalConstants | An class providing predefined properties of physical constants. | Class | org.openscience.cdk | CDK |
| PiBondingMovementReaction | IReactionProcess which tries to reproduce the delocalization of electrons which are unsaturated bonds from conjugated rings. | Class | org.openscience.cdk.reaction.type | CDK |
| 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 | Class | org.openscience.cdk.qsar.descriptors.atompair | CDK |
| 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). | Class | org.openscience.cdk.charges | CDK |
| PiElectronegativityDescriptor | Pi electronegativity is given by X = a + bq + c(q*q) This descriptor uses these parameters: | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| PMPConvention | Class | org.openscience.cdk.io.cml | CDK | |
| PMPFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PMPReader | Reads an frames from a PMP formated input. | Class | org.openscience.cdk.io | CDK |
| Point | Class | org.openscience.cdk.graph.rebond | CDK | |
| Point2dDifference | Difference between two boolean[]'s. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| Point3dDifference | Difference between two boolean[]'s. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| Polarizability | Calculation of the polarizability of a molecule by the method of Kang and Jhon and Gasteiger based on and | Class | org.openscience.cdk.charges | CDK |
| Polymer | Subclass of Molecule to store Polymer specific attributes that a Polymer has. | Class | org.openscience.cdk | CDK |
| Polymer | Subclass of Molecule to store Polymer specific attributes that a Polymer has. | Class | org.openscience.cdk.silent | CDK |
| PostFilter | Class that cleans redundant mappings from the solution set. | Class | org.openscience.cdk.smsd.filters | CDK |
| POVRayFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PQSChemFormat | Class | org.openscience.cdk.io.formats | CDK | |
| Primes | Class | org.openscience.cdk.math | CDK | |
| ProblemMarker | Tool to mark IChemObject's as having a problem. | Class | org.openscience.cdk.validate | CDK |
| ProductsBoxGenerator | Generate the symbols for radicals. | Class | org.openscience.cdk.renderer.generators | CDK |
| Projector | Tool to make projections from 3D to 2DKeywords:projection in 2D | Class | org.openscience.cdk.geometry | CDK |
| PropertiesListener | Answers the questions by looking up the values in a Properties object. | Class | org.openscience.cdk.io.listener | CDK |
| ProteinBuilderTool | Class that facilitates building protein structures. | Class | org.openscience.cdk.tools | CDK |
| ProteinPocketFinder | The detection of pocket and cavities in a bioPolymer is done similar to the program TODO: Optimisation of the cubic grid placement | Class | org.openscience.cdk.protein | CDK |
| ProtonAffinityHOSEDescriptor | This class returns the proton affinity of an atom containing. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| ProtonTotalPartialChargeDescriptor | The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE). | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| PseudoAtom | Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc. | Class | org.openscience.cdk | CDK |
| PseudoAtom | Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc. | Class | org.openscience.cdk.silent | CDK |
| PubChemASNFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemCompoundsXMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemCompoundXMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubchemFingerprinter | Generates a Pubchem fingerprint for a molecule. | Class | org.openscience.cdk.fingerprint | CDK |
| PubChemFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemSubstancesASNFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemSubstancesXMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemSubstanceXMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemXMLHelper | Helper class to parse PubChem XML documents. | Class | org.openscience.cdk.io.pubchemxml | CDK |
| QChemFormat | Class | org.openscience.cdk.io.formats | CDK | |
| QSARConvention | This is an implementation for the CDK convention. | Class | org.openscience.cdk.io.cml | CDK |
| QSARCustomizer | Customizer for the libio-cml Convertor to be able to export details for QSAR descriptors calculated for Molecules. | Class | org.openscience.cdk.libio.cml | CDK |
| QuadTo | Make a quadratic curve in the path. | Class | org.openscience.cdk.renderer.elements.path | CDK |
| Quaternion | This class handles quaternions. | Class | org.openscience.cdk.math | CDK |
| QueryAtomContainer | Class | org.openscience.cdk.isomorphism.matchers | CDK | |
