Binary compatibility report for the CDK library between 1.4.19 and 1.5.0 versions

Test Info

Library Name	CDK
Version #1	1.4.19
Version #2	1.5.0

Test Results

Total Java ARchives	1
Total Methods / Classes	32628 / 3559
Verdict	Incompatible (7.1%)

Problem Summary

	Severity	Count
Added Methods	-	463
Removed Methods	High	857
Problems with Data Types	High	133
	Medium	30
	Low	37
Problems with Methods	High	12
	Medium	0
	Low	2
Other Changes in Data Types	-	26

Added Methods (463)

cdk-1.5.0.jar, AbstractRenderer.class
package org.openscience.cdk.renderer
AbstractRenderer.AbstractRenderer ( )

cdk-1.5.0.jar, AbstractValidator.class
package org.openscience.cdk.validate
AbstractValidator.validateMolecule ( IAtomContainer subject ) :  ValidationReport
AbstractValidator.validateMoleculeSet ( IAtomContainerSet subject ) :  ValidationReport

cdk-1.5.0.jar, AdductionLPMechanism.class
package org.openscience.cdk.reaction.mechanism
AdductionLPMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, AdductionPBMechanism.class
package org.openscience.cdk.reaction.mechanism
AdductionPBMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, AdductionProtonLPReaction.class
package org.openscience.cdk.reaction.type
AdductionProtonLPReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, AdductionProtonPBReaction.class
package org.openscience.cdk.reaction.type
AdductionProtonPBReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, AdductionSodiumLPReaction.class
package org.openscience.cdk.reaction.type
AdductionSodiumLPReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, AtomContainerAtomPermutor.class
package org.openscience.cdk.graph
AtomContainerAtomPermutor.containerFromPermutation ( int[ ] permutation ) :  IAtomContainer

cdk-1.5.0.jar, AtomContainerBondPermutor.class
package org.openscience.cdk.graph
AtomContainerBondPermutor.containerFromPermutation ( int[ ] permutation ) :  IAtomContainer

cdk-1.5.0.jar, AtomContainerPermutor.class
package org.openscience.cdk.graph
AtomContainerPermutor.AtomContainerPermutor ( int size, IAtomContainer atomContainer )
AtomContainerPermutor.containerFromPermutation ( int[ ] p1 ) [abstract] :  IAtomContainer
AtomContainerPermutor.randomNext ( ) :  IAtomContainer

cdk-1.5.0.jar, AtomPlacer.class
package org.openscience.cdk.layout
AtomPlacer.getInitialLongestChain ( IAtomContainer molecule ) :  IAtomContainer
AtomPlacer.getLongestUnplacedChain ( IAtomContainer molecule, IAtom startAtom ) :  IAtomContainer

cdk-1.5.0.jar, AtomTypeTools.class
package org.openscience.cdk.tools
AtomTypeTools.assignAtomTypePropertiesToAtom ( IAtomContainer molecule ) :  IRingSet
AtomTypeTools.assignAtomTypePropertiesToAtom ( IAtomContainer molecule, boolean aromaticity ) :  IRingSet

cdk-1.5.0.jar, BasicValidator.class
package org.openscience.cdk.validate
BasicValidator.validateMolecule ( IAtomContainer subject ) :  ValidationReport

cdk-1.5.0.jar, BoundsCalculator.class
package org.openscience.cdk.renderer
BoundsCalculator.calculateBounds ( IAtomContainerSet moleculeSet ) [static] :  Rectangle2D

cdk-1.5.0.jar, CarbonylEliminationReaction.class
package org.openscience.cdk.reaction.type
CarbonylEliminationReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, CDKMCSHandler.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKMCSHandler.getUncommon ( IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds ) :  IAtomContainerSet

cdk-1.5.0.jar, CDKSubGraphHandler.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKSubGraphHandler.getUncommon ( IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds ) :  IAtomContainerSet

cdk-1.5.0.jar, CDKUtilities.class
package org.openscience.cdk.tools
CDKUtilities.fixAromaticityForXLogP ( IAtomContainer m ) [static] :  void
CDKUtilities.fixNitroGroups2 ( IAtomContainer m ) [static] :  boolean
CDKUtilities.fixSulphurH ( IAtomContainer m ) [static] :  void

cdk-1.5.0.jar, ChemModel.class
package org.openscience.cdk
ChemModel.getMoleculeSet ( ) :  IAtomContainerSet
ChemModel.setMoleculeSet ( IAtomContainerSet setOfMolecules ) :  void
package org.openscience.cdk.silent
ChemModel.getMoleculeSet ( ) :  IAtomContainerSet
ChemModel.setMoleculeSet ( IAtomContainerSet setOfMolecules ) :  void

cdk-1.5.0.jar, ConnectivityChecker.class
package org.openscience.cdk.graph
ConnectivityChecker.partitionIntoMolecules ( IAtomContainer atomContainer ) [static] :  IAtomContainerSet

cdk-1.5.0.jar, Convertor.class
package org.openscience.cdk.libio.cml
Convertor.cdkAtomContainerSetToCMLList ( IAtomContainerSet moleculeSet ) :  CMLMoleculeList
package org.openscience.cdk.libio.jena
Convertor.model2Molecule ( Model model, IChemObjectBuilder builder ) [static] :  IAtomContainer
Convertor.molecule2Model ( IAtomContainer molecule ) [static] :  Model

cdk-1.5.0.jar, CTFileQueryBond.class
package org.openscience.cdk.isomorphism.matchers
CTFileQueryBond.CTFileQueryBond ( )
CTFileQueryBond.getType ( ) :  CTFileQueryBond.Type
CTFileQueryBond.matches ( IBond bond ) :  boolean
CTFileQueryBond.setType ( CTFileQueryBond.Type type ) :  void

cdk-1.5.0.jar, DataFeaturesTool.class
package org.openscience.cdk.tools
DataFeaturesTool.getSupportedDataFeatures ( IAtomContainer molecule ) [static] :  int

cdk-1.5.0.jar, DebugChemModel.class
package org.openscience.cdk.debug
DebugChemModel.getMoleculeSet ( ) :  IAtomContainerSet
DebugChemModel.setMoleculeSet ( IAtomContainerSet setOfMolecules ) :  void

cdk-1.5.0.jar, DebugReaction.class
package org.openscience.cdk.debug
DebugReaction.addAgent ( IAtomContainer agent ) :  void
DebugReaction.addProduct ( IAtomContainer product ) :  void
DebugReaction.addProduct ( IAtomContainer product, Double coefficient ) :  void
DebugReaction.addReactant ( IAtomContainer reactant ) :  void
DebugReaction.addReactant ( IAtomContainer reactant, Double coefficient ) :  void
DebugReaction.getAgents ( ) :  IAtomContainerSet
DebugReaction.getProductCoefficient ( IAtomContainer product ) :  Double
DebugReaction.getProducts ( ) :  IAtomContainerSet
DebugReaction.getReactantCoefficient ( IAtomContainer reactant ) :  Double
DebugReaction.getReactants ( ) :  IAtomContainerSet
DebugReaction.setProductCoefficient ( IAtomContainer product, Double coefficient ) :  boolean
DebugReaction.setProducts ( IAtomContainerSet products ) :  void
DebugReaction.setReactantCoefficient ( IAtomContainer reactant, Double coefficient ) :  boolean
DebugReaction.setReactants ( IAtomContainerSet reactants ) :  void

cdk-1.5.0.jar, DeduceBondSystemTool.class
package org.openscience.cdk.smiles
DeduceBondSystemTool.fixAromaticBondOrders ( IAtomContainer atomContainer ) :  IAtomContainer
DeduceBondSystemTool.isOK ( IAtomContainer m ) :  boolean

cdk-1.5.0.jar, ElectronImpactNBEReaction.class
package org.openscience.cdk.reaction.type
ElectronImpactNBEReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, ElectronImpactPDBReaction.class
package org.openscience.cdk.reaction.type
ElectronImpactPDBReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, ElectronImpactSDBReaction.class
package org.openscience.cdk.reaction.type
ElectronImpactSDBReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, EStateFingerprinter.class
package org.openscience.cdk.fingerprint
EStateFingerprinter.getRawFingerprint ( IAtomContainer iAtomContainer ) :  Map

cdk-1.5.0.jar, ExtAtomContainerManipulator.class
package org.openscience.cdk.smsd.tools
ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID ( IAtomContainer atomContainer ) [static] :  IAtomContainer

cdk-1.5.0.jar, ExtendedFingerprinter.class
package org.openscience.cdk.fingerprint
ExtendedFingerprinter.getRawFingerprint ( IAtomContainer iAtomContainer ) :  Map

cdk-1.5.0.jar, FiguerasSSSRFinder.class
package org.openscience.cdk.ringsearch
FiguerasSSSRFinder.findSSSR ( IAtomContainer mol ) :  RingSet

cdk-1.5.0.jar, Fingerprinter.class
package org.openscience.cdk.fingerprint
Fingerprinter.getRawFingerprint ( IAtomContainer iAtomContainer ) :  Map

cdk-1.5.0.jar, ForceFieldConfigurator.class
package org.openscience.cdk.modeling.builder3d
ForceFieldConfigurator.assignAtomTyps ( IAtomContainer molecule ) :  IRingSet

cdk-1.5.0.jar, GaussianInputWriter.class
package org.openscience.cdk.io.program
GaussianInputWriter.writeMolecule ( IAtomContainer mol ) :  void

cdk-1.5.0.jar, HeterolyticCleavageMechanism.class
package org.openscience.cdk.reaction.mechanism
HeterolyticCleavageMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, HeterolyticCleavagePBReaction.class
package org.openscience.cdk.reaction.type
HeterolyticCleavagePBReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, HeterolyticCleavageSBReaction.class
package org.openscience.cdk.reaction.type
HeterolyticCleavageSBReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, HomolyticCleavageMechanism.class
package org.openscience.cdk.reaction.mechanism
HomolyticCleavageMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, HomolyticCleavageReaction.class
package org.openscience.cdk.reaction.type
HomolyticCleavageReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, HOSECodeGenerator.class
package org.openscience.cdk.tools
HOSECodeGenerator.getSpheres ( IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize ) :  List[ ]

cdk-1.5.0.jar, HyperconjugationReaction.class
package org.openscience.cdk.reaction.type
HyperconjugationReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, IChemModel.class
package org.openscience.cdk.interfaces
IChemModel.getMoleculeSet ( ) [abstract] :  IAtomContainerSet
IChemModel.setMoleculeSet ( IAtomContainerSet p1 ) [abstract] :  void

cdk-1.5.0.jar, IFingerprinter.class
package org.openscience.cdk.fingerprint
IFingerprinter.getRawFingerprint ( IAtomContainer p1 ) [abstract] :  Map

cdk-1.5.0.jar, InverseSymbolSetQueryAtom.class
package org.openscience.cdk.isomorphism.matchers
InverseSymbolSetQueryAtom.getSymbolSet ( ) :  Set

cdk-1.5.0.jar, IReaction.class
package org.openscience.cdk.interfaces
IReaction.addAgent ( IAtomContainer p1 ) [abstract] :  void
IReaction.addProduct ( IAtomContainer p1 ) [abstract] :  void
IReaction.addProduct ( IAtomContainer p1, Double p2 ) [abstract] :  void
IReaction.addReactant ( IAtomContainer p1 ) [abstract] :  void
IReaction.addReactant ( IAtomContainer p1, Double p2 ) [abstract] :  void
IReaction.getAgents ( ) [abstract] :  IAtomContainerSet
IReaction.getProductCoefficient ( IAtomContainer p1 ) [abstract] :  Double
IReaction.getProducts ( ) [abstract] :  IAtomContainerSet
IReaction.getReactantCoefficient ( IAtomContainer p1 ) [abstract] :  Double
IReaction.getReactants ( ) [abstract] :  IAtomContainerSet
IReaction.setProductCoefficient ( IAtomContainer p1, Double p2 ) [abstract] :  boolean
IReaction.setProducts ( IAtomContainerSet p1 ) [abstract] :  void
IReaction.setReactantCoefficient ( IAtomContainer p1, Double p2 ) [abstract] :  boolean
IReaction.setReactants ( IAtomContainerSet p1 ) [abstract] :  void

cdk-1.5.0.jar, IReactionMechanism.class
package org.openscience.cdk.reaction
IReactionMechanism.initiate ( IAtomContainerSet p1, ArrayList p2, ArrayList p3 ) [abstract] :  IReaction

cdk-1.5.0.jar, IReactionProcess.class
package org.openscience.cdk.reaction
IReactionProcess.initiate ( IAtomContainerSet p1, IAtomContainerSet p2 ) [abstract] :  IReactionSet

cdk-1.5.0.jar, IsoAlkanes.class
package org.openscience.cdk.templates.saturatedhydrocarbons
IsoAlkanes.getIsobutane ( ) [static] :  IAtomContainer
IsoAlkanes.getIsohexane ( ) [static] :  IAtomContainer
IsoAlkanes.getIsopentane ( ) [static] :  IAtomContainer

cdk-1.5.0.jar, IsomorphismTester.class
package org.openscience.cdk.isomorphism
IsomorphismTester.isIsomorphic ( IAtomContainer mol1, IAtomContainer mol2 ) :  boolean
IsomorphismTester.isIsomorphic ( IAtomContainer mol2 ) :  boolean
IsomorphismTester.IsomorphismTester ( IAtomContainer mol )

cdk-1.5.0.jar, IValidator.class
package org.openscience.cdk.validate
IValidator.validateMolecule ( IAtomContainer p1 ) [abstract] :  ValidationReport
IValidator.validateMoleculeSet ( IAtomContainerSet p1 ) [abstract] :  ValidationReport

cdk-1.5.0.jar, LingoFingerprinter.class
package org.openscience.cdk.fingerprint
LingoFingerprinter.getFingerprint ( IAtomContainer iAtomContainer ) :  BitSet
LingoFingerprinter.getRawFingerprint ( IAtomContainer atomContainer ) :  Map
LingoFingerprinter.getSize ( ) :  int
LingoFingerprinter.LingoFingerprinter ( )
LingoFingerprinter.LingoFingerprinter ( int q )

cdk-1.5.0.jar, LingoSimilarity.class
package org.openscience.cdk.similarity
LingoSimilarity.calculate ( Map features1, Map features2 ) [static] :  float

cdk-1.5.0.jar, MACCSFingerprinter.class
package org.openscience.cdk.fingerprint
MACCSFingerprinter.getRawFingerprint ( IAtomContainer iAtomContainer ) :  Map

cdk-1.5.0.jar, MDLV3000Reader.class
package org.openscience.cdk.io
MDLV3000Reader.accepts ( IChemObject object ) :  boolean
MDLV3000Reader.readMolecule ( IChemObjectBuilder builder ) :  IAtomContainer

cdk-1.5.0.jar, ModelBuilder3D.class
package org.openscience.cdk.modeling.builder3d
ModelBuilder3D.generate3DCoordinates ( IAtomContainer molecule, boolean clone ) :  IAtomContainer

cdk-1.5.0.jar, Mol2Writer.class
package org.openscience.cdk.io
Mol2Writer.writeMolecule ( IAtomContainer mol ) :  void

cdk-1.5.0.jar, MolecularFormulaManipulator.class
package org.openscience.cdk.tools.manipulator
MolecularFormulaManipulator.getAtomContainer ( String formulaString, IChemObjectBuilder builder ) [static] :  IAtomContainer

cdk-1.5.0.jar, MoleculeBuilder.class
package org.openscience.cdk.iupac.parser
MoleculeBuilder.buildMolecule ( int mainChain, Vector attachedSubstituents, Vector attachedGroups, boolean isMainCyclic, String name ) :  IAtomContainer

cdk-1.5.0.jar, MoleculeFactory.class
package org.openscience.cdk.templates
MoleculeFactory.loadMolecule ( String inFile ) [static] :  IAtomContainer
MoleculeFactory.make123Triazole ( ) [static] :  IAtomContainer
MoleculeFactory.make124Triazole ( ) [static] :  IAtomContainer
MoleculeFactory.make4x3CondensedRings ( ) [static] :  IAtomContainer
MoleculeFactory.makeAdenine ( ) [static] :  IAtomContainer
MoleculeFactory.makeAlkane ( int chainLength ) [static] :  IAtomContainer
MoleculeFactory.makeAlphaPinene ( ) [static] :  IAtomContainer
MoleculeFactory.makeAzulene ( ) [static] :  IAtomContainer
MoleculeFactory.makeBenzene ( ) [static] :  IAtomContainer
MoleculeFactory.makeBicycloRings ( ) [static] :  IAtomContainer
MoleculeFactory.makeBiphenyl ( ) [static] :  IAtomContainer
MoleculeFactory.makeBranchedAliphatic ( ) [static] :  IAtomContainer
MoleculeFactory.makeCyclobutadiene ( ) [static] :  IAtomContainer
MoleculeFactory.makeCyclobutane ( ) [static] :  IAtomContainer
MoleculeFactory.makeCyclohexane ( ) [static] :  IAtomContainer
MoleculeFactory.makeCyclohexene ( ) [static] :  IAtomContainer
MoleculeFactory.makeCyclopentane ( ) [static] :  IAtomContainer
MoleculeFactory.makeDiamantane ( ) [static] :  IAtomContainer
MoleculeFactory.makeEthylCyclohexane ( ) [static] :  IAtomContainer
MoleculeFactory.makeEthylPropylPhenantren ( ) [static] :  IAtomContainer
MoleculeFactory.makeFusedRings ( ) [static] :  IAtomContainer
MoleculeFactory.makeImidazole ( ) [static] :  IAtomContainer
MoleculeFactory.makeIndole ( ) [static] :  IAtomContainer
MoleculeFactory.makeIsothiazole ( ) [static] :  IAtomContainer
MoleculeFactory.makeIsoxazole ( ) [static] :  IAtomContainer
MoleculeFactory.makeMethylDecaline ( ) [static] :  IAtomContainer
MoleculeFactory.makeOxadiazole ( ) [static] :  IAtomContainer
MoleculeFactory.makeOxazole ( ) [static] :  IAtomContainer
MoleculeFactory.makePhenylAmine ( ) [static] :  IAtomContainer
MoleculeFactory.makePhenylEthylBenzene ( ) [static] :  IAtomContainer
MoleculeFactory.makePiperidine ( ) [static] :  IAtomContainer
MoleculeFactory.makePropylCycloPropane ( ) [static] :  IAtomContainer
MoleculeFactory.makePyrazole ( ) [static] :  IAtomContainer
MoleculeFactory.makePyridazine ( ) [static] :  IAtomContainer
MoleculeFactory.makePyridine ( ) [static] :  IAtomContainer
MoleculeFactory.makePyridineOxide ( ) [static] :  IAtomContainer
MoleculeFactory.makePyrimidine ( ) [static] :  IAtomContainer
MoleculeFactory.makePyrrole ( ) [static] :  IAtomContainer
MoleculeFactory.makePyrroleAnion ( ) [static] :  IAtomContainer
MoleculeFactory.makeQuinone ( ) [static] :  IAtomContainer
MoleculeFactory.makeSingleRing ( ) [static] :  IAtomContainer
MoleculeFactory.makeSpiroRings ( ) [static] :  IAtomContainer
MoleculeFactory.makeSteran ( ) [static] :  IAtomContainer
MoleculeFactory.makeTetrahydropyran ( ) [static] :  IAtomContainer
MoleculeFactory.makeTetrazole ( ) [static] :  IAtomContainer
MoleculeFactory.makeThiadiazole ( ) [static] :  IAtomContainer
MoleculeFactory.makeThiazole ( ) [static] :  IAtomContainer
MoleculeFactory.makeTriazine ( ) [static] :  IAtomContainer

