- MACIE_RXN - Static variable in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- main(String[]) - Static method in class aamtool.ReactionDecoder
-
- main(String[]) - Static method in class aamtool.rgroup.ECRgroupFrequency
-
- make(IMappingAlgorithm, IReaction, boolean, Map<Integer, IAtomContainer>, Map<Integer, IAtomContainer>, GameTheoryMatrix) - Static method in class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryFactory
-
- makeAtomsMapOfBondsMap(List<CDKRMap>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
-
This makes a map of matching atoms out of a map of matching bonds as
produced by the get(Subgraph|Ismorphism)Map methods.
- makeAtomsMapsOfBondsMaps(List<List<CDKRMap>>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
-
This makes maps of matching atoms out of a maps of matching bonds as
produced by the get(Subgraph|Ismorphism)Maps methods.
- makeBlankImage(int, int) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
-
- makeBlankImage(int, int, Color) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
-
- makeBlankImage(int, int) - Method in class uk.ac.ebi.reactionblast.tools.Reader
-
- makeBlankImage(int, int) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- makeBondMapsOfAtomMaps(IAtomContainer, IAtomContainer, List<AtomAtomMapping>) - Method in class org.openscience.smsd.BaseMapping
-
Returns bond maps between sourceAtomCount and targetAtomCount molecules
based on the atoms
- makeEdge(int, int, String, String, String) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
-
- makeGraph() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
-
- makeIndexMap(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
-
- makeLabelMap(IReaction) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
-
- makeLeftToRighHighlightedReactionToFile(IReaction, AbstractDirectReactionLayout, AbstractAWTReactionLayout, int, int, boolean, File) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
-
- makeLeftToRighHighlightedReactionToFile(IReaction, int, int, boolean, File) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
-
- makeMoleculeFromSignature(String) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
-
Convert a signature string into a molecule.
- makePatternFingerprint(Map<String, Double>) - Static method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
-
- makePatternFingerprint(Collection<String>, Collection<Double>) - Static method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
-
- makeReactionCenterHighlightedReactionToFile(IReaction, AbstractDirectReactionLayout, AbstractAWTReactionLayout, int, int, File) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
-
- makeTopToBottomRHighlightedReactionToFile(IReaction, int, int, File) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
-
- makeVertex(String) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
-
- map(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
-
- map(String, String) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
-
- map(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.Reader
-
- Map1ValueComparator - Class in org.openscience.smsd.algorithm.vflib
-
- Map1ValueComparator(SortOrder) - Constructor for class org.openscience.smsd.algorithm.vflib.Map1ValueComparator
-
- Map2ValueComparator - Class in org.openscience.smsd.algorithm.vflib
-
- Map2ValueComparator(SortOrder) - Constructor for class org.openscience.smsd.algorithm.vflib.Map2ValueComparator
-
- mapAttributes(A, Map<String, String>) - Method in class uk.ac.ebi.centres.io.CytoscapeWriter
-
- MappingGraph - Class in uk.ac.ebi.reactionblast.mapping.blocks
-
A graph of the atom-atom mappings in a reaction - each vertex of the graph is
a mapping between a pair of atoms, and an edge connects mappings whose
endpoints (atoms) are connected (bonded).
- MappingGraph(IReaction) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.MappingGraph
-
- MappingGraph(List<DefinedMapping>) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.MappingGraph
-
- MappingHandler - Class in uk.ac.ebi.reactionblast.mapping.helper
-
- MappingHandler() - Constructor for class uk.ac.ebi.reactionblast.mapping.helper.MappingHandler
-
- MappingReferenceResolver - Class in uk.ac.ebi.reactionblast.mapping.fixer
-
Simple class to ensure that the atoms referred to in an atom-atom mapping are the same object reference as in the
atom containers of the reactants and products.
- MappingSolution - Class in uk.ac.ebi.reactionblast.mechanism
-
- MappingSolution(BondChangeCalculator, IMappingAlgorithm, IReaction, Reactor, double, int, int, int, int, int, int, double) - Constructor for class uk.ac.ebi.reactionblast.mechanism.MappingSolution
-
- MappingTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
-
- MappingTransformation() - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.MappingTransformation
-
- MappingUtility - Class in uk.ac.ebi.reactionblast.tools
-
- MappingUtility() - Constructor for class uk.ac.ebi.reactionblast.tools.MappingUtility
-
- mapReaction(IReaction, boolean) - Method in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- mapReactions(IReactionSet, boolean) - Method in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- markBondChanges() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
-
set bond change flag
- MassNumberAccessor<A> - Interface in uk.ac.ebi.centres.priority.access
-
Wrapper provides access to a given an atom's mass number (of type A) to priority rules that require it.
- MassNumberRule<A> - Class in uk.ac.ebi.centres.priority
-
An abstract class for constitutional priority based on mass number.
- MassNumberRule(MassNumberAccessor<A>) - Constructor for class uk.ac.ebi.centres.priority.MassNumberRule
-
Constructs an mass number comparator that uses the provided accessor to fetch the mass number for a given atom.
- Match - Class in org.openscience.smsd.algorithm.vflib.map
-
Holds matching query and target nodes.
- Match(INode, IAtom) - Constructor for class org.openscience.smsd.algorithm.vflib.map.Match
-
Constructor
- matcher(Holder) - Static method in class uk.ac.ebi.reactionblast.mapping.graph.GraphMatcher
-
- matches(IAtom) - Method in interface org.openscience.smsd.algorithm.matchers.AtomMatcher
-
- matches(IBond) - Method in interface org.openscience.smsd.algorithm.matchers.BondMatcher
-
- matches(IAtom) - Method in class org.openscience.smsd.algorithm.matchers.DefaultAtomMatcher
- matches(IAtom) - Method in class org.openscience.smsd.algorithm.matchers.DefaultAtomTypeMatcher
- matches(IBond) - Method in class org.openscience.smsd.algorithm.matchers.DefaultBondMatcher
- matches(IBond, IBond, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.matchers.DefaultMatcher
-
- matches(IBond) - Method in class org.openscience.smsd.helper.BondEnergy
-
- matches(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.fingerprints.IQueryTool
-
Perform a SMARTS match and check whether the query is present in the target molecule.
- matches(IAtomContainer, boolean) - Method in interface uk.ac.ebi.reactionblast.fingerprints.IQueryTool
-
Perform a SMARTS match and check whether the query is present in the target molecule.
- matches(IBond.Stereo[]) - Method in class uk.ac.ebi.reactionblast.stereo.wedge.WedgeRule
-
Match a list of IBond.Stereo
s to the pattern list of stereos,
allowing for circular permutation of the list.
- Maths - Class in uk.ac.ebi.reactionblast.tools.matrix
-
- MatrixPrinter - Class in uk.ac.ebi.reactionblast.mechanism.helper
-
- MAX_ENERGY - Static variable in class org.openscience.smsd.filters.EnergyFilter
-
- McGregor - Class in org.openscience.smsd.algorithm.mcgregor
-
Class which reports MCS solutions based on the McGregor algorithm published
in 1982.
- McGregor(IAtomContainer, IAtomContainer, List<List<Integer>>, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.algorithm.mcgregor.McGregor
-
Constructor for the McGregor algorithm.
- McGregor(IQueryAtomContainer, IAtomContainer, List<List<Integer>>) - Constructor for class org.openscience.smsd.algorithm.mcgregor.McGregor
-
Constructor for the McGregor algorithm.
- McGregorChecks - Class in org.openscience.smsd.algorithm.mcgregor
-
Class to perform check/methods for McGregor class.
- McgregorHelper - Class in org.openscience.smsd.algorithm.mcgregor
-
Helper Class for McGregor algorithm.
- McgregorHelper(boolean, int, List<Integer>, int, int, List<Integer>, List<Integer>, List<String>, List<String>, int, int, List<Integer>, List<Integer>, List<String>, List<String>) - Constructor for class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
-
Stores the variables
- mcsMatch(Holder, boolean, Integer, Integer, BitSet, BitSet) - Method in class uk.ac.ebi.reactionblast.mapping.graph.GraphMatching
-
- mcsMatch(Holder, boolean, Integer, Integer, BitSet, BitSet) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.IGraphMatching
-
- MCSPlus - Class in org.openscience.smsd.algorithm.mcsplus
-
This class handles MCS plus algorithm which is a combination of c-clique
algorithm and McGregor algorithm.
- MCSPlus(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.algorithm.mcsplus.MCSPlus
-
- MCSPlus(IQueryAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.algorithm.mcsplus.MCSPlus
-
- MCSPlusHandler - Class in org.openscience.smsd.algorithm.mcsplus
-
This class acts as a handler class for MCSPlus algorithm.
- MCSPlusHandler(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.algorithm.mcsplus.MCSPlusHandler
-
Constructor for the MCS Plus algorithm class
- MCSPlusHandler(IQueryAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.algorithm.mcsplus.MCSPlusHandler
-
Constructor for the MCS Plus algorithm class
- MCSS - Class in org.openscience.smsd.mcss
-
- MCSS(List<IAtomContainer>, JobType, int) - Constructor for class org.openscience.smsd.mcss.MCSS
-
- MCSS(List<IAtomContainer>, JobType, int, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.mcss.MCSS
-
- MCSSeedGenerator - Class in org.openscience.smsd.algorithm.vflib.seeds
-
This class should be used to find MCS between source graph and target graph.
- MCSSeedGenerator(IAtomContainer, IAtomContainer, boolean, boolean, boolean, Algorithm) - Constructor for class org.openscience.smsd.algorithm.vflib.seeds.MCSSeedGenerator
-
- MCSSeedGenerator(IQueryAtomContainer, IAtomContainer, Algorithm) - Constructor for class org.openscience.smsd.algorithm.vflib.seeds.MCSSeedGenerator
-
- MCSSolution - Class in uk.ac.ebi.reactionblast.mapping.graph
-
- MCSSolution(int, int, IAtomContainer, IAtomContainer, AtomAtomMapping) - Constructor for class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
-
- MCSSThread - Class in org.openscience.smsd.mcss
-
- MCSSThread(List<IAtomContainer>, JobType, int) - Constructor for class org.openscience.smsd.mcss.MCSSThread
-
- MCSSThread(List<IAtomContainer>, JobType, int, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.mcss.MCSSThread
-
- MCSThread - