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# Classes and Interfaces in #CDK - 1170 results found.
NameDescriptionTypePackageFrameworkJavaDoc
ABINITFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
AbstractAtomicDescriptorAbstract atomic descriptor class with helper functions for descriptors that require the whole molecule to calculate the descriptor values,Classorg.openscience.cdk.qsarCDKjavadoc
AbstractAWTDrawVisitorPartial implementation of the IDrawVisitor interface for the AWT widget toolkit, allowing molecules to be rendered with toolkits based onClassorg.openscience.cdk.renderer.visitorCDKjavadoc
AbstractBondDescriptorAbstract bond descriptor class with helper functions for descriptors that require the whole molecule to calculate the descriptor values,Classorg.openscience.cdk.qsarCDKjavadoc
AbstractDifferenceClassorg.openscience.cdk.tools.diff.treeCDKjavadoc
AbstractDifferenceListDiff between two IChemObjects.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
AbstractGeneratorParameterAbstract class to provide the base functionality for IGeneratorParameter implementations.Classorg.openscience.cdk.renderer.generators.parameterCDKjavadoc
AbstractMCSInterface for all MCS algorithms.Interfaceorg.openscience.cdk.smsd.interfacesCDKjavadoc
AbstractMCSAlgorithmInterface for MCS search algorithm.Interfaceorg.openscience.cdk.smsd.interfacesCDKjavadoc
AbstractReactionLabellerClassorg.openscience.cdk.smsd.labellingCDKjavadoc
AbstractRendererThe base class for all renderers, handling the core aspects of rendering such as the location of the model in 'model space' and the location onClassorg.openscience.cdk.rendererCDKjavadoc
AbstractSelectionAn abstract selection of IChemObjects.Classorg.openscience.cdk.renderer.selectionCDKjavadoc
AbstractSubGraphInterface class for reporting only substructure searches.Interfaceorg.openscience.cdk.smsd.interfacesCDKjavadoc
AbstractValidatorAbstract validator that does nothing but provide all the methods that the ValidatorInterface requires.Classorg.openscience.cdk.validateCDKjavadoc
Aces2FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
AcidicGroupCountDescriptorReturns the number of acidic groups.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AdductFormulaClass defining an adduct object in a MolecularFormula.Classorg.openscience.cdk.formulaCDKjavadoc
AdductFormulaClass defining an adduct object in a MolecularFormula.Classorg.openscience.cdk.silentCDKjavadoc
AdductionLPMechanismThis mechanism adduct together two fragments.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
AdductionPBMechanismThis mechanism adduct together two fragments due to a double bond.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
AdductionProtonLPReactionIReactionProcess which produces a protonation.Classorg.openscience.cdk.reaction.typeCDKjavadoc
AdductionProtonPBReactionIReactionProcess which produces a protonation to double bond.Classorg.openscience.cdk.reaction.typeCDKjavadoc
AdductionSodiumLPReactionIReactionProcess which produces an adduction of the Sodium.Classorg.openscience.cdk.reaction.typeCDKjavadoc
ADFFormatClassorg.openscience.cdk.io.formatsCDKjavadoc

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AdjacencyMatrixCalculator for a adjacency matrix representation of this AtomContainer.Classorg.openscience.cdk.graph.matrixCDKjavadoc
AlchemyFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
AlgorithmThis class represents various algorithm type supported by SMSD.Interfaceorg.openscience.cdk.smsd.interfacesCDKjavadoc
AliphaticAtomThis matcher any non-aromatic atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
AliphaticSymbolAtomThis smarts atom matches aliphatic atom with element symbol specifiedSee Also:Serialized FormKeywords:SMARTSClassorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
AllRingsFinderFinds the Set of all Rings.Classorg.openscience.cdk.ringsearchCDKjavadoc
AllRingsFinderModFinds the Set of all Rings.Classorg.openscience.cdk.ringsearchCDKjavadoc
ALOGPDescriptorThis class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity .Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AminoAcidA AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Classorg.openscience.cdkCDKjavadoc
AminoAcidA AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Classorg.openscience.cdk.silentCDKjavadoc
AminoAcidCountDescriptorClass that returns the number of each amino acid in an atom container.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AminoAcidManipulatorClass with convenience methods that provide methods to manipulateAuthor:Egon WillighagenCreated on:2005-08-19Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
AminoAcidsTool that provides templates for the (natural) amino acids.Classorg.openscience.cdk.templatesCDKjavadoc
AngularMomentumThis class is used to calculate angular momentum states.Classorg.openscience.cdk.math.qmCDKjavadoc
AnyAtomThis matcher any Atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
AnyOrderQueryBondThis matches a bond of any orderSee Also:Serialized FormKeywords:SMARTSClassorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
APolDescriptorSum of the atomic polarizabilities (including implicit hydrogens).Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AromaticAtomThis matcher any aromatic atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
AromaticAtomsCountDescriptorClass that returns the number of aromatic atoms in an atom container.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AromaticBondsCountDescriptorThis Class contains a method that returns the number of aromatic atoms in an AtomContainer.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AromaticityCalculatorClassorg.openscience.cdk.aromaticityCDKjavadoc
AromaticOrSingleQueryBondThis matches an aromatic or a single bond, used when no bond is specified between an atomSee Also:Serialized FormKeywords:SMARTSClassorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
AromaticQueryBondThis matches an aromatic bondSee Also:Serialized FormKeywords:SMARTSClassorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
AromaticSymbolAtomThis class matches aromatic atom with element symbol specified.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
ArrowElementIRenderingElement for linear arrows.Classorg.openscience.cdk.renderer.elementsCDKjavadoc

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AssociationBase class for storing interactions like hydrogen bonds and ionic interactions.Classorg.openscience.cdkCDKjavadoc
ASTAliphaticAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTAnyAtomAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTAromaticAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTAtomAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTAtomicMassAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTAtomicNumberAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTChargeAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTChiralityAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTElementAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTExplicitAtomAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTExplicitConnectivityAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTExplicitHighAndBondAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTExplicitHighAndExpressionAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTGroupAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTHybrdizationNumberAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTImplicitHCountAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTImplicitHighAndBondAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTImplicitHighAndExpressionAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTLowAndBondAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTLowAndExpressionAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTNonCHHeavyAtomAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTNotBondAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTNotExpressionAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTOrBondAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc

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ASTOrExpressionAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTPeriodicGroupNumberAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTPrimitiveAtomExpressionAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTReactionAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTRecursiveSmartsExpressionAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTRingConnectivityAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTRingIdentifierAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTRingMembershipAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTSimpleBondAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTSmallestRingSizeAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTSmartsAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTStartAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTTotalConnectivityAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTTotalHCountAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ASTValenceAn AST node.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
AtomRepresents the idea of an chemical atom.Classorg.openscience.cdkCDKjavadoc
AtomRepresents the idea of an chemical atom.Classorg.openscience.cdk.silentCDKjavadoc
AtomContainerBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.Classorg.openscience.cdkCDKjavadoc
AtomContainerBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.Classorg.openscience.cdk.silentCDKjavadoc
AtomContainerAtomPermutorThis class iterates through all possible permutations of the atom order in a given atom container.Classorg.openscience.cdk.graphCDKjavadoc
AtomContainerAtomPermutorClassorg.openscience.cdk.smsd.labellingCDKjavadoc
AtomContainerBondPermutorThis class allows to iterate trough the set of all possible permutations of the bond order in a given atom container.Classorg.openscience.cdk.graphCDKjavadoc
AtomContainerBoundsGeneratorIGenerator that draws a rectangular around the IAtomContainer.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
AtomContainerComparatorCompares two IAtomContainers for order with the following criteria with decreasing priority: Compare molecular weight (heavy atoms only)Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
AtomContainerComparatorBy2DCenterCompares two IAtomContainers based on their 2D position.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc

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AtomContainerDiffCompares two IAtomContainer classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
AtomContainerManipulatorClass with convenience methods that provide methods to manipulate AtomContainer's.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
AtomContainerPermutorThe permutation code here is based on a pseudo code example on a tutorial site created and maintained by Phillip P.Classorg.openscience.cdk.graphCDKjavadoc
AtomContainerPrinterClassorg.openscience.cdk.smsd.labellingCDKjavadoc
AtomContainerRendererA general renderer for IAtomContainers.Classorg.openscience.cdk.rendererCDKjavadoc
AtomContainerSetA set of AtomContainers.Classorg.openscience.cdkCDKjavadoc
AtomContainerSetA set of AtomContainers.Classorg.openscience.cdk.silentCDKjavadoc
AtomContainerSetManipulatorClassorg.openscience.cdk.tools.manipulatorCDKjavadoc
AtomCountDescriptorIDescriptor based on the number of atoms of a certain element type.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AtomDegreeDescriptorThis class returns the number of not-Hs substituents of an atom, also defined as "atom degree".Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
AtomDiffCompares two IAtom classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
AtomHybridizationDescriptorThis class returns the hybridization of an atom.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
AtomHybridizationVSEPRDescriptorThis class returns the hybridization of an atom.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
AtomicNumberAtomThis matches an atom using the atomic number.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
AtomicNumberDifferenceDescriptorDescribes the imbalance in atomic number of the IBond.Classorg.openscience.cdk.qsar.descriptors.bondCDKjavadoc
AtomicPropertiesProvides atomic property values for descriptor calculations.Classorg.openscience.cdk.toolsCDKjavadoc
AtomMappingToolsClassorg.openscience.cdk.isomorphismCDKjavadoc
AtomMassGeneratorIGenerator that can render mass number information of atoms.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
AtomMassSymbolElementRendering element that shows the IAtom mass number information.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
AtomMatcherInterface for the AtomMatcher (atoms) in graph.Interfaceorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
AtomNumberGeneratorClassorg.openscience.cdk.renderer.generatorsCDKjavadoc
AtomParityRepresents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms.Classorg.openscience.cdkCDKjavadoc
AtomParityRepresents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms.Classorg.openscience.cdk.silentCDKjavadoc
AtomPlacerMethods for generating coordinates for atoms in various situations.Classorg.openscience.cdk.layoutCDKjavadoc
AtomPlacer3DPlace aliphatic chains with Z matrix method.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc

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AtomSignature The signature for a molecule rooted at a particular A signature is a description of the connectivity of a molecule, in the formClassorg.openscience.cdk.signatureCDKjavadoc
AtomSymbolElementA text element with added information.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
AtomTetrahedralLigandPlacer3DA set of static utility classes for geometric calculations on Atoms.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
AtomToolsA set of static utility classes for geometric calculations on Atoms.Classorg.openscience.cdk.geometryCDKjavadoc
AtomTypeThe base class for atom types.Classorg.openscience.cdkCDKjavadoc
AtomTypeThe base class for atom types.Classorg.openscience.cdk.silentCDKjavadoc
AtomTypeChargesAssigns charges to atom types.Classorg.openscience.cdk.chargesCDKjavadoc
AtomTypeDiffCompares two IAtomType classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
AtomTypeFactoryGeneral class for defining AtomTypes.Classorg.openscience.cdk.configCDKjavadoc
AtomTypeHandlerSAX Handler for the AtomTypeReader.Classorg.openscience.cdk.config.atomtypesCDKjavadoc
AtomTypeHybridizationDifferenceIDifference between two IAtomType.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
AtomTypeManipulatorClass with utilities for the AtomType class.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
AtomTypeMapperAn AtomTypeMapper allows the mapping of atom types between atom type schemes.Classorg.openscience.cdk.atomtype.mapperCDKjavadoc
AtomTypeReaderXML Reader for the CDKBasedAtomTypeConfigurator.Classorg.openscience.cdk.config.atomtypesCDKjavadoc
AtomTypeToolsAtomTypeTools is a helper class for assigning atom types to an atom.Classorg.openscience.cdk.toolsCDKjavadoc
AtomValenceDescriptorThis class returns the valence of an atom.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
AtomValenceToolThis class returns the valence of an atom.Classorg.openscience.cdk.qsarCDKjavadoc
AttachedGroupHolds data on a specific functional group or substituent.Classorg.openscience.cdk.iupac.parserCDKjavadoc
AutocorrelationDescriptorChargeThis class calculates ATS autocorrelation descriptor, where the weight equalAuthor:FedericoBelongs to the set:qsar-descriptorsCreated on:2007-02-27Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AutocorrelationDescriptorMassThis class calculates ATS autocorrelation descriptor, where the weight equal to the scaled atomic mass .Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AutocorrelationDescriptorPolarizabilityThis class calculates ATS autocorrelation descriptor, where the weight equalAuthor:FedericoBelongs to the set:qsar-descriptorsCreated on:2007-03-01Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
AverageBondLengthCalculatorUtility class for calculating the average bond length for various IChemObject subtypes : IReaction, IMoleculeSet, IChemModel, and IReactionSet.Classorg.openscience.cdk.rendererCDKjavadoc
AWTDrawVisitor widget toolkit, allowing molecules to be rendered with toolkits based on AWT, like the Java reference graphics platform Swing.Classorg.openscience.cdk.renderer.visitorCDKjavadoc
AWTFontManagerAWT-specific font manager.Classorg.openscience.cdk.renderer.fontCDKjavadoc
BadMatrixFormatExceptionClassorg.openscience.cdk.graph.invariant.exceptionCDKjavadoc

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BasicAtomGeneratorGenerates basic IRenderingElements for atoms in an atom container.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
BasicBondGeneratorGenerator for elements from bonds.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
BasicGeneratorCombination generator for basic drawing of molecules.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
BasicGroupCountDescriptorReturns the number of basic groups.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
BasicSceneGeneratorThis generator does not create any elements, but acts as a holding place for various generator parameters used by most drawings, such as the zoom,Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
BasicValidatorValidator which tests a number of basic chemical semantics.Classorg.openscience.cdk.validateCDKjavadoc
BCUTDescriptorEigenvalue based descriptor noted for its utility in chemical diversity.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
BFSShortestPathUtility class that finds the shortest bond path between two atoms using a breadth first search.Classorg.openscience.cdk.graphCDKjavadoc
BGFFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
BiconnectivityInspectorFinds the biconnected components of a graph.Classorg.openscience.cdk.graphCDKjavadoc
BinaryTreeClass to construct a Binary tree for McGregor search.Classorg.openscience.cdk.smsd.helperCDKjavadoc
BioPolymerA BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.Classorg.openscience.cdkCDKjavadoc
BioPolymerA BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.Classorg.openscience.cdk.silentCDKjavadoc
BKKCKCFThis class implements Bron-Kerbosch clique detection algorithm as it is described in [F.Classorg.openscience.cdk.smsd.algorithm.mcsplusCDKjavadoc
Bond considered to be a number of electrons connecting two or more of atoms.Classorg.openscience.cdkCDKjavadoc
Bond considered to be a number of electrons connecting two or more of atoms.Classorg.openscience.cdk.silentCDKjavadoc
BondCountDescriptorIDescriptor based on the number of bonds of a certain bond order.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
BondDiffCompares two IBond classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
BondEnergiesClass that stores bond breaking/formation energy between two atoms.Classorg.openscience.cdk.smsd.toolsCDKjavadoc
BondEnergyHelper class defining the energy for a bond type.Classorg.openscience.cdk.smsd.helperCDKjavadoc
BondManipulatorClass with convenience methods that provide methods to manipulate AtomContainer's.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
BondMatcherInterface for the BondMatcher (bonds) in graph.Interfaceorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
BondOrderDifferenceIDifference between two IBond.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
BondPartialPiChargeDescriptorThe calculation of bond-pi Partial charge is calculated determining the difference the Partial Pi Charge on atoms Classorg.openscience.cdk.qsar.descriptors.bondCDKjavadoc
BondPartialSigmaChargeDescriptorThe calculation of bond-sigma Partial charge is calculated determining the difference the Partial Sigma Charge on atoms Classorg.openscience.cdk.qsar.descriptors.bondCDKjavadoc

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BondPartialTChargeDescriptorThe calculation of bond total Partial charge is calculated determining the difference the Partial Total Charge on atoms Classorg.openscience.cdk.qsar.descriptors.bondCDKjavadoc
BondSigmaElectronegativityDescriptorThe calculation of bond-Polarizability is calculated determining the difference the Sigma electronegativity on atoms A and B of a bond.Classorg.openscience.cdk.qsar.descriptors.bondCDKjavadoc
BondsToAtomDescriptorThis class returns the number of bonds on the shortest path between two atoms.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
BondToolsA set of static utility classes for geometric calculations on IBonds.Classorg.openscience.cdk.geometryCDKjavadoc
BooleanArrayDifferenceDifference between two boolean[]'s.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
BooleanDifferenceIDifference between two Booleans.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
BooleanIOSettingAn class for a reader setting which must be of type String.Classorg.openscience.cdk.io.settingCDKjavadoc
BooleanResultObject that provides access to the calculated descriptor value.Classorg.openscience.cdk.qsar.resultCDKjavadoc
BooleanResultTypeIDescriptorResult type for booleans.Classorg.openscience.cdk.qsar.resultCDKjavadoc
BoundsCalculatorUtility class for calculating the 2D bounding rectangles (bounds) of various IChemObject subtypes - IChemModel, IReactionSet, IReaction,Classorg.openscience.cdk.rendererCDKjavadoc
BoundsGeneratorProduce a bounding rectangle for various chem objects.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
BPolDescriptorSum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens) with polarizabilities taken fromClassorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
BremserOneSphereHOSECodePredictorClassorg.openscience.cdk.toolsCDKjavadoc
BSFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
BsptBSP-Tree stands for Binary Space Partitioning Tree.Classorg.openscience.cdk.graph.rebondCDKjavadoc
CacaoCartesianFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CacaoInternalFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CACheFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CanonicalLabelerCanonically labels an atom container implementing the algorithm published in David Weininger et.Classorg.openscience.cdk.graph.invariantCDKjavadoc
CanonicalLabellingAdaptorClassorg.openscience.cdk.smsd.labellingCDKjavadoc
CarbonTypesDescriptorTopological descriptor characterizing the carbon connectivity.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
CarbonylEliminationReactionIReactionProcess which participate mass spectrum process.Classorg.openscience.cdk.reaction.typeCDKjavadoc
CASNumberTools to work with CAS registry numbers.Classorg.openscience.cdk.indexCDKjavadoc
CDKHelper class to provide general information about this CDK library.Classorg.openscience.cdkCDKjavadoc
CDKHelper class to provide a Java API to the CDK OWL ontology, following the design of similar namespace classes in the Jena library, like RDF.Classorg.openscience.cdk.libio.jenaCDKjavadoc

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CDK2DAtomColorsGives a short table of atom colors for 2D display.Classorg.openscience.cdk.renderer.colorCDKjavadoc
CDKAtomColorsGives a short table of atom colors for 3D display.Classorg.openscience.cdk.renderer.colorCDKjavadoc
CDKAtomTypeMatcherAtom Type matcher that perceives atom types as defined in the CDK atom type list org/openscience/cdk/dict/data/cdk-atom-types.Classorg.openscience.cdk.atomtypeCDKjavadoc
CDKBasedAtomTypeConfiguratorAtomType resource that reads the atom type configuration from an XML file.Classorg.openscience.cdk.configCDKjavadoc
CDKConstantsAn interface providing predefined values for a number of constants used throughout the CDK.Classorg.openscience.cdkCDKjavadoc
CDKConventionThis is an implementation for the CDK convention.Classorg.openscience.cdk.io.cmlCDKjavadoc
CDKDictionaryReferencesThis class transforms implicit references to dictionary of CDK objects into explicit references.Classorg.openscience.cdk.dictCDKjavadoc
CDKExceptionException that is thrown by CDK classes when some problem has occured.Classorg.openscience.cdk.exceptionCDKjavadoc
CDKHueckelAromaticityDetectorClassorg.openscience.cdk.aromaticityCDKjavadoc
CDKHydrogenAdderAdds implicit hydrogens based on atom type definitions.Classorg.openscience.cdk.toolsCDKjavadoc
CDKMCSHandlerThis class acts as a handler class for CDKMCS algorithm.Classorg.openscience.cdk.smsd.algorithm.rgraphCDKjavadoc
CDKOWLFormatSerializes a CDK model into the Web Ontology Language using theBelongs to the set:io-formatsClassorg.openscience.cdk.io.formatsCDKjavadoc
CDKOWLReaderReads content from a CDK OWL serialization.Classorg.openscience.cdk.io.rdfCDKjavadoc
CDKOWLWriterSerializes the data model into CDK OWL.Classorg.openscience.cdk.io.rdfCDKjavadoc
CDKPopupMenuBasically, identical to the JPopupMenu class, except that this menu can also contain the source for which it was popped up.Classorg.openscience.cdk.controllerCDKjavadoc
CDKRGraphThis class implements the Resolution Graph (CDKRGraph).Classorg.openscience.cdk.smsd.algorithm.rgraphCDKjavadoc
CDKRMapAn 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.Classorg.openscience.cdk.smsd.algorithm.rgraphCDKjavadoc
CDKRMapHandlerThis algorithm derives from the algorithm described in [Tonnelier, C.Classorg.openscience.cdk.smsd.algorithm.rgraphCDKjavadoc
CDKRNodeNode of the resolution graphe (RGraph) An CDKRNode represents an association betwwen two edges of the source graphs G1 and G2 that are compared.Classorg.openscience.cdk.smsd.algorithm.rgraphCDKjavadoc
CDKSourceCodeFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CDKSourceCodeWriterConverts a Molecule into CDK source code that would build the same molecule.Classorg.openscience.cdk.ioCDKjavadoc
CDKSubGraphHandlerThis class acts as a handler class for CDKMCS algorithm.Classorg.openscience.cdk.smsd.algorithm.rgraphCDKjavadoc
CDKUtilitiesUtility class written by Todd Martin, for help in his QSAR descriptors and SMILES parser.Classorg.openscience.cdk.toolsCDKjavadoc
CDKValencyCheckerClassorg.openscience.cdk.toolsCDKjavadoc
CDKValidatorThis Validator tests the internal datastructures, and tries to detect inconsistencies in it.Classorg.openscience.cdk.validateCDKjavadoc

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ChargeGroupA ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.Classorg.openscience.cdk.libio.mdCDKjavadoc
ChargeRuleThis class validate if the charge in the IMolecularFormula correspond with a specific value.Classorg.openscience.cdk.formula.rulesCDKjavadoc
Chem3D_Cartesian_1FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
Chem3D_Cartesian_2FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
ChemDrawFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
ChemFileA Object containing a number of ChemSequences.Classorg.openscience.cdkCDKjavadoc
ChemFileA Object containing a number of ChemSequences.Classorg.openscience.cdk.silentCDKjavadoc
ChemFileManipulatorClass with convenience methods that provide methods from methods from ChemObjects within the ChemFile.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
ChemGraphClassorg.openscience.cdk.structgen.stochastic.operatorCDKjavadoc
ChemicalFiltersClass that ranks MCS final solution according to the chemical rules.Classorg.openscience.cdk.smsd.filtersCDKjavadoc
ChemModelAn object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, Classorg.openscience.cdkCDKjavadoc
ChemModelAn object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, Classorg.openscience.cdk.silentCDKjavadoc
ChemModelManipulatorClass with convenience methods that provide methods from methods from ChemObjects within the ChemModel.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
ChemModelRendererA general renderer for IChemModels, IReactions, and IMolecules.Classorg.openscience.cdk.rendererCDKjavadoc
ChemObjectThe base class for all chemical objects in this cdk.Classorg.openscience.cdkCDKjavadoc
ChemObjectThe base class for all chemical objects in this cdk.Classorg.openscience.cdk.silentCDKjavadoc
ChemObjectChangeEventEvent fired by cdk classes to their registered listeners in case something changes within them.Classorg.openscience.cdk.eventCDKjavadoc
ChemObjectDiffCompares two IChemObject classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
ChemObjectDifferenceIDifference between two IChemObjects.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
ChemSequenceA sequence of ChemModels, which can, for example, be used to store the course of a reaction.Classorg.openscience.cdkCDKjavadoc
ChemSequenceA sequence of ChemModels, which can, for example, be used to store the course of a reaction.Classorg.openscience.cdk.silentCDKjavadoc
ChemSequenceManipulatorClass with convenience methods that provide methods from methods from ChemObjects within the ChemSequence.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
ChemtoolFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
ChiChainDescriptorEvaluates chi chain descriptors.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
ChiClusterDescriptorEvaluates chi cluster descriptors.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc

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ChiPathClusterDescriptorEvaluates chi path cluster descriptors.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
ChiPathDescriptorEvaluates chi path descriptors.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
ChiralityAtomThis matches an atom with chirality property.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
CIFFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CIFReaderThis is not a reader for the CIF and mmCIF crystallographic formats.Classorg.openscience.cdk.ioCDKjavadoc
CIPLigandRuleCompares to ILigands based on CIP sequences sub rules.Classorg.openscience.cdk.geometry.cip.rulesCDKjavadoc
CIPToolTool to help determine the R,S and stereochemistry definitions of a subset of the CIP rules .Classorg.openscience.cdk.geometry.cipCDKjavadoc
CloseIndicates the closing point of the path.Classorg.openscience.cdk.renderer.elements.pathCDKjavadoc
ClosedShellJobCalculates the orbitals and orbital energies of electron systemsAuthor:Stephan Michels Created on:2001-06-14Classorg.openscience.cdk.math.qmCDKjavadoc
CMLCoreModuleCore CML 1.Classorg.openscience.cdk.io.cmlCDKjavadoc
CMLErrorHandlerCDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document.Classorg.openscience.cdk.io.cmlCDKjavadoc
CMLFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CMLHandlerSAX2 implementation for CML XML fragment reading.Classorg.openscience.cdk.io.cmlCDKjavadoc
CMLReactionModuleClassorg.openscience.cdk.io.cmlCDKjavadoc
CMLReaderReads a molecule in CML 1.Classorg.openscience.cdk.ioCDKjavadoc
CMLResolverThis class resolves DOCTYPE declaration for Chemical Markup Language (CML) files and uses a local version for validation.Classorg.openscience.cdk.io.cmlCDKjavadoc
CMLRSSFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CMLStackLow weigth alternative to Sun's Stack class.Classorg.openscience.cdk.io.cmlCDKjavadoc
CMLWriterSerializes a IMoleculeSet or a IMolecule object to CML 2 code.Classorg.openscience.cdk.ioCDKjavadoc
ComplexThis class handles complex values.Classorg.openscience.cdk.mathCDKjavadoc
ConformerContainerA memory-efficient data structure to store conformers for a single molecule.Classorg.openscience.cdkCDKjavadoc
ConjugatedPiSystemsDetectorClassorg.openscience.cdk.graph.invariantCDKjavadoc
ConnectionCountAtomThis matcher checks the total valency of the Atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
ConnectionMatrixCalculator for a connection matrix representation of this AtomContainer.Classorg.openscience.cdk.graph.matrixCDKjavadoc
ConnectivityCheckerTool class for checking whether the (sub)structure in an AtomContainer is connected.Classorg.openscience.cdk.graphCDKjavadoc

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ConvertorKeywords:CML, class convertorRequires:java1.Classorg.openscience.cdk.libio.cmlCDKjavadoc
ConvertorHelper class that converts a CDK IChemObject into RDF using a Jena model and the CDK data model ontology.Classorg.openscience.cdk.libio.jenaCDKjavadoc
CovalentRadiusDescriptorThis class return the covalent radius of a given atom.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
CPKAtomColorsColors atoms using CPK color scheme .Classorg.openscience.cdk.renderer.colorCDKjavadoc
CPSADescriptorCalculates 29 Charged Partial Surface Area (CPSA) descriptors.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
CRK2DFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CRK3DFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CrossoverMachineModified molecular structures by applying crossover operator on a pair of parent structures and generate a pair of offspring structures.Classorg.openscience.cdk.structgen.stochastic.operatorCDKjavadoc
CrystalClass representing a molecular crystal.Classorg.openscience.cdkCDKjavadoc
CrystalClass representing a molecular crystal.Classorg.openscience.cdk.silentCDKjavadoc
CrystalGeometryToolsA set of static methods for working with crystal coordinates.Classorg.openscience.cdk.geometryCDKjavadoc
CrystClustFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CrystClustReaderClassorg.openscience.cdk.ioCDKjavadoc
CrystClustWriterRather stupid file format used for storing crystal information.Classorg.openscience.cdk.ioCDKjavadoc
CTXFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
CTXReaderReader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files.Classorg.openscience.cdk.ioCDKjavadoc
CubicToA cubic curve in the path.Classorg.openscience.cdk.renderer.elements.pathCDKjavadoc
CustomSerializerCustom Serializer with the sole purpose and functionality to not output the XML declaration.Classorg.openscience.cdk.io.cmlCDKjavadoc
CycleBasisA minimum basis of all cycles in a graph.Classorg.openscience.cdk.ringsearch.cyclebasisCDKjavadoc
DaltonFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
DataFeaturesClass with constants for possible data features defined in the a Data Feature Ontology.Classorg.openscience.cdk.toolsCDKjavadoc
DataFeaturesToolUtility that helps determine which data features are present.Classorg.openscience.cdk.toolsCDKjavadoc
DeAromatizationToolMethods that takes a ring of which all bonds are aromatic, and assigns single and double bonds.Classorg.openscience.cdk.toolsCDKjavadoc
DebugAdductFormulaClassorg.openscience.cdk.debugCDKjavadoc
DebugAminoAcidDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc

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DebugAtomDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugAtomContainerDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugAtomContainerSetDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugAtomParityDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugAtomTypeDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugBioPolymerDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugBondDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugChemFileDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugChemModelDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugChemObjectDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugChemObjectBuilderClassorg.openscience.cdk.debugCDKjavadoc
DebugChemSequenceDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugCrystalDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugElectronContainerDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugElementDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugFragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.Classorg.openscience.cdk.debugCDKjavadoc
DebugIsotopeDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugLonePairDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugMappingDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugMolecularFormulaClassorg.openscience.cdk.debugCDKjavadoc
DebugMolecularFormulaSetClassorg.openscience.cdk.debugCDKjavadoc
DebugMoleculeDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugMoleculeSetDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugMonomerDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugPDBAtomDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc

