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F

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