- Feature - Class in uk.ac.ebi.reactionblast.fingerprints
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- Feature(String, double) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.Feature
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- Feature(String) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.Feature
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- FilesystemMoleculeDataSource - Class in uk.ac.ebi.reactionblast.io.filesystem
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- FilesystemMoleculeDataSource(String) - Constructor for class uk.ac.ebi.reactionblast.io.filesystem.FilesystemMoleculeDataSource
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- FilesystemMoleculeDataStore - Class in uk.ac.ebi.reactionblast.io.filesystem
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- FilesystemMoleculeDataStore(String) - Constructor for class uk.ac.ebi.reactionblast.io.filesystem.FilesystemMoleculeDataStore
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- FilesystemReactionDataSource - Class in uk.ac.ebi.reactionblast.io.filesystem
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- FilesystemReactionDataSource(String) - Constructor for class uk.ac.ebi.reactionblast.io.filesystem.FilesystemReactionDataSource
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- FilesystemReactionDataStore - Class in uk.ac.ebi.reactionblast.io.filesystem
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- FilesystemReactionDataStore(String) - Constructor for class uk.ac.ebi.reactionblast.io.filesystem.FilesystemReactionDataStore
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- filledWedgeWidth - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
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- fillMap(Map<Integer, Double>) - Method in class org.openscience.smsd.filters.EnergyFilter
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- fillMap(Map<Integer, Integer>) - Method in class org.openscience.smsd.filters.FragmentFilter
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- fillMap(Map<Integer, T>) - Method in interface org.openscience.smsd.filters.IChemicalFilter
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- fillMap(Map<Integer, Double>) - Method in class org.openscience.smsd.filters.StereoFilter
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- filter(List<List<Integer>>) - Static method in class org.openscience.smsd.filters.PostFilter
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Creates a new instance of Post Filter and removes redundant mapping(s).
- filterAtoms(int, Collection<List<IAtom>>, Collection<IAtom>) - Method in class org.openscience.smsd.ring.RingFilter
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- filterAtoms(IAtomContainer, Collection<IAtom>) - Method in class org.openscience.smsd.ring.RingFilter
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- findMappedConnectedComponents(IReaction, List<DefinedMapping>) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapper
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- findRings(IAtomContainer) - Static method in class org.openscience.smsd.ring.HanserRingFinder
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Returns Collection of atoms in Rings based on Hanser Ring Finding method
- findRootSystems(RBlastReaction) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.SignatureRootFinder
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- findRootSystems(IReaction, List<IBond>, List<IAtom>) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.SignatureRootFinder
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- findRootSystems(IAtomContainer, List<IBond>, List<IAtom>) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.SignatureRootFinder
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- findRootSystems(IReaction, List<String>) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.SignatureRootFinder
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- FingerPrintContainer - Class in uk.ac.ebi.reactionblast.containers
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- FingerprintGenerator - Class in uk.ac.ebi.reactionblast.fingerprints
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- FingerprintGenerator() - Constructor for class uk.ac.ebi.reactionblast.fingerprints.FingerprintGenerator
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- FingerprintSubset - Class in uk.ac.ebi.reactionblast.fingerprints.tools
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- FingerprintType - Class in aamtool.rgroup
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- FingerprintType(Set<String>, Set<String>, Set<String>) - Constructor for class aamtool.rgroup.FingerprintType
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- fixCoordinates(IReaction) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.layout.CoordinateFixer
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- fixDativeBonds(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
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This method is a workaround by assigning dative bonds to single
- FixedLabeller - Class in uk.ac.ebi.reactionblast.signature
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- FixedLabeller(int[]) - Constructor for class uk.ac.ebi.reactionblast.signature.FixedLabeller
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- formatMDLFloat(float) - Static method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
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Formats a float to fit into the connectiontable and changes it to a
String.
- formatMDLFloat(float) - Static method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
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Formats a float to fit into the connection table and changes it to a
String.
- formatMDLInt(int, int) - Static method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
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Formats an integer to fit into the connection table and changes it to a
String.
- formatMDLInt(int, int) - Static method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
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Formats an integer to fit into the connection table and changes it to a
String.
- formatMDLString(String, int) - Static method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
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Formats a String to fit into the connectiontable.
- formatMDLString(String, int) - Static method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
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Formats a String to fit into the connection table.
- Fragment - Class in org.openscience.smsd.mcss
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- Fragment(IAtomContainer) - Constructor for class org.openscience.smsd.mcss.Fragment
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- FragmentFilter - Class in org.openscience.smsd.filters
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Filter the results based on fragment size.
- FullTetrahedralWedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
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- FullTetrahedralWedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.FullTetrahedralWedgeRule
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