| QueryAtomContainerCreator | Class | org.openscience.cdk.isomorphism.matchers | CDK | |
| QueryCompiler | This class creates an template for MCS/substructure query. | Class | org.openscience.cdk.smsd.algorithm.vflib.query | CDK |
| QueryProcessor | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK | |
| Queue | Class | org.openscience.cdk.ringsearch | CDK | |
| RadicalChargeSiteInitiationHReaction | IReactionProcess which participate mass spectrum process. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalChargeSiteInitiationReaction | IReactionProcess which participate mass spectrum process. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalGenerator | Generate the symbols for radicals. | Class | org.openscience.cdk.renderer.generators | CDK |
| RadicalSiteHrAlphaReaction | This reaction could be represented as [A*]-(C)_2-C3[H] => A([H])-(C_2)-[C3*]. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteHrBetaReaction | This reaction could be represented as [A*]-(C)_3-C4[H] => A([H])-(C_3)-[C4*]. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteHrDeltaReaction | This reaction could be represented as [A*]-(C)_4-C5[H] => A([H])-(C_4)-[C5*]. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteHrGammaReaction | This reaction could be represented as [A*]-C1-C2-C3[H] => A([H])-C1-C2-[C3*]. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteInitiationHReaction | IReactionProcess which participate mass spectrum process. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteInitiationReaction | IReactionProcess which participate mass spectrum process. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteIonizationMechanism | This mechanism extracts an atom because of the stabilization of a radical. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| RadicalSiteRearrangementMechanism | This mechanism displaces an Atom or substructure (R) from one position to an other. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| RadicalSiteRrAlphaReaction | This reaction could be represented as [A*]-(C)_2-C3[R] => A([RH])-(C_2)-[C3*]. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteRrBetaReaction | This reaction could be represented as [A*]-(C)_3-C4[R] => A([R])-(C_3)-[C4*]. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteRrDeltaReaction | This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*]. | Class | org.openscience.cdk.reaction.type | CDK |
| RadicalSiteRrGammaReaction | This reaction could be represented as [A*]-(C)_5-C6[R] => A([R])-(C_5)-[C6*]. | Class | org.openscience.cdk.reaction.type | CDK |
| RandomAccessReader | Random access to text files of compounds. | Class | org.openscience.cdk.io.random | CDK |
| RandomAccessSDFReader | Random access of SDF file. | Class | org.openscience.cdk.io.random | CDK |
| RandomGenerator | RandomGenerator is a generator of Constitutional Isomers. | Class | org.openscience.cdk.structgen | CDK |
| RandomNumbersTool | Class supplying useful methods to generate random numbers. | Class | org.openscience.cdk.math | CDK |
| RasmolColors | Atom coloring following RasMol/Chime Color scheme http://www. | Class | org.openscience.cdk.renderer.color | CDK |
| RawCopyFormat | Class | org.openscience.cdk.io.formats | CDK | |
| RDBERule | Ring Double Bond Equivalents (RDBE) or Double Bond Equivalents (DBE) are calculated from valence values of | Class | org.openscience.cdk.formula.rules | CDK |
| RDFCalculator | Calculator of radial distribution functions. | Class | org.openscience.cdk.geometry | CDK |
| RDFProtonDescriptor_G3R | This class calculates G3R proton descriptors used in neural networks for H1 NMR shift . | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| RDFProtonDescriptor_GDR | This class calculates GDR proton descriptors used in neural networks for H1 NMR shift . | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| RDFProtonDescriptor_GHR | This class calculates GHR proton descriptors used in neural networks for H1 NMR shift . | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| RDFProtonDescriptor_GHR_topol | This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift . | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| RDFProtonDescriptor_GSR | This class calculates GDR proton descriptors used in neural networks for H1 NMR shift . | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| ReactantsBoxGenerator | Generate the symbols for radicals. | Class | org.openscience.cdk.renderer.generators | CDK |
| Reaction | Represents the idea of a chemical reaction. | Class | org.openscience.cdk | CDK |