cdk-1.5.0.jar, MoleculeFeaturesTool.class
package org.openscience.cdk.tools.features
MoleculeFeaturesTool.hasElementSymbols ( IAtomContainer molecule ) [static] :  boolean
MoleculeFeaturesTool.hasFormalCharges ( IAtomContainer molecule ) [static] :  boolean
MoleculeFeaturesTool.hasGraphRepresentation ( IAtomContainer molecule ) [static] :  boolean
MoleculeFeaturesTool.hasPartialCharges ( IAtomContainer molecule ) [static] :  boolean

cdk-1.5.0.jar, MoleculeSetManipulator.class
package org.openscience.cdk.tools.manipulator
MoleculeSetManipulator.getAllAtomContainers ( IAtomContainerSet set ) [static] :  List
MoleculeSetManipulator.getAllChemObjects ( IAtomContainerSet set ) [static] :  List
MoleculeSetManipulator.getAllIDs ( IAtomContainerSet set ) [static] :  List
MoleculeSetManipulator.getRelevantAtomContainer ( IAtomContainerSet moleculeSet, IAtom atom ) [static] :  IAtomContainer
MoleculeSetManipulator.getRelevantAtomContainer ( IAtomContainerSet moleculeSet, IBond bond ) [static] :  IAtomContainer
MoleculeSetManipulator.getTotalCharge ( IAtomContainerSet set ) [static] :  double
MoleculeSetManipulator.getTotalFormalCharge ( IAtomContainerSet set ) [static] :  double
MoleculeSetManipulator.getTotalHydrogenCount ( IAtomContainerSet set ) [static] :  int
MoleculeSetManipulator.removeAtomAndConnectedElectronContainers ( IAtomContainerSet set, IAtom atom ) [static] :  void
MoleculeSetManipulator.removeElectronContainer ( IAtomContainerSet set, IElectronContainer electrons ) [static] :  void
MoleculeSetManipulator.setAtomProperties ( IAtomContainerSet set, Object propKey, Object propVal ) [static] :  void

cdk-1.5.0.jar, MoleculeSignature.class
package org.openscience.cdk.signature
MoleculeSignature.MoleculeSignature ( IAtomContainer molecule, int height )

cdk-1.5.0.jar, NomParser.class
package org.openscience.cdk.iupac.parser
NomParser.generate ( String stringToParse ) [static] :  IAtomContainer

cdk-1.5.0.jar, ParseException.class
package org.openscience.cdk.iupac.parser
ParseException.getMessage ( ) :  String
package org.openscience.cdk.smiles.smarts.parser
ParseException.getMessage ( ) :  String

cdk-1.5.0.jar, PathTools.class
package org.openscience.cdk.graph
PathTools.breadthFirstSearch ( IAtomContainer atomContainer, List sphere, IAtomContainer molecule ) [static] :  void
PathTools.breadthFirstSearch ( IAtomContainer atomContainer, List sphere, IAtomContainer molecule, int max ) [static] :  void

cdk-1.5.0.jar, PDBWriter.class
package org.openscience.cdk.io
PDBWriter.writeMolecule ( IAtomContainer molecule ) :  void

cdk-1.5.0.jar, Permutor.class
package org.openscience.cdk.graph
Permutor.calculateMaxRank ( ) :  int
Permutor.getCurrentPermutation ( ) :  int[ ]
Permutor.getNextPermutation ( ) :  int[ ]
Permutor.getRandomNextPermutation ( ) :  int[ ]
Permutor.getRank ( ) :  int
Permutor.hasNext ( ) :  boolean
Permutor.Permutor ( int size )
Permutor.setPermutation ( int[ ] permutation ) :  void
Permutor.setRank ( int rank ) :  void

cdk-1.5.0.jar, PiBondingMovementReaction.class
package org.openscience.cdk.reaction.type
PiBondingMovementReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, PubchemFingerprinter.class
package org.openscience.cdk.fingerprint
PubchemFingerprinter.getRawFingerprint ( IAtomContainer iAtomContainer ) :  Map

cdk-1.5.0.jar, PubChemXMLHelper.class
package org.openscience.cdk.io.pubchemxml
PubChemXMLHelper.parseAtomCharges ( XmlPullParser parser, IAtomContainer molecule ) :  void
PubChemXMLHelper.parseAtomElements ( XmlPullParser parser, IAtomContainer molecule ) :  void
PubChemXMLHelper.parseCompoundsBlock ( XmlPullParser parser ) :  IAtomContainerSet
PubChemXMLHelper.parseMolecule ( XmlPullParser parser, IChemObjectBuilder builder ) :  IAtomContainer
PubChemXMLHelper.parserAtomBlock ( XmlPullParser parser, IAtomContainer molecule ) :  void
PubChemXMLHelper.parserBondBlock ( XmlPullParser parser, IAtomContainer molecule ) :  void
PubChemXMLHelper.parserCompoundInfoData ( XmlPullParser parser, IAtomContainer molecule ) :  void
PubChemXMLHelper.parserCoordBlock ( XmlPullParser parser, IAtomContainer molecule ) :  void

cdk-1.5.0.jar, QueryAtom.class
package org.openscience.cdk.isomorphism.matchers
QueryAtom.getAtomicNumber ( ) :  Integer
QueryAtom.getAtomTypeName ( ) :  String
QueryAtom.getBondOrderSum ( ) :  Double
QueryAtom.getCharge ( ) :  Double
QueryAtom.getCovalentRadius ( ) :  Double
QueryAtom.getExactMass ( ) :  Double
QueryAtom.getFormalCharge ( ) :  Integer
QueryAtom.getFormalNeighbourCount ( ) :  Integer
QueryAtom.getFractionalPoint3d ( ) :  Point3d
QueryAtom.getHybridization ( ) :  IAtomType.Hybridization
QueryAtom.getImplicitHydrogenCount ( ) :  Integer
QueryAtom.getMassNumber ( ) :  Integer
QueryAtom.getMaxBondOrder ( ) :  IBond.Order
QueryAtom.getNaturalAbundance ( ) :  Double
QueryAtom.getPoint2d ( ) :  Point2d
QueryAtom.getPoint3d ( ) :  Point3d
QueryAtom.getStereoParity ( ) :  Integer
QueryAtom.getSymbol ( ) :  String
QueryAtom.getValency ( ) :  Integer
QueryAtom.QueryAtom ( )
QueryAtom.QueryAtom ( String symbol )
QueryAtom.setAtomicNumber ( Integer atomicNumber ) :  void
QueryAtom.setAtomTypeName ( String identifier ) :  void
QueryAtom.setBondOrderSum ( Double bondOrderSum ) :  void
QueryAtom.setCharge ( Double charge ) :  void
QueryAtom.setCovalentRadius ( Double radius ) :  void
QueryAtom.setExactMass ( Double exactMass ) :  void
QueryAtom.setFormalCharge ( Integer charge ) :  void
QueryAtom.setFormalNeighbourCount ( Integer count ) :  void
QueryAtom.setFractionalPoint3d ( Point3d point3d ) :  void
QueryAtom.setHybridization ( IAtomType.Hybridization hybridization ) :  void
QueryAtom.setImplicitHydrogenCount ( Integer hydrogenCount ) :  void
QueryAtom.setMassNumber ( Integer massNumber ) :  void
QueryAtom.setMaxBondOrder ( IBond.Order maxBondOrder ) :  void
QueryAtom.setNaturalAbundance ( Double naturalAbundance ) :  void
QueryAtom.setPoint2d ( Point2d point2d ) :  void
QueryAtom.setPoint3d ( Point3d point3d ) :  void
QueryAtom.setStereoParity ( Integer stereoParity ) :  void
QueryAtom.setSymbol ( String symbol ) :  void
QueryAtom.setValency ( Integer valency ) :  void

cdk-1.5.0.jar, QueryAtomContainer.class
package org.openscience.cdk.isomorphism.matchers
QueryAtomContainer.addBond ( int atom1, int atom2, IBond.Order order ) :  void
QueryAtomContainer.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
QueryAtomContainer.addElectronContainer ( IElectronContainer electronContainer ) :  void
QueryAtomContainer.addLonePair ( ILonePair lonePair ) :  void
QueryAtomContainer.addLonePair ( int atomID ) :  void
QueryAtomContainer.addSingleElectron ( int atomID ) :  void
QueryAtomContainer.addSingleElectron ( ISingleElectron singleElectron ) :  void
QueryAtomContainer.addStereoElement ( IStereoElement element ) :  void
QueryAtomContainer.atoms ( ) :  Iterable
QueryAtomContainer.bonds ( ) :  Iterable
QueryAtomContainer.clone ( ) :  Object
QueryAtomContainer.contains ( IAtom atom ) :  boolean
QueryAtomContainer.contains ( IBond bond ) :  boolean
QueryAtomContainer.contains ( IElectronContainer electronContainer ) :  boolean
QueryAtomContainer.contains ( ILonePair lonePair ) :  boolean
QueryAtomContainer.contains ( ISingleElectron singleElectron ) :  boolean
QueryAtomContainer.electronContainers ( ) :  Iterable
QueryAtomContainer.getAtom ( int number ) :  IAtom
QueryAtomContainer.getAtomCount ( ) :  int
QueryAtomContainer.getAtomNumber ( IAtom atom ) :  int
QueryAtomContainer.getBond ( IAtom atom1, IAtom atom2 ) :  IBond
QueryAtomContainer.getBond ( int number ) :  IBond
QueryAtomContainer.getBondCount ( ) :  int
QueryAtomContainer.getBondNumber ( IAtom atom1, IAtom atom2 ) :  int
QueryAtomContainer.getBondNumber ( IBond bond ) :  int
QueryAtomContainer.getBondOrderSum ( IAtom atom ) :  double *DEPRECATED*
QueryAtomContainer.getConnectedAtomsCount ( IAtom atom ) :  int
QueryAtomContainer.getConnectedAtomsList ( IAtom atom ) :  List
QueryAtomContainer.getConnectedBondsCount ( IAtom atom ) :  int
QueryAtomContainer.getConnectedBondsCount ( int atomNumber ) :  int
QueryAtomContainer.getConnectedBondsList ( IAtom atom ) :  List
QueryAtomContainer.getConnectedElectronContainersList ( IAtom atom ) :  List
QueryAtomContainer.getConnectedLonePairsCount ( IAtom atom ) :  int
QueryAtomContainer.getConnectedLonePairsList ( IAtom atom ) :  List
QueryAtomContainer.getConnectedSingleElectronsCount ( IAtom atom ) :  int
QueryAtomContainer.getConnectedSingleElectronsList ( IAtom atom ) :  List
QueryAtomContainer.getElectronContainer ( int number ) :  IElectronContainer
QueryAtomContainer.getElectronContainerCount ( ) :  int
QueryAtomContainer.getFirstAtom ( ) :  IAtom
QueryAtomContainer.getLastAtom ( ) :  IAtom
QueryAtomContainer.getLonePair ( int number ) :  ILonePair
QueryAtomContainer.getLonePairCount ( ) :  int
QueryAtomContainer.getLonePairNumber ( ILonePair lonePair ) :  int
QueryAtomContainer.getMaximumBondOrder ( IAtom atom ) :  IBond.Order
QueryAtomContainer.getMinimumBondOrder ( IAtom atom ) :  IBond.Order
QueryAtomContainer.getSingleElectron ( int number ) :  ISingleElectron
QueryAtomContainer.getSingleElectronCount ( ) :  int
QueryAtomContainer.getSingleElectronNumber ( ISingleElectron singleElectron ) :  int
QueryAtomContainer.lonePairs ( ) :  Iterable
QueryAtomContainer.QueryAtomContainer ( IAtomContainer container )
QueryAtomContainer.QueryAtomContainer ( int atomCount, int bondCount, int lpCount, int seCount )
QueryAtomContainer.remove ( IAtomContainer atomContainer ) :  void
QueryAtomContainer.removeAllBonds ( ) :  void
QueryAtomContainer.removeAllElectronContainers ( ) :  void
QueryAtomContainer.removeAllElements ( ) :  void
QueryAtomContainer.removeAtom ( IAtom atom ) :  void
QueryAtomContainer.removeAtom ( int position ) :  void
QueryAtomContainer.removeAtomAndConnectedElectronContainers ( IAtom atom ) :  void
QueryAtomContainer.removeBond ( IAtom atom1, IAtom atom2 ) :  IBond
QueryAtomContainer.removeBond ( IBond bond ) :  void
QueryAtomContainer.removeBond ( int position ) :  IBond
QueryAtomContainer.removeElectronContainer ( IElectronContainer electronContainer ) :  void
QueryAtomContainer.removeElectronContainer ( int number ) :  IElectronContainer
QueryAtomContainer.removeLonePair ( ILonePair lonePair ) :  void
QueryAtomContainer.removeLonePair ( int position ) :  ILonePair
QueryAtomContainer.removeSingleElectron ( int position ) :  ISingleElectron
QueryAtomContainer.removeSingleElectron ( ISingleElectron singleElectron ) :  void
QueryAtomContainer.setAtom ( int number, IAtom atom ) :  void
QueryAtomContainer.setAtoms ( IAtom[ ] atoms ) :  void
QueryAtomContainer.setBonds ( IBond[ ] bonds ) :  void
QueryAtomContainer.singleElectrons ( ) :  Iterable
QueryAtomContainer.stateChanged ( IChemObjectChangeEvent event ) :  void
QueryAtomContainer.stereoElements ( ) :  Iterable

cdk-1.5.0.jar, QueryBond.class
package org.openscience.cdk.isomorphism.matchers
QueryBond.atoms ( ) :  Iterable
QueryBond.clone ( ) :  Object
QueryBond.compare ( Object object ) :  boolean
QueryBond.contains ( IAtom atom ) :  boolean
QueryBond.get2DCenter ( ) :  Point2d
QueryBond.get3DCenter ( ) :  Point3d
QueryBond.getAtom ( int position ) :  IAtom
QueryBond.getAtomCount ( ) :  int
QueryBond.getConnectedAtom ( IAtom atom ) :  IAtom
QueryBond.getConnectedAtoms ( IAtom atom ) :  IAtom[ ]
QueryBond.getElectronCount ( ) :  Integer
QueryBond.getOrder ( ) :  IBond.Order
QueryBond.getStereo ( ) :  IBond.Stereo
QueryBond.isConnectedTo ( IBond bond ) :  boolean
QueryBond.QueryBond ( )
QueryBond.QueryBond ( IAtom atom1, IAtom atom2 )
QueryBond.QueryBond ( IAtom atom1, IAtom atom2, IBond.Order order )
QueryBond.QueryBond ( IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo )
QueryBond.QueryBond ( IAtom[ ] atoms )
QueryBond.QueryBond ( IAtom[ ] atoms, IBond.Order order )
QueryBond.setAtom ( IAtom atom, int position ) :  void
QueryBond.setAtoms ( IAtom[ ] atoms ) :  void
QueryBond.setElectronCount ( Integer electronCount ) :  void
QueryBond.setOrder ( IBond.Order order ) :  void
QueryBond.setStereo ( IBond.Stereo stereo ) :  void
QueryBond.toString ( ) :  String

cdk-1.5.0.jar, QueryChemObject.class
package org.openscience.cdk.isomorphism.matchers
QueryChemObject.addListener ( IChemObjectListener col ) :  void
QueryChemObject.clone ( ) :  Object
QueryChemObject.getBuilder ( ) :  IChemObjectBuilder
QueryChemObject.getFlag ( int flag_type ) :  boolean
QueryChemObject.getFlags ( ) :  boolean[ ]
QueryChemObject.getID ( ) :  String
QueryChemObject.getListenerCount ( ) :  int
QueryChemObject.getNotification ( ) :  boolean
QueryChemObject.getProperties ( ) :  Map
QueryChemObject.getProperty ( Object description ) :  Object
QueryChemObject.matches ( IAtom atom ) :  boolean
QueryChemObject.notifyChanged ( ) :  void
QueryChemObject.notifyChanged ( IChemObjectChangeEvent evt ) :  void
QueryChemObject.QueryChemObject ( )
QueryChemObject.removeListener ( IChemObjectListener col ) :  void
QueryChemObject.removeProperty ( Object description ) :  void
QueryChemObject.setFlag ( int flag_type, boolean flag_value ) :  void
QueryChemObject.setFlags ( boolean[ ] flagsNew ) :  void
QueryChemObject.setID ( String identifier ) :  void
QueryChemObject.setNotification ( boolean bool ) :  void
QueryChemObject.setProperties ( Map properties ) :  void
QueryChemObject.setProperty ( Object description, Object property ) :  void