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DebugPDBMonomerDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugPDBPolymerDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugPDBStructureDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugPolymerDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugPseudoAtomDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugReactionDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugReactionSchemeDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugReactionSetDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugRingDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugRingSetDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugSingleElectronDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DebugStrandDebugging data class.Classorg.openscience.cdk.debugCDKjavadoc
DeduceBondSystemToolTool that tries to deduce bond orders based on connectivity and hybridization for a number of common ring systems of up to seven-membered rings.Classorg.openscience.cdk.smilesCDKjavadoc
DefaultBondMatcherChecks if a bond is matching between query and target molecules.Classorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
DefaultChemObjectBuilderClassorg.openscience.cdkCDKjavadoc
DefaultChemObjectReaderAbstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.Classorg.openscience.cdk.ioCDKjavadoc
DefaultChemObjectWriterAbstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.Classorg.openscience.cdk.ioCDKjavadoc
DefaultEventChemObjectReaderAbstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.Classorg.openscience.cdk.io.iterator.eventCDKjavadoc
DefaultIteratingChemObjectReaderAbstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.Classorg.openscience.cdk.io.iteratorCDKjavadoc
DefaultMatcherChecks if atom is matching between query and target molecules.Classorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
DefaultMCSPlusAtomMatcherChecks if atom is matching between query and target molecules.Classorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
DefaultRandomAccessChemObjectReaderAbstract class that IRandomAccessChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.Classorg.openscience.cdk.io.randomCDKjavadoc
DefaultRGraphAtomMatcherChecks if atom is matching between query and target molecules.Classorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
DefaultVFAtomMatcherChecks if atom is matching between query and target molecules.Classorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
DefaultVFBondMatcherChecks if a bond is matching between query and target molecules.Classorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc

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DegreeAtomThis matcher checks the number of connections of the checked Atom with other Atom's.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
DescriptorEngineA class that provides access to automatic descriptor calculation and more.Classorg.openscience.cdk.qsarCDKjavadoc
DescriptorExceptionException that is thrown by descriptor routines when a problem has occured.Classorg.openscience.cdk.qsarCDKjavadoc
DescriptorSpecificationClass that is used to distribute descriptor specifications.Classorg.openscience.cdk.qsarCDKjavadoc
DescriptorValueClass that is used to store descriptor values as IChemObject properties.Classorg.openscience.cdk.qsarCDKjavadoc
DictionaryDictionary with entries.Classorg.openscience.cdk.dictCDKjavadoc
DictionaryDatabaseDatabase of dictionaries listing entries with compounds, fragmentsAuthor:Egon WillighagenKeywords:dictionaryCreated on:2003-04-06Required library to be able to run this class:xom.Classorg.openscience.cdk.dictCDKjavadoc
DictionaryHandlerClass for unmarshalling a dictionary schema file.Classorg.openscience.cdk.dictCDKjavadoc
DictionaryValidatorValidates the existence of references to dictionaries.Classorg.openscience.cdk.validateCDKjavadoc
DictRefObject that can be used as key in IChemObject.Classorg.openscience.cdk.dictCDKjavadoc
DistanceMomentFast similarity measure for 3D structures.Classorg.openscience.cdk.similarityCDKjavadoc
DistanceToAtomDescriptorThis class returns the 3D distance between two atoms.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
DMol3FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
DOCK5FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
DoubleArrayResultClassorg.openscience.cdk.qsar.resultCDKjavadoc
DoubleArrayResultTypeIDescriptorResult type for booleans.Classorg.openscience.cdk.qsar.resultCDKjavadoc
DoubleBondAcceptingAromaticityDetectorClassorg.openscience.cdk.aromaticityCDKjavadoc
DoubleBondStereochemistryStereochemistry specification for double bonds.Classorg.openscience.cdk.stereoCDKjavadoc
DoubleDifferenceIDifference between two Double.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
DoubleResultClassorg.openscience.cdk.qsar.resultCDKjavadoc
DoubleResultTypeIDescriptorResult type for booleans.Classorg.openscience.cdk.qsar.resultCDKjavadoc
EccentricConnectivityIndexDescriptorA topological descriptor combining distance and adjacency information.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
EdgeBuilderClass for building/storing edges (bonds) in the graph with bond query capabilities.Classorg.openscience.cdk.smsd.algorithm.vflib.builderCDKjavadoc
EffectiveAtomPolarizabilityDescriptorEffective polarizability of an heavy atom This descriptor uses these parameters:Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
ElectronContainerBase class for entities containing electrons, like bonds, orbitals, lone-pairs.Classorg.openscience.cdkCDKjavadoc

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ElectronContainerBase class for entities containing electrons, like bonds, orbitals, lone-pairs.Classorg.openscience.cdk.silentCDKjavadoc
ElectronContainerDiffCompares two IChemObject classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
ElectronegativityCalculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).Classorg.openscience.cdk.chargesCDKjavadoc
ElectronImpactNBEReactionIReactionProcess which make an electron impact for for Non-Bonding Electron Lost.Classorg.openscience.cdk.reaction.typeCDKjavadoc
ElectronImpactPDBReactionIReactionProcess which make an electron impact for pi-Bond Dissociation.Classorg.openscience.cdk.reaction.typeCDKjavadoc
ElectronImpactSDBReactionIReactionProcess which make an electron impact for Sigma Bond Dissociation.Classorg.openscience.cdk.reaction.typeCDKjavadoc
Element Use the IsotopeFactory to get a ready-to-use elements by symbol or atomic number:Classorg.openscience.cdkCDKjavadoc
Element Use the IsotopeFactory to get a ready-to-use elements by symbol or atomic number:Classorg.openscience.cdk.silentCDKjavadoc
ElementComparatorCompares elements based on the order commonly used in molecular formula.Classorg.openscience.cdk.toolsCDKjavadoc
ElementDiffCompares two IElement classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
ElementGroupA group of rendering elements, of any type.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
ElementRuleThis class validate if the occurrence of the IElements in the IMolecularFormula are into a limits.Classorg.openscience.cdk.formula.rulesCDKjavadoc
ElementsList of elements.Classorg.openscience.cdk.configCDKjavadoc
EntryEntry in a Dictionary.Classorg.openscience.cdk.dictCDKjavadoc
EntryReactEntry in a Dictionary for reactions.Classorg.openscience.cdk.dictCDKjavadoc
EnzymeResidueLocatorAtom that represents part of an residue in an enzyme, like Arg255.Classorg.openscience.cdkCDKjavadoc
EquivalentClassPartitionerAn algorithm for topological symmetry.Classorg.openscience.cdk.graph.invariantCDKjavadoc
EStateAtomTypeMatcherDetermines the EState atom types.Classorg.openscience.cdk.atomtypeCDKjavadoc
EStateFingerprinterThis fingerprinter generates 79 bit fingerprints using the E-State The E-State fragments are those described in and Classorg.openscience.cdk.fingerprintCDKjavadoc
EStateFragmentsA class representing the 79 E-state atom types in terms of SMARTS.Classorg.openscience.cdk.config.fragmentsCDKjavadoc
EventCMLHandlerCDO object needed as interface with the JCFL library for reading CML in a event based manner.Classorg.openscience.cdk.io.iterator.eventCDKjavadoc
EventCMLReaderReads a molecule in CML 1.Classorg.openscience.cdk.io.iterator.eventCDKjavadoc
ExactMappingThis class handles MCS between two identical molecules.Classorg.openscience.cdk.smsd.algorithm.mcsplusCDKjavadoc
ExhaustiveFragmenterGenerate fragments exhaustively.Classorg.openscience.cdk.fragmentCDKjavadoc
ExplicitConnectionAtomThis smarts atom matches any atom with a certain number of explicitSee Also:Serialized FormKeywords:SMARTSClassorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc

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ExtAtomContainerManipulatorClass that handles some customised features for SMSD atom containers.Classorg.openscience.cdk.smsd.toolsCDKjavadoc
ExtendedAtomGeneratorA generator for atoms with mass, charge, etc.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
ExtendedFingerprinterGenerates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional bits describing ringClassorg.openscience.cdk.fingerprintCDKjavadoc
FenskeHall_ZMatrixFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
FiguerasSSSRFinderFinds the Smallest Set of Smallest Rings.Classorg.openscience.cdk.ringsearchCDKjavadoc
FinalMappingsClass that stores raw mapping(s) after each algorithm is executed.Classorg.openscience.cdk.smsd.helperCDKjavadoc
FingerprinterGenerates a fingerprint for a given AtomContainer.Classorg.openscience.cdk.fingerprintCDKjavadoc
FingerprinterToolTool with helper methods for IFingerprint.Classorg.openscience.cdk.fingerprintCDKjavadoc
FingerprintFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
FixBondOrdersToolClass to Fix bond orders at present for Aromatic Rings only.Classorg.openscience.cdk.smilesCDKjavadoc
FixedSizeStackA LIFO queue for result structures.Classorg.openscience.cdk.toolsCDKjavadoc
FMFDescriptorAn implementation of the FMF descriptor characterizing complexity of a molecule.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
ForceFieldConfiguratorReads 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.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
FormalChargeAtomThis matcher checks the formal charge of the Atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
FormatFactoryA factory for recognizing chemical file formats.Classorg.openscience.cdk.ioCDKjavadoc
FormatStringBufferA class for formatting output similar to the C printf command.Classorg.openscience.cdk.toolsCDKjavadoc
FortranFormatConverts a String representation of a Fortran double to a double.Classorg.openscience.cdk.mathCDKjavadoc
FragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.Classorg.openscience.cdkCDKjavadoc
FragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.Classorg.openscience.cdk.silentCDKjavadoc
FragmentComplexityDescriptorClass that returns the complexity of a system.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
FragmentUtilsHelper methods for fragmentation algorithms.Classorg.openscience.cdk.fragmentCDKjavadoc
GamessFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
GamessReaderA reader for GAMESS log file.Classorg.openscience.cdk.ioCDKjavadoc
GasteigerMarsiliPartialChargesThe calculation of the Gasteiger Marsili (PEOE) partial charges is based on .Classorg.openscience.cdk.chargesCDKjavadoc
GasteigerPEPEPartialChargesThe calculation of the Gasteiger (PEPE) partial charges is based on .Classorg.openscience.cdk.chargesCDKjavadoc

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Gaussian03FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
Gaussian03ReaderA reader for Gaussian03 output.Classorg.openscience.cdk.ioCDKjavadoc
Gaussian90FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
Gaussian92FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
Gaussian94FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
Gaussian95FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
Gaussian98FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
Gaussian98ReaderA reader for Gaussian98 output.Classorg.openscience.cdk.ioCDKjavadoc
GaussianInputFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
GaussianInputWriterFile writer thats generates input files for Gaussian calculation jobs.Classorg.openscience.cdk.io.programCDKjavadoc
GeneralPathA path of rendering elements from the elements.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
GenerateCompatibilityGraphThis class generates compatibility graph between query and target molecule.Classorg.openscience.cdk.smsd.algorithm.mcsplusCDKjavadoc
Geometry3DValidatorValidates the 3D geometry of the model.Classorg.openscience.cdk.validateCDKjavadoc
GeometryToolsA set of static utility classes for geometric calculations and operations.Classorg.openscience.cdk.geometryCDKjavadoc
GhemicalMMFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
GhemicalMMReader http://www.Classorg.openscience.cdk.ioCDKjavadoc
GhemicalSPMFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
GIMatrixThis 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)Classorg.openscience.cdk.graph.invariantCDKjavadoc
GraphOnlyFingerprinterSpecialized version of the Fingerprinter which does not take bond ordersAuthor:egonwSee Also:FingerprinterKeywords:fingerprint, similarityCreated on:2007-01-11Classorg.openscience.cdk.fingerprintCDKjavadoc
GraphRendererModelThis class handles a set of function for the GraphRendererAuthor:Stephan Michels Created on:2001-07-02Classorg.openscience.cdk.rendererCDKjavadoc
GravitationalIndexDescriptorIDescriptor characterizing the mass distribution of the molecule.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
GridGeneratorGenerates a grid of points in 3D space within given boundaries.Classorg.openscience.cdk.toolsCDKjavadoc
GROMOS96FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
HanserRingFinderFinds the Set of all Rings.Classorg.openscience.cdk.smsd.ringCDKjavadoc
HBondAcceptorCountDescriptorThis descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the The following groups are counted as hydrogen bond acceptors:Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc

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HBondDonorCountDescriptorThis descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the The following groups are counted as hydrogen bond donors:Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
HeterolyticCleavageMechanismThis mechanism displaces the chemical bond to an Atom.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
HeterolyticCleavagePBReactionIReactionProcess which a bond is broken displacing the electron to one of the atoms.Classorg.openscience.cdk.reaction.typeCDKjavadoc
HeterolyticCleavageSBReactionIReactionProcess which a bond is broken displacing the electron to one of the atoms.Classorg.openscience.cdk.reaction.typeCDKjavadoc
HINFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
HINReaderReads an object from HIN formated input.Classorg.openscience.cdk.ioCDKjavadoc
HINWriterWriter that outputs in the HIN format.Classorg.openscience.cdk.ioCDKjavadoc
HomolyticCleavageMechanismThis mechanism breaks the chemical bond between atoms.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
HomolyticCleavageReactionIReactionProcess which breaks the bond homogeneously leading to radical ions.Classorg.openscience.cdk.reaction.typeCDKjavadoc
HOSECodeAnalyserAnalyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula.Classorg.openscience.cdk.toolsCDKjavadoc
HOSECodeGeneratorGenerates HOSE codes .Classorg.openscience.cdk.toolsCDKjavadoc
HuLuIndexToolClassorg.openscience.cdk.graph.invariantCDKjavadoc
HybridizationFingerprinterGenerates a fingerprint for a given IAtomContainer.Classorg.openscience.cdk.fingerprintCDKjavadoc
HybridizationNumberAtomThis matcher checks the hybridization state of an atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
HybridizationRatioDescriptorIMolecularDescriptor that reports the fraction of sp3 carbons to sp2 carbons.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
HydrogenAtomThis matches Hydrogen atoms.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
HydrogenPlacerThis is a wrapper class for some existing methods in AtomPlacer.Classorg.openscience.cdk.layoutCDKjavadoc
HyperconjugationReactionHyperconjugationReaction is the stabilizing interaction that results from the interaction of the electrons in a s-bond (for our case only C-H)Classorg.openscience.cdk.reaction.typeCDKjavadoc
IAdductFormulaClass defining an adduct object in a MolecularFormula.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IAminoAcidA AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IAtomRepresents the idea of an chemical atom.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IAtomColorerInterface to a class for coloring atoms.Interfaceorg.openscience.cdk.renderer.colorCDKjavadoc
IAtomContainerBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IAtomContainerSetA set of AtomContainers.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IAtomicDescriptorClasses that implement this interface are QSAR descriptor calculators.Interfaceorg.openscience.cdk.qsarCDKjavadoc

