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