| Reaction | Represents the idea of a chemical reaction. | Class | org.openscience.cdk.silent | CDK |
| ReactionArrowGenerator | Generate the arrow for a reaction. | Class | org.openscience.cdk.renderer.generators | CDK |
| ReactionBoxGenerator | Generate the symbols for radicals. | Class | org.openscience.cdk.renderer.generators | CDK |
| ReactionChain | Classes that extends the definition of reaction to a chain reaction. | Class | org.openscience.cdk.reaction | CDK |
| ReactionEngine | The base class for all chemical reactions objects in this cdk. | Class | org.openscience.cdk.reaction | CDK |
| ReactionManipulator | Class | org.openscience.cdk.tools.manipulator | CDK | |
| ReactionPlusGenerator | Generate the arrow for a reaction. | Class | org.openscience.cdk.renderer.generators | CDK |
| ReactionRenderer | A general renderer for IChemModels, IReactions, and IMolecules. | Class | org.openscience.cdk.renderer | CDK |
| ReactionSceneGenerator | Generator for general reaction scene components. | Class | org.openscience.cdk.renderer.generators | CDK |
| ReactionSceneGenerator .ArrowHeadWidth | Double which indicates how wide the arrow head is in screen pixels. | Class | org.openscience.cdk.renderer.generators | CDK |
| ReactionSceneGenerator .ShowReactionBoxes | Boolean that indicates if boxes are drawn around the reaction. | Class | org.openscience.cdk.renderer.generators | CDK |
| ReactionScheme | Classes that extends the definition of reaction to a scheme. | Class | org.openscience.cdk | CDK |
| ReactionScheme | Classes that extends the definition of reaction to a scheme. | Class | org.openscience.cdk.silent | CDK |
| ReactionSchemeManipulator | Class | org.openscience.cdk.tools.manipulator | CDK | |
| ReactionSet | A set of reactions, for example those taking part in a reaction. | Class | org.openscience.cdk | CDK |
| ReactionSet | A set of reactions, for example those taking part in a reaction. | Class | org.openscience.cdk.silent | CDK |
| ReactionSetManipulator | Class | org.openscience.cdk.tools.manipulator | CDK | |
| ReactionSetRenderer | A general renderer for IChemModels, IReactions, and IMolecules. | Class | org.openscience.cdk.renderer | CDK |
| ReactionSpecification | Class that is used to distribute reactions specifications. | Class | org.openscience.cdk.reaction | CDK |
| ReaderEvent | Signals that something has happened in a file reader. | Class | org.openscience.cdk.io | CDK |
| ReaderFactory | A factory for creating ChemObjectReaders. | Class | org.openscience.cdk.io | CDK |
| RearrangementAnionReaction | IReactionProcess which participate in movement resonance. | Class | org.openscience.cdk.reaction.type | CDK |
| RearrangementCationReaction | IReactionProcess which participate in movement resonance. | Class | org.openscience.cdk.reaction.type | CDK |
| RearrangementChargeMechanism | This mechanism displaces the charge(radical, charge + or charge -) because of a double bond which is associated. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| RearrangementLonePairReaction | IReactionProcess which participate in movement resonance. | Class | org.openscience.cdk.reaction.type | CDK |
| RearrangementRadicalReaction | IReactionProcess which participate in movement resonance. | Class | org.openscience.cdk.reaction.type | CDK |
| RebondTool | Provides tools to rebond a molecule from 3D coordinates only. | Class | org.openscience.cdk.graph.rebond | CDK |
| RectangleElement | A rectangle, with width and height. | Class | org.openscience.cdk.renderer.elements | CDK |
| RecursiveSmartsAtom | This matches recursive smarts atoms. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| RemovingSEofBMechanism | This mechanism extracts a single electron from a bonding orbital which located in an bond. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| RemovingSEofNBMechanism | This mechanism extracts a single electron from a non-bonding orbital which located in a ILonePair container. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| RendererModel | Model for IRenderer that contains settings for drawing objects. | Class | org.openscience.cdk.renderer | CDK |
| RendererModel .ColorHash | The color hash is used to color substructures. | Class | org.openscience.cdk.renderer | CDK |
| RendererModel .ExternalHighlightColor | The color used to highlight external selections. | Class | org.openscience.cdk.renderer | CDK |
| Residue | A residue is a named, numbered collection of atoms in an MDMolecule. | Class | org.openscience.cdk.libio.md | CDK |
| RGraph | This class implements the Resolution Graph (RGraph). | Class | org.openscience.cdk.isomorphism.mcss | CDK |