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IAtomPairDescriptorClasses that implement this interface are QSAR descriptor calculators.Interfaceorg.openscience.cdk.qsarCDKjavadoc
IAtomParityRepresents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IAtomTypeThe base class for atom types.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IAtomTypeConfiguratorInterfaceorg.openscience.cdk.configCDKjavadoc
IAtomTypeGuesserClasses that implement this interface are atom type guessers.Interfaceorg.openscience.cdk.atomtypeCDKjavadoc
IAtomTypeMatcherClasses that implement this interface are atom type matchers.Interfaceorg.openscience.cdk.atomtypeCDKjavadoc
IBioPolymerA BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IBond considered to be a number of electrons connecting two ore more atoms.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IBondDescriptorClasses that implement this interface are QSAR descriptor calculators.Interfaceorg.openscience.cdk.qsarCDKjavadoc
ICanonicalMoleculeLabellerInterfaceorg.openscience.cdk.smsd.labellingCDKjavadoc
ICanonicalReactionLabellerInterfaceorg.openscience.cdk.smsd.labellingCDKjavadoc
ICDKChangeListenerA ChangeListener for the CDK, to be independent from the Swing package.Interfaceorg.openscience.cdk.eventCDKjavadoc
ICDKObjectThe base class for all data objects in this CDK.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
ICDKSelectionChangeListenerA ChangeListener for the CDK, to be independent from the Swing package.Interfaceorg.openscience.cdk.eventCDKjavadoc
IChargeCalculatorInterfaceorg.openscience.cdk.chargesCDKjavadoc
IChemFileAn IChemObject containing a number of ChemSequences.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IChemFormatThis class is the interface that all ChemFormat's should implement.Interfaceorg.openscience.cdk.io.formatsCDKjavadoc
IChemFormatMatcherThis interface is used for classes that are able to match a certain chemical file format.Interfaceorg.openscience.cdk.io.formatsCDKjavadoc
IChemModelAn object containig multiple MoleculeSet and the other lower level concepts like rings, sequences, Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IChemObjectThe base class for all chemical objects in this cdk.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IChemObjectBuilderInterfaceorg.openscience.cdk.interfacesCDKjavadoc
IChemObjectChangeEventEvent fired by CDK IChemObject classes to their registered listeners in case something changed within them.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IChemObjectIOThis class is the interface that all IO readers should implement.Interfaceorg.openscience.cdk.ioCDKjavadoc
IChemObjectIOListenerAllows monitoring of progress of file reader activities.Interfaceorg.openscience.cdk.io.listenerCDKjavadoc
IChemObjectListenerClasses implementing this interface must implement this method such that they react appropriately to changes in the object theyInterfaceorg.openscience.cdk.interfacesCDKjavadoc

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IChemObjectReaderThis interface specifies the common functionality all IO readers should provide.Interfaceorg.openscience.cdk.ioCDKjavadoc
IChemObjectReaderErrorHandlerInterface for classes aimed to handle IChemObjectReader errors.Interfaceorg.openscience.cdk.ioCDKjavadoc
IChemObjectSelectionInterfaceorg.openscience.cdk.renderer.selectionCDKjavadoc
IChemObjectWriterThis class is the interface that all IO writers should implement.Interfaceorg.openscience.cdk.ioCDKjavadoc
IChemSequenceA sequence of ChemModels, which can, for example, be used to store the course of a reaction.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
ICMLConventionThis interface describes the procedures classes must implement to be plugable into the CMLHandler.Interfaceorg.openscience.cdk.io.cmlCDKjavadoc
ICMLCustomizerInterface for classes that allow the Convertor to be customized for certain features.Interfaceorg.openscience.cdk.libio.cmlCDKjavadoc
ICMLModuleThis interface describes the procedures classes must implement to be plugable into the CMLHandler.Interfaceorg.openscience.cdk.io.cmlCDKjavadoc
ICrystalClass representing a molecular crystal.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IDCreatorClass that provides methods to give unique IDs to ChemObjects.Classorg.openscience.cdk.toolsCDKjavadoc
IDeduceBondOrderToolA common interface for tools that deduce bond orders from connectivity and optionally additional information, like number of implicit orInterfaceorg.openscience.cdk.toolsCDKjavadoc
IDescriptorClasses that implement this interface are QSAR descriptor calculators.Interfaceorg.openscience.cdk.qsarCDKjavadoc
IDescriptorResultObject that provides access to the calculated descriptor value.Interfaceorg.openscience.cdk.qsar.resultCDKjavadoc
IDifferenceInterfaceorg.openscience.cdk.tools.diff.treeCDKjavadoc
IDifferenceListIDifference between two Objects which contains one or more child IDifference objects.Interfaceorg.openscience.cdk.tools.diff.treeCDKjavadoc
IDoubleBondStereochemistryStereochemistry specification for double bond stereochemistry.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IDrawVisitorAn IDrawVisitor is an IRenderingVisitor that can be customized and knows about fonts and other rendering parameters.Interfaceorg.openscience.cdk.renderer.visitorCDKjavadoc
IEdgeInterface for the Edges (bonds) in graph.Interfaceorg.openscience.cdk.smsd.algorithm.vflib.interfacesCDKjavadoc
IElectronContainerBase class for entities containing electrons, like bonds, orbitals, lone-pairs.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IElectronicPropertyCalculatorInterfaceorg.openscience.cdk.chargesCDKjavadoc
IElementInterfaceorg.openscience.cdk.interfacesCDKjavadoc
IEventChemObjectReaderInterface for an iterating molecule reader.Interfaceorg.openscience.cdk.io.iterator.eventCDKjavadoc
IFinalMappingInterface for mappings.Interfaceorg.openscience.cdk.smsd.interfacesCDKjavadoc
IFingerprinterInterface for fingerprint calculators.Interfaceorg.openscience.cdk.fingerprintCDKjavadoc
IFontManagerAn interface for managing the drawing of fonts at different zoom levels.Interfaceorg.openscience.cdk.renderer.fontCDKjavadoc

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IFragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IFragmenterAn interface for classes implementing fragmentation algorithms.Interfaceorg.openscience.cdk.fragmentCDKjavadoc
IFunctionA class, which has a function value should implement this interface.Interfaceorg.openscience.cdk.mathCDKjavadoc
IGeneratorAn IGenerator converts chemical entities into parts of the chemical drawing expressed as IRenderingElements.Interfaceorg.openscience.cdk.renderer.generatorsCDKjavadoc
IGeneratorParameterParameter from some rendering of the 2D diagram.Interfaceorg.openscience.cdk.renderer.generatorsCDKjavadoc
IGraphMatrixInterfaceorg.openscience.cdk.graph.matrixCDKjavadoc
IImplementationSpecificationInterface that is used to describe the specification of a certain implementation of an algorithm.Interfaceorg.openscience.cdkCDKjavadoc
IIsotopeUsed to store and retrieve data of a particular isotope.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IIteratingChemObjectReaderInterface for an iterating molecule reader.Interfaceorg.openscience.cdk.io.iteratorCDKjavadoc
ILigandConcept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.Interfaceorg.openscience.cdk.geometry.cipCDKjavadoc
ILoggingToolUseful for logging messages.Interfaceorg.openscience.cdk.toolsCDKjavadoc
ILonePairA LonePair is an orbital primarily located with one Atom, containingKeywords:orbital, lone-pairInterfaceorg.openscience.cdk.interfacesCDKjavadoc
IMapperInterface for the mappings (mapped objects).Interfaceorg.openscience.cdk.smsd.algorithm.vflib.interfacesCDKjavadoc
IMappingRepresents a mapping of two atoms.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IMatrixThis class contains a complex matrix.Classorg.openscience.cdk.mathCDKjavadoc
IMCSBaseInterface that holds basic core interface for all MCS algorithm.Interfaceorg.openscience.cdk.smsd.interfacesCDKjavadoc
IMolecularDescriptorClasses that implement this interface are QSAR descriptor calculators for IMolecule objects.Interfaceorg.openscience.cdk.qsarCDKjavadoc
IMolecularFormulaClass defining a molecular formula object.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IMolecularFormulaSetClass defining a molecular formula object.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IMoleculeRepresents a set of Molecules.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IMoleculeSetRepresents a set of Molecules.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IMonomerA Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IMouseEventRelayWidget toolkit-independent interface to relay for mouse events.Interfaceorg.openscience.cdk.controllerCDKjavadoc
ImplicitHCountAtomThis matcher checks the number of implicit hydrogens of the Atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
ImplicitHydrogenLigandSubclass of Ligand to which no further recursion must be applied.Classorg.openscience.cdk.geometry.cipCDKjavadoc

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INChIContentProcessorToolTool to help process INChI 1.Classorg.openscience.cdk.io.inchiCDKjavadoc
INChIFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
InChIGeneratorThis class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer.Classorg.openscience.cdk.inchiCDKjavadoc
InChIGeneratorFactoryFactory providing access to InChIGenerator and InChIToStructure.Classorg.openscience.cdk.inchiCDKjavadoc
INChIHandlerSAX2 implementation for INChI XML fragment parsing.Classorg.openscience.cdk.io.inchiCDKjavadoc
InChINumbersToolsTool for calculating atom numbers using the InChI algorithm.Classorg.openscience.cdk.graph.invariantCDKjavadoc
INChIPlainTextFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
INChIPlainTextReaderReads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document.Classorg.openscience.cdk.ioCDKjavadoc
INChIReaderReads the content of a IUPAC/NIST Chemical Identifier (INChI) document.Classorg.openscience.cdk.ioCDKjavadoc
InChITautomerGeneratorCreates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI.Classorg.openscience.cdk.tautomersCDKjavadoc
InChIToStructureThis class generates a CDK IAtomContainer from an InChI string.Classorg.openscience.cdk.inchiCDKjavadoc
IncorrectUseOfCDKCoreClassErrorError that is thrown by debug implementations of the core CDK classes.Classorg.openscience.cdk.exceptionCDKjavadoc
IndexOutOfBoundsExceptionClassorg.openscience.cdk.graph.invariant.exceptionCDKjavadoc
InductiveAtomicHardnessDescriptorInductive atomic hardness of an atom in a polyatomic system can be defined as the "resistance" to a change of the atomic charge.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
InductiveAtomicSoftnessDescriptorInductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
InductivePartialChargesThe calculation of the inductive partial atomic charges and equalization of effective electronegativities is based on .Classorg.openscience.cdk.chargesCDKjavadoc
INodeInterface for the Node (atomss) in graph.Interfaceorg.openscience.cdk.smsd.algorithm.vflib.interfacesCDKjavadoc
IntegerArrayResultClassorg.openscience.cdk.qsar.resultCDKjavadoc
IntegerArrayResultTypeIDescriptorResult type for booleans.Classorg.openscience.cdk.qsar.resultCDKjavadoc
IntegerDifferenceIDifference between two Integer.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
IntegerIOSettingAn class for a reader setting which must be of type String.Classorg.openscience.cdk.io.settingCDKjavadoc
IntegerResultObject that provides access to the calculated descriptor value.Classorg.openscience.cdk.qsar.resultCDKjavadoc
IntegerResultTypeIDescriptorResult type for booleans.Classorg.openscience.cdk.qsar.resultCDKjavadoc
InvalidSmilesExceptionClassorg.openscience.cdk.exceptionCDKjavadoc
InverseSymbolSetQueryAtomA QueryAtom that matches all symbols but those in this container.Classorg.openscience.cdk.isomorphism.matchersCDKjavadoc

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InvPairThis is used to hold the invariance numbers for the canonical labeling ofSee Also:Serialized FormClassorg.openscience.cdk.smilesCDKjavadoc
IonizationPotentialToolThis class contains the necessary information to predict ionization potential energy.Classorg.openscience.cdk.toolsCDKjavadoc
IOSettingAn interface for reader settings.Classorg.openscience.cdk.io.settingCDKjavadoc
IParameterReactInterface for classes that generate parameters used in reactions.Interfaceorg.openscience.cdk.reaction.type.parametersCDKjavadoc
IPAtomicHOSEDescriptorThis class returns the ionization potential of an atom containg lone pair electrons.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
IPAtomicLearningDescriptorThis class returns the ionization potential of an atom containing lone pair electrons.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
IPBondLearningDescriptorThis class returns the ionization potential of a Bond.Classorg.openscience.cdk.qsar.descriptors.bondCDKjavadoc
IPDBAtomA PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IPDBMonomerRepresents the idea of an protein monomer as found in PDB files.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IPDBPolymerA PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IPDBStructureRepresents the idea of an chemical structure.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IPMolecularLearningDescriptorThis class returns the ionization potential of a molecule.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
IPolymerSubclass of Molecule to store Polymer specific attributes that a Polymer has.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IPseudoAtomRepresents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IQueryInterface for the query molecule/graph.Interfaceorg.openscience.cdk.smsd.algorithm.vflib.interfacesCDKjavadoc
IQueryAtomDefines the ability to be matched against IAtom's.Interfaceorg.openscience.cdk.isomorphism.matchersCDKjavadoc
IQueryAtomContainerGeneral concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester.Interfaceorg.openscience.cdk.isomorphism.matchersCDKjavadoc
IQueryBondDefines the abililty to be matched against IBond's.Interfaceorg.openscience.cdk.isomorphism.matchersCDKjavadoc
IQueryCompilerInterface for the query graph generator.Interfaceorg.openscience.cdk.smsd.algorithm.vflib.interfacesCDKjavadoc
IRandomAccessChemObjectReaderExtension of ListIterator.Interfaceorg.openscience.cdk.io.randomCDKjavadoc
IRDFWeightFunctionWeight function used in the RDFCalculator.Interfaceorg.openscience.cdk.geometryCDKjavadoc
IReactionRepresents the idea of a chemical reaction.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IReactionMechanismClasses that implement this interface are reaction mechanisms.Interfaceorg.openscience.cdk.reactionCDKjavadoc
IReactionProcessClasses that implement this interface are Reactions types.Interfaceorg.openscience.cdk.reactionCDKjavadoc
IReactionSchemeClasses that implement this interface of a scheme.Interfaceorg.openscience.cdk.interfacesCDKjavadoc

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IReactionSetA set of reactions, for example those taking part in a reaction.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IReaderListenerAllows monitoring of progress of file reader activities.Interfaceorg.openscience.cdk.io.listenerCDKjavadoc
IRendererInterface that all 2D renderers implement.Interfaceorg.openscience.cdk.rendererCDKjavadoc
IRenderingElementWidget toolkit-independent, abstract definition of something to be drawn.Interfaceorg.openscience.cdk.renderer.elementsCDKjavadoc
IRenderingVisitorAn IRenderingVisitor is responsible of converting an abstract chemical drawing into a widget set specific drawing.Interfaceorg.openscience.cdk.renderer.elementsCDKjavadoc
IResourceFormatThis class is the interface that all ResourceFormat's should implement.Interfaceorg.openscience.cdk.io.formatsCDKjavadoc
IRGroupQueryInterface definition for Rgroup query classes.Interfaceorg.openscience.cdk.isomorphism.matchersCDKjavadoc
IRingClass representing a ring structure in a molecule.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IRingSetMaintains a set of Ring objects.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IRuleInterface which groups all method that validate a IMolecularFormula.Interfaceorg.openscience.cdk.formula.rulesCDKjavadoc
ISequenceSubRuleSequence sub rule used in the CIP method to decide which of the two ligands takes precedence .Interfaceorg.openscience.cdk.geometry.cip.rulesCDKjavadoc
ISimpleChemObjectReaderThis class is the interface that all IO readers should implement.Interfaceorg.openscience.cdk.ioCDKjavadoc
ISingleElectronA Single Electron is an orbital which is occupied by only one electron.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IsoAlkanesThis class contains methods for generating simple organic alkanes.Classorg.openscience.cdk.templates.saturatedhydrocarbonsCDKjavadoc
IsomorphismThis class implements the Isomorphism- a multipurpose structure comparison tool.Classorg.openscience.cdk.smsdCDKjavadoc
IsomorphismTesterA too simplistic implementation of an isomorphism test for chemical graphs.Classorg.openscience.cdk.isomorphismCDKjavadoc
IsotopeUsed to store and retrieve data of a particular isotope.Classorg.openscience.cdkCDKjavadoc
IsotopeUsed to store and retrieve data of a particular isotope.Classorg.openscience.cdk.silentCDKjavadoc
IsotopeContainerThis class defines a isotope container.Classorg.openscience.cdk.formulaCDKjavadoc
IsotopeDiffCompares two IIsotope classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
IsotopeFactoryUsed to store and return data of a particular isotope.Classorg.openscience.cdk.configCDKjavadoc
IsotopeHandlerReads an isotope list in CML2 format.Classorg.openscience.cdk.config.isotopesCDKjavadoc
IsotopePatternThis class defines the properties of a deisotoped pattern distribution.Classorg.openscience.cdk.formulaCDKjavadoc
IsotopePatternGeneratorGenerates all Combinatorial chemical isotopes given a structure.Classorg.openscience.cdk.formulaCDKjavadoc
IsotopePatternManipulatorClass to manipulate IsotopePattern objects.Classorg.openscience.cdk.formulaCDKjavadoc