cdk-1.5.0.jar, RadicalChargeSiteInitiationHReaction.class
package org.openscience.cdk.reaction.type
RadicalChargeSiteInitiationHReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalChargeSiteInitiationReaction.class
package org.openscience.cdk.reaction.type
RadicalChargeSiteInitiationReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteHrAlphaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteHrAlphaReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteHrBetaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteHrBetaReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteHrDeltaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteHrDeltaReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteHrGammaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteHrGammaReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteInitiationHReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteInitiationHReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteInitiationReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteInitiationReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteIonizationMechanism.class
package org.openscience.cdk.reaction.mechanism
RadicalSiteIonizationMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, RadicalSiteRearrangementMechanism.class
package org.openscience.cdk.reaction.mechanism
RadicalSiteRearrangementMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, RadicalSiteRrAlphaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteRrAlphaReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteRrBetaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteRrBetaReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteRrDeltaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteRrDeltaReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RadicalSiteRrGammaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteRrGammaReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RandomGenerator.class
package org.openscience.cdk.structgen
RandomGenerator.getMolecule ( ) :  IAtomContainer
RandomGenerator.proposeStructure ( ) :  IAtomContainer
RandomGenerator.RandomGenerator ( IAtomContainer molecule )
RandomGenerator.setMolecule ( IAtomContainer molecule ) :  void

cdk-1.5.0.jar, Reaction.class
package org.openscience.cdk
Reaction.addAgent ( IAtomContainer agent ) :  void
Reaction.addProduct ( IAtomContainer product ) :  void
Reaction.addProduct ( IAtomContainer product, Double coefficient ) :  void
Reaction.addReactant ( IAtomContainer reactant ) :  void
Reaction.addReactant ( IAtomContainer reactant, Double coefficient ) :  void
Reaction.getAgents ( ) :  IAtomContainerSet
Reaction.getProductCoefficient ( IAtomContainer product ) :  Double
Reaction.getProducts ( ) :  IAtomContainerSet
Reaction.getReactantCoefficient ( IAtomContainer reactant ) :  Double
Reaction.getReactants ( ) :  IAtomContainerSet
Reaction.setProductCoefficient ( IAtomContainer product, Double coefficient ) :  boolean
Reaction.setProducts ( IAtomContainerSet setOfMolecules ) :  void
Reaction.setReactantCoefficient ( IAtomContainer reactant, Double coefficient ) :  boolean
Reaction.setReactants ( IAtomContainerSet setOfMolecules ) :  void
package org.openscience.cdk.silent
Reaction.addAgent ( IAtomContainer agent ) :  void
Reaction.addProduct ( IAtomContainer product ) :  void
Reaction.addProduct ( IAtomContainer product, Double coefficient ) :  void
Reaction.addReactant ( IAtomContainer reactant ) :  void
Reaction.addReactant ( IAtomContainer reactant, Double coefficient ) :  void
Reaction.getAgents ( ) :  IAtomContainerSet
Reaction.getProductCoefficient ( IAtomContainer product ) :  Double
Reaction.getProducts ( ) :  IAtomContainerSet
Reaction.getReactantCoefficient ( IAtomContainer reactant ) :  Double
Reaction.getReactants ( ) :  IAtomContainerSet
Reaction.setProductCoefficient ( IAtomContainer product, Double coefficient ) :  boolean
Reaction.setProducts ( IAtomContainerSet setOfMolecules ) :  void
Reaction.setReactantCoefficient ( IAtomContainer reactant, Double coefficient ) :  boolean
Reaction.setReactants ( IAtomContainerSet setOfMolecules ) :  void

cdk-1.5.0.jar, ReactionManipulator.class
package org.openscience.cdk.tools.manipulator
ReactionManipulator.getAllMolecules ( IReaction reaction ) [static] :  IAtomContainerSet
ReactionManipulator.getAllProducts ( IReaction reaction ) [static] :  IAtomContainerSet
ReactionManipulator.getAllReactants ( IReaction reaction ) [static] :  IAtomContainerSet

cdk-1.5.0.jar, ReactionSchemeManipulator.class
package org.openscience.cdk.tools.manipulator
ReactionSchemeManipulator.getAllAtomContainers ( IReactionScheme scheme ) [static] :  IAtomContainerSet
ReactionSchemeManipulator.getAllAtomContainers ( IReactionScheme scheme, IAtomContainerSet molSet ) [static] :  IAtomContainerSet
ReactionSchemeManipulator.getAtomContainerSet ( IAtomContainer origenMol, IAtomContainer finalMol, IReactionScheme reactionScheme ) [static] :  ArrayList

cdk-1.5.0.jar, ReactionSetManipulator.class
package org.openscience.cdk.tools.manipulator
ReactionSetManipulator.getAllMolecules ( IReactionSet set ) [static] :  IAtomContainerSet

cdk-1.5.0.jar, RearrangementAnionReaction.class
package org.openscience.cdk.reaction.type
RearrangementAnionReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RearrangementCationReaction.class
package org.openscience.cdk.reaction.type
RearrangementCationReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RearrangementChargeMechanism.class
package org.openscience.cdk.reaction.mechanism
RearrangementChargeMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, RearrangementLonePairReaction.class
package org.openscience.cdk.reaction.type
RearrangementLonePairReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RearrangementRadicalReaction.class
package org.openscience.cdk.reaction.type
RearrangementRadicalReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, RemovingSEofBMechanism.class
package org.openscience.cdk.reaction.mechanism
RemovingSEofBMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, RemovingSEofNBMechanism.class
package org.openscience.cdk.reaction.mechanism
RemovingSEofNBMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, RingPlacer.class
package org.openscience.cdk.layout
RingPlacer.getMolecule ( ) :  IAtomContainer
RingPlacer.setMolecule ( IAtomContainer molecule ) :  void

cdk-1.5.0.jar, SharingAnionReaction.class
package org.openscience.cdk.reaction.type
SharingAnionReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, SharingChargeDBReaction.class
package org.openscience.cdk.reaction.type
SharingChargeDBReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, SharingChargeSBReaction.class
package org.openscience.cdk.reaction.type
SharingChargeSBReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, SharingElectronMechanism.class
package org.openscience.cdk.reaction.mechanism
SharingElectronMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, SharingLonePairReaction.class
package org.openscience.cdk.reaction.type
SharingLonePairReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, SignatureFingerprinter.class
package org.openscience.cdk.fingerprint
SignatureFingerprinter.getFingerprint ( IAtomContainer iAtomContainer ) :  BitSet
SignatureFingerprinter.getRawFingerprint ( IAtomContainer atomContainer ) :  Map
SignatureFingerprinter.getSize ( ) :  int
SignatureFingerprinter.SignatureFingerprinter ( )
SignatureFingerprinter.SignatureFingerprinter ( int depth )

cdk-1.5.0.jar, SingleStructureRandomGenerator.class
package org.openscience.cdk.structgen
SingleStructureRandomGenerator.generate ( ) :  IAtomContainer

cdk-1.5.0.jar, SmilesParser.class
package org.openscience.cdk.smiles
SmilesParser.parseSmiles ( String smiles ) :  IAtomContainer

cdk-1.5.0.jar, SMILESWriter.class
package org.openscience.cdk.io
SMILESWriter.writeAtomContainer ( IAtomContainer molecule ) :  void
SMILESWriter.writeAtomContainerSet ( IAtomContainerSet som ) :  void

cdk-1.5.0.jar, SMSDNormalizer.class
package org.openscience.cdk.normalize
SMSDNormalizer.makeDeepCopy ( IAtomContainer container ) [static] :  IAtomContainer

cdk-1.5.0.jar, StructureDiagramGenerator.class
package org.openscience.cdk.layout
StructureDiagramGenerator.getMolecule ( ) :  IAtomContainer
StructureDiagramGenerator.setMolecule ( IAtomContainer mol, boolean clone ) :  void
StructureDiagramGenerator.setMolecule ( IAtomContainer molecule ) :  void
StructureDiagramGenerator.StructureDiagramGenerator ( IAtomContainer molecule )

cdk-1.5.0.jar, StructureResonanceGenerator.class
package org.openscience.cdk.tools
StructureResonanceGenerator.getContainer ( IAtomContainer molecule, IAtom atom ) :  IAtomContainer
StructureResonanceGenerator.getContainer ( IAtomContainer molecule, IBond bond ) :  IAtomContainer
StructureResonanceGenerator.getContainers ( IAtomContainer molecule ) :  IAtomContainerSet
StructureResonanceGenerator.getStructures ( IAtomContainer molecule ) :  IAtomContainerSet

cdk-1.5.0.jar, SubstructureFingerprinter.class
package org.openscience.cdk.fingerprint
SubstructureFingerprinter.getRawFingerprint ( IAtomContainer iAtomContainer ) :  Map

cdk-1.5.0.jar, SymbolSetQueryAtom.class
package org.openscience.cdk.isomorphism.matchers
SymbolSetQueryAtom.getSymbolSet ( ) :  Set

cdk-1.5.0.jar, Tanimoto.class
package org.openscience.cdk.similarity
Tanimoto.calculate ( Map features1, Map features2 ) [static] :  float

cdk-1.5.0.jar, TautomerizationMechanism.class
package org.openscience.cdk.reaction.mechanism
TautomerizationMechanism.initiate ( IAtomContainerSet atomContainerSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.5.0.jar, TautomerizationReaction.class
package org.openscience.cdk.reaction.type
TautomerizationReaction.initiate ( IAtomContainerSet reactants, IAtomContainerSet agents ) :  IReactionSet

cdk-1.5.0.jar, TemplateExtractor.class
package org.openscience.cdk.modeling.builder3d
TemplateExtractor.removeLoopBonds ( IAtomContainer molecule, int position ) :  IAtomContainer
TemplateExtractor.writeChemModel ( IAtomContainerSet som, String file, String endFix ) :  void

cdk-1.5.0.jar, Type.class
package org.openscience.cdk.isomorphism.matchers
CTFileQueryBond.Type.valueOf ( String name ) [static] :  CTFileQueryBond.Type
CTFileQueryBond.Type.values ( ) [static] :  CTFileQueryBond.Type[ ]

cdk-1.5.0.jar, VABCVolume.class
package org.openscience.cdk.geometry.volume
VABCVolume.calculate ( IAtomContainer molecule ) [static] :  double

cdk-1.5.0.jar, ValidatorEngine.class
package org.openscience.cdk.validate
ValidatorEngine.validateMolecule ( IAtomContainer subject ) :  ValidationReport
ValidatorEngine.validateMoleculeSet ( IAtomContainerSet subject ) :  ValidationReport

cdk-1.5.0.jar, VicinitySampler.class
package org.openscience.cdk.structgen
VicinitySampler.sample ( IAtomContainer ac ) [static] :  List

cdk-1.5.0.jar, XYZWriter.class
package org.openscience.cdk.io
XYZWriter.writeMolecule ( IAtomContainer mol ) :  void

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Removed Methods (857)

cdk-1.4.19.jar, AbstractMCS.class
package org.openscience.cdk.smsd.interfaces
AbstractMCS.init ( IMolecule p1, IMolecule p2, boolean p3, boolean p4 ) [abstract] :  void

cdk-1.4.19.jar, AbstractRenderer.class
package org.openscience.cdk.renderer
AbstractRenderer.AbstractRenderer ( RendererModel rendererModel )

cdk-1.4.19.jar, AbstractValidator.class
package org.openscience.cdk.validate
AbstractValidator.validateMolecule ( IMolecule subject ) :  ValidationReport
AbstractValidator.validateMoleculeSet ( IMoleculeSet subject ) :  ValidationReport

cdk-1.4.19.jar, AdductionLPMechanism.class
package org.openscience.cdk.reaction.mechanism
AdductionLPMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, AdductionPBMechanism.class
package org.openscience.cdk.reaction.mechanism
AdductionPBMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, AdductionProtonLPReaction.class
package org.openscience.cdk.reaction.type
AdductionProtonLPReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, AdductionProtonPBReaction.class
package org.openscience.cdk.reaction.type
AdductionProtonPBReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, AdductionSodiumLPReaction.class
package org.openscience.cdk.reaction.type
AdductionSodiumLPReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, ArrowHeadWidth.class
package org.openscience.cdk.renderer.generators
ReactionSceneGenerator.ArrowHeadWidth.getDefault ( ) :  Double
ReactionSceneGenerator.ArrowHeadWidth.getDefault ( ) :  Object
ReactionSceneGenerator.ArrowHeadWidth.ReactionSceneGenerator.ArrowHeadWidth ( )

cdk-1.4.19.jar, AtomAtomMappingLineColor.class
package org.openscience.cdk.renderer.generators
MappingGenerator.AtomAtomMappingLineColor.getDefault ( ) :  Color
MappingGenerator.AtomAtomMappingLineColor.getDefault ( ) :  Object
MappingGenerator.AtomAtomMappingLineColor.MappingGenerator.AtomAtomMappingLineColor ( )

cdk-1.4.19.jar, AtomColorer.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.AtomColorer.AtomNumberGenerator.AtomColorer ( )
AtomNumberGenerator.AtomColorer.getDefault ( ) :  IAtomColorer
AtomNumberGenerator.AtomColorer.getDefault ( ) :  Object

cdk-1.4.19.jar, AtomContainer.class
package org.openscience.cdk
AtomContainer.isEmpty ( ) :  boolean
AtomContainer.setStereoElements ( List elements ) :  void
package org.openscience.cdk.silent
AtomContainer.isEmpty ( ) :  boolean
AtomContainer.setStereoElements ( List elements ) :  void

cdk-1.4.19.jar, AtomContainerAtomPermutor.class
package org.openscience.cdk.graph
AtomContainerAtomPermutor.initObjectArray ( ) :  void

cdk-1.4.19.jar, AtomContainerBondPermutor.class
package org.openscience.cdk.graph
AtomContainerBondPermutor.initObjectArray ( ) :  void

cdk-1.4.19.jar, AtomContainerBoundsGenerator.class
package org.openscience.cdk.renderer.generators
AtomContainerBoundsGenerator.AtomContainerBoundsGenerator ( )
AtomContainerBoundsGenerator.generate ( IAtomContainer container, RendererModel model ) :  IRenderingElement
AtomContainerBoundsGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
AtomContainerBoundsGenerator.getParameters ( ) :  List

cdk-1.4.19.jar, AtomContainerPermutor.class
package org.openscience.cdk.graph
AtomContainerPermutor.AtomContainerPermutor ( )
AtomContainerPermutor.initBookkeeping ( ) :  void
AtomContainerPermutor.setAtomContainer ( IAtomContainer ac ) :  void

cdk-1.4.19.jar, AtomContainerRenderer.class
package org.openscience.cdk.renderer
AtomContainerRenderer.AtomContainerRenderer ( RendererModel rendererModel, List generators, IFontManager fontManager )

cdk-1.4.19.jar, AtomContainerSet.class
package org.openscience.cdk
AtomContainerSet.isEmpty ( ) :  boolean
package org.openscience.cdk.silent
AtomContainerSet.isEmpty ( ) :  boolean

cdk-1.4.19.jar, AtomMassGenerator.class
package org.openscience.cdk.renderer.generators
AtomMassGenerator.AtomMassGenerator ( )
AtomMassGenerator.showCarbon ( IAtom atom, IAtomContainer container, RendererModel model ) :  boolean

cdk-1.4.19.jar, AtomMassSymbolElement.class
package org.openscience.cdk.renderer.elements
AtomMassSymbolElement.AtomMassSymbolElement ( double xCoord, double yCoord, String symbol, Integer formalCharge, Integer hydrogenCount, int alignment, Integer atomMass, Color color )

cdk-1.4.19.jar, AtomNumberGenerator.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.AtomNumberGenerator ( )
AtomNumberGenerator.generate ( IAtomContainer container, RendererModel model ) :  IRenderingElement
AtomNumberGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
AtomNumberGenerator.getParameters ( ) :  List

cdk-1.4.19.jar, AtomNumberTextColor.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.AtomNumberTextColor.AtomNumberGenerator.AtomNumberTextColor ( )
AtomNumberGenerator.AtomNumberTextColor.getDefault ( ) :  Color
AtomNumberGenerator.AtomNumberTextColor.getDefault ( ) :  Object

cdk-1.4.19.jar, AtomParity.class
package org.openscience.cdk
AtomParity.map ( Map atoms, Map bonds ) :  IAtomParity
AtomParity.map ( Map x0, Map x1 ) :  IStereoElement
package org.openscience.cdk.silent
AtomParity.map ( Map atoms, Map bonds ) :  IAtomParity
AtomParity.map ( Map x0, Map x1 ) :  IStereoElement

cdk-1.4.19.jar, AtomPlacer.class
package org.openscience.cdk.layout
AtomPlacer.getInitialLongestChain ( IMolecule molecule ) :  IAtomContainer
AtomPlacer.getLongestUnplacedChain ( IMolecule molecule, IAtom startAtom ) :  IAtomContainer

cdk-1.4.19.jar, AtomTypeTools.class
package org.openscience.cdk.tools
AtomTypeTools.assignAtomTypePropertiesToAtom ( IMolecule molecule ) :  IRingSet
AtomTypeTools.assignAtomTypePropertiesToAtom ( IMolecule molecule, boolean aromaticity ) :  IRingSet

cdk-1.4.19.jar, AverageBondLengthCalculator.class
package org.openscience.cdk.renderer
AverageBondLengthCalculator.AverageBondLengthCalculator ( )
AverageBondLengthCalculator.calculateAverageBondLength ( IMoleculeSet moleculeSet ) [static] :  double

cdk-1.4.19.jar, BasicValidator.class
package org.openscience.cdk.validate
BasicValidator.validateMolecule ( IMolecule subject ) :  ValidationReport

cdk-1.4.19.jar, BoundsCalculator.class
package org.openscience.cdk.renderer
BoundsCalculator.calculateBounds ( IMoleculeSet moleculeSet ) [static] :  Rectangle2D

cdk-1.4.19.jar, BoundsColor.class
package org.openscience.cdk.renderer.generators
BoundsGenerator.BoundsColor.BoundsGenerator.BoundsColor ( )
BoundsGenerator.BoundsColor.getDefault ( ) :  Color
BoundsGenerator.BoundsColor.getDefault ( ) :  Object

cdk-1.4.19.jar, BoundsGenerator.class
package org.openscience.cdk.renderer.generators
BoundsGenerator.BoundsGenerator ( )
BoundsGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
BoundsGenerator.generate ( IReaction reaction, RendererModel model ) :  IRenderingElement
BoundsGenerator.getParameters ( ) :  List

cdk-1.4.19.jar, CarbonylEliminationReaction.class
package org.openscience.cdk.reaction.type
CarbonylEliminationReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, CDKMCSHandler.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKMCSHandler.getUncommon ( IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds ) :  IMoleculeSet

cdk-1.4.19.jar, CDKSubGraphHandler.class
package org.openscience.cdk.smsd.algorithm.rgraph
CDKSubGraphHandler.getUncommon ( IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds ) :  IMoleculeSet