| RGroup | Represents a single substitute structure in an RGroupList. | Class | org.openscience.cdk.isomorphism.matchers | CDK |
| RGroupList | Represents a list of Rgroup substitutes to be associated with someAuthor:Mark RijnbeekKeywords:Rgroup, R group, R-group | Class | org.openscience.cdk.isomorphism.matchers | CDK |
| RGroupQuery | Represents information contained in a Symyx RGfile (R-group query file). | Class | org.openscience.cdk.isomorphism.matchers | CDK |
| RGroupQueryFormat | Format for Symyx RGfiles (Rgroup query files). | Class | org.openscience.cdk.io.formats | CDK |
| RGroupQueryReader | A reader for Symyx' Rgroup files (RGFiles). | Class | org.openscience.cdk.io | CDK |
| RGroupQueryWriter | A writer for Symyx' Rgroup files (RGFiles). | Class | org.openscience.cdk.io | CDK |
| Ring | Class representing a ring structure in a molecule. | Class | org.openscience.cdk | CDK |
| Ring | Class representing a ring structure in a molecule. | Class | org.openscience.cdk.silent | CDK |
| RingAtom | This matches an atom in a specific size ring. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| RingBond | This smarts bond matches any bond that is in a ring. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| RingElement | Class | org.openscience.cdk.renderer.elements | CDK | |
| RingFilter | Class | org.openscience.cdk.smsd.ring | CDK | |
| RingFinder | Interface | org.openscience.cdk.smsd.ring | CDK | |
| RingGenerator | Generates just the aromatic indicators for rings : circles, or light-gray inner bonds, depending on the value of CDKStyleAromaticity. | Class | org.openscience.cdk.renderer.generators | CDK |
| RingGenerator .CDKStyleAromaticity | Depicts aromaticity of rings in the original CDK style. | Class | org.openscience.cdk.renderer.generators | CDK |
| RingGenerator .RingProportion | The proportion of a ring bounds to use to draw the ring. | Class | org.openscience.cdk.renderer.generators | CDK |
| RingGenerator .ShowAromaticity | Class | org.openscience.cdk.renderer.generators | CDK | |
| RingIdentifierAtom | This encapsulates an atom with a ring identifier, with an optional ring bond specified. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| RingManipulator | Class | org.openscience.cdk.tools.manipulator | CDK | |
| RingMembershipAtom | This query atom matches any atom with a certain number of SSSR. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| RingPartitioner | Partitions a RingSet into RingSets of connected rings. | Class | org.openscience.cdk.ringsearch | CDK |
| RingPlacer | Class providing methods for generating coordinates for ring atoms. | Class | org.openscience.cdk.layout | CDK |
| RingSet | Maintains a set of Ring objects. | Class | org.openscience.cdk | CDK |
| RingSet | Maintains a set of Ring objects. | Class | org.openscience.cdk.silent | CDK |
| RingSetManipulator | Class | org.openscience.cdk.tools.manipulator | CDK | |
| RingSizeComparator | Class | org.openscience.cdk.tools.manipulator | CDK | |
| 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. | Class | org.openscience.cdk.isomorphism.mcss | CDK |
| RNode | Node of the resolution graphe (RGraph) An RNode represents an association betwwen two edges of the source graphs G1 and G2 that are compared. | Class | org.openscience.cdk.isomorphism.mcss | CDK |
| RotatableBondsCountDescriptor | The number of rotatable bonds is given by the SMARTS specified by Daylight on This descriptor uses these parameters: | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| RssWriter | Generates an RSS feed. | Class | org.openscience.cdk.io | CDK |
| RuleOfFiveDescriptor | This Class contains a method that returns the number failures of the Lipinski's Rule Of 5. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| SaturationChecker | Provides methods for checking whether an atoms valences are saturated with respect to a particular atom type. | Class | org.openscience.cdk.tools | CDK |
| SDFFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SDFWriter | Writes MDL SD files (). | Class | org.openscience.cdk.io | CDK |
| SetReactionCenter | Class extension of ParameterReact class which defines if a reaction is set already the reaction centerAuthor:miguelrojasch | Class | org.openscience.cdk.reaction.type.parameters | CDK |
| SharingAnionReaction | IReactionProcess which participate in movement resonance. | Class | org.openscience.cdk.reaction.type | CDK |
| SharingChargeDBReaction | IReactionProcess which participate in movement resonance. | Class | org.openscience.cdk.reaction.type | CDK |