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IsotopePatternRuleThis class validate if the Isotope Pattern from a given IMolecularFormula correspond with other to compare.Classorg.openscience.cdk.formula.rulesCDKjavadoc
IsotopePatternSimilarityThis class gives a score hit of similarity between two different isotope abundance pattern.Classorg.openscience.cdk.formulaCDKjavadoc
IsotopeReaderReader that instantiates an XML parser and customized handler to process the isotope information in the CML2 isotope data file.Classorg.openscience.cdk.config.isotopesCDKjavadoc
IsProtonInAromaticSystemDescriptorThis 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, Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
IsProtonInConjugatedPiSystemDescriptorThis class evaluates if a proton is joined to a conjugated system.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
IStateInterface for the storing the states of the mapping in the VF algorithm.Interfaceorg.openscience.cdk.smsd.algorithm.vflib.interfacesCDKjavadoc
IStereoElementRepresents the concept of a stereo element in the molecule.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IStrandA Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IStructureGenerationListenerInterfaceorg.openscience.cdk.structgenCDKjavadoc
IteratingMDLConformerReaderIterate over conformers of a collection of molecules stored in SDF format.Classorg.openscience.cdk.io.iteratorCDKjavadoc
IteratingMDLReaderIterating MDL SDF reader.Classorg.openscience.cdk.io.iteratorCDKjavadoc
IteratingPCCompoundASNReaderIterating PubChem PCCompound ASN reader.Classorg.openscience.cdk.io.iteratorCDKjavadoc
IteratingPCCompoundXMLReaderIterating PubChem PCCompound ASN.Classorg.openscience.cdk.io.iteratorCDKjavadoc
IteratingPCSubstancesXMLReaderIterating PubChem PC-Substances ASN.Classorg.openscience.cdk.io.iteratorCDKjavadoc
IteratingSMILESReaderIterating SMILES file reader.Classorg.openscience.cdk.io.iteratorCDKjavadoc
ITetrahedralChiralityStereochemistry specification for quadrivalent atoms.Interfaceorg.openscience.cdk.interfacesCDKjavadoc
IValencyCheckerA common interface for SaturationChecker and ValencyChecker.Interfaceorg.openscience.cdk.toolsCDKjavadoc
IValidatorInterface that Validators need to implement to be used in validation.Interfaceorg.openscience.cdk.validateCDKjavadoc
IVectorClassorg.openscience.cdk.mathCDKjavadoc
IViewEventRelayInterfaceorg.openscience.cdk.controllerCDKjavadoc
IWriterListenerInterfaceorg.openscience.cdk.io.listenerCDKjavadoc
JaguarFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
JCPAction2DSuperclass of all JChemPaint GUI actionsAuthor:steinbeckSee Also:Serialized FormClassorg.openscience.cdk.rendererCDKjavadoc
JJTSMARTSParserStateClassorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
JMEFormatClassorg.openscience.cdk.io.formatsCDKjavadoc

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JMOLANIMATIONConventionClassorg.openscience.cdk.io.cmlCDKjavadoc
KabschAlignmentAligns two structures to minimize the RMSD using the Kabsch algorithm.Classorg.openscience.cdk.geometry.alignmentCDKjavadoc
KappaShapeIndicesDescriptorKier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; a description is given at: http://www.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
KierHallSmartsDescriptorA fragment count descriptor that uses e-state fragments.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
KlekotaRothFingerprinterSMARTS based substructure fingerprint based on Chemical substructures that enrich for biological activity .Classorg.openscience.cdk.fingerprintCDKjavadoc
LabelContainerClass that handles atoms and assignes an integer lable to them.Classorg.openscience.cdk.smsd.helperCDKjavadoc
LargestChainDescriptorClass that returns the number of atoms in the largest chain.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
LargestPiSystemDescriptorClass that returns the number of atoms in the largest pi system.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
LengthOverBreadthDescriptorEvaluates length over breadth descriptors.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
LigandConcept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.Classorg.openscience.cdk.geometry.cipCDKjavadoc
LineElementA line between two points.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
LineToA line element in the path.Classorg.openscience.cdk.renderer.elements.pathCDKjavadoc
LoggingToolUseful for logging messages.Classorg.openscience.cdk.toolsCDKjavadoc
LoggingToolFactoryFactory used to instantiate a ILoggingTool.Classorg.openscience.cdk.toolsCDKjavadoc
LogicalOperatorAtomThis class matches a logical operator that connects two query atomsSee Also:Serialized FormKeywords:SMARTSClassorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
LogicalOperatorBondThis class matches a logical operator that connects two query bonds.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
LonePairA LonePair is an orbital primarily located with one Atom, containingSee Also:Serialized FormKeywords:orbital, lone-pairClassorg.openscience.cdkCDKjavadoc
LonePairA LonePair is an orbital primarily located with one Atom, containingSee Also:Serialized FormKeywords:orbital, lone-pairClassorg.openscience.cdk.silentCDKjavadoc
LonePairDiffCompares two ILonePair classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
LonePairElectronCheckerProvides methods for checking whether an atoms lone pair electrons are saturated with respect to a particular atom type.Classorg.openscience.cdk.toolsCDKjavadoc
LonePairGeneratorGenerate the symbols for lone pairs.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
LongestAliphaticChainDescriptorClass that returns the number of atoms in the longest aliphatic chain.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
MACCSFingerprinterThis fingerprinter generates 166 bit MACCS keys.Classorg.openscience.cdk.fingerprintCDKjavadoc
MacroModelFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MannholdLogPDescriptorPrediction of logP based on the number of carbon and hetero atoms.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc

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MappingA Mapping is an relation between two ChemObjects in a non-chemical entity.Classorg.openscience.cdkCDKjavadoc
MappingA Mapping is an relation between two ChemObjects in a non-chemical entity.Classorg.openscience.cdk.silentCDKjavadoc
MappingGeneratorClassorg.openscience.cdk.renderer.generatorsCDKjavadoc
MassAtomThis class matches an atom based on the atomic mass.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
MassToFormulaToolTool to determine molecular formula consistent with a given accurate mass.Classorg.openscience.cdk.formulaCDKjavadoc
MatchHolds matching query and target nodes.Classorg.openscience.cdk.smsd.algorithm.vflib.mapCDKjavadoc
MathToolsClass providing convenience methods for simple mathematical operations.Classorg.openscience.cdk.mathCDKjavadoc
MatrixThis class contains a matrix.Classorg.openscience.cdk.mathCDKjavadoc
MatrixNotInvertibleExceptionClassorg.openscience.cdk.graph.invariant.exceptionCDKjavadoc
McGregorClass which reports MCS solutions based on the McGregor algorithm The SMSD algorithm is described in this paper.Classorg.openscience.cdk.smsd.algorithm.mcgregorCDKjavadoc
McGregorChecksClass to perform check/methods for McGregor class.Classorg.openscience.cdk.smsd.algorithm.mcgregorCDKjavadoc
McgregorHelperHelper Class for McGregor algorithm.Classorg.openscience.cdk.smsd.algorithm.mcgregorCDKjavadoc
MCSPlusThis class handles MCS plus algorithm which is a combination of c-clique algorithm and McGregor algorithm.Classorg.openscience.cdk.smsd.algorithm.mcsplusCDKjavadoc
MCSPlusHandlerThis class acts as a handler class for MCSPlus algorithm.Classorg.openscience.cdk.smsd.algorithm.mcsplusCDKjavadoc
MDEDescriptorCalculates the Molecular Distance Edge descriptor described in .Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
MDLFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MDLMolConventionClassorg.openscience.cdk.io.cmlCDKjavadoc
MDLReaderReads a molecule from the original MDL MOL or SDF file .Classorg.openscience.cdk.ioCDKjavadoc
MDLRXNFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MDLRXNReaderReads a molecule from an MDL RXN file .Classorg.openscience.cdk.ioCDKjavadoc
MDLRXNV2000ReaderReads a molecule from an MDL RXN file .Classorg.openscience.cdk.ioCDKjavadoc
MDLRXNV3000FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MDLRXNV3000ReaderClass that implements the new MDL mol format introduced in August 2002.Classorg.openscience.cdk.ioCDKjavadoc
MDLRXNWriterWrites a reaction to a MDL rxn or SDF file.Classorg.openscience.cdk.ioCDKjavadoc
MDLV2000FormatClassorg.openscience.cdk.io.formatsCDKjavadoc

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MDLV2000ReaderReads content from MDL molfiles and SD files.Classorg.openscience.cdk.ioCDKjavadoc
MDLV2000WriterWrites MDL molfiles, which contains a single molecule (see ).Classorg.openscience.cdk.ioCDKjavadoc
MDLV3000FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MDLV3000ReaderClass that implements the MDL mol V3000 format.Classorg.openscience.cdk.ioCDKjavadoc
MDMoleculeClassorg.openscience.cdk.libio.mdCDKjavadoc
MDMoleculeConventionClassorg.openscience.cdk.io.cmlCDKjavadoc
MDMoleculeCustomizerCustomize persistence of MDMolecule by adding support for residues and charge groups.Classorg.openscience.cdk.libio.cmlCDKjavadoc
MinimalPathIteratorIterates over all shortest paths between two vertices in an undirected, unweighted graph.Classorg.openscience.cdk.graphCDKjavadoc
MM2AtomTypeMatcherClass implements methods to assign mmff94 atom types for a specific atom in an molecule.Classorg.openscience.cdk.atomtypeCDKjavadoc
MM2BasedAtomTypePatternClass stores hose code patterns to identify mm2 force field atom types.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
MM2BasedParameterSetReaderAtomType list configurator that uses the ParameterSet originally defined in mm2.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
MMElementRuleThis class validate if the occurrence of the IElements in the IMolecularFormula, for metabolites, are into a maximal limit according paper: .Classorg.openscience.cdk.formula.rulesCDKjavadoc
MMFF94AtomTypeMatcherClass implements methods to assign mmff94 atom types for a specific atom in an molecule.Classorg.openscience.cdk.atomtypeCDKjavadoc
MMFF94BasedAtomTypePatternClass stores hose code patterns to identify mm2 force field atom typesAuthor:chhoppeCreated on:2004-09-07Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
MMFF94BasedParameterSetReaderAtomType list configurator that uses the ParameterSet originally defined in mmff94.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
MMFF94ParametersCallSet the right atoms order to get the parameters.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
MMFF94PartialChargesThe calculation of the MMFF94 partial charges.Classorg.openscience.cdk.chargesCDKjavadoc
MMODFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
ModelBuilder3DThe main class to generate the 3D coordinates of a molecule ModelBuilder3D.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
Mol2FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
Mol2ReaderReads a molecule from an Mol2 file, such as written by Sybyl.Classorg.openscience.cdk.ioCDKjavadoc
Mol2WriterAn output Writer that writes molecular data into the Tripos Mol2 format.Classorg.openscience.cdk.ioCDKjavadoc
MolecularFormulaClass defining a molecular formula object.Classorg.openscience.cdk.formulaCDKjavadoc
MolecularFormulaClass defining a molecular formula object.Classorg.openscience.cdk.silentCDKjavadoc
MolecularFormulaChecker Validate a molecular formula given in IMolecularformula object.Classorg.openscience.cdk.formulaCDKjavadoc

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MolecularFormulaManipulatorClass with convenience methods that provide methods to manipulate IMolecularFormula's.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
MolecularFormulaRangeClass defining a expanded molecular formula object.Classorg.openscience.cdk.formulaCDKjavadoc
MolecularFormulaRangeManipulatorClass with convenience methods that provide methods to manipulate MolecularFormulaRange's.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
MolecularFormulaSetClass defining an set object of MolecularFormulas.Classorg.openscience.cdk.formulaCDKjavadoc
MolecularFormulaSetClass defining an set object of MolecularFormulas.Classorg.openscience.cdk.silentCDKjavadoc
MolecularFormulaSetManipulatorClass with convenience methods that provide methods to manipulate MolecularFormulaSet's.Classorg.openscience.cdk.tools.manipulatorCDKjavadoc
MoleculeRepresents the concept of a chemical molecule, an object composed of atoms connected by bonds.Classorg.openscience.cdkCDKjavadoc
MoleculeRepresents the concept of a chemical molecule, an object composed of atoms connected by bonds.Classorg.openscience.cdk.silentCDKjavadoc
MoleculeBuilderTakes in parsed Tokens from NomParser and contains rules to convert those tokens to a Molecule.Classorg.openscience.cdk.iupac.parserCDKjavadoc
MoleculeFactoryThis class contains methods for generating simple organic molecules.Classorg.openscience.cdk.templatesCDKjavadoc
MoleculeFeaturesToolUtility that helps determine which data features are present.Classorg.openscience.cdk.tools.featuresCDKjavadoc
MoleculeFromSignatureBuilderBuilds a molecule from a signature.Classorg.openscience.cdk.signatureCDKjavadoc
MoleculeGraphsUtility class to create a molecule graph for use with JGraphT.Classorg.openscience.cdk.graphCDKjavadoc
MoleculeSanityCheckClass that cleans a molecule before MCS search.Classorg.openscience.cdk.smsd.toolsCDKjavadoc
MoleculeSetA set of molecules, for example those taking part in a reaction.Classorg.openscience.cdkCDKjavadoc
MoleculeSetA set of molecules, for example those taking part in a reaction.Classorg.openscience.cdk.silentCDKjavadoc
MoleculeSetManipulatorClassorg.openscience.cdk.tools.manipulatorCDKjavadoc
MoleculeSetRendererA general renderer for IChemModels, IReactions, and IMolecules.Classorg.openscience.cdk.rendererCDKjavadoc
MoleculeSignature A molecule signature is a way to produce AtomSignatures and to get the canonical signature string for a molecule.Classorg.openscience.cdk.signatureCDKjavadoc
MoleculeSignatureLabellingAdaptorClassorg.openscience.cdk.smsd.labellingCDKjavadoc
MolHandlerClass that handles molecules for MCS search.Classorg.openscience.cdk.smsd.toolsCDKjavadoc
MomentOfInertiaDescriptorA descriptor that calculates the moment of inertia and radius of gyration.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
MonomerA Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.Classorg.openscience.cdkCDKjavadoc
MonomerA Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.Classorg.openscience.cdk.silentCDKjavadoc
MOPAC2002FormatClassorg.openscience.cdk.io.formatsCDKjavadoc