cdk-1.4.19.jar, CDKUtilities.class
package org.openscience.cdk.tools
CDKUtilities.fixAromaticityForXLogP ( IMolecule m ) [static] :  void
CDKUtilities.fixNitroGroups2 ( IMolecule m ) [static] :  boolean
CDKUtilities.fixSulphurH ( IMolecule m ) [static] :  void

cdk-1.4.19.jar, ChemModel.class
package org.openscience.cdk
ChemModel.getMoleculeSet ( ) :  IMoleculeSet
ChemModel.isEmpty ( ) :  boolean
ChemModel.setMoleculeSet ( IMoleculeSet setOfMolecules ) :  void
package org.openscience.cdk.silent
ChemModel.getMoleculeSet ( ) :  IMoleculeSet
ChemModel.isEmpty ( ) :  boolean
ChemModel.setMoleculeSet ( IMoleculeSet setOfMolecules ) :  void

cdk-1.4.19.jar, ChemModelRenderer.class
package org.openscience.cdk.renderer
ChemModelRenderer.calculateDiagramBounds ( IChemModel model ) :  Rectangle
ChemModelRenderer.calculateDiagramBounds ( IChemObject x0 ) :  Rectangle
ChemModelRenderer.calculateScaleForBondLength ( double modelBondLength ) :  double
ChemModelRenderer.ChemModelRenderer ( List generators, IFontManager fontManager )
ChemModelRenderer.ChemModelRenderer ( List generators, List reactionGenerators, IFontManager fontManager )
ChemModelRenderer.getGenerators ( ) :  List
ChemModelRenderer.paint ( IChemModel chemModel, IDrawVisitor drawVisitor ) :  Rectangle
ChemModelRenderer.paint ( IChemModel chemModel, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) :  void
ChemModelRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) :  Rectangle
ChemModelRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) :  void
ChemModelRenderer.repaint ( IDrawVisitor drawVisitor ) :  void
ChemModelRenderer.setScale ( IChemModel chemModel ) :  void
ChemModelRenderer.setScale ( IChemObject x0 ) :  void
ChemModelRenderer.setup ( IChemModel chemModel, Rectangle screen ) :  void
ChemModelRenderer.setup ( IChemObject x0, Rectangle x1 ) :  void

cdk-1.4.19.jar, ColorByType.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.ColorByType.AtomNumberGenerator.ColorByType ( )
AtomNumberGenerator.ColorByType.getDefault ( ) :  Boolean
AtomNumberGenerator.ColorByType.getDefault ( ) :  Object

cdk-1.4.19.jar, Conformation.class
package org.openscience.cdk.interfaces
IDoubleBondStereochemistry.Conformation.valueOf ( String name ) [static] :  IDoubleBondStereochemistry.Conformation
IDoubleBondStereochemistry.Conformation.values ( ) [static] :  IDoubleBondStereochemistry.Conformation[ ]

cdk-1.4.19.jar, ConnectivityChecker.class
package org.openscience.cdk.graph
ConnectivityChecker.partitionIntoMolecules ( IAtomContainer atomContainer ) [static] :  IMoleculeSet

cdk-1.4.19.jar, Convertor.class
package org.openscience.cdk.libio.cml
Convertor.cdkMoleculeSetToCMLList ( IMoleculeSet moleculeSet ) :  CMLMoleculeList
Convertor.cdkMoleculeToCMLMolecule ( IMolecule structure ) :  CMLMolecule
package org.openscience.cdk.libio.jena
Convertor.model2Molecule ( Model model, IChemObjectBuilder builder ) [static] :  IMolecule
Convertor.molecule2Model ( IMolecule molecule ) [static] :  Model

cdk-1.4.19.jar, DataFeaturesTool.class
package org.openscience.cdk.tools
DataFeaturesTool.getSupportedDataFeatures ( IMolecule molecule ) [static] :  int

cdk-1.4.19.jar, DebugAtomContainer.class
package org.openscience.cdk.debug
DebugAtomContainer.isEmpty ( ) :  boolean
DebugAtomContainer.setStereoElements ( List elements ) :  void

cdk-1.4.19.jar, DebugAtomContainerSet.class
package org.openscience.cdk.debug
DebugAtomContainerSet.isEmpty ( ) :  boolean

cdk-1.4.19.jar, DebugAtomParity.class
package org.openscience.cdk.debug
DebugAtomParity.map ( Map atoms, Map bonds ) :  IAtomParity
DebugAtomParity.map ( Map x0, Map x1 ) :  IStereoElement

cdk-1.4.19.jar, DebugChemModel.class
package org.openscience.cdk.debug
DebugChemModel.isEmpty ( ) :  boolean
DebugChemModel.setMoleculeSet ( IMoleculeSet setOfMolecules ) :  void

cdk-1.4.19.jar, DebugCrystal.class
package org.openscience.cdk.debug
DebugCrystal.isEmpty ( ) :  boolean

cdk-1.4.19.jar, DebugMolecule.class
package org.openscience.cdk.debug
DebugMolecule.add ( IAtomContainer atomContainer ) :  void
DebugMolecule.addAtom ( IAtom atom ) :  void
DebugMolecule.addBond ( IBond bond ) :  void
DebugMolecule.addBond ( int atom1, int atom2, IBond.Order order ) :  void
DebugMolecule.addBond ( int atom1, int atom2, IBond.Order order, IBond.Stereo stereo ) :  void
DebugMolecule.addElectronContainer ( IElectronContainer electronContainer ) :  void
DebugMolecule.addListener ( IChemObjectListener col ) :  void
DebugMolecule.addLonePair ( ILonePair ec ) :  void
DebugMolecule.addLonePair ( int atomID ) :  void
DebugMolecule.addSingleElectron ( int atomID ) :  void
DebugMolecule.addSingleElectron ( ISingleElectron ec ) :  void
DebugMolecule.addStereoElement ( IStereoElement parity ) :  void
DebugMolecule.atoms ( ) :  Iterable
DebugMolecule.bonds ( ) :  Iterable
DebugMolecule.clone ( ) :  IAtomContainer
DebugMolecule.clone ( ) :  IMolecule
DebugMolecule.clone ( ) :  Object
DebugMolecule.contains ( IAtom atom ) :  boolean
DebugMolecule.contains ( IBond bond ) :  boolean
DebugMolecule.contains ( IElectronContainer electronContainer ) :  boolean
DebugMolecule.contains ( ILonePair ec ) :  boolean
DebugMolecule.contains ( ISingleElectron ec ) :  boolean
DebugMolecule.DebugMolecule ( )
DebugMolecule.DebugMolecule ( IAtomContainer container )
DebugMolecule.DebugMolecule ( int atomCount, int electronContainerCount, int lonePairCount, int singleElectronCount )
DebugMolecule.electronContainers ( ) :  Iterable
DebugMolecule.getAtom ( int number ) :  IAtom
DebugMolecule.getAtomCount ( ) :  int
DebugMolecule.getAtomNumber ( IAtom atom ) :  int
DebugMolecule.getBond ( IAtom atom1, IAtom atom2 ) :  IBond
DebugMolecule.getBond ( int number ) :  IBond
DebugMolecule.getBondCount ( ) :  int
DebugMolecule.getBondNumber ( IAtom atom1, IAtom atom2 ) :  int
DebugMolecule.getBondNumber ( IBond bond ) :  int
DebugMolecule.getBondOrderSum ( IAtom atom ) :  double
DebugMolecule.getBuilder ( ) :  IChemObjectBuilder
DebugMolecule.getConnectedAtomsCount ( IAtom atom ) :  int
DebugMolecule.getConnectedAtomsList ( IAtom atom ) :  List
DebugMolecule.getConnectedBondsCount ( IAtom atom ) :  int
DebugMolecule.getConnectedBondsList ( IAtom atom ) :  List
DebugMolecule.getConnectedElectronContainersList ( IAtom atom ) :  List
DebugMolecule.getConnectedLonePairsCount ( IAtom atom ) :  int
DebugMolecule.getConnectedLonePairsList ( IAtom atom ) :  List
DebugMolecule.getConnectedSingleElectronsCount ( IAtom atom ) :  int
DebugMolecule.getConnectedSingleElectronsList ( IAtom atom ) :  List
DebugMolecule.getElectronContainer ( int number ) :  IElectronContainer
DebugMolecule.getElectronContainerCount ( ) :  int
DebugMolecule.getFirstAtom ( ) :  IAtom
DebugMolecule.getFlag ( int flag_type ) :  boolean
DebugMolecule.getFlags ( ) :  boolean[ ]
DebugMolecule.getID ( ) :  String
DebugMolecule.getLastAtom ( ) :  IAtom
DebugMolecule.getListenerCount ( ) :  int
DebugMolecule.getLonePair ( int number ) :  ILonePair
DebugMolecule.getLonePairCount ( ) :  int
DebugMolecule.getLonePairNumber ( ILonePair bond ) :  int
DebugMolecule.getMaximumBondOrder ( IAtom atom ) :  IBond.Order
DebugMolecule.getMinimumBondOrder ( IAtom atom ) :  IBond.Order
DebugMolecule.getProperties ( ) :  Map
DebugMolecule.getProperty ( Object description ) :  Object
DebugMolecule.getSingleElectron ( int number ) :  ISingleElectron
DebugMolecule.getSingleElectronCount ( ) :  int
DebugMolecule.getSingleElectronNumber ( ISingleElectron bond ) :  int
DebugMolecule.lonePairs ( ) :  Iterable
DebugMolecule.notifyChanged ( ) :  void
DebugMolecule.notifyChanged ( IChemObjectChangeEvent evt ) :  void
DebugMolecule.remove ( IAtomContainer atomContainer ) :  void
DebugMolecule.removeAllBonds ( ) :  void
DebugMolecule.removeAllElectronContainers ( ) :  void
DebugMolecule.removeAllElements ( ) :  void
DebugMolecule.removeAtom ( IAtom atom ) :  void
DebugMolecule.removeAtom ( int position ) :  void
DebugMolecule.removeAtomAndConnectedElectronContainers ( IAtom atom ) :  void
DebugMolecule.removeBond ( IAtom atom1, IAtom atom2 ) :  IBond
DebugMolecule.removeBond ( IBond bond ) :  void
DebugMolecule.removeBond ( int pos ) :  IBond
DebugMolecule.removeElectronContainer ( IElectronContainer electronContainer ) :  void
DebugMolecule.removeElectronContainer ( int position ) :  IElectronContainer
DebugMolecule.removeListener ( IChemObjectListener col ) :  void
DebugMolecule.removeLonePair ( ILonePair ec ) :  void
DebugMolecule.removeLonePair ( int pos ) :  ILonePair
DebugMolecule.removeProperty ( Object description ) :  void
DebugMolecule.removeSingleElectron ( int pos ) :  ISingleElectron
DebugMolecule.removeSingleElectron ( ISingleElectron ec ) :  void
DebugMolecule.setAtom ( int number, IAtom atom ) :  void
DebugMolecule.setAtoms ( IAtom[ ] atoms ) :  void
DebugMolecule.setFlag ( int flag_type, boolean flag_value ) :  void
DebugMolecule.setFlags ( boolean[ ] flagsNew ) :  void
DebugMolecule.setID ( String identifier ) :  void
DebugMolecule.setProperties ( Map properties ) :  void
DebugMolecule.setProperty ( Object description, Object property ) :  void
DebugMolecule.singleElectrons ( ) :  Iterable
DebugMolecule.stereoElements ( ) :  Iterable

cdk-1.4.19.jar, DebugMoleculeSet.class
package org.openscience.cdk.debug
DebugMoleculeSet.add ( IAtomContainerSet atomContainerSet ) :  void
DebugMoleculeSet.add ( IMoleculeSet moleculeSet ) :  void
DebugMoleculeSet.addAtomContainer ( IAtomContainer atomContainer ) :  void
DebugMoleculeSet.addAtomContainer ( IAtomContainer atomContainer, double multiplier ) :  void
DebugMoleculeSet.addListener ( IChemObjectListener col ) :  void
DebugMoleculeSet.addMolecule ( IMolecule molecule ) :  void
DebugMoleculeSet.atomContainers ( ) :  Iterable
DebugMoleculeSet.clone ( ) :  Object
DebugMoleculeSet.DebugMoleculeSet ( )
DebugMoleculeSet.getAtomContainer ( int number ) :  IAtomContainer
DebugMoleculeSet.getAtomContainerCount ( ) :  int
DebugMoleculeSet.getBuilder ( ) :  IChemObjectBuilder
DebugMoleculeSet.getFlag ( int flag_type ) :  boolean
DebugMoleculeSet.getFlags ( ) :  boolean[ ]
DebugMoleculeSet.getID ( ) :  String
DebugMoleculeSet.getListenerCount ( ) :  int
DebugMoleculeSet.getMolecule ( int number ) :  IMolecule
DebugMoleculeSet.getMoleculeCount ( ) :  int
DebugMoleculeSet.getMultiplier ( IAtomContainer container ) :  Double
DebugMoleculeSet.getMultiplier ( int number ) :  Double
DebugMoleculeSet.getMultipliers ( ) :  Double[ ]
DebugMoleculeSet.getProperties ( ) :  Map
DebugMoleculeSet.getProperty ( Object description ) :  Object
DebugMoleculeSet.molecules ( ) :  Iterable
DebugMoleculeSet.notifyChanged ( ) :  void
DebugMoleculeSet.notifyChanged ( IChemObjectChangeEvent evt ) :  void
DebugMoleculeSet.removeAllAtomContainers ( ) :  void
DebugMoleculeSet.removeAtomContainer ( IAtomContainer atomContainer ) :  void
DebugMoleculeSet.removeAtomContainer ( int pos ) :  void
DebugMoleculeSet.removeListener ( IChemObjectListener col ) :  void
DebugMoleculeSet.removeProperty ( Object description ) :  void
DebugMoleculeSet.replaceAtomContainer ( int position, IAtomContainer container ) :  void
DebugMoleculeSet.setFlag ( int flag_type, boolean flag_value ) :  void
DebugMoleculeSet.setFlags ( boolean[ ] flagsNew ) :  void
DebugMoleculeSet.setID ( String identifier ) :  void
DebugMoleculeSet.setMolecules ( IMolecule[ ] molecules ) :  void
DebugMoleculeSet.setMultiplier ( IAtomContainer container, Double multiplier ) :  boolean
DebugMoleculeSet.setMultiplier ( int position, Double multiplier ) :  void
DebugMoleculeSet.setMultipliers ( Double[ ] newMultipliers ) :  boolean
DebugMoleculeSet.setProperties ( Map properties ) :  void
DebugMoleculeSet.setProperty ( Object description, Object property ) :  void

cdk-1.4.19.jar, DebugReaction.class
package org.openscience.cdk.debug
DebugReaction.addAgent ( IMolecule agent ) :  void
DebugReaction.addProduct ( IMolecule product ) :  void
DebugReaction.addProduct ( IMolecule product, Double coefficient ) :  void
DebugReaction.addReactant ( IMolecule reactant ) :  void
DebugReaction.addReactant ( IMolecule reactant, Double coefficient ) :  void
DebugReaction.getProductCoefficient ( IMolecule product ) :  Double
DebugReaction.getReactantCoefficient ( IMolecule reactant ) :  Double
DebugReaction.setProductCoefficient ( IMolecule product, Double coefficient ) :  boolean
DebugReaction.setProducts ( IMoleculeSet products ) :  void
DebugReaction.setReactantCoefficient ( IMolecule reactant, Double coefficient ) :  boolean
DebugReaction.setReactants ( IMoleculeSet reactants ) :  void

cdk-1.4.19.jar, DebugReactionSet.class
package org.openscience.cdk.debug
DebugReactionSet.isEmpty ( ) :  boolean

cdk-1.4.19.jar, DeduceBondSystemTool.class
package org.openscience.cdk.smiles
DeduceBondSystemTool.fixAromaticBondOrders ( IMolecule molecule ) :  IMolecule
DeduceBondSystemTool.isOK ( IMolecule m ) :  boolean

cdk-1.4.19.jar, DoubleBondAcceptingAromaticityDetector.class
package org.openscience.cdk.aromaticity
DoubleBondAcceptingAromaticityDetector.detectAromaticity ( IAtomContainer atomContainer ) [static] :  boolean
DoubleBondAcceptingAromaticityDetector.DoubleBondAcceptingAromaticityDetector ( )

cdk-1.4.19.jar, DoubleBondStereochemistry.class
package org.openscience.cdk.stereo
DoubleBondStereochemistry.DoubleBondStereochemistry ( IBond stereoBond, IBond[ ] ligandBonds, IDoubleBondStereochemistry.Conformation stereo )
DoubleBondStereochemistry.getBonds ( ) :  IBond[ ]
DoubleBondStereochemistry.getBuilder ( ) :  IChemObjectBuilder
DoubleBondStereochemistry.getStereo ( ) :  IDoubleBondStereochemistry.Conformation
DoubleBondStereochemistry.getStereoBond ( ) :  IBond
DoubleBondStereochemistry.map ( Map atoms, Map bonds ) :  IDoubleBondStereochemistry
DoubleBondStereochemistry.map ( Map x0, Map x1 ) :  IStereoElement
DoubleBondStereochemistry.setBuilder ( IChemObjectBuilder builder ) :  void

cdk-1.4.19.jar, ElectronImpactNBEReaction.class
package org.openscience.cdk.reaction.type
ElectronImpactNBEReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, ElectronImpactPDBReaction.class
package org.openscience.cdk.reaction.type
ElectronImpactPDBReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, ElectronImpactSDBReaction.class
package org.openscience.cdk.reaction.type
ElectronImpactSDBReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, ExtAtomContainerManipulator.class
package org.openscience.cdk.smsd.tools
ExtAtomContainerManipulator.makeDeepCopy ( IMolecule container ) [static] :  IMolecule
ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID ( IAtomContainer atomContainer ) [static] :  IMolecule

cdk-1.4.19.jar, ExtendedAtomGenerator.class
package org.openscience.cdk.renderer.generators
ExtendedAtomGenerator.ExtendedAtomGenerator ( )
ExtendedAtomGenerator.generate ( IAtomContainer container, IAtom atom, RendererModel model ) :  IRenderingElement
ExtendedAtomGenerator.getParameters ( ) :  List