| SharingChargeSBReaction | IReactionProcess which participate in movement resonance. | Class | org.openscience.cdk.reaction.type | CDK |
| SharingElectronMechanism | This mechanism displaces the charge (lonePair) because of deficiency of charge. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| SharingLonePairReaction | IReactionProcess which participate in movement resonance. | Class | org.openscience.cdk.reaction.type | CDK |
| ShelXFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ShelXReader | A reader for ShelX output (RES) files. | Class | org.openscience.cdk.io | CDK |
| ShelXWriter | Serializes a MoleculeSet or a Molecule object to ShelX code. | Class | org.openscience.cdk.io | CDK |
| SigmaElectronegativityDescriptor | Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| 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. | Class | org.openscience.cdk.signature | CDK |
| SignatureReactionCanoniser | Class | org.openscience.cdk.smsd.labelling | CDK | |
| SilentChemObjectBuilder | Class | org.openscience.cdk.silent | CDK | |
| SimpleBasisSet | This class will generate a simple base set for a atom container. | Class | org.openscience.cdk.math.qm | CDK |
| SimpleCharStream | An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing). | Class | org.openscience.cdk.iupac.parser | CDK |
| SimpleCharStream | An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing). | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| SimpleCycle | A cycle in a graph G is a subgraph in which every vertex has even degree. | Class | org.openscience.cdk.ringsearch.cyclebasis | CDK |
| SimpleCycleBasis | Auxiliary class for CycleBasis. | Class | org.openscience.cdk.ringsearch.cyclebasis | CDK |
| SimpleNode | Basic implementation of AST nodes. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| SingleElectron | A Single Electron is an orbital which is occupied by only one electron. | Class | org.openscience.cdk.silent | CDK |
| SingleElectron | A Single Electron is an orbital which is occupied by only one electron. | Class | org.openscience.cdk | CDK |
| SingleElectronDiff | Compares two ISingleElectron classes. | Class | org.openscience.cdk.tools.diff | CDK |
| SingleMapping | This class handles single atom mapping. | Class | org.openscience.cdk.smsd.algorithm.single | CDK |
| SingleMappingHandler | This is a handler class for single atom mappingAuthor:Syed Asad Rahman | Class | org.openscience.cdk.smsd.algorithm.single | CDK |
| SingleStructureRandomGenerator | Randomly generates a single, connected, correctly bonded structure for a given molecular formula. | Class | org.openscience.cdk.structgen | CDK |
| SmallestRingAtom | This smarts atom matches any atom with the smallest SSSR size being a See Also:Serialized FormKeywords:SMARTS | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| Smarts2MQLVisitor | An AST tree visitor. | Class | org.openscience.cdk.smiles.smarts.parser.visitor | CDK |
| SMARTSAtom | Abstract smarts atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| SMARTSBond | Abstract smarts bond. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| SmartsDumpVisitor | An AST Tree visitor. | Class | org.openscience.cdk.smiles.smarts.parser.visitor | CDK |
| SMARTSFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SMARTSParser | This parser implements a nearly complete subset of the SMARTS syntax as defined on Example code using SMARTS substructure search looks like: | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| SMARTSParserConstants | Token literal values and constants. | Interface | org.openscience.cdk.smiles.smarts.parser | CDK |
| SMARTSParserTokenManager | Class | org.openscience.cdk.smiles.smarts.parser | CDK | |
| SMARTSParserTreeConstants | Interface | org.openscience.cdk.smiles.smarts.parser | CDK | |
| SMARTSParserVisitor | Interface | org.openscience.cdk.smiles.smarts.parser | CDK | |
| SMARTSQueryTool | This class provides a easy to use wrapper around SMARTS matching functionality. | Class | org.openscience.cdk.smiles.smarts | CDK |
| SmartsQueryVisitor | An AST tree visitor. | Class | org.openscience.cdk.smiles.smarts.parser.visitor | CDK |
| SMILESFIXFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SMILESFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SmilesGenerator | Generates SMILES strings . | Class | org.openscience.cdk.smiles | CDK |
| SmilesParser | Parses a SMILES string and an AtomContainer. | Class | org.openscience.cdk.smiles | CDK |
| SmilesReactionCanoniser | Class | org.openscience.cdk.smsd.labelling | CDK | |
| SMILESReader | This Reader reads files which has one SMILES string on each line, where the format is given as below: | Class | org.openscience.cdk.io | CDK |