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MOPAC7FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MOPAC93FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MOPAC97FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MorganNumbersToolsTool for calculating Morgan numbers .Classorg.openscience.cdk.graph.invariantCDKjavadoc
MoSSOutputFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MoSSOutputReaderReader for MoSS output files which present the results of a substructure mining study.Classorg.openscience.cdk.ioCDKjavadoc
MoveToA 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.Classorg.openscience.cdk.renderer.elements.pathCDKjavadoc
MPQCFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
MurckoFragmenterAn implementation of the Murcko fragmenation method .Classorg.openscience.cdk.fragmentCDKjavadoc
NeighborListCreates a list of atoms neighboring each atom in the molecule.Classorg.openscience.cdk.geometry.surfaceCDKjavadoc
NitrogenRuleThis class validate if the rule of nitrogen is kept.Classorg.openscience.cdk.formula.rulesCDKjavadoc
NNAdductFormulaClassorg.openscience.cdk.nonotifyCDKjavadoc
NNAminoAcidClassorg.openscience.cdk.nonotifyCDKjavadoc
NNAtomClassorg.openscience.cdk.nonotifyCDKjavadoc
NNAtomContainerClassorg.openscience.cdk.nonotifyCDKjavadoc
NNAtomContainerSetClassorg.openscience.cdk.nonotifyCDKjavadoc
NNAtomParityClassorg.openscience.cdk.nonotifyCDKjavadoc
NNAtomTypeClassorg.openscience.cdk.nonotifyCDKjavadoc
NNBioPolymerClassorg.openscience.cdk.nonotifyCDKjavadoc
NNBondClassorg.openscience.cdk.nonotifyCDKjavadoc
NNChemFileClassorg.openscience.cdk.nonotifyCDKjavadoc
NNChemModelClassorg.openscience.cdk.nonotifyCDKjavadoc
NNChemObjectClassorg.openscience.cdk.nonotifyCDKjavadoc
NNChemSequenceClassorg.openscience.cdk.nonotifyCDKjavadoc
NNCrystalClassorg.openscience.cdk.nonotifyCDKjavadoc

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NNElectronContainerClassorg.openscience.cdk.nonotifyCDKjavadoc
NNElementClassorg.openscience.cdk.nonotifyCDKjavadoc
NNFragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.Classorg.openscience.cdk.nonotifyCDKjavadoc
NNIsotopeClassorg.openscience.cdk.nonotifyCDKjavadoc
NNLonePairClassorg.openscience.cdk.nonotifyCDKjavadoc
NNMappingClassorg.openscience.cdk.nonotifyCDKjavadoc
NNMolecularFormulaClassorg.openscience.cdk.nonotifyCDKjavadoc
NNMolecularFormulaSetClassorg.openscience.cdk.nonotifyCDKjavadoc
NNMoleculeClassorg.openscience.cdk.nonotifyCDKjavadoc
NNMoleculeSetClassorg.openscience.cdk.nonotifyCDKjavadoc
NNMonomerClassorg.openscience.cdk.nonotifyCDKjavadoc
NNPDBAtomClassorg.openscience.cdk.nonotifyCDKjavadoc
NNPDBMonomerClassorg.openscience.cdk.nonotifyCDKjavadoc
NNPDBPolymerClassorg.openscience.cdk.nonotifyCDKjavadoc
NNPDBStructureClassorg.openscience.cdk.nonotifyCDKjavadoc
NNPolymerClassorg.openscience.cdk.nonotifyCDKjavadoc
NNPseudoAtomClassorg.openscience.cdk.nonotifyCDKjavadoc
NNReactionClassorg.openscience.cdk.nonotifyCDKjavadoc
NNReactionSchemeClassorg.openscience.cdk.nonotifyCDKjavadoc
NNReactionSetClassorg.openscience.cdk.nonotifyCDKjavadoc
NNRingClassorg.openscience.cdk.nonotifyCDKjavadoc
NNRingSetClassorg.openscience.cdk.nonotifyCDKjavadoc
NNSingleElectronClassorg.openscience.cdk.nonotifyCDKjavadoc
NNStrandClassorg.openscience.cdk.nonotifyCDKjavadoc
NodeAll AST nodes must implement this interface.Interfaceorg.openscience.cdk.smiles.smarts.parserCDKjavadoc

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NodeBuilderClass for building/storing nodes (atoms) in the graph with atom query capabilities.Classorg.openscience.cdk.smsd.algorithm.vflib.builderCDKjavadoc
NomParserA class partly generated by JavaCC which breaks down the chemical name into computable subparts and passes these parts to the MoleculeBuilder.Classorg.openscience.cdk.iupac.parserCDKjavadoc
NomParserConstantsToken literal values and constants.Interfaceorg.openscience.cdk.iupac.parserCDKjavadoc
NomParserTokenManagerClassorg.openscience.cdk.iupac.parserCDKjavadoc
NonCHHeavyAtomThis matcher any heavy atom that is not C or H.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
NoNotificationChemObjectBuilderClassorg.openscience.cdk.nonotifyCDKjavadoc
NormalizerAdjusts parts of an AtomContainer to the congiguratin of a fragment.Classorg.openscience.cdk.normalizeCDKjavadoc
NoSuchAtomExceptionException that is thrown when an Atom is requested or required that does not exist in the relevant environment.Classorg.openscience.cdk.exceptionCDKjavadoc
NoSuchAtomTypeExceptionException that may be thrown when an atom type is looked up or perceived but no such atom type was found.Classorg.openscience.cdk.exceptionCDKjavadoc
NumericalSurfaceA class representing the solvent acessible surface area surface of a molecule.Classorg.openscience.cdk.geometry.surfaceCDKjavadoc
NWChemFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
OneElectronJobCalculates the orbitals and orbital energies of electron systems without electron electron interactionsClassorg.openscience.cdk.math.qmCDKjavadoc
OptionIOSettingAn class for a reader setting which must be found in the list of possible settings.Classorg.openscience.cdk.io.settingCDKjavadoc
OrbitA list of atom indices, and the label of the orbit.Classorg.openscience.cdk.signatureCDKjavadoc
OrbitalsThis class represents a set of orbitalsAuthor:Stephan Michels Created on:2001-06-14Classorg.openscience.cdk.math.qmCDKjavadoc
OrderQueryBondClassorg.openscience.cdk.isomorphism.matchersCDKjavadoc
OrderQueryBondThis matches a bond with a certain bond order.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
OrderQueryBondOrderOnlyIQueryBond that matches IBond object only based on bond order, and disregarding any aromaticity flag.Classorg.openscience.cdk.isomorphism.matchersCDKjavadoc
OvalElementAn oval element (should) have both a width and a height.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
OverlapResolverHelper class for Structure Diagram Generation.Classorg.openscience.cdk.layoutCDKjavadoc
OWLAtomTypeHandlerSAX Handler for the OWLAtomTypeReader.Classorg.openscience.cdk.config.atomtypesCDKjavadoc
OWLAtomTypeMappingHandlerSAX Handler for the OWLAtomTypeMappingReader.Classorg.openscience.cdk.config.atomtypesCDKjavadoc
OWLAtomTypeMappingReaderXML Reader for the OWLBasedAtomTypeConfigurator.Classorg.openscience.cdk.config.atomtypesCDKjavadoc
OWLAtomTypeReaderXML Reader for the OWLBasedAtomTypeConfigurator.Classorg.openscience.cdk.config.atomtypesCDKjavadoc
OWLBasedAtomTypeConfiguratorAtomType resource that reads the atom type configuration from an OWL file.Classorg.openscience.cdk.configCDKjavadoc

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OWLFileDictionary with entries build from an OWL file.Classorg.openscience.cdk.dictCDKjavadoc
OWLReactDictionary with entries build from an OWL React.Classorg.openscience.cdk.dictCDKjavadoc
ParameterReactClass which defines the allowed parameters of a reaction.Classorg.openscience.cdk.reaction.type.parametersCDKjavadoc
ParseExceptionThis exception is thrown when parse errors are encountered.Classorg.openscience.cdk.iupac.parserCDKjavadoc
ParseExceptionThis exception is thrown when parse errors are encountered.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
PartialAtomicChargeColorsClass defining the color which with atoms are colored.Classorg.openscience.cdk.renderer.colorCDKjavadoc
PartialFilledStructureMergerRandomly generates a single, connected, correctly bonded structure from a number of fragments.Classorg.openscience.cdk.structgen.stochasticCDKjavadoc
PartialPiChargeDescriptorThe calculation of pi partial charges in pi-bonded systems of an heavy atom was made by Saller-Gasteiger.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
PartialSigmaChargeDescriptorThe calculation of sigma partial charges in sigma-bonded systems of an heavy atom was made by Marsilli-Gasteiger.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
PartialTChargeMMFF94DescriptorThe calculation of total partial charges of an heavy atom is based on MMFF94 model.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
PartialTChargePEOEDescriptorThe calculation of total partial charges of an heavy atom is based on Partial Equalization of Electronegativity method (PEOE-PEPE) from Gasteiger.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
PathClassorg.openscience.cdk.ringsearchCDKjavadoc
PathBuilderBuilder class for paths.Classorg.openscience.cdk.renderer.elements.pathCDKjavadoc
PathEdgeClassorg.openscience.cdk.smsd.ringCDKjavadoc
PathElementClassorg.openscience.cdk.renderer.elements.pathCDKjavadoc
PathElementA path composed of points.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
PathGraphClassorg.openscience.cdk.smsd.ringCDKjavadoc
PathToolsTools class with methods for handling molecular graphs.Classorg.openscience.cdk.graphCDKjavadoc
PCCompoundASNReaderReads an object from ASN formated input for PubChem Compound entries.Classorg.openscience.cdk.ioCDKjavadoc
PCCompoundXMLReaderReads an object from ASN.Classorg.openscience.cdk.ioCDKjavadoc
PCModelFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PCSubstanceXMLReaderReads an object from ASN formated input for PubChem Compound entries.Classorg.openscience.cdk.ioCDKjavadoc
PDBAtomRepresents the idea of an atom as used in PDB files.Classorg.openscience.cdk.protein.dataCDKjavadoc
PDBAtomRepresents the idea of an atom as used in PDB files.Classorg.openscience.cdk.silentCDKjavadoc
PDBAtomCustomizerCustomizer for the libio-cml Convertor to be able to export details forAuthor:egonwBelongs to the set:libio-cml-customizersCreated on:2005-05-04Requires:java1.Classorg.openscience.cdk.libio.cmlCDKjavadoc

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PDBConvention This is a lousy implementation, though.Classorg.openscience.cdk.io.cmlCDKjavadoc
PDBFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PDBMLFormatXML version of the PDB format.Classorg.openscience.cdk.io.formatsCDKjavadoc
PDBMonomerRepresents the idea of an monomer as used in PDB files.Classorg.openscience.cdk.protein.dataCDKjavadoc
PDBMonomerRepresents the idea of an monomer as used in PDB files.Classorg.openscience.cdk.silentCDKjavadoc
PDBPolymerAn entry in the PDB database.Classorg.openscience.cdk.protein.dataCDKjavadoc
PDBPolymerAn entry in the PDB database.Classorg.openscience.cdk.silentCDKjavadoc
PDBReaderReads the contents of a PDBFile.Classorg.openscience.cdk.ioCDKjavadoc
PDBStrandAn entry in the PDB database.Classorg.openscience.cdk.protein.dataCDKjavadoc
PDBStructureHolder for secundary protein structure elements.Classorg.openscience.cdk.protein.dataCDKjavadoc
PDBStructureHolder for secundary protein structure elements.Classorg.openscience.cdk.silentCDKjavadoc
PDBWriterSaves small molecules in a rudimentary PDB format.Classorg.openscience.cdk.ioCDKjavadoc
PeriodicGroupNumberAtomThis matcher checks the periodic group number of an atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
PeriodicTableRepresents elements of the Periodic Table.Classorg.openscience.cdk.tools.periodictableCDKjavadoc
PeriodicTablePositionDescriptorThis class returns the period in the periodic table of an atom belonging to an atom container This descriptor uses these parameters:Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
PermutorGeneral permutation generator, that uses orderly generation by ranking and unranking.Classorg.openscience.cdk.smsd.labellingCDKjavadoc
PetitjeanNumberDescriptorAccording to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
PetitjeanShapeIndexDescriptorEvaluates the Petitjean shape indices, These original Petitjean number was described by Petitjean ()Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
PharmacophoreAngleBondRepresents an angle relationship between three pharmacophore groups.Classorg.openscience.cdk.pharmacophoreCDKjavadoc
PharmacophoreAtomA representation of a pharmacophore group.Classorg.openscience.cdk.pharmacophoreCDKjavadoc
PharmacophoreBondRepresents a distance relationship between two pharmacophore groups.Classorg.openscience.cdk.pharmacophoreCDKjavadoc
PharmacophoreMatcherIdentifies atoms whose 3D arrangement matches a specified pharmacophore query.Classorg.openscience.cdk.pharmacophoreCDKjavadoc
PharmacophoreQueryRepresents a colleciton of pharmacophore groups and constraints.Classorg.openscience.cdk.pharmacophoreCDKjavadoc
PharmacophoreQueryAngleBondRepresents a pharmacophore query angle constraint.Classorg.openscience.cdk.pharmacophoreCDKjavadoc
PharmacophoreQueryAtomRepresents a query pharmacophore group.Classorg.openscience.cdk.pharmacophoreCDKjavadoc

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PharmacophoreQueryBondRepresents a pharmacophore query distance constraint.Classorg.openscience.cdk.pharmacophoreCDKjavadoc
PharmacophoreUtilsProvides some utility methods for pharmacophore handling.Classorg.openscience.cdk.pharmacophoreCDKjavadoc
PhysicalConstantsAn class providing predefined properties of physical constants.Classorg.openscience.cdkCDKjavadoc
PiBondingMovementReactionIReactionProcess which tries to reproduce the delocalization of electrons which are unsaturated bonds from conjugated rings.Classorg.openscience.cdk.reaction.typeCDKjavadoc
PiContactDetectionDescriptorThis 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 directlyClassorg.openscience.cdk.qsar.descriptors.atompairCDKjavadoc
PiElectronegativityCalculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).Classorg.openscience.cdk.chargesCDKjavadoc
PiElectronegativityDescriptorPi electronegativity is given by X = a + bq + c(q*q) This descriptor uses these parameters:Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
PMPConventionClassorg.openscience.cdk.io.cmlCDKjavadoc
PMPFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PMPReaderReads an frames from a PMP formated input.Classorg.openscience.cdk.ioCDKjavadoc
PointClassorg.openscience.cdk.graph.rebondCDKjavadoc
Point2dDifferenceDifference between two boolean[]'s.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
Point3dDifferenceDifference between two boolean[]'s.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc
PolarizabilityCalculation of the polarizability of a molecule by the method of Kang and Jhon and Gasteiger based on and Classorg.openscience.cdk.chargesCDKjavadoc
PolymerSubclass of Molecule to store Polymer specific attributes that a Polymer has.Classorg.openscience.cdkCDKjavadoc
PolymerSubclass of Molecule to store Polymer specific attributes that a Polymer has.Classorg.openscience.cdk.silentCDKjavadoc
PostFilterClass that cleans redundant mappings from the solution set.Classorg.openscience.cdk.smsd.filtersCDKjavadoc
POVRayFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PQSChemFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PrimesClassorg.openscience.cdk.mathCDKjavadoc
ProblemMarkerTool to mark IChemObject's as having a problem.Classorg.openscience.cdk.validateCDKjavadoc
ProductsBoxGeneratorGenerate the symbols for radicals.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
ProjectorTool to make projections from 3D to 2DKeywords:projection in 2DClassorg.openscience.cdk.geometryCDKjavadoc
PropertiesListenerAnswers the questions by looking up the values in a Properties object.Classorg.openscience.cdk.io.listenerCDKjavadoc
ProteinBuilderToolClass that facilitates building protein structures.Classorg.openscience.cdk.toolsCDKjavadoc