cdk-1.4.19.jar, FiguerasSSSRFinder.class
package org.openscience.cdk.ringsearch
FiguerasSSSRFinder.findSSSR ( Molecule mol ) :  RingSet

cdk-1.4.19.jar, FixBondOrdersTool.class
package org.openscience.cdk.smiles
FixBondOrdersTool.FixBondOrdersTool ( )
FixBondOrdersTool.isInterrupted ( ) :  boolean
FixBondOrdersTool.kekuliseAromaticRings ( IMolecule molecule ) :  IMolecule
FixBondOrdersTool.setInterrupted ( boolean interrupted ) :  void

cdk-1.4.19.jar, ForceFieldConfigurator.class
package org.openscience.cdk.modeling.builder3d
ForceFieldConfigurator.assignAtomTyps ( IMolecule molecule ) :  IRingSet

cdk-1.4.19.jar, GaussianInputWriter.class
package org.openscience.cdk.io.program
GaussianInputWriter.writeMolecule ( IMolecule mol ) :  void

cdk-1.4.19.jar, HeterolyticCleavageMechanism.class
package org.openscience.cdk.reaction.mechanism
HeterolyticCleavageMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, HeterolyticCleavagePBReaction.class
package org.openscience.cdk.reaction.type
HeterolyticCleavagePBReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, HeterolyticCleavageSBReaction.class
package org.openscience.cdk.reaction.type
HeterolyticCleavageSBReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, HomolyticCleavageMechanism.class
package org.openscience.cdk.reaction.mechanism
HomolyticCleavageMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, HomolyticCleavageReaction.class
package org.openscience.cdk.reaction.type
HomolyticCleavageReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, HOSECodeGenerator.class
package org.openscience.cdk.tools
HOSECodeGenerator.getSpheres ( IMolecule ac, IAtom root, int noOfSpheres, boolean ringsize ) :  List[ ]

cdk-1.4.19.jar, HyperconjugationReaction.class
package org.openscience.cdk.reaction.type
HyperconjugationReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, IAtomContainer.class
package org.openscience.cdk.interfaces
IAtomContainer.isEmpty ( ) [abstract] :  boolean
IAtomContainer.setStereoElements ( List p1 ) [abstract] :  void

cdk-1.4.19.jar, IAtomContainerSet.class
package org.openscience.cdk.interfaces
IAtomContainerSet.isEmpty ( ) [abstract] :  boolean

cdk-1.4.19.jar, IAtomParity.class
package org.openscience.cdk.interfaces
IAtomParity.map ( Map p1, Map p2 ) [abstract] :  IAtomParity

cdk-1.4.19.jar, IChemModel.class
package org.openscience.cdk.interfaces
IChemModel.getMoleculeSet ( ) [abstract] :  IMoleculeSet
IChemModel.isEmpty ( ) [abstract] :  boolean
IChemModel.setMoleculeSet ( IMoleculeSet p1 ) [abstract] :  void

cdk-1.4.19.jar, IDoubleBondStereochemistry.class
package org.openscience.cdk.interfaces
IDoubleBondStereochemistry.getBonds ( ) [abstract] :  IBond[ ]
IDoubleBondStereochemistry.getStereo ( ) [abstract] :  IDoubleBondStereochemistry.Conformation
IDoubleBondStereochemistry.getStereoBond ( ) [abstract] :  IBond
IDoubleBondStereochemistry.map ( Map p1, Map p2 ) [abstract] :  IDoubleBondStereochemistry

cdk-1.4.19.jar, IMolecule.class
package org.openscience.cdk.interfaces
IMolecule.clone ( ) [abstract] :  IMolecule

cdk-1.4.19.jar, IMoleculeSet.class
package org.openscience.cdk.interfaces
IMoleculeSet.add ( IMoleculeSet p1 ) [abstract] :  void
IMoleculeSet.addMolecule ( IMolecule p1 ) [abstract] :  void
IMoleculeSet.getMolecule ( int p1 ) [abstract] :  IMolecule
IMoleculeSet.getMoleculeCount ( ) [abstract] :  int
IMoleculeSet.molecules ( ) [abstract] :  Iterable
IMoleculeSet.setMolecules ( IMolecule[ ] p1 ) [abstract] :  void

cdk-1.4.19.jar, InverseSymbolSetQueryAtom.class
package org.openscience.cdk.isomorphism.matchers
InverseSymbolSetQueryAtom.getSymbolSet ( ) :  HashSet

cdk-1.4.19.jar, IReaction.class
package org.openscience.cdk.interfaces
IReaction.addAgent ( IMolecule p1 ) [abstract] :  void
IReaction.addProduct ( IMolecule p1 ) [abstract] :  void
IReaction.addProduct ( IMolecule p1, Double p2 ) [abstract] :  void
IReaction.addReactant ( IMolecule p1 ) [abstract] :  void
IReaction.addReactant ( IMolecule p1, Double p2 ) [abstract] :  void
IReaction.getAgents ( ) [abstract] :  IMoleculeSet
IReaction.getProductCoefficient ( IMolecule p1 ) [abstract] :  Double
IReaction.getProducts ( ) [abstract] :  IMoleculeSet
IReaction.getReactantCoefficient ( IMolecule p1 ) [abstract] :  Double
IReaction.getReactants ( ) [abstract] :  IMoleculeSet
IReaction.setProductCoefficient ( IMolecule p1, Double p2 ) [abstract] :  boolean
IReaction.setProducts ( IMoleculeSet p1 ) [abstract] :  void
IReaction.setReactantCoefficient ( IMolecule p1, Double p2 ) [abstract] :  boolean
IReaction.setReactants ( IMoleculeSet p1 ) [abstract] :  void

cdk-1.4.19.jar, IReactionMechanism.class
package org.openscience.cdk.reaction
IReactionMechanism.initiate ( IMoleculeSet p1, ArrayList p2, ArrayList p3 ) [abstract] :  IReaction

cdk-1.4.19.jar, IReactionProcess.class
package org.openscience.cdk.reaction
IReactionProcess.initiate ( IMoleculeSet p1, IMoleculeSet p2 ) [abstract] :  IReactionSet

cdk-1.4.19.jar, IReactionSet.class
package org.openscience.cdk.interfaces
IReactionSet.isEmpty ( ) [abstract] :  boolean

cdk-1.4.19.jar, IRingSet.class
package org.openscience.cdk.interfaces
IRingSet.isEmpty ( ) [abstract] :  boolean

cdk-1.4.19.jar, IsoAlkanes.class
package org.openscience.cdk.templates.saturatedhydrocarbons
IsoAlkanes.getIsobutane ( ) [static] :  Molecule
IsoAlkanes.getIsohexane ( ) [static] :  Molecule
IsoAlkanes.getIsopentane ( ) [static] :  Molecule

cdk-1.4.19.jar, Isomorphism.class
package org.openscience.cdk.smsd
Isomorphism.init ( IMolecule reactant, IMolecule product, boolean removeHydrogen, boolean cleanAndConfigureMolecule ) :  void

cdk-1.4.19.jar, IsomorphismTester.class
package org.openscience.cdk.isomorphism
IsomorphismTester.isIsomorphic ( IMolecule mol1, IMolecule mol2 ) :  boolean
IsomorphismTester.isIsomorphic ( IMolecule mol2 ) :  boolean
IsomorphismTester.IsomorphismTester ( IMolecule mol )

cdk-1.4.19.jar, IsotopeFactory.class
package org.openscience.cdk.config
IsotopeFactory.getIsotopes ( ) :  IIsotope[ ]
IsotopeFactory.getIsotopes ( double exactMass, double difference ) :  IIsotope[ ]

cdk-1.4.19.jar, IStereoElement.class
package org.openscience.cdk.interfaces
IStereoElement.map ( Map p1, Map p2 ) [abstract] :  IStereoElement

cdk-1.4.19.jar, IteratingMDLReader.class
package org.openscience.cdk.io.iterator
IteratingMDLReader.IteratingMDLReader ( InputStream in, IChemObjectBuilder builder, boolean skip )
IteratingMDLReader.IteratingMDLReader ( Reader in, IChemObjectBuilder builder, boolean skip )
IteratingMDLReader.setSkip ( boolean skip ) :  void

cdk-1.4.19.jar, IteratingSMILESReader.class
package org.openscience.cdk.io.iterator
IteratingSMILESReader.IteratingSMILESReader ( InputStream in )

cdk-1.4.19.jar, ITetrahedralChirality.class
package org.openscience.cdk.interfaces
ITetrahedralChirality.map ( Map p1, Map p2 ) [abstract] :  ITetrahedralChirality

cdk-1.4.19.jar, IValidator.class
package org.openscience.cdk.validate
IValidator.validateMolecule ( IMolecule p1 ) [abstract] :  ValidationReport
IValidator.validateMoleculeSet ( IMoleculeSet p1 ) [abstract] :  ValidationReport

cdk-1.4.19.jar, JJTSMARTSParserState.class
package org.openscience.cdk.smiles.smarts.parser
JJTSMARTSParserState.JJTSMARTSParserState ( )

cdk-1.4.19.jar, LonePairGenerator.class
package org.openscience.cdk.renderer.generators
LonePairGenerator.generate ( IAtomContainer container, RendererModel model ) :  IRenderingElement
LonePairGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
LonePairGenerator.getParameters ( ) :  List
LonePairGenerator.LonePairGenerator ( )

cdk-1.4.19.jar, MappingGenerator.class
package org.openscience.cdk.renderer.generators
MappingGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
MappingGenerator.generate ( IReaction reaction, RendererModel model ) :  IRenderingElement
MappingGenerator.getParameters ( ) :  List
MappingGenerator.MappingGenerator ( )

cdk-1.4.19.jar, MappingLineWidth.class
package org.openscience.cdk.renderer.generators
MappingGenerator.MappingLineWidth.getDefault ( ) :  Double
MappingGenerator.MappingLineWidth.getDefault ( ) :  Object
MappingGenerator.MappingLineWidth.MappingGenerator.MappingLineWidth ( )

cdk-1.4.19.jar, MDLV3000Reader.class
package org.openscience.cdk.io
MDLV3000Reader.readMolecule ( IChemObjectBuilder builder ) :  IMolecule

cdk-1.4.19.jar, ModelBuilder3D.class
package org.openscience.cdk.modeling.builder3d
ModelBuilder3D.generate3DCoordinates ( IMolecule molecule, boolean clone ) :  IMolecule

cdk-1.4.19.jar, Mol2Writer.class
package org.openscience.cdk.io
Mol2Writer.writeMolecule ( IMolecule mol ) :  void

cdk-1.4.19.jar, Molecule.class
package org.openscience.cdk
Molecule.clone ( ) :  IAtomContainer
Molecule.clone ( ) :  IMolecule
Molecule.clone ( ) :  Object
Molecule.Molecule ( )
Molecule.Molecule ( IAtomContainer container )
Molecule.Molecule ( int atomCount, int bondCount, int lonePairCount, int singleElectronCount )
Molecule.toString ( ) :  String
package org.openscience.cdk.silent
Molecule.clone ( ) :  IAtomContainer
Molecule.clone ( ) :  IMolecule
Molecule.clone ( ) :  Object
Molecule.Molecule ( )
Molecule.Molecule ( IAtomContainer container )
Molecule.Molecule ( int atomCount, int bondCount, int lonePairCount, int singleElectronCount )
Molecule.toString ( ) :  String

cdk-1.4.19.jar, MoleculeBuilder.class
package org.openscience.cdk.iupac.parser
MoleculeBuilder.buildMolecule ( int mainChain, Vector attachedSubstituents, Vector attachedGroups, boolean isMainCyclic, String name ) :  Molecule

cdk-1.4.19.jar, MoleculeFactory.class
package org.openscience.cdk.templates
MoleculeFactory.loadMolecule ( String inFile ) [static] :  IMolecule
MoleculeFactory.make123Triazole ( ) [static] :  Molecule
MoleculeFactory.make124Triazole ( ) [static] :  Molecule
MoleculeFactory.make4x3CondensedRings ( ) [static] :  Molecule
MoleculeFactory.makeAdenine ( ) [static] :  IMolecule
MoleculeFactory.makeAlkane ( int chainLength ) [static] :  Molecule
MoleculeFactory.makeAlphaPinene ( ) [static] :  Molecule
MoleculeFactory.makeAzulene ( ) [static] :  Molecule
MoleculeFactory.makeBenzene ( ) [static] :  Molecule
MoleculeFactory.makeBicycloRings ( ) [static] :  Molecule
MoleculeFactory.makeBiphenyl ( ) [static] :  Molecule
MoleculeFactory.makeBranchedAliphatic ( ) [static] :  Molecule
MoleculeFactory.makeCyclobutadiene ( ) [static] :  Molecule
MoleculeFactory.makeCyclobutane ( ) [static] :  Molecule
MoleculeFactory.makeCyclohexane ( ) [static] :  Molecule
MoleculeFactory.makeCyclohexene ( ) [static] :  Molecule
MoleculeFactory.makeCyclopentane ( ) [static] :  Molecule
MoleculeFactory.makeDiamantane ( ) [static] :  Molecule
MoleculeFactory.makeEthylCyclohexane ( ) [static] :  Molecule
MoleculeFactory.makeEthylPropylPhenantren ( ) [static] :  Molecule
MoleculeFactory.makeFusedRings ( ) [static] :  Molecule
MoleculeFactory.makeImidazole ( ) [static] :  Molecule
MoleculeFactory.makeIndole ( ) [static] :  Molecule
MoleculeFactory.makeIsothiazole ( ) [static] :  Molecule
MoleculeFactory.makeIsoxazole ( ) [static] :  Molecule
MoleculeFactory.makeMethylDecaline ( ) [static] :  Molecule
MoleculeFactory.makeOxadiazole ( ) [static] :  Molecule
MoleculeFactory.makeOxazole ( ) [static] :  Molecule
MoleculeFactory.makePhenylAmine ( ) [static] :  Molecule
MoleculeFactory.makePhenylEthylBenzene ( ) [static] :  Molecule
MoleculeFactory.makePiperidine ( ) [static] :  Molecule
MoleculeFactory.makePropylCycloPropane ( ) [static] :  Molecule
MoleculeFactory.makePyrazole ( ) [static] :  Molecule
MoleculeFactory.makePyridazine ( ) [static] :  Molecule
MoleculeFactory.makePyridine ( ) [static] :  Molecule
MoleculeFactory.makePyridineOxide ( ) [static] :  Molecule
MoleculeFactory.makePyrimidine ( ) [static] :  Molecule
MoleculeFactory.makePyrrole ( ) [static] :  Molecule
MoleculeFactory.makePyrroleAnion ( ) [static] :  Molecule
MoleculeFactory.makeQuinone ( ) [static] :  Molecule
MoleculeFactory.makeSingleRing ( ) [static] :  Molecule
MoleculeFactory.makeSpiroRings ( ) [static] :  Molecule
MoleculeFactory.makeSteran ( ) [static] :  Molecule
MoleculeFactory.makeTetrahydropyran ( ) [static] :  Molecule
MoleculeFactory.makeTetrazole ( ) [static] :  Molecule
MoleculeFactory.makeThiadiazole ( ) [static] :  Molecule
MoleculeFactory.makeThiazole ( ) [static] :  Molecule
MoleculeFactory.makeTriazine ( ) [static] :  Molecule

cdk-1.4.19.jar, MoleculeFeaturesTool.class
package org.openscience.cdk.tools.features
MoleculeFeaturesTool.hasElementSymbols ( IMolecule molecule ) [static] :  boolean
MoleculeFeaturesTool.hasFormalCharges ( IMolecule molecule ) [static] :  boolean
MoleculeFeaturesTool.hasGraphRepresentation ( IMolecule molecule ) [static] :  boolean
MoleculeFeaturesTool.hasPartialCharges ( IMolecule molecule ) [static] :  boolean

cdk-1.4.19.jar, MoleculeSet.class
package org.openscience.cdk
MoleculeSet.add ( IMoleculeSet moleculeSet ) :  void
MoleculeSet.addAtomContainer ( IAtomContainer atomContainer ) :  void
MoleculeSet.addAtomContainer ( IAtomContainer atomContainer, double multiplier ) :  void
MoleculeSet.addMolecule ( IMolecule molecule ) :  void
MoleculeSet.clone ( ) :  Object
MoleculeSet.getMolecule ( int number ) :  IMolecule
MoleculeSet.getMoleculeCount ( ) :  int
MoleculeSet.molecules ( ) :  Iterable
MoleculeSet.MoleculeSet ( )
MoleculeSet.setMolecules ( IMolecule[ ] molecules ) :  void
MoleculeSet.stateChanged ( IChemObjectChangeEvent event ) :  void
MoleculeSet.toString ( ) :  String
package org.openscience.cdk.silent
MoleculeSet.add ( IMoleculeSet moleculeSet ) :  void
MoleculeSet.addAtomContainer ( IAtomContainer atomContainer ) :  void
MoleculeSet.addAtomContainer ( IAtomContainer atomContainer, double multiplier ) :  void
MoleculeSet.addMolecule ( IMolecule molecule ) :  void
MoleculeSet.clone ( ) :  Object
MoleculeSet.getMolecule ( int number ) :  IMolecule
MoleculeSet.getMoleculeCount ( ) :  int
MoleculeSet.molecules ( ) :  Iterable
MoleculeSet.MoleculeSet ( )
MoleculeSet.setMolecules ( IMolecule[ ] molecules ) :  void
MoleculeSet.stateChanged ( IChemObjectChangeEvent event ) :  void
MoleculeSet.toString ( ) :  String

cdk-1.4.19.jar, MoleculeSetManipulator.class
package org.openscience.cdk.tools.manipulator
MoleculeSetManipulator.getAllAtomContainers ( IMoleculeSet set ) [static] :  List
MoleculeSetManipulator.getAllChemObjects ( IMoleculeSet set ) [static] :  List
MoleculeSetManipulator.getAllIDs ( IMoleculeSet set ) [static] :  List
MoleculeSetManipulator.getRelevantAtomContainer ( IMoleculeSet moleculeSet, IAtom atom ) [static] :  IAtomContainer
MoleculeSetManipulator.getRelevantAtomContainer ( IMoleculeSet moleculeSet, IBond bond ) [static] :  IAtomContainer
MoleculeSetManipulator.getTotalCharge ( IMoleculeSet set ) [static] :  double
MoleculeSetManipulator.getTotalFormalCharge ( IMoleculeSet set ) [static] :  double
MoleculeSetManipulator.getTotalHydrogenCount ( IMoleculeSet set ) [static] :  int
MoleculeSetManipulator.removeAtomAndConnectedElectronContainers ( IMoleculeSet set, IAtom atom ) [static] :  void
MoleculeSetManipulator.removeElectronContainer ( IMoleculeSet set, IElectronContainer electrons ) [static] :  void
MoleculeSetManipulator.setAtomProperties ( IMoleculeSet set, Object propKey, Object propVal ) [static] :  void