| SmilesValencyChecker | Small customization of ValencyHybridChecker suggested by Todd Martin specially tuned for SMILES parsing. | Class | org.openscience.cdk.tools | CDK |
| SMILESWriter | Writes the SMILES strings to a plain text file. | Class | org.openscience.cdk.io | CDK |
| SMSDNormalizer | This class containes set of modules required to clean a molecule before subjecting it for MCS search. | Class | org.openscience.cdk.normalize | CDK |
| SpanningTree | Spanning tree of a molecule. | Class | org.openscience.cdk.graph | CDK |
| SpartanFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SSSRFinder | Finds the Smallest Set of Smallest Rings. | Class | org.openscience.cdk.ringsearch | CDK |
| StabilizationCharges | The stabilization of the positive and the negative charge obtained (e. | Class | org.openscience.cdk.charges | CDK |
| StabilizationPlusChargeDescriptor | The stabilization of the positive charge (e. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| StandardSubstructureSets | Class | org.openscience.cdk.fingerprint | CDK | |
| StereoBond | This query bond matches bonds with specific stereo type. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| StereoTool | Methods to determine or check the stereo class of a set of atoms. | Class | org.openscience.cdk.stereo | CDK |
| StereoTool .SquarePlanarShape | The shape that four atoms take in a plane. | Class | org.openscience.cdk.stereo | CDK |
| StereoTool .StereoClass | Currently unused, but intended for the StereoTool to indicate what it 'means' by an assignment of some atoms to a class. | Class | org.openscience.cdk.stereo | CDK |
| StereoTool .TetrahedralSign | The handedness of a tetrahedron, in terms of the point-plane distance of three of the corners, compared to the fourth. | Class | org.openscience.cdk.stereo | CDK |
| Strand | A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms. | Class | org.openscience.cdk.silent | CDK |
| Strand | A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms. | Class | org.openscience.cdk | CDK |
| StringDifference | IDifference between two String. | Class | org.openscience.cdk.tools.diff.tree | CDK |
| StringIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
| StructGenAtomTypeGuesser | AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol. | Class | org.openscience.cdk.atomtype | CDK |
| StructGenMatcher | AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol. | Class | org.openscience.cdk.atomtype | CDK |
| StructureDiagramGenerator | Generates 2D coordinates for a molecule for which only connectivity is known or the coordinates have been discarded for some reason. | Class | org.openscience.cdk.layout | CDK |
| StructureResonanceGenerator | This class try to generate resonance structure for a determinate molecule. | Class | org.openscience.cdk.tools | CDK |
| SubstructureFingerprinter | IFingerprinter that gives a bit set which has a size equal to the number of substructures it was constructed from. | Class | org.openscience.cdk.fingerprint | CDK |
| SVGFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SwingEventRelay | Class | org.openscience.cdk.controller | CDK | |
| SwingGUIListener | Allows processing of IOSetting quesions which are passed to the user by using Swing dialogs. | Class | org.openscience.cdk.io.listener | CDK |
| SwingMouseEventRelay | Class | org.openscience.cdk.controller | CDK | |
| SwissArmyKnife | A set of utilities which did not really fit into any other categoryAuthor:steinbeckCreated on:2001-06-19 | Class | org.openscience.cdk.tools | CDK |
| SybylAtomTypeMatcher | Atom Type matcher for Sybyl atom types. | Class | org.openscience.cdk.atomtype | CDK |
| SybylDescriptorFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SymbolAndChargeQueryAtom | Class | org.openscience.cdk.isomorphism.matchers | CDK | |
| SymbolChargeIDQueryAtom | Class | org.openscience.cdk.isomorphism.matchers | CDK | |
| SymbolQueryAtom | Class | org.openscience.cdk.isomorphism.matchers | CDK | |
| SymbolSetQueryAtom | A QueryAtom that matches all symbols in this container. | Class | org.openscience.cdk.isomorphism.matchers | CDK |
| SystemOutLoggingTool | the System. | Class | org.openscience.cdk.tools | CDK |
| TaeAminoAcidDescriptor | An implementation of the TAE descriptors for amino acids. | Class | org.openscience.cdk.qsar.descriptors.protein | CDK |
| Tanimoto | Calculates the Tanimoto coefficient for a given pair of two fingerprint bitsets or real valued feature vectors. | Class | org.openscience.cdk.similarity | CDK |
| TargetProcessor | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK | |
