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WarpCoreEjection - Exception in uk.ac.ebi.centres.exception
 
WarpCoreEjection() - Constructor for exception uk.ac.ebi.centres.exception.WarpCoreEjection
 
WedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
 
WedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.WedgeRule
 
WedgeStereoAnalyser - Class in uk.ac.ebi.reactionblast.stereo.wedge
Analyse the stereo wedges around an atom, to determine if they are correct.
WedgeStereoAnalysisResult - Enum in uk.ac.ebi.reactionblast.stereo.wedge
 
WedgeStereoComparisonResult - Class in uk.ac.ebi.reactionblast.stereo.compare
Tool for comparing chiralities.
WedgeStereoComparisonResult(IAtom, IAtomContainer, WedgeStereoAnalysisResult, IAtom, IAtomContainer, WedgeStereoAnalysisResult) - Constructor for class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
WedgeStereoComparisonTool - Class in uk.ac.ebi.reactionblast.stereo.compare
Tool to check mapped pairs of atoms, to see if they have compatible stereo wedges.
WedgeStereoLifter - Class in uk.ac.ebi.reactionblast.stereo.wedge
'Lifts' the 2D wedge stereo representation into a 3D one.
WedgeStereoLifter() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.WedgeStereoLifter
 
wiggleLineWidth - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
write() - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
write() - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
write() - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
write() - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
write() - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
 
write() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
write() - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
write(IChemObject) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
Writes a IChemObject to the MDL RXN file formated output.
write(IChemObject) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
Writes a IChemObject to the MDL molfile formated output.
writeAtomValue(BufferedWriter, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
 
writeAttributes() - Method in class uk.ac.ebi.centres.io.CytoscapeWriter
 
writeBEMatrix(File, BEMatrix) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.MatrixPrinter
 
writeBMatrix(File) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
writeBMatrix(File) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
writeBMatrix(File) - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
writeBondChanges(File) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
Print the atom changes
writeBondChanges(File) - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
Print the bond changes
writeCompoundFingerPrints() - Method in interface uk.ac.ebi.reactionblast.interfaces.IReactionBuilder
write the fingerprints in a file
writeCompoundInChI() - Method in interface uk.ac.ebi.reactionblast.interfaces.IReactionBuilder
write the InChi into a file
writeEMatrix(File) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
writeEMatrix(File) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
writeEMatrix(File) - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
writeFiles(String, ReactionMechanismTool) - Method in class uk.ac.ebi.aamtool.Annotator
 
writeFormalAtomicCharges(BufferedWriter, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
 
writeFormalIsotope(BufferedWriter, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
 
writeMappingRXN(Reactor, String, String) - Static method in class uk.ac.ebi.reactionblast.mapping.CallableAtomMappingTool
Creates mapping PDFs for all the processed reaction mappings
writeMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
Writes a Molecule to an OutputStream in MDL sdf format.
writeReactionMatrix(File, RMatrix) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.MatrixPrinter
 
writeReactions() - Method in interface uk.ac.ebi.reactionblast.interfaces.IReactionBuilder
write the reaction in a file
writeRGroups(BufferedWriter, List<Integer>) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
 
writeRMatrix(File) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
writeRMatrix(File) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
writeRMatrix(File) - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
writeSgroupProperty(IAtomContainer, BufferedWriter) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
 
writeSif() - Method in class uk.ac.ebi.centres.io.CytoscapeWriter
 
writeSimilarityMatrix(List<SimilarityResult>, String) - Method in class uk.ac.ebi.aamtool.Annotator
 
writeToFile(Image, String, String) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
writeToFile(Image, String, String) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
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