cdk-1.4.19.jar, MoleculeSetRenderer.class
package org.openscience.cdk.renderer
MoleculeSetRenderer.calculateDiagramBounds ( IChemObject x0 ) :  Rectangle
MoleculeSetRenderer.calculateDiagramBounds ( IMoleculeSet moleculeSet ) :  Rectangle
MoleculeSetRenderer.calculateScaleForBondLength ( double modelBondLength ) :  double
MoleculeSetRenderer.generateDiagram ( IChemObject x0 ) :  IRenderingElement
MoleculeSetRenderer.generateDiagram ( IMoleculeSet molecules ) :  IRenderingElement
MoleculeSetRenderer.getGenerators ( ) :  List
MoleculeSetRenderer.MoleculeSetRenderer ( List generators, IFontManager fontManager )
MoleculeSetRenderer.MoleculeSetRenderer ( RendererModel rendererModel, List generators, IFontManager fontManager )
MoleculeSetRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) :  Rectangle
MoleculeSetRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) :  void
MoleculeSetRenderer.paint ( IMoleculeSet molecules, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) :  void
MoleculeSetRenderer.paint ( IMoleculeSet moleculeSet, IDrawVisitor drawVisitor ) :  Rectangle
MoleculeSetRenderer.setScale ( IChemObject x0 ) :  void
MoleculeSetRenderer.setScale ( IMoleculeSet moleculeSet ) :  void
MoleculeSetRenderer.setup ( IChemObject x0, Rectangle x1 ) :  void
MoleculeSetRenderer.setup ( IMoleculeSet moleculeSet, Rectangle screen ) :  void
MoleculeSetRenderer.shift ( Rectangle screenBounds, Rectangle diagramBounds ) :  Rectangle

cdk-1.4.19.jar, MoleculeSignature.class
package org.openscience.cdk.signature
MoleculeSignature.MoleculeSignature ( IMolecule molecule, int height )

cdk-1.4.19.jar, NNAdductFormula.class
package org.openscience.cdk.nonotify
NNAdductFormula.getBuilder ( ) :  IChemObjectBuilder
NNAdductFormula.NNAdductFormula ( )
NNAdductFormula.NNAdductFormula ( IMolecularFormula formula )

cdk-1.4.19.jar, NNAminoAcid.class
package org.openscience.cdk.nonotify
NNAminoAcid.addListener ( IChemObjectListener col ) :  void
NNAminoAcid.getBuilder ( ) :  IChemObjectBuilder
NNAminoAcid.NNAminoAcid ( )

cdk-1.4.19.jar, NNAtom.class
package org.openscience.cdk.nonotify
NNAtom.addListener ( IChemObjectListener col ) :  void
NNAtom.getBuilder ( ) :  IChemObjectBuilder
NNAtom.NNAtom ( )
NNAtom.NNAtom ( IElement element )
NNAtom.NNAtom ( String elementSymbol )
NNAtom.NNAtom ( String elementSymbol, Point2d point2d )
NNAtom.NNAtom ( String elementSymbol, Point3d point3d )

cdk-1.4.19.jar, NNAtomContainer.class
package org.openscience.cdk.nonotify
NNAtomContainer.addListener ( IChemObjectListener col ) :  void
NNAtomContainer.getBuilder ( ) :  IChemObjectBuilder
NNAtomContainer.NNAtomContainer ( )
NNAtomContainer.NNAtomContainer ( IAtomContainer container )
NNAtomContainer.NNAtomContainer ( int atomCount, int electronContainerCount, int lonePairCount, int singleElectronCount )

cdk-1.4.19.jar, NNAtomContainerSet.class
package org.openscience.cdk.nonotify
NNAtomContainerSet.addListener ( IChemObjectListener col ) :  void
NNAtomContainerSet.getBuilder ( ) :  IChemObjectBuilder
NNAtomContainerSet.NNAtomContainerSet ( )

cdk-1.4.19.jar, NNAtomParity.class
package org.openscience.cdk.nonotify
NNAtomParity.map ( Map atoms, Map bonds ) :  IAtomParity
NNAtomParity.map ( Map x0, Map x1 ) :  IStereoElement
NNAtomParity.NNAtomParity ( IAtom centralAtom, IAtom first, IAtom second, IAtom third, IAtom fourth, int parity )

cdk-1.4.19.jar, NNAtomType.class
package org.openscience.cdk.nonotify
NNAtomType.addListener ( IChemObjectListener col ) :  void
NNAtomType.getBuilder ( ) :  IChemObjectBuilder
NNAtomType.NNAtomType ( IElement element )
NNAtomType.NNAtomType ( String elementSymbol )
NNAtomType.NNAtomType ( String identifier, String elementSymbol )

cdk-1.4.19.jar, NNBioPolymer.class
package org.openscience.cdk.nonotify
NNBioPolymer.addListener ( IChemObjectListener col ) :  void
NNBioPolymer.getBuilder ( ) :  IChemObjectBuilder
NNBioPolymer.NNBioPolymer ( )

cdk-1.4.19.jar, NNBond.class
package org.openscience.cdk.nonotify
NNBond.addListener ( IChemObjectListener col ) :  void
NNBond.getBuilder ( ) :  IChemObjectBuilder
NNBond.NNBond ( )
NNBond.NNBond ( IAtom atom1, IAtom atom2 )
NNBond.NNBond ( IAtom atom1, IAtom atom2, IBond.Order order )
NNBond.NNBond ( IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo )
NNBond.NNBond ( IAtom[ ] atoms )
NNBond.NNBond ( IAtom[ ] atoms, IBond.Order order )

cdk-1.4.19.jar, NNChemFile.class
package org.openscience.cdk.nonotify
NNChemFile.addListener ( IChemObjectListener col ) :  void
NNChemFile.getBuilder ( ) :  IChemObjectBuilder
NNChemFile.NNChemFile ( )

cdk-1.4.19.jar, NNChemModel.class
package org.openscience.cdk.nonotify
NNChemModel.addListener ( IChemObjectListener col ) :  void
NNChemModel.getBuilder ( ) :  IChemObjectBuilder
NNChemModel.NNChemModel ( )

cdk-1.4.19.jar, NNChemObject.class
package org.openscience.cdk.nonotify
NNChemObject.addListener ( IChemObjectListener col ) :  void
NNChemObject.getBuilder ( ) :  IChemObjectBuilder
NNChemObject.NNChemObject ( )
NNChemObject.NNChemObject ( IChemObject object )

cdk-1.4.19.jar, NNChemSequence.class
package org.openscience.cdk.nonotify
NNChemSequence.addListener ( IChemObjectListener col ) :  void
NNChemSequence.getBuilder ( ) :  IChemObjectBuilder
NNChemSequence.NNChemSequence ( )

cdk-1.4.19.jar, NNCrystal.class
package org.openscience.cdk.nonotify
NNCrystal.addListener ( IChemObjectListener col ) :  void
NNCrystal.getBuilder ( ) :  IChemObjectBuilder
NNCrystal.NNCrystal ( )
NNCrystal.NNCrystal ( IAtomContainer container )

cdk-1.4.19.jar, NNElectronContainer.class
package org.openscience.cdk.nonotify
NNElectronContainer.addListener ( IChemObjectListener col ) :  void
NNElectronContainer.getBuilder ( ) :  IChemObjectBuilder
NNElectronContainer.NNElectronContainer ( )

cdk-1.4.19.jar, NNElement.class
package org.openscience.cdk.nonotify
NNElement.addListener ( IChemObjectListener col ) :  void
NNElement.getBuilder ( ) :  IChemObjectBuilder
NNElement.NNElement ( )
NNElement.NNElement ( IElement element )
NNElement.NNElement ( String symbol )
NNElement.NNElement ( String symbol, int atomicNumber )

cdk-1.4.19.jar, NNFragmentAtom.class
package org.openscience.cdk.nonotify
NNFragmentAtom.addListener ( IChemObjectListener col ) :  void
NNFragmentAtom.getBuilder ( ) :  IChemObjectBuilder
NNFragmentAtom.NNFragmentAtom ( )

cdk-1.4.19.jar, NNIsotope.class
package org.openscience.cdk.nonotify
NNIsotope.addListener ( IChemObjectListener col ) :  void
NNIsotope.getBuilder ( ) :  IChemObjectBuilder
NNIsotope.NNIsotope ( IElement element )
NNIsotope.NNIsotope ( int atomicNumber, String elementSymbol, double exactMass, double abundance )
NNIsotope.NNIsotope ( int atomicNumber, String elementSymbol, int massNumber, double exactMass, double abundance )
NNIsotope.NNIsotope ( String elementSymbol )
NNIsotope.NNIsotope ( String elementSymbol, int massNumber )

cdk-1.4.19.jar, NNLonePair.class
package org.openscience.cdk.nonotify
NNLonePair.addListener ( IChemObjectListener col ) :  void
NNLonePair.getBuilder ( ) :  IChemObjectBuilder
NNLonePair.NNLonePair ( )
NNLonePair.NNLonePair ( IAtom atom )

cdk-1.4.19.jar, NNMapping.class
package org.openscience.cdk.nonotify
NNMapping.addListener ( IChemObjectListener col ) :  void
NNMapping.getBuilder ( ) :  IChemObjectBuilder
NNMapping.NNMapping ( IChemObject objectOne, IChemObject objectTwo )

cdk-1.4.19.jar, NNMolecularFormula.class
package org.openscience.cdk.nonotify
NNMolecularFormula.getBuilder ( ) :  IChemObjectBuilder
NNMolecularFormula.NNMolecularFormula ( )

cdk-1.4.19.jar, NNMolecularFormulaSet.class
package org.openscience.cdk.nonotify
NNMolecularFormulaSet.getBuilder ( ) :  IChemObjectBuilder
NNMolecularFormulaSet.NNMolecularFormulaSet ( )
NNMolecularFormulaSet.NNMolecularFormulaSet ( IMolecularFormula formula )

cdk-1.4.19.jar, NNMolecule.class
package org.openscience.cdk.nonotify
NNMolecule.addListener ( IChemObjectListener col ) :  void
NNMolecule.getBuilder ( ) :  IChemObjectBuilder
NNMolecule.NNMolecule ( )
NNMolecule.NNMolecule ( IAtomContainer container )
NNMolecule.NNMolecule ( int atomCount, int bondCount, int lonePairCount, int singleElectronCount )

cdk-1.4.19.jar, NNMoleculeSet.class
package org.openscience.cdk.nonotify
NNMoleculeSet.addListener ( IChemObjectListener col ) :  void
NNMoleculeSet.getBuilder ( ) :  IChemObjectBuilder
NNMoleculeSet.NNMoleculeSet ( )

cdk-1.4.19.jar, NNMonomer.class
package org.openscience.cdk.nonotify
NNMonomer.addListener ( IChemObjectListener col ) :  void
NNMonomer.getBuilder ( ) :  IChemObjectBuilder
NNMonomer.NNMonomer ( )

cdk-1.4.19.jar, NNPDBAtom.class
package org.openscience.cdk.nonotify
NNPDBAtom.addListener ( IChemObjectListener col ) :  void
NNPDBAtom.getBuilder ( ) :  IChemObjectBuilder
NNPDBAtom.NNPDBAtom ( IElement element )
NNPDBAtom.NNPDBAtom ( String elementSymbol )
NNPDBAtom.NNPDBAtom ( String elementSymbol, Point3d point3d )

cdk-1.4.19.jar, NNPDBMonomer.class
package org.openscience.cdk.nonotify
NNPDBMonomer.addListener ( IChemObjectListener col ) :  void
NNPDBMonomer.getBuilder ( ) :  IChemObjectBuilder
NNPDBMonomer.NNPDBMonomer ( )

cdk-1.4.19.jar, NNPDBPolymer.class
package org.openscience.cdk.nonotify
NNPDBPolymer.addListener ( IChemObjectListener col ) :  void
NNPDBPolymer.getBuilder ( ) :  IChemObjectBuilder
NNPDBPolymer.NNPDBPolymer ( )

cdk-1.4.19.jar, NNPDBStructure.class
package org.openscience.cdk.nonotify
NNPDBStructure.addListener ( IChemObjectListener col ) :  void
NNPDBStructure.getBuilder ( ) :  IChemObjectBuilder
NNPDBStructure.NNPDBStructure ( )

cdk-1.4.19.jar, NNPolymer.class
package org.openscience.cdk.nonotify
NNPolymer.addListener ( IChemObjectListener col ) :  void
NNPolymer.getBuilder ( ) :  IChemObjectBuilder
NNPolymer.NNPolymer ( )

cdk-1.4.19.jar, NNPseudoAtom.class
package org.openscience.cdk.nonotify
NNPseudoAtom.addListener ( IChemObjectListener col ) :  void
NNPseudoAtom.getBuilder ( ) :  IChemObjectBuilder
NNPseudoAtom.NNPseudoAtom ( )
NNPseudoAtom.NNPseudoAtom ( IAtom atom )
NNPseudoAtom.NNPseudoAtom ( IElement element )
NNPseudoAtom.NNPseudoAtom ( String label )
NNPseudoAtom.NNPseudoAtom ( String label, Point2d point2d )
NNPseudoAtom.NNPseudoAtom ( String label, Point3d point3d )

cdk-1.4.19.jar, NNReaction.class
package org.openscience.cdk.nonotify
NNReaction.addListener ( IChemObjectListener col ) :  void
NNReaction.getBuilder ( ) :  IChemObjectBuilder
NNReaction.NNReaction ( )

cdk-1.4.19.jar, NNReactionScheme.class
package org.openscience.cdk.nonotify
NNReactionScheme.addListener ( IChemObjectListener col ) :  void
NNReactionScheme.getBuilder ( ) :  IChemObjectBuilder
NNReactionScheme.NNReactionScheme ( )

cdk-1.4.19.jar, NNReactionSet.class
package org.openscience.cdk.nonotify
NNReactionSet.addListener ( IChemObjectListener col ) :  void
NNReactionSet.getBuilder ( ) :  IChemObjectBuilder
NNReactionSet.NNReactionSet ( )

cdk-1.4.19.jar, NNRing.class
package org.openscience.cdk.nonotify
NNRing.addListener ( IChemObjectListener col ) :  void
NNRing.getBuilder ( ) :  IChemObjectBuilder
NNRing.NNRing ( )
NNRing.NNRing ( IAtomContainer atomContainer )
NNRing.NNRing ( int ringSize )
NNRing.NNRing ( int ringSize, String elementSymbol )

cdk-1.4.19.jar, NNRingSet.class
package org.openscience.cdk.nonotify
NNRingSet.addListener ( IChemObjectListener col ) :  void
NNRingSet.getBuilder ( ) :  IChemObjectBuilder
NNRingSet.NNRingSet ( )

cdk-1.4.19.jar, NNSingleElectron.class
package org.openscience.cdk.nonotify
NNSingleElectron.addListener ( IChemObjectListener col ) :  void
NNSingleElectron.getBuilder ( ) :  IChemObjectBuilder
NNSingleElectron.NNSingleElectron ( )
NNSingleElectron.NNSingleElectron ( IAtom atom )

cdk-1.4.19.jar, NNStrand.class
package org.openscience.cdk.nonotify
NNStrand.addListener ( IChemObjectListener col ) :  void
NNStrand.getBuilder ( ) :  IChemObjectBuilder
NNStrand.NNStrand ( )

cdk-1.4.19.jar, NomParser.class
package org.openscience.cdk.iupac.parser
NomParser.generate ( String stringToParse ) [static] :  Molecule
NomParser.NomParser ( InputStream stream, String encoding )
NomParser.ReInit ( InputStream stream, String encoding ) :  void

cdk-1.4.19.jar, NoNotificationChemObjectBuilder.class
package org.openscience.cdk.nonotify
NoNotificationChemObjectBuilder.getInstance ( ) [static] :  IChemObjectBuilder
NoNotificationChemObjectBuilder.newInstance ( Class clazz, Object[ ] params ) :  ICDKObject

cdk-1.4.19.jar, Offset.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.Offset.AtomNumberGenerator.Offset ( )
AtomNumberGenerator.Offset.getDefault ( ) :  Object
AtomNumberGenerator.Offset.getDefault ( ) :  Vector2d

cdk-1.4.19.jar, Order.class
package org.openscience.cdk.interfaces
IBond.Order.numeric ( ) :  Integer

cdk-1.4.19.jar, PathTools.class
package org.openscience.cdk.graph
PathTools.breadthFirstSearch ( IAtomContainer atomContainer, List sphere, IMolecule molecule ) [static] :  void
PathTools.breadthFirstSearch ( IAtomContainer atomContainer, List sphere, IMolecule molecule, int max ) [static] :  void

cdk-1.4.19.jar, PDBWriter.class
package org.openscience.cdk.io
PDBWriter.writeMolecule ( IMolecule molecule ) :  void

cdk-1.4.19.jar, PiBondingMovementReaction.class
package org.openscience.cdk.reaction.type
PiBondingMovementReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, PiContactDetectionDescriptor.class
package org.openscience.cdk.qsar.descriptors.atompair
PiContactDetectionDescriptor.calculate ( IAtom first, IAtom second, IAtomContainer atomContainer ) :  DescriptorValue
PiContactDetectionDescriptor.getDescriptorNames ( ) :  String[ ]
PiContactDetectionDescriptor.getParameterNames ( ) :  String[ ]
PiContactDetectionDescriptor.getParameters ( ) :  Object[ ]
PiContactDetectionDescriptor.getParameterType ( String name ) :  Object
PiContactDetectionDescriptor.getSpecification ( ) :  DescriptorSpecification
PiContactDetectionDescriptor.PiContactDetectionDescriptor ( )
PiContactDetectionDescriptor.setParameters ( Object[ ] params ) :  void

cdk-1.4.19.jar, ProductsBoxGenerator.class
package org.openscience.cdk.renderer.generators
ProductsBoxGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
ProductsBoxGenerator.generate ( IReaction reaction, RendererModel model ) :  IRenderingElement
ProductsBoxGenerator.getParameters ( ) :  List
ProductsBoxGenerator.ProductsBoxGenerator ( )