| TargetProperties | Class for building/storing nodes (atoms) in the graph with atom query capabilities. | Class | org.openscience.cdk.smsd.algorithm.vflib.builder | CDK |
| TautomerizationMechanism | This mechanism produces the tautomerization chemical reaction between two tautomers. | Class | org.openscience.cdk.reaction.mechanism | CDK |
| TautomerizationReaction | IReactionProcess which produces a tautomerization chemical reaction. | Class | org.openscience.cdk.reaction.type | CDK |
| TemplateExtractor | Helper class that help setup a template library of CDK's Builder3D. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| TemplateHandler | Helper class for Structure Diagram Generation. | Class | org.openscience.cdk.layout | CDK |
| TemplateHandler3D | Helper class for ModelBuilder3D. | Class | org.openscience.cdk.modeling.builder3d | CDK |
| Tessellate | Performs a tessellation of the unit sphere. | Class | org.openscience.cdk.geometry.surface | CDK |
| TestClass | Class | org.openscience.cdk.annotations | CDK | |
| TestMethod | Class | org.openscience.cdk.annotations | CDK | |
| TetrahedralChirality | Stereochemistry specification for quadrivalent atoms. | Class | org.openscience.cdk.stereo | CDK |
| TextElement | Text element as used in the chemical drawing. | Class | org.openscience.cdk.renderer.elements | CDK |
| TextGroupElement | A group of text elements, particularly the element symbol (eg: "C") surrounded by other annotations such as mass number, charge, etc. | Class | org.openscience.cdk.renderer.elements | CDK |
| TextGroupElement .Position | Compass-point positions for text element annotation children. | Class | org.openscience.cdk.renderer.elements | CDK |
| TextGUIListener | Allows processing of IOSetting quesions which are passed to the user by using the System. | Class | org.openscience.cdk.io.listener | CDK |
| TimeManager | Class that handles execution time of the MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |
| TimeOut | Class that manages MCS timeout. | Class | org.openscience.cdk.smsd.global | CDK |
| TinkerMM2Format | Class | org.openscience.cdk.io.formats | CDK | |
| TinkerXYZFormat | Class | org.openscience.cdk.io.formats | CDK | |
| Token | Describes the input token stream. | Class | org.openscience.cdk.iupac.parser | CDK |
| Token | Describes the input token stream. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| TokenMgrError | Token Manager Error. | Class | org.openscience.cdk.iupac.parser | CDK |
| TokenMgrError | Token Manager Error. | Class | org.openscience.cdk.smiles.smarts.parser | CDK |
| ToleranceRangeRule | This class validate if the mass from an IMolecularFormula is between the tolerance range give a experimental mass. | Class | org.openscience.cdk.formula.rules | CDK |
| TopologicalMatrix | Calculator for a topological matrix representation of this AtomContainer. | Class | org.openscience.cdk.graph.matrix | CDK |
| TotalConnectionAtom | This matches an atom using total number of connections. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| TotalHCountAtom | This matcher checks the formal charge of the Atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| TotalRingConnectionAtom | This matcher checks the number of ring connections of the checked Atom with other Atom's. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| TotalValencyAtom | This matcher checks the total valency of the Atom. | Class | org.openscience.cdk.isomorphism.matchers.smarts | CDK |
| TPSADescriptor | Calculation of topological polar surface area based on fragment contributions (TPSA) . | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| Triangle | Representation of a triangle in 3D. | Class | org.openscience.cdk.geometry.surface | CDK |
| TurboMoleFormat | Class | org.openscience.cdk.io.formats | CDK | |
| TXTBasedAtomTypeConfigurator | AtomType list configurator that uses the AtomTypes originally defined in Jmol v5. | Class | org.openscience.cdk.config | CDK |
| Type | The type of the path elements. | Class | org.openscience.cdk.renderer.elements.path | CDK |
| UndoAdapter | An undo adapter for updating the state of the undo components according to the new state of the undo history list. | Class | org.openscience.cdk.controller | CDK |
| UniChemXYZFormat | Class | org.openscience.cdk.io.formats | CDK | |
| UnsupportedChemObjectException | Class | org.openscience.cdk.exception | CDK | |
| VABCDescriptor | Volume descriptor using the method implemented in the VABCVolume class. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| VABCVolume | Calculates the Van der Waals volume using the method proposed in . | Class | org.openscience.cdk.geometry.volume | CDK |