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ProteinPocketFinderThe detection of pocket and cavities in a bioPolymer is done similar to the program TODO: Optimisation of the cubic grid placementClassorg.openscience.cdk.proteinCDKjavadoc
ProtonAffinityHOSEDescriptorThis class returns the proton affinity of an atom containing.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
ProtonTotalPartialChargeDescriptorThe calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE).Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
PseudoAtomRepresents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Classorg.openscience.cdkCDKjavadoc
PseudoAtomRepresents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Classorg.openscience.cdk.silentCDKjavadoc
PubChemASNFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PubChemCompoundsXMLFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PubChemCompoundXMLFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PubchemFingerprinterGenerates a Pubchem fingerprint for a molecule.Classorg.openscience.cdk.fingerprintCDKjavadoc
PubChemFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PubChemSubstancesASNFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PubChemSubstancesXMLFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PubChemSubstanceXMLFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
PubChemXMLHelperHelper class to parse PubChem XML documents.Classorg.openscience.cdk.io.pubchemxmlCDKjavadoc
QChemFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
QSARConventionThis is an implementation for the CDK convention.Classorg.openscience.cdk.io.cmlCDKjavadoc
QSARCustomizerCustomizer for the libio-cml Convertor to be able to export details for QSAR descriptors calculated for Molecules.Classorg.openscience.cdk.libio.cmlCDKjavadoc
QuadToMake a quadratic curve in the path.Classorg.openscience.cdk.renderer.elements.pathCDKjavadoc
QuaternionThis class handles quaternions.Classorg.openscience.cdk.mathCDKjavadoc
QueryAtomContainerClassorg.openscience.cdk.isomorphism.matchersCDKjavadoc
QueryAtomContainerCreatorClassorg.openscience.cdk.isomorphism.matchersCDKjavadoc
QueryCompilerThis class creates an template for MCS/substructure query.Classorg.openscience.cdk.smsd.algorithm.vflib.queryCDKjavadoc
QueryProcessorClassorg.openscience.cdk.smsd.algorithm.mcgregorCDKjavadoc
QueueClassorg.openscience.cdk.ringsearchCDKjavadoc
RadicalChargeSiteInitiationHReactionIReactionProcess which participate mass spectrum process.Classorg.openscience.cdk.reaction.typeCDKjavadoc

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RadicalChargeSiteInitiationReactionIReactionProcess which participate mass spectrum process.Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalGeneratorGenerate the symbols for radicals.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
RadicalSiteHrAlphaReaction This reaction could be represented as [A*]-(C)_2-C3[H] => A([H])-(C_2)-[C3*].Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteHrBetaReaction This reaction could be represented as [A*]-(C)_3-C4[H] => A([H])-(C_3)-[C4*].Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteHrDeltaReaction This reaction could be represented as [A*]-(C)_4-C5[H] => A([H])-(C_4)-[C5*].Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteHrGammaReaction This reaction could be represented as [A*]-C1-C2-C3[H] => A([H])-C1-C2-[C3*].Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteInitiationHReactionIReactionProcess which participate mass spectrum process.Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteInitiationReactionIReactionProcess which participate mass spectrum process.Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteIonizationMechanismThis mechanism extracts an atom because of the stabilization of a radical.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
RadicalSiteRearrangementMechanismThis mechanism displaces an Atom or substructure (R) from one position to an other.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
RadicalSiteRrAlphaReaction This reaction could be represented as [A*]-(C)_2-C3[R] => A([RH])-(C_2)-[C3*].Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteRrBetaReaction This reaction could be represented as [A*]-(C)_3-C4[R] => A([R])-(C_3)-[C4*].Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteRrDeltaReaction This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*].Classorg.openscience.cdk.reaction.typeCDKjavadoc
RadicalSiteRrGammaReaction This reaction could be represented as [A*]-(C)_5-C6[R] => A([R])-(C_5)-[C6*].Classorg.openscience.cdk.reaction.typeCDKjavadoc
RandomAccessReaderRandom access to text files of compounds.Classorg.openscience.cdk.io.randomCDKjavadoc
RandomAccessSDFReaderRandom access of SDF file.Classorg.openscience.cdk.io.randomCDKjavadoc
RandomGeneratorRandomGenerator is a generator of Constitutional Isomers.Classorg.openscience.cdk.structgenCDKjavadoc
RandomNumbersToolClass supplying useful methods to generate random numbers.Classorg.openscience.cdk.mathCDKjavadoc
RasmolColorsAtom coloring following RasMol/Chime Color scheme http://www.Classorg.openscience.cdk.renderer.colorCDKjavadoc
RawCopyFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
RDBERuleRing Double Bond Equivalents (RDBE) or Double Bond Equivalents (DBE) are calculated from valence values of Classorg.openscience.cdk.formula.rulesCDKjavadoc
RDFCalculatorCalculator of radial distribution functions.Classorg.openscience.cdk.geometryCDKjavadoc
RDFProtonDescriptor_G3RThis class calculates G3R proton descriptors used in neural networks for H1 NMR shift .Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
RDFProtonDescriptor_GDRThis class calculates GDR proton descriptors used in neural networks for H1 NMR shift .Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
RDFProtonDescriptor_GHRThis class calculates GHR proton descriptors used in neural networks for H1 NMR shift .Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc

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RDFProtonDescriptor_GHR_topolThis class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift .Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
RDFProtonDescriptor_GSRThis class calculates GDR proton descriptors used in neural networks for H1 NMR shift .Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
ReactantsBoxGeneratorGenerate the symbols for radicals.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
ReactionRepresents the idea of a chemical reaction.Classorg.openscience.cdkCDKjavadoc
ReactionRepresents the idea of a chemical reaction.Classorg.openscience.cdk.silentCDKjavadoc
ReactionArrowGeneratorGenerate the arrow for a reaction.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
ReactionBoxGeneratorGenerate the symbols for radicals.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
ReactionChainClasses that extends the definition of reaction to a chain reaction.Classorg.openscience.cdk.reactionCDKjavadoc
ReactionEngineThe base class for all chemical reactions objects in this cdk.Classorg.openscience.cdk.reactionCDKjavadoc
ReactionManipulatorClassorg.openscience.cdk.tools.manipulatorCDKjavadoc
ReactionPlusGeneratorGenerate the arrow for a reaction.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
ReactionRendererA general renderer for IChemModels, IReactions, and IMolecules.Classorg.openscience.cdk.rendererCDKjavadoc
ReactionSceneGeneratorGenerator for general reaction scene components.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc
ReactionSchemeClasses that extends the definition of reaction to a scheme.Classorg.openscience.cdkCDKjavadoc
ReactionSchemeClasses that extends the definition of reaction to a scheme.Classorg.openscience.cdk.silentCDKjavadoc
ReactionSchemeManipulatorClassorg.openscience.cdk.tools.manipulatorCDKjavadoc
ReactionSetA set of reactions, for example those taking part in a reaction.Classorg.openscience.cdkCDKjavadoc
ReactionSetA set of reactions, for example those taking part in a reaction.Classorg.openscience.cdk.silentCDKjavadoc
ReactionSetManipulatorClassorg.openscience.cdk.tools.manipulatorCDKjavadoc
ReactionSetRendererA general renderer for IChemModels, IReactions, and IMolecules.Classorg.openscience.cdk.rendererCDKjavadoc
ReactionSpecificationClass that is used to distribute reactions specifications.Classorg.openscience.cdk.reactionCDKjavadoc
ReaderEventSignals that something has happened in a file reader.Classorg.openscience.cdk.ioCDKjavadoc
ReaderFactoryA factory for creating ChemObjectReaders.Classorg.openscience.cdk.ioCDKjavadoc
RearrangementAnionReactionIReactionProcess which participate in movement resonance.Classorg.openscience.cdk.reaction.typeCDKjavadoc
RearrangementCationReactionIReactionProcess which participate in movement resonance.Classorg.openscience.cdk.reaction.typeCDKjavadoc

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RearrangementChargeMechanismThis mechanism displaces the charge(radical, charge + or charge -) because of a double bond which is associated.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
RearrangementLonePairReactionIReactionProcess which participate in movement resonance.Classorg.openscience.cdk.reaction.typeCDKjavadoc
RearrangementRadicalReactionIReactionProcess which participate in movement resonance.Classorg.openscience.cdk.reaction.typeCDKjavadoc
RebondToolProvides tools to rebond a molecule from 3D coordinates only.Classorg.openscience.cdk.graph.rebondCDKjavadoc
RectangleElementA rectangle, with width and height.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
RecursiveSmartsAtomThis matches recursive smarts atoms.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
RemovingSEofBMechanismThis mechanism extracts a single electron from a bonding orbital which located in an bond.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
RemovingSEofNBMechanismThis mechanism extracts a single electron from a non-bonding orbital which located in a ILonePair container.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
RendererModelModel for IRenderer that contains settings for drawing objects.Classorg.openscience.cdk.rendererCDKjavadoc
ResidueA residue is a named, numbered collection of atoms in an MDMolecule.Classorg.openscience.cdk.libio.mdCDKjavadoc
RGraphThis class implements the Resolution Graph (RGraph).Classorg.openscience.cdk.isomorphism.mcssCDKjavadoc
RGroupRepresents a single substitute structure in an RGroupList.Classorg.openscience.cdk.isomorphism.matchersCDKjavadoc
RGroupListRepresents a list of Rgroup substitutes to be associated with someAuthor:Mark RijnbeekKeywords:Rgroup, R group, R-groupClassorg.openscience.cdk.isomorphism.matchersCDKjavadoc
RGroupQueryRepresents information contained in a Symyx RGfile (R-group query file).Classorg.openscience.cdk.isomorphism.matchersCDKjavadoc
RGroupQueryFormatFormat for Symyx RGfiles (Rgroup query files).Classorg.openscience.cdk.io.formatsCDKjavadoc
RGroupQueryReaderA reader for Symyx' Rgroup files (RGFiles).Classorg.openscience.cdk.ioCDKjavadoc
RGroupQueryWriterA writer for Symyx' Rgroup files (RGFiles).Classorg.openscience.cdk.ioCDKjavadoc
RingClass representing a ring structure in a molecule.Classorg.openscience.cdkCDKjavadoc
RingClass representing a ring structure in a molecule.Classorg.openscience.cdk.silentCDKjavadoc
RingAtomThis matches an atom in a specific size ring.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
RingBondThis smarts bond matches any bond that is in a ring.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
RingElementClassorg.openscience.cdk.renderer.elementsCDKjavadoc
RingFilterClassorg.openscience.cdk.smsd.ringCDKjavadoc
RingFinderInterfaceorg.openscience.cdk.smsd.ringCDKjavadoc
RingGeneratorGenerates just the aromatic indicators for rings : circles, or light-gray inner bonds, depending on the value of CDKStyleAromaticity.Classorg.openscience.cdk.renderer.generatorsCDKjavadoc

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RingIdentifierAtomThis encapsulates an atom with a ring identifier, with an optional ring bond specified.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
RingManipulatorClassorg.openscience.cdk.tools.manipulatorCDKjavadoc
RingMembershipAtomThis query atom matches any atom with a certain number of SSSR.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
RingPartitionerPartitions a RingSet into RingSets of connected rings.Classorg.openscience.cdk.ringsearchCDKjavadoc
RingPlacerClass providing methods for generating coordinates for ring atoms.Classorg.openscience.cdk.layoutCDKjavadoc
RingSetMaintains a set of Ring objects.Classorg.openscience.cdkCDKjavadoc
RingSetMaintains a set of Ring objects.Classorg.openscience.cdk.silentCDKjavadoc
RingSetManipulatorClassorg.openscience.cdk.tools.manipulatorCDKjavadoc
RingSizeComparatorClassorg.openscience.cdk.tools.manipulatorCDKjavadoc
RMapAn 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.Classorg.openscience.cdk.isomorphism.mcssCDKjavadoc
RNodeNode of the resolution graphe (RGraph) An RNode represents an association betwwen two edges of the source graphs G1 and G2 that are compared.Classorg.openscience.cdk.isomorphism.mcssCDKjavadoc
RotatableBondsCountDescriptorThe number of rotatable bonds is given by the SMARTS specified by Daylight on This descriptor uses these parameters:Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
RssWriterGenerates an RSS feed.Classorg.openscience.cdk.ioCDKjavadoc
RuleOfFiveDescriptorThis Class contains a method that returns the number failures of the Lipinski's Rule Of 5.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
SaturationCheckerProvides methods for checking whether an atoms valences are saturated with respect to a particular atom type.Classorg.openscience.cdk.toolsCDKjavadoc
SDFFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
SDFWriterWrites MDL SD files ().Classorg.openscience.cdk.ioCDKjavadoc
SetReactionCenterClass extension of ParameterReact class which defines if a reaction is set already the reaction centerAuthor:miguelrojaschClassorg.openscience.cdk.reaction.type.parametersCDKjavadoc
SharingAnionReactionIReactionProcess which participate in movement resonance.Classorg.openscience.cdk.reaction.typeCDKjavadoc
SharingChargeDBReactionIReactionProcess which participate in movement resonance.Classorg.openscience.cdk.reaction.typeCDKjavadoc
SharingChargeSBReactionIReactionProcess which participate in movement resonance.Classorg.openscience.cdk.reaction.typeCDKjavadoc
SharingElectronMechanismThis mechanism displaces the charge (lonePair) because of deficiency of charge.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
SharingLonePairReactionIReactionProcess which participate in movement resonance.Classorg.openscience.cdk.reaction.typeCDKjavadoc
ShelXFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
ShelXReaderA reader for ShelX output (RES) files.Classorg.openscience.cdk.ioCDKjavadoc