cdk-1.4.19.jar, PubChemXMLHelper.class
package org.openscience.cdk.io.pubchemxml
PubChemXMLHelper.parseAtomCharges ( XmlPullParser parser, IMolecule molecule ) :  void
PubChemXMLHelper.parseAtomElements ( XmlPullParser parser, IMolecule molecule ) :  void
PubChemXMLHelper.parseCompoundsBlock ( XmlPullParser parser ) :  IMoleculeSet
PubChemXMLHelper.parseMolecule ( XmlPullParser parser, IChemObjectBuilder builder ) :  IMolecule
PubChemXMLHelper.parserAtomBlock ( XmlPullParser parser, IMolecule molecule ) :  void
PubChemXMLHelper.parserBondBlock ( XmlPullParser parser, IMolecule molecule ) :  void
PubChemXMLHelper.parserCompoundInfoData ( XmlPullParser parser, IMolecule molecule ) :  void
PubChemXMLHelper.parserCoordBlock ( XmlPullParser parser, IMolecule molecule ) :  void

cdk-1.4.19.jar, RadicalChargeSiteInitiationHReaction.class
package org.openscience.cdk.reaction.type
RadicalChargeSiteInitiationHReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalChargeSiteInitiationReaction.class
package org.openscience.cdk.reaction.type
RadicalChargeSiteInitiationReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalGenerator.class
package org.openscience.cdk.renderer.generators
RadicalGenerator.generate ( IAtomContainer container, RendererModel model ) :  IRenderingElement
RadicalGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
RadicalGenerator.getParameters ( ) :  List
RadicalGenerator.RadicalGenerator ( )

cdk-1.4.19.jar, RadicalSiteHrAlphaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteHrAlphaReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteHrBetaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteHrBetaReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteHrDeltaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteHrDeltaReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteHrGammaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteHrGammaReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteInitiationHReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteInitiationHReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteInitiationReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteInitiationReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteIonizationMechanism.class
package org.openscience.cdk.reaction.mechanism
RadicalSiteIonizationMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, RadicalSiteRearrangementMechanism.class
package org.openscience.cdk.reaction.mechanism
RadicalSiteRearrangementMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, RadicalSiteRrAlphaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteRrAlphaReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteRrBetaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteRrBetaReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteRrDeltaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteRrDeltaReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RadicalSiteRrGammaReaction.class
package org.openscience.cdk.reaction.type
RadicalSiteRrGammaReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RandomGenerator.class
package org.openscience.cdk.structgen
RandomGenerator.getMolecule ( ) :  IMolecule
RandomGenerator.proposeStructure ( ) :  IMolecule
RandomGenerator.RandomGenerator ( IMolecule molecule )
RandomGenerator.setMolecule ( IMolecule molecule ) :  void

cdk-1.4.19.jar, ReactantsBoxGenerator.class
package org.openscience.cdk.renderer.generators
ReactantsBoxGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
ReactantsBoxGenerator.generate ( IReaction reaction, RendererModel model ) :  IRenderingElement
ReactantsBoxGenerator.getParameters ( ) :  List
ReactantsBoxGenerator.ReactantsBoxGenerator ( )

cdk-1.4.19.jar, Reaction.class
package org.openscience.cdk
Reaction.addAgent ( IMolecule agent ) :  void
Reaction.addProduct ( IMolecule product ) :  void
Reaction.addProduct ( IMolecule product, Double coefficient ) :  void
Reaction.addReactant ( IMolecule reactant ) :  void
Reaction.addReactant ( IMolecule reactant, Double coefficient ) :  void
Reaction.getAgents ( ) :  IMoleculeSet
Reaction.getProductCoefficient ( IMolecule product ) :  Double
Reaction.getProducts ( ) :  IMoleculeSet
Reaction.getReactantCoefficient ( IMolecule reactant ) :  Double
Reaction.getReactants ( ) :  IMoleculeSet
Reaction.setProductCoefficient ( IMolecule product, Double coefficient ) :  boolean
Reaction.setProducts ( IMoleculeSet setOfMolecules ) :  void
Reaction.setReactantCoefficient ( IMolecule reactant, Double coefficient ) :  boolean
Reaction.setReactants ( IMoleculeSet setOfMolecules ) :  void
package org.openscience.cdk.silent
Reaction.addAgent ( IMolecule agent ) :  void
Reaction.addProduct ( IMolecule product ) :  void
Reaction.addProduct ( IMolecule product, Double coefficient ) :  void
Reaction.addReactant ( IMolecule reactant ) :  void
Reaction.addReactant ( IMolecule reactant, Double coefficient ) :  void
Reaction.getAgents ( ) :  IMoleculeSet
Reaction.getProductCoefficient ( IMolecule product ) :  Double
Reaction.getProducts ( ) :  IMoleculeSet
Reaction.getReactantCoefficient ( IMolecule reactant ) :  Double
Reaction.getReactants ( ) :  IMoleculeSet
Reaction.setProductCoefficient ( IMolecule product, Double coefficient ) :  boolean
Reaction.setProducts ( IMoleculeSet setOfMolecules ) :  void
Reaction.setReactantCoefficient ( IMolecule reactant, Double coefficient ) :  boolean
Reaction.setReactants ( IMoleculeSet setOfMolecules ) :  void

cdk-1.4.19.jar, ReactionArrowGenerator.class
package org.openscience.cdk.renderer.generators
ReactionArrowGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
ReactionArrowGenerator.generate ( IReaction reaction, RendererModel model ) :  IRenderingElement
ReactionArrowGenerator.getParameters ( ) :  List
ReactionArrowGenerator.ReactionArrowGenerator ( )

cdk-1.4.19.jar, ReactionBoxGenerator.class
package org.openscience.cdk.renderer.generators
ReactionBoxGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
ReactionBoxGenerator.generate ( IReaction reaction, RendererModel model ) :  IRenderingElement
ReactionBoxGenerator.getParameters ( ) :  List
ReactionBoxGenerator.ReactionBoxGenerator ( )

cdk-1.4.19.jar, ReactionManipulator.class
package org.openscience.cdk.tools.manipulator
ReactionManipulator.getAllMolecules ( IReaction reaction ) [static] :  IMoleculeSet
ReactionManipulator.getAllProducts ( IReaction reaction ) [static] :  IMoleculeSet
ReactionManipulator.getAllReactants ( IReaction reaction ) [static] :  IMoleculeSet

cdk-1.4.19.jar, ReactionPlusGenerator.class
package org.openscience.cdk.renderer.generators
ReactionPlusGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
ReactionPlusGenerator.generate ( IReaction reaction, RendererModel model ) :  IRenderingElement
ReactionPlusGenerator.getParameters ( ) :  List
ReactionPlusGenerator.ReactionPlusGenerator ( )

cdk-1.4.19.jar, ReactionRenderer.class
package org.openscience.cdk.renderer
ReactionRenderer.calculateDiagramBounds ( IChemObject x0 ) :  Rectangle
ReactionRenderer.calculateDiagramBounds ( IReaction reaction ) :  Rectangle
ReactionRenderer.calculateScaleForBondLength ( double modelBondLength ) :  double
ReactionRenderer.generateDiagram ( IChemObject x0 ) :  IRenderingElement
ReactionRenderer.generateDiagram ( IReaction reaction ) :  IRenderingElement
ReactionRenderer.getGenerators ( ) :  List
ReactionRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) :  Rectangle
ReactionRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) :  void
ReactionRenderer.paint ( IReaction reaction, IDrawVisitor drawVisitor ) :  Rectangle
ReactionRenderer.paint ( IReaction reaction, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) :  void
ReactionRenderer.ReactionRenderer ( List generators, IFontManager fontManager )
ReactionRenderer.ReactionRenderer ( List generators, List reactionGenerators, IFontManager fontManager )
ReactionRenderer.ReactionRenderer ( RendererModel rendererModel, List generators, IFontManager fontManager )
ReactionRenderer.setScale ( IChemObject x0 ) :  void
ReactionRenderer.setScale ( IReaction reaction ) :  void
ReactionRenderer.setup ( IChemObject x0, Rectangle x1 ) :  void
ReactionRenderer.setup ( IReaction reaction, Rectangle screen ) :  void

cdk-1.4.19.jar, ReactionSceneGenerator.class
package org.openscience.cdk.renderer.generators
ReactionSceneGenerator.generate ( IChemObject x0, RendererModel x1 ) :  IRenderingElement
ReactionSceneGenerator.generate ( IReaction reaction, RendererModel model ) :  IRenderingElement
ReactionSceneGenerator.getParameters ( ) :  List
ReactionSceneGenerator.ReactionSceneGenerator ( )

cdk-1.4.19.jar, ReactionSchemeManipulator.class
package org.openscience.cdk.tools.manipulator
ReactionSchemeManipulator.getAllMolecules ( IReactionScheme scheme ) [static] :  IMoleculeSet
ReactionSchemeManipulator.getAllMolecules ( IReactionScheme scheme, IMoleculeSet molSet ) [static] :  IMoleculeSet
ReactionSchemeManipulator.getMoleculeSet ( IMolecule origenMol, IMolecule finalMol, IReactionScheme reactionScheme ) [static] :  ArrayList

cdk-1.4.19.jar, ReactionSet.class
package org.openscience.cdk
ReactionSet.isEmpty ( ) :  boolean
package org.openscience.cdk.silent
ReactionSet.isEmpty ( ) :  boolean

cdk-1.4.19.jar, ReactionSetManipulator.class
package org.openscience.cdk.tools.manipulator
ReactionSetManipulator.getAllMolecules ( IReactionSet set ) [static] :  IMoleculeSet

cdk-1.4.19.jar, ReactionSetRenderer.class
package org.openscience.cdk.renderer
ReactionSetRenderer.calculateDiagramBounds ( IChemObject x0 ) :  Rectangle
ReactionSetRenderer.calculateDiagramBounds ( IReactionSet reactionSet ) :  Rectangle
ReactionSetRenderer.calculateScaleForBondLength ( double modelBondLength ) :  double
ReactionSetRenderer.getGenerators ( ) :  List
ReactionSetRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) :  Rectangle
ReactionSetRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) :  void
ReactionSetRenderer.paint ( IReactionSet reactionSet, IDrawVisitor drawVisitor ) :  Rectangle
ReactionSetRenderer.paint ( IReactionSet reactionSet, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) :  void
ReactionSetRenderer.ReactionSetRenderer ( List generators, IFontManager fontManager )
ReactionSetRenderer.ReactionSetRenderer ( List generators, List reactionGenerators, IFontManager fontManager )
ReactionSetRenderer.ReactionSetRenderer ( RendererModel rendererModel, List generators, IFontManager fontManager )
ReactionSetRenderer.ReactionSetRenderer ( RendererModel rendererModel, List generators, List reactionGenerators, IFontManager fontManager )
ReactionSetRenderer.setScale ( IChemObject x0 ) :  void
ReactionSetRenderer.setScale ( IReactionSet reactionSet ) :  void
ReactionSetRenderer.setup ( IChemObject x0, Rectangle x1 ) :  void
ReactionSetRenderer.setup ( IReactionSet reactionSet, Rectangle screen ) :  void

cdk-1.4.19.jar, RearrangementAnionReaction.class
package org.openscience.cdk.reaction.type
RearrangementAnionReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RearrangementCationReaction.class
package org.openscience.cdk.reaction.type
RearrangementCationReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RearrangementChargeMechanism.class
package org.openscience.cdk.reaction.mechanism
RearrangementChargeMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, RearrangementLonePairReaction.class
package org.openscience.cdk.reaction.type
RearrangementLonePairReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RearrangementRadicalReaction.class
package org.openscience.cdk.reaction.type
RearrangementRadicalReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, RemovingSEofBMechanism.class
package org.openscience.cdk.reaction.mechanism
RemovingSEofBMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, RemovingSEofNBMechanism.class
package org.openscience.cdk.reaction.mechanism
RemovingSEofNBMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, RingPlacer.class
package org.openscience.cdk.layout
RingPlacer.getMolecule ( ) :  IMolecule
RingPlacer.setMolecule ( IMolecule molecule ) :  void

cdk-1.4.19.jar, SDFWriter.class
package org.openscience.cdk.io
SDFWriter.SDFWriter ( OutputStream output, Set propertiesToWrite )
SDFWriter.SDFWriter ( Set propertiesToWrite )
SDFWriter.SDFWriter ( Writer out, Set propertiesToWrite )

cdk-1.4.19.jar, SharingAnionReaction.class
package org.openscience.cdk.reaction.type
SharingAnionReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, SharingChargeDBReaction.class
package org.openscience.cdk.reaction.type
SharingChargeDBReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, SharingChargeSBReaction.class
package org.openscience.cdk.reaction.type
SharingChargeSBReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, SharingElectronMechanism.class
package org.openscience.cdk.reaction.mechanism
SharingElectronMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, SharingLonePairReaction.class
package org.openscience.cdk.reaction.type
SharingLonePairReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, ShowAtomAtomMapping.class
package org.openscience.cdk.renderer.generators
MappingGenerator.ShowAtomAtomMapping.getDefault ( ) :  Boolean
MappingGenerator.ShowAtomAtomMapping.getDefault ( ) :  Object
MappingGenerator.ShowAtomAtomMapping.MappingGenerator.ShowAtomAtomMapping ( )

cdk-1.4.19.jar, ShowAtomTypeNames.class
package org.openscience.cdk.renderer.generators
ExtendedAtomGenerator.ShowAtomTypeNames.ExtendedAtomGenerator.ShowAtomTypeNames ( )
ExtendedAtomGenerator.ShowAtomTypeNames.getDefault ( ) :  Boolean
ExtendedAtomGenerator.ShowAtomTypeNames.getDefault ( ) :  Object

cdk-1.4.19.jar, ShowImplicitHydrogens.class
package org.openscience.cdk.renderer.generators
ExtendedAtomGenerator.ShowImplicitHydrogens.ExtendedAtomGenerator.ShowImplicitHydrogens ( )
ExtendedAtomGenerator.ShowImplicitHydrogens.getDefault ( ) :  Boolean
ExtendedAtomGenerator.ShowImplicitHydrogens.getDefault ( ) :  Object

cdk-1.4.19.jar, ShowReactionBoxes.class
package org.openscience.cdk.renderer.generators
ReactionSceneGenerator.ShowReactionBoxes.getDefault ( ) :  Boolean
ReactionSceneGenerator.ShowReactionBoxes.getDefault ( ) :  Object
ReactionSceneGenerator.ShowReactionBoxes.ReactionSceneGenerator.ShowReactionBoxes ( )

cdk-1.4.19.jar, SimpleCharStream.class
package org.openscience.cdk.iupac.parser
SimpleCharStream.getTabSize ( int i ) :  int
SimpleCharStream.ReInit ( InputStream dstream, String encoding ) :  void
SimpleCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn ) :  void
SimpleCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize ) :  void
SimpleCharStream.setTabSize ( int i ) :  void
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding )
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding, int startline, int startcolumn )
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize )
package org.openscience.cdk.smiles.smarts.parser
SimpleCharStream.getTabSize ( int i ) :  int
SimpleCharStream.ReInit ( InputStream dstream, String encoding ) :  void
SimpleCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn ) :  void
SimpleCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize ) :  void
SimpleCharStream.setTabSize ( int i ) :  void
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding )
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding, int startline, int startcolumn )
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize )

cdk-1.4.19.jar, SingleStructureRandomGenerator.class
package org.openscience.cdk.structgen
SingleStructureRandomGenerator.generate ( ) :  IMolecule

cdk-1.4.19.jar, SMARTSParser.class
package org.openscience.cdk.smiles.smarts.parser
SMARTSParser.ReInit ( InputStream stream, String encoding ) :  void
SMARTSParser.SMARTSParser ( InputStream stream, String encoding )

cdk-1.4.19.jar, SmilesParser.class
package org.openscience.cdk.smiles
SmilesParser.parseSmiles ( String smiles ) :  IMolecule

cdk-1.4.19.jar, SMILESReader.class
package org.openscience.cdk.io
SMILESReader.SMILESReader ( Reader input, IChemObjectBuilder builder )

cdk-1.4.19.jar, SMILESWriter.class
package org.openscience.cdk.io
SMILESWriter.writeMolecule ( IMolecule molecule ) :  void
SMILESWriter.writeMoleculeSet ( IMoleculeSet som ) :  void

cdk-1.4.19.jar, SMSDNormalizer.class
package org.openscience.cdk.normalize
SMSDNormalizer.makeDeepCopy ( IAtomContainer container ) [static] :  IMolecule

cdk-1.4.19.jar, StructureDiagramGenerator.class
package org.openscience.cdk.layout
StructureDiagramGenerator.getBondLength ( ) :  double
StructureDiagramGenerator.getMolecule ( ) :  IMolecule
StructureDiagramGenerator.setMolecule ( IMolecule mol, boolean clone ) :  void
StructureDiagramGenerator.setMolecule ( IMolecule molecule ) :  void
StructureDiagramGenerator.StructureDiagramGenerator ( IMolecule molecule )

cdk-1.4.19.jar, StructureResonanceGenerator.class
package org.openscience.cdk.tools
StructureResonanceGenerator.getContainer ( IMolecule molecule, IAtom atom ) :  IAtomContainer
StructureResonanceGenerator.getContainer ( IMolecule molecule, IBond bond ) :  IAtomContainer
StructureResonanceGenerator.getContainers ( IMolecule molecule ) :  IAtomContainerSet
StructureResonanceGenerator.getStructures ( IMolecule molecule ) :  IMoleculeSet

cdk-1.4.19.jar, SymbolSetQueryAtom.class
package org.openscience.cdk.isomorphism.matchers
SymbolSetQueryAtom.getSymbolSet ( ) :  HashSet

cdk-1.4.19.jar, TautomerizationMechanism.class
package org.openscience.cdk.reaction.mechanism
TautomerizationMechanism.initiate ( IMoleculeSet moleculeSet, ArrayList atomList, ArrayList bondList ) :  IReaction

cdk-1.4.19.jar, TautomerizationReaction.class
package org.openscience.cdk.reaction.type
TautomerizationReaction.initiate ( IMoleculeSet reactants, IMoleculeSet agents ) :  IReactionSet

cdk-1.4.19.jar, TemplateExtractor.class
package org.openscience.cdk.modeling.builder3d
TemplateExtractor.removeLoopBonds ( IMolecule molecule, int position ) :  IMolecule
TemplateExtractor.writeChemModel ( IMoleculeSet som, String file, String endFix ) :  void

cdk-1.4.19.jar, TetrahedralChirality.class
package org.openscience.cdk.stereo
TetrahedralChirality.map ( Map atoms, Map bonds ) :  ITetrahedralChirality
TetrahedralChirality.map ( Map x0, Map x1 ) :  IStereoElement

cdk-1.4.19.jar, Token.class
package org.openscience.cdk.iupac.parser
Token.getValue ( ) :  Object
Token.newToken ( int ofKind, String image ) [static] :  Token
Token.Token ( int kind )
Token.Token ( int kind, String image )
package org.openscience.cdk.smiles.smarts.parser
Token.getValue ( ) :  Object
Token.newToken ( int ofKind, String image ) [static] :  Token
Token.Token ( int kind )
Token.Token ( int kind, String image )

cdk-1.4.19.jar, VABCVolume.class
package org.openscience.cdk.geometry.volume
VABCVolume.calculate ( IMolecule molecule ) [static] :  double

cdk-1.4.19.jar, ValidatorEngine.class
package org.openscience.cdk.validate
ValidatorEngine.validateMolecule ( IMolecule subject ) :  ValidationReport
ValidatorEngine.validateMoleculeSet ( IMoleculeSet subject ) :  ValidationReport

cdk-1.4.19.jar, VicinitySampler.class
package org.openscience.cdk.structgen
VicinitySampler.sample ( IMolecule ac ) [static] :  List

cdk-1.4.19.jar, WillDrawAtomNumbers.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.WillDrawAtomNumbers.AtomNumberGenerator.WillDrawAtomNumbers ( )
AtomNumberGenerator.WillDrawAtomNumbers.getDefault ( ) :  Boolean
AtomNumberGenerator.WillDrawAtomNumbers.getDefault ( ) :  Object

cdk-1.4.19.jar, XYZWriter.class
package org.openscience.cdk.io
XYZWriter.writeMolecule ( IMolecule mol ) :  void

to the top

Problems with Data Types, High Severity (133)