| VAdjMaDescriptor | Vertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| ValidationReport | A report on validation of chemical semantics. | Class | org.openscience.cdk.validate | CDK |
| ValidationTest | Error found during sematical validation of a IChemObject. | Class | org.openscience.cdk.validate | CDK |
| ValidatorEngine | Engine that performs the validation by traversing the IChemObject hierarchy. | Class | org.openscience.cdk.validate | CDK |
| VASPFormat | Class | org.openscience.cdk.io.formats | CDK | |
| VASPReader | Read output files generated with the VASP software. | Class | org.openscience.cdk.io | CDK |
| VdWRadiusDescriptor | This class return the VdW radius of a given atom. | Class | org.openscience.cdk.qsar.descriptors.atomic | CDK |
| Vector | This class handles vectors. | Class | org.openscience.cdk.math | CDK |
| VFAtomMatcher | Interface for the AtomMatcher (atoms) in graph. | Interface | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| VFBondMatcher | Interface for the BondMatcher (bonds) in graph. | Interface | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| VFlibMCSHandler | This class should be used to find MCS between query graph and target graph. | Class | org.openscience.cdk.smsd.algorithm.vflib | CDK |
| VFlibSubStructureHandler | This is an ultra fast method to report if query is a substructure for target molecule. | Class | org.openscience.cdk.smsd.algorithm.vflib | CDK |
| VFlibTurboHandler | This is an ultra fast method to report if query is a substructure for target molecule. | Class | org.openscience.cdk.smsd.algorithm.vflib | CDK |
| VFMapper | This class finds MCS between query and target molecules using VF2 algorithm. | Class | org.openscience.cdk.smsd.algorithm.vflib.map | CDK |
| VFMCSMapper | This class finds MCS between query and target molecules using VF2 algorithm. | Class | org.openscience.cdk.smsd.algorithm.vflib.map | CDK |
| VFQueryBuilder | Class for parsing and generating query graph. | Class | org.openscience.cdk.smsd.algorithm.vflib.builder | CDK |
| VFState | This class finds mapping states between query and targetAuthor:Syed Asad Rahman | Class | org.openscience.cdk.smsd.algorithm.vflib.map | CDK |
| Vibration | A molecular vibration composed of a set of atom vectors. | Class | org.openscience.cdk | CDK |
| VicinitySampler | The VicinitySampler is a generator of Constitutional Isomers. | Class | org.openscience.cdk.structgen | CDK |
| ViewmolFormat | Class | org.openscience.cdk.io.formats | CDK | |
| VisitedAtoms | Helper class for the CIPTool to keep track of which atoms have already been visited. | Class | org.openscience.cdk.geometry.cip | CDK |
| WedgeLineElement | A 'wedge' is a triangle aligned along a bond that indicates stereochemistry. | Class | org.openscience.cdk.renderer.elements | CDK |
| WedgeLineElement .Direction | Class | org.openscience.cdk.renderer.elements | CDK | |
| WeightDescriptor | IDescriptor based on the weight of atoms of a certain element type. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| WeightedPathDescriptor | Evaluates the weighted path descriptors. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| WHIMDescriptor | Holistic descriptors described by Todeschini et al . | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| WienerNumbersDescriptor | This descriptor calculates the Wiener numbers. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| WriterFactory | Helper tool to create IChemObjectWriters. | Class | org.openscience.cdk.io | CDK |
| XEDFormat | Class | org.openscience.cdk.io.formats | CDK | |
| XLogPDescriptor | Prediction of logP based on the atom-type method called XLogP. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| XYZFormat | Class | org.openscience.cdk.io.formats | CDK | |
| XYZReader | Reads an object from XYZ formated input. | Class | org.openscience.cdk.io | CDK |
| XYZWriter | Class | org.openscience.cdk.io | CDK | |
| YasaraFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ZagrebIndexDescriptor | Zagreb index: the sum of the squares of atom degree over all heavy atoms i. | Class | org.openscience.cdk.qsar.descriptors.molecular | CDK |
| ZindoFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ZMatrixFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ZMatrixReader | It reads Z matrices like in Gaussian input files. | Class | org.openscience.cdk.io | CDK |
| ZMatrixTools | A set of static utility classes for dealing with Z matrices. | Class | org.openscience.cdk.geometry | CDK |