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ShelXWriterSerializes a MoleculeSet or a Molecule object to ShelX code.Classorg.openscience.cdk.ioCDKjavadoc
SigmaElectronegativityDescriptorAtomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
SignatureQuotientGraphA 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.Classorg.openscience.cdk.signatureCDKjavadoc
SignatureReactionCanoniserClassorg.openscience.cdk.smsd.labellingCDKjavadoc
SilentChemObjectBuilderClassorg.openscience.cdk.silentCDKjavadoc
SimpleBasisSetThis class will generate a simple base set for a atom container.Classorg.openscience.cdk.math.qmCDKjavadoc
SimpleCharStreamAn implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).Classorg.openscience.cdk.iupac.parserCDKjavadoc
SimpleCharStreamAn implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
SimpleCycleA cycle in a graph G is a subgraph in which every vertex has even degree.Classorg.openscience.cdk.ringsearch.cyclebasisCDKjavadoc
SimpleCycleBasisAuxiliary class for CycleBasis.Classorg.openscience.cdk.ringsearch.cyclebasisCDKjavadoc
SimpleNodeBasic implementation of AST nodes.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
SingleElectronA Single Electron is an orbital which is occupied by only one electron.Classorg.openscience.cdk.silentCDKjavadoc
SingleElectronA Single Electron is an orbital which is occupied by only one electron.Classorg.openscience.cdkCDKjavadoc
SingleElectronDiffCompares two ISingleElectron classes.Classorg.openscience.cdk.tools.diffCDKjavadoc
SingleMappingThis class handles single atom mapping.Classorg.openscience.cdk.smsd.algorithm.singleCDKjavadoc
SingleMappingHandlerThis is a handler class for single atom mappingAuthor:Syed Asad Rahman Classorg.openscience.cdk.smsd.algorithm.singleCDKjavadoc
SingleStructureRandomGeneratorRandomly generates a single, connected, correctly bonded structure for a given molecular formula.Classorg.openscience.cdk.structgenCDKjavadoc
SmallestRingAtomThis smarts atom matches any atom with the smallest SSSR size being a See Also:Serialized FormKeywords:SMARTSClassorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
Smarts2MQLVisitorAn AST tree visitor.Classorg.openscience.cdk.smiles.smarts.parser.visitorCDKjavadoc
SMARTSAtomAbstract smarts atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
SMARTSBondAbstract smarts bond.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
SmartsDumpVisitorAn AST Tree visitor.Classorg.openscience.cdk.smiles.smarts.parser.visitorCDKjavadoc
SMARTSFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
SMARTSParserThis parser implements a nearly complete subset of the SMARTS syntax as defined on Example code using SMARTS substructure search looks like:Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
SMARTSParserConstantsToken literal values and constants.Interfaceorg.openscience.cdk.smiles.smarts.parserCDKjavadoc

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SMARTSParserTokenManagerClassorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
SMARTSParserTreeConstantsInterfaceorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
SMARTSParserVisitorInterfaceorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
SMARTSQueryToolThis class provides a easy to use wrapper around SMARTS matching functionality.Classorg.openscience.cdk.smiles.smartsCDKjavadoc
SmartsQueryVisitorAn AST tree visitor.Classorg.openscience.cdk.smiles.smarts.parser.visitorCDKjavadoc
SMILESFIXFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
SMILESFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
SmilesGeneratorGenerates SMILES strings .Classorg.openscience.cdk.smilesCDKjavadoc
SmilesParserParses a SMILES string and an AtomContainer.Classorg.openscience.cdk.smilesCDKjavadoc
SmilesReactionCanoniserClassorg.openscience.cdk.smsd.labellingCDKjavadoc
SMILESReaderThis Reader reads files which has one SMILES string on each line, where the format is given as below:Classorg.openscience.cdk.ioCDKjavadoc
SmilesValencyCheckerSmall customization of ValencyHybridChecker suggested by Todd Martin specially tuned for SMILES parsing.Classorg.openscience.cdk.toolsCDKjavadoc
SMILESWriterWrites the SMILES strings to a plain text file.Classorg.openscience.cdk.ioCDKjavadoc
SMSDNormalizerThis class containes set of modules required to clean a molecule before subjecting it for MCS search.Classorg.openscience.cdk.normalizeCDKjavadoc
SpanningTreeSpanning tree of a molecule.Classorg.openscience.cdk.graphCDKjavadoc
SpartanFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
SSSRFinderFinds the Smallest Set of Smallest Rings.Classorg.openscience.cdk.ringsearchCDKjavadoc
StabilizationChargesThe stabilization of the positive and the negative charge obtained (e.Classorg.openscience.cdk.chargesCDKjavadoc
StabilizationPlusChargeDescriptorThe stabilization of the positive charge (e.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
StandardSubstructureSetsClassorg.openscience.cdk.fingerprintCDKjavadoc
StereoBondThis query bond matches bonds with specific stereo type.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
StereoToolMethods to determine or check the stereo class of a set of atoms.Classorg.openscience.cdk.stereoCDKjavadoc
StrandA Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.Classorg.openscience.cdk.silentCDKjavadoc
StrandA Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.Classorg.openscience.cdkCDKjavadoc
StringDifferenceIDifference between two String.Classorg.openscience.cdk.tools.diff.treeCDKjavadoc

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StringIOSettingAn class for a reader setting which must be of type String.Classorg.openscience.cdk.io.settingCDKjavadoc
StructGenAtomTypeGuesserAtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.Classorg.openscience.cdk.atomtypeCDKjavadoc
StructGenMatcherAtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.Classorg.openscience.cdk.atomtypeCDKjavadoc
StructureDiagramGeneratorGenerates 2D coordinates for a molecule for which only connectivity is known or the coordinates have been discarded for some reason.Classorg.openscience.cdk.layoutCDKjavadoc
StructureResonanceGeneratorThis class try to generate resonance structure for a determinate molecule.Classorg.openscience.cdk.toolsCDKjavadoc
SubstructureFingerprinterIFingerprinter that gives a bit set which has a size equal to the number of substructures it was constructed from.Classorg.openscience.cdk.fingerprintCDKjavadoc
SVGFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
SwingEventRelayClassorg.openscience.cdk.controllerCDKjavadoc
SwingGUIListenerAllows processing of IOSetting quesions which are passed to the user by using Swing dialogs.Classorg.openscience.cdk.io.listenerCDKjavadoc
SwingMouseEventRelayClassorg.openscience.cdk.controllerCDKjavadoc
SwissArmyKnifeA set of utilities which did not really fit into any other categoryAuthor:steinbeckCreated on:2001-06-19Classorg.openscience.cdk.toolsCDKjavadoc
SybylAtomTypeMatcherAtom Type matcher for Sybyl atom types.Classorg.openscience.cdk.atomtypeCDKjavadoc
SybylDescriptorFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
SymbolAndChargeQueryAtomClassorg.openscience.cdk.isomorphism.matchersCDKjavadoc
SymbolChargeIDQueryAtomClassorg.openscience.cdk.isomorphism.matchersCDKjavadoc
SymbolQueryAtomClassorg.openscience.cdk.isomorphism.matchersCDKjavadoc
SymbolSetQueryAtomA QueryAtom that matches all symbols in this container.Classorg.openscience.cdk.isomorphism.matchersCDKjavadoc
SystemOutLoggingTool the System.Classorg.openscience.cdk.toolsCDKjavadoc
TaeAminoAcidDescriptorAn implementation of the TAE descriptors for amino acids.Classorg.openscience.cdk.qsar.descriptors.proteinCDKjavadoc
TanimotoCalculates the Tanimoto coefficient for a given pair of two fingerprint bitsets or real valued feature vectors.Classorg.openscience.cdk.similarityCDKjavadoc
TargetProcessorClassorg.openscience.cdk.smsd.algorithm.mcgregorCDKjavadoc
TargetPropertiesClass for building/storing nodes (atoms) in the graph with atom query capabilities.Classorg.openscience.cdk.smsd.algorithm.vflib.builderCDKjavadoc
TautomerizationMechanismThis mechanism produces the tautomerization chemical reaction between two tautomers.Classorg.openscience.cdk.reaction.mechanismCDKjavadoc
TautomerizationReactionIReactionProcess which produces a tautomerization chemical reaction.Classorg.openscience.cdk.reaction.typeCDKjavadoc
TemplateExtractorHelper class that help setup a template library of CDK's Builder3D.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc

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TemplateHandlerHelper class for Structure Diagram Generation.Classorg.openscience.cdk.layoutCDKjavadoc
TemplateHandler3DHelper class for ModelBuilder3D.Classorg.openscience.cdk.modeling.builder3dCDKjavadoc
TessellatePerforms a tessellation of the unit sphere.Classorg.openscience.cdk.geometry.surfaceCDKjavadoc
TestClassClassorg.openscience.cdk.annotationsCDKjavadoc
TestMethodClassorg.openscience.cdk.annotationsCDKjavadoc
TetrahedralChiralityStereochemistry specification for quadrivalent atoms.Classorg.openscience.cdk.stereoCDKjavadoc
TextElementText element as used in the chemical drawing.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
TextGroupElementA group of text elements, particularly the element symbol (eg: "C") surrounded by other annotations such as mass number, charge, etc.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
TextGUIListenerAllows processing of IOSetting quesions which are passed to the user by using the System.Classorg.openscience.cdk.io.listenerCDKjavadoc
TimeManagerClass that handles execution time of the MCS search.Classorg.openscience.cdk.smsd.toolsCDKjavadoc
TimeOutClass that manages MCS timeout.Classorg.openscience.cdk.smsd.globalCDKjavadoc
TinkerMM2FormatClassorg.openscience.cdk.io.formatsCDKjavadoc
TinkerXYZFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
TokenDescribes the input token stream.Classorg.openscience.cdk.iupac.parserCDKjavadoc
TokenDescribes the input token stream.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
TokenMgrErrorToken Manager Error.Classorg.openscience.cdk.iupac.parserCDKjavadoc
TokenMgrErrorToken Manager Error.Classorg.openscience.cdk.smiles.smarts.parserCDKjavadoc
ToleranceRangeRuleThis class validate if the mass from an IMolecularFormula is between the tolerance range give a experimental mass.Classorg.openscience.cdk.formula.rulesCDKjavadoc
TopologicalMatrixCalculator for a topological matrix representation of this AtomContainer.Classorg.openscience.cdk.graph.matrixCDKjavadoc
TotalConnectionAtomThis matches an atom using total number of connections.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
TotalHCountAtomThis matcher checks the formal charge of the Atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
TotalRingConnectionAtomThis matcher checks the number of ring connections of the checked Atom with other Atom's.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
TotalValencyAtomThis matcher checks the total valency of the Atom.Classorg.openscience.cdk.isomorphism.matchers.smartsCDKjavadoc
TPSADescriptorCalculation of topological polar surface area based on fragment contributions (TPSA) .Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
TriangleRepresentation of a triangle in 3D.Classorg.openscience.cdk.geometry.surfaceCDKjavadoc

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TurboMoleFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
TXTBasedAtomTypeConfiguratorAtomType list configurator that uses the AtomTypes originally defined in Jmol v5.Classorg.openscience.cdk.configCDKjavadoc
TypeThe type of the path elements.Classorg.openscience.cdk.renderer.elements.pathCDKjavadoc
UndoAdapterAn undo adapter for updating the state of the undo components according to the new state of the undo history list.Classorg.openscience.cdk.controllerCDKjavadoc
UniChemXYZFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
UnsupportedChemObjectExceptionClassorg.openscience.cdk.exceptionCDKjavadoc
VABCDescriptorVolume descriptor using the method implemented in the VABCVolume class.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
VABCVolumeCalculates the Van der Waals volume using the method proposed in .Classorg.openscience.cdk.geometry.volumeCDKjavadoc
VAdjMaDescriptorVertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
ValidationReportA report on validation of chemical semantics.Classorg.openscience.cdk.validateCDKjavadoc
ValidationTestError found during sematical validation of a IChemObject.Classorg.openscience.cdk.validateCDKjavadoc
ValidatorEngineEngine that performs the validation by traversing the IChemObject hierarchy.Classorg.openscience.cdk.validateCDKjavadoc
VASPFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
VASPReaderRead output files generated with the VASP software.Classorg.openscience.cdk.ioCDKjavadoc
VdWRadiusDescriptorThis class return the VdW radius of a given atom.Classorg.openscience.cdk.qsar.descriptors.atomicCDKjavadoc
VectorThis class handles vectors.Classorg.openscience.cdk.mathCDKjavadoc
VFAtomMatcherInterface for the AtomMatcher (atoms) in graph.Interfaceorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
VFBondMatcherInterface for the BondMatcher (bonds) in graph.Interfaceorg.openscience.cdk.smsd.algorithm.matchersCDKjavadoc
VFlibMCSHandlerThis class should be used to find MCS between query graph and target graph.Classorg.openscience.cdk.smsd.algorithm.vflibCDKjavadoc
VFlibSubStructureHandlerThis is an ultra fast method to report if query is a substructure for target molecule.Classorg.openscience.cdk.smsd.algorithm.vflibCDKjavadoc
VFlibTurboHandlerThis is an ultra fast method to report if query is a substructure for target molecule.Classorg.openscience.cdk.smsd.algorithm.vflibCDKjavadoc
VFMapperThis class finds MCS between query and target molecules using VF2 algorithm.Classorg.openscience.cdk.smsd.algorithm.vflib.mapCDKjavadoc
VFMCSMapperThis class finds MCS between query and target molecules using VF2 algorithm.Classorg.openscience.cdk.smsd.algorithm.vflib.mapCDKjavadoc
VFQueryBuilderClass for parsing and generating query graph.Classorg.openscience.cdk.smsd.algorithm.vflib.builderCDKjavadoc
VFStateThis class finds mapping states between query and targetAuthor:Syed Asad Rahman Classorg.openscience.cdk.smsd.algorithm.vflib.mapCDKjavadoc

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VibrationA molecular vibration composed of a set of atom vectors.Classorg.openscience.cdkCDKjavadoc
VicinitySamplerThe VicinitySampler is a generator of Constitutional Isomers.Classorg.openscience.cdk.structgenCDKjavadoc
ViewmolFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
VisitedAtomsHelper class for the CIPTool to keep track of which atoms have already been visited.Classorg.openscience.cdk.geometry.cipCDKjavadoc
WedgeLineElementA 'wedge' is a triangle aligned along a bond that indicates stereochemistry.Classorg.openscience.cdk.renderer.elementsCDKjavadoc
WeightDescriptorIDescriptor based on the weight of atoms of a certain element type.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
WeightedPathDescriptorEvaluates the weighted path descriptors.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
WHIMDescriptorHolistic descriptors described by Todeschini et al .Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
WienerNumbersDescriptorThis descriptor calculates the Wiener numbers.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
WriterFactoryHelper tool to create IChemObjectWriters.Classorg.openscience.cdk.ioCDKjavadoc
XEDFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
XLogPDescriptorPrediction of logP based on the atom-type method called XLogP.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
XYZFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
XYZReaderReads an object from XYZ formated input.Classorg.openscience.cdk.ioCDKjavadoc
XYZWriterClassorg.openscience.cdk.ioCDKjavadoc
YasaraFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
ZagrebIndexDescriptorZagreb index: the sum of the squares of atom degree over all heavy atoms i.Classorg.openscience.cdk.qsar.descriptors.molecularCDKjavadoc
ZindoFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
ZMatrixFormatClassorg.openscience.cdk.io.formatsCDKjavadoc
ZMatrixReaderIt reads Z matrices like in Gaussian input files.Classorg.openscience.cdk.ioCDKjavadoc
ZMatrixToolsA set of static utility classes for dealing with Z matrices.Classorg.openscience.cdk.geometryCDKjavadoc

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