	Change	Effect
1	Type of field setOfMolecules has been changed from interfaces.IMoleculeSet to interfaces.IAtomContainerSet.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	Type of field agents has been changed from interfaces.IMoleculeSet to interfaces.IAtomContainerSet.	A client program may be interrupted by NoSuchFieldError exception.
2	Type of field products has been changed from interfaces.IMoleculeSet to interfaces.IAtomContainerSet.	A client program may be interrupted by NoSuchFieldError exception.
3	Type of field reactants has been changed from interfaces.IMoleculeSet to interfaces.IAtomContainerSet.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	Field FLEROVIUM of type org.openscience.cdk.interfaces.IElement has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.
2	Field LIVERMORIUM of type org.openscience.cdk.interfaces.IElement has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	Abstract method isEmpty ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
2	Abstract method setStereoElements ( List ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Abstract method isEmpty ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Abstract method map ( Map, Map ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Abstract method getMoleculeSet ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
2	Abstract method isEmpty ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
3	Abstract method setMoleculeSet ( IMoleculeSet ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	This interface has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This interface has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This interface has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	Removed super-interface IMolecule.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Abstract method addAgent ( IMolecule ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
2	Abstract method addProduct ( IMolecule ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
3	Abstract method addProduct ( IMolecule, Double ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
4	Abstract method addReactant ( IMolecule ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
5	Abstract method addReactant ( IMolecule, Double ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
6	Abstract method getAgents ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
7	Abstract method getProductCoefficient ( IMolecule ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
8	Abstract method getProducts ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
9	Abstract method getReactantCoefficient ( IMolecule ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
10	Abstract method getReactants ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
11	Abstract method setProductCoefficient ( IMolecule, Double ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
12	Abstract method setProducts ( IMoleculeSet ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
13	Abstract method setReactantCoefficient ( IMolecule, Double ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
14	Abstract method setReactants ( IMoleculeSet ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Abstract method isEmpty ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Abstract method isEmpty ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Abstract method map ( Map, Map ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Abstract method map ( Map, Map ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Type of field currentMoleculeSet has been changed from org.openscience.cdk.interfaces.IMoleculeSet to org.openscience.cdk.interfaces.IAtomContainerSet.	A client program may be interrupted by NoSuchFieldError exception.
2	Field atomAromaticities of type java.util.List has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	Field tabSize of type int has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	Removed super-interface java.io.Serializable.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

cdk-1.4.19.jar
package org.openscience.cdk
[+] ChemModel (1)
[+] Molecule (1)
[+] MoleculeSet (1)
[+] Reaction (3)

package org.openscience.cdk.aromaticity
[+] DoubleBondAcceptingAromaticityDetector (1)

package org.openscience.cdk.config
[+] Elements (2)

package org.openscience.cdk.debug
[+] DebugMolecule (1)
[+] DebugMoleculeSet (1)

package org.openscience.cdk.interfaces
[+] IAtomContainer (2)
[+] IAtomContainerSet (1)
[+] IAtomParity (1)
[+] IChemModel (3)
[+] IDoubleBondStereochemistry (1)
[+] IDoubleBondStereochemistry.Conformation (1)
[+] IMolecule (1)
[+] IMoleculeSet (1)
[+] IPolymer (1)
[+] IReaction (14)
[+] IReactionSet (1)
[+] IRingSet (1)
[+] IStereoElement (1)
[+] ITetrahedralChirality (1)

package org.openscience.cdk.io.cml
[+] CMLCoreModule (2)

package org.openscience.cdk.iupac.parser
[+] SimpleCharStream (1)
[+] Token (1)

package org.openscience.cdk.nonotify
[+] NNAdductFormula (1)
[+] NNAminoAcid (1)
[+] NNAtom (1)
[+] NNAtomContainer (1)
[+] NNAtomContainerSet (1)
[+] NNAtomParity (1)
[+] NNAtomType (1)
[+] NNBioPolymer (1)
[+] NNBond (1)
[+] NNChemFile (1)
[+] NNChemModel (1)
[+] NNChemObject (1)
[+] NNChemSequence (1)
[+] NNCrystal (1)
[+] NNElectronContainer (1)
[+] NNElement (1)
[+] NNFragmentAtom (1)
[+] NNIsotope (1)
[+] NNLonePair (1)
[+] NNMapping (1)
[+] NNMolecularFormula (1)
[+] NNMolecularFormulaSet (1)
[+] NNMolecule (1)
[+] NNMoleculeSet (1)
[+] NNMonomer (1)
[+] NNPDBAtom (1)
[+] NNPDBMonomer (1)
[+] NNPDBPolymer (1)
[+] NNPDBStructure (1)
[+] NNPolymer (1)
[+] NNPseudoAtom (1)
[+] NNReaction (1)
[+] NNReactionScheme (1)
[+] NNReactionSet (1)
[+] NNRing (1)
[+] NNRingSet (1)
[+] NNSingleElectron (1)
[+] NNStrand (1)
[+] NoNotificationChemObjectBuilder (1)

package org.openscience.cdk.qsar.descriptors.atompair
[+] PiContactDetectionDescriptor (1)

package org.openscience.cdk.reaction
[+] IReactionMechanism (1)
[+] IReactionProcess (1)

package org.openscience.cdk.renderer
[+] ChemModelRenderer (1)
[+] MoleculeSetRenderer (1)
[+] ReactionRenderer (1)
[+] ReactionSetRenderer (1)

package org.openscience.cdk.renderer.elements
[+] AtomMassSymbolElement (1)

package org.openscience.cdk.renderer.generators
[+] AtomContainerBoundsGenerator (1)
[+] AtomMassGenerator (1)
[+] AtomNumberGenerator (1)
[+] AtomNumberGenerator.AtomColorer (1)
[+] AtomNumberGenerator.AtomNumberTextColor (1)
[+] AtomNumberGenerator.ColorByType (1)
[+] AtomNumberGenerator.Offset (1)
[+] AtomNumberGenerator.WillDrawAtomNumbers (1)
[+] BoundsGenerator (1)
[+] BoundsGenerator.BoundsColor (1)
[+] ExtendedAtomGenerator (1)
[+] ExtendedAtomGenerator.ShowAtomTypeNames (1)
[+] ExtendedAtomGenerator.ShowImplicitHydrogens (1)
[+] LonePairGenerator (1)
[+] MappingGenerator (1)
[+] MappingGenerator.AtomAtomMappingLineColor (1)
[+] MappingGenerator.MappingLineWidth (1)
[+] MappingGenerator.ShowAtomAtomMapping (1)
[+] ProductsBoxGenerator (1)
[+] RadicalGenerator (1)
[+] ReactantsBoxGenerator (1)
[+] ReactionArrowGenerator (1)
[+] ReactionBoxGenerator (1)
[+] ReactionPlusGenerator (1)
[+] ReactionSceneGenerator (1)
[+] ReactionSceneGenerator.ArrowHeadWidth (1)
[+] ReactionSceneGenerator.ShowReactionBoxes (1)

package org.openscience.cdk.silent
[+] ChemModel (1)
[+] Molecule (1)
[+] MoleculeSet (1)
[+] Reaction (3)

package org.openscience.cdk.smiles
[+] FixBondOrdersTool (1)

package org.openscience.cdk.smiles.smarts.parser
[+] SimpleCharStream (1)
[+] SMARTSParserTokenManager (1)
[+] Token (1)

package org.openscience.cdk.smsd.interfaces
[+] AbstractMCS (1)

package org.openscience.cdk.stereo
[+] DoubleBondStereochemistry (1)

package org.openscience.cdk.validate
[+] IValidator (2)

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Problems with Methods, High Severity (12)

cdk-1.4.19.jar, JJTSMARTSParserState
package org.openscience.cdk.smiles.smarts.parser
[+] JJTSMARTSParserState.clearNodeScope ( Node n ) :  void (1)
[+] JJTSMARTSParserState.closeNodeScope ( Node n, boolean condition ) :  void (1)
[+] JJTSMARTSParserState.closeNodeScope ( Node n, int num ) :  void (1)
[+] JJTSMARTSParserState.nodeArity ( ) :  int (1)
[+] JJTSMARTSParserState.nodeCreated ( ) :  boolean (1)
[+] JJTSMARTSParserState.openNodeScope ( Node n ) :  void (1)
[+] JJTSMARTSParserState.peekNode ( ) :  Node (1)
[+] JJTSMARTSParserState.popNode ( ) :  Node (1)
[+] JJTSMARTSParserState.pushNode ( Node n ) :  void (1)
[+] JJTSMARTSParserState.reset ( ) :  void (1)
[+] JJTSMARTSParserState.rootNode ( ) :  Node (1)

cdk-1.4.19.jar, Tanimoto
package org.openscience.cdk.similarity
[+] Tanimoto.Tanimoto ( ) (1)

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Problems with Data Types, Medium Severity (30)

cdk-1.4.19.jar
package org.openscience.cdk
[+] Polymer (1)

package org.openscience.cdk.interfaces
[+] IChemModel (2)
[+] IReaction (12)

package org.openscience.cdk.isomorphism.matchers
[+] InverseSymbolSetQueryAtom (1)
[+] OrderQueryBond (1)
[+] OrderQueryBondOrderOnly (1)
[+] QueryAtomContainer (1)
[+] RGroupQuery (1)
[+] SymbolAndChargeQueryAtom (1)
[+] SymbolChargeIDQueryAtom (1)
[+] SymbolQueryAtom (1)
[+] SymbolSetQueryAtom (1)

package org.openscience.cdk.isomorphism.matchers.smarts
[+] SMARTSAtom (1)
[+] SMARTSBond (1)

package org.openscience.cdk.libio.md
[+] MDMolecule (1)

package org.openscience.cdk.reaction
[+] IReactionProcess (1)

package org.openscience.cdk.silent
[+] Polymer (1)

package org.openscience.cdk.smiles
[+] InvPair (1)

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Problems with Data Types, Low Severity (37)

cdk-1.4.19.jar
package org.openscience.cdk
[+] AminoAcid (1)
[+] AtomContainer (1)
[+] BioPolymer (1)
[+] CDKConstants (1)
[+] Crystal (1)
[+] Monomer (1)
[+] Polymer (1)
[+] Ring (1)
[+] Strand (1)

package org.openscience.cdk.debug
[+] DebugAminoAcid (1)
[+] DebugAtomContainer (1)
[+] DebugBioPolymer (1)
[+] DebugChemModel (1)
[+] DebugCrystal (1)
[+] DebugMonomer (1)
[+] DebugPolymer (1)
[+] DebugReaction (3)
[+] DebugRing (1)
[+] DebugStrand (1)

package org.openscience.cdk.fingerprint
[+] PubchemFingerprinter (1)

package org.openscience.cdk.graph
[+] AtomContainerPermutor (2)

package org.openscience.cdk.protein.data
[+] PDBMonomer (1)
[+] PDBPolymer (1)

package org.openscience.cdk.qsar
[+] DescriptorEngine (1)

package org.openscience.cdk.silent
[+] AminoAcid (1)
[+] AtomContainer (1)
[+] BioPolymer (1)
[+] Crystal (1)
[+] Monomer (1)
[+] PDBMonomer (1)
[+] PDBPolymer (1)
[+] Polymer (1)
[+] Ring (1)
[+] Strand (1)

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Problems with Methods, Low Severity (2)

cdk-1.4.19.jar, SMARTSParser
package org.openscience.cdk.smiles.smarts.parser
[+] SMARTSParser.parse ( String smarts ) [static] : QueryAtomContainer (1)

cdk-1.4.19.jar, SMARTSQueryTool
package org.openscience.cdk.smiles.smarts
[+] SMARTSQueryTool.SMARTSQueryTool ( String smarts ) (1)

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Other Changes in Data Types (26)

cdk-1.4.19.jar
package org.openscience.cdk.fingerprint
[+] IFingerprinter (1)

package org.openscience.cdk.graph
[+] AtomContainerPermutor (1)

package org.openscience.cdk.interfaces
[+] IPolymer (1)
[+] IReaction (2)

package org.openscience.cdk.io
[+] IChemObjectIO (1)

package org.openscience.cdk.isomorphism.matchers
[+] IQueryBond (1)
[+] QueryAtomContainer (10)

package org.openscience.cdk.iupac.parser
[+] NomParser (1)
[+] ParseException (1)

package org.openscience.cdk.layout
[+] HydrogenPlacer (2)

package org.openscience.cdk.reaction
[+] IReactionMechanism (1)

package org.openscience.cdk.smiles.smarts.parser
[+] ParseException (1)
[+] SMARTSParser (1)

package org.openscience.cdk.validate
[+] IValidator (2)

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Java ARchives (1)

cdk-1.4.19.jar

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	Change	Effect
1	Abstract method getMoleculeSet ( ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method endElement ( CMLStack, String, String, String ) and may not be implemented by old clients.
2	Abstract method setMoleculeSet ( IAtomContainerSet ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method readChemFile ( IChemFile ) and may not be implemented by old clients.

	Change	Effect
1	Abstract method addAgent ( IAtomContainer ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method endElement ( CMLStack, String, String, String ) and may not be implemented by old clients.
2	Abstract method addProduct ( IAtomContainer ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method endElement ( CMLStack, String, String, String ) and may not be implemented by old clients.
3	Abstract method addProduct ( IAtomContainer, Double ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method reverse ( IReaction ) and may not be implemented by old clients.
4	Abstract method addReactant ( IAtomContainer ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method endElement ( CMLStack, String, String, String ) and may not be implemented by old clients.
5	Abstract method addReactant ( IAtomContainer, Double ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method reverse ( IReaction ) and may not be implemented by old clients.
6	Abstract method getAgents ( ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method cdkReactionToCMLReaction ( IReaction, boolean ) and may not be implemented by old clients.
7	Abstract method getProductCoefficient ( IAtomContainer ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method reverse ( IReaction ) and may not be implemented by old clients.
8	Abstract method getProducts ( ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method removeAtomAndConnectedElectronContainers ( IReaction, IAtom ) and may not be implemented by old clients.
9	Abstract method getReactantCoefficient ( IAtomContainer ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method reverse ( IReaction ) and may not be implemented by old clients.
10	Abstract method getReactants ( ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method removeAtomAndConnectedElectronContainers ( IReaction, IAtom ) and may not be implemented by old clients.
11	Abstract method setProducts ( IAtomContainerSet ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method labelReaction ( IReaction, ICanonicalMoleculeLabeller ) and may not be implemented by old clients.
12	Abstract method setReactants ( IAtomContainerSet ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method labelReaction ( IReaction, ICanonicalMoleculeLabeller ) and may not be implemented by old clients.

	Change	Effect
1	Method getAgents ( ) has been moved up type hierarchy to getAgents ( )	Method getAgents ( ) will be called instead of getAgents ( ) in a client program.
2	Method getProducts ( ) has been moved up type hierarchy to getProducts ( )	Method getProducts ( ) will be called instead of getProducts ( ) in a client program.
3	Method getReactants ( ) has been moved up type hierarchy to getReactants ( )	Method getReactants ( ) will be called instead of getReactants ( ) in a client program.

	Change	Effect
1	Added super-class Permutor.	A static field from a super-interface of a client class may hide a field (with the same name) inherited from new super-class and cause IncompatibleClassChangeError exception.
2	Method hasNext ( ) has been moved up type hierarchy to hasNext ( )	Method hasNext ( ) will be called instead of hasNext ( ) in a client program.

	Change	Effect
1	Abstract method setProductCoefficient ( IAtomContainer, Double ) has been added to this interface.	No effect.
2	Abstract method setReactantCoefficient ( IAtomContainer, Double ) has been added to this interface.	No effect.

	Change	Effect
1	Abstract method validateMolecule ( IMolecule ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.
2	Abstract method validateMoleculeSet ( IMoleculeSet ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Field atomCount has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
2	Field atoms has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
3	Field bondCount has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
4	Field bonds has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
5	Field growArraySize has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
6	Field lonePairCount has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
7	Field lonePairs has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
8	Field singleElectronCount has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
9	Field singleElectrons has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
10	Field stereoElements has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.

	Change	Effect
1	Field debug has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
2	Field debug1 has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.

	Change	Effect
1	Abstract method validateMolecule ( IAtomContainer ) has been added to this interface.	No effect.
2	Abstract method validateMoleculeSet ( IAtomContainerSet ) has been added to this interface.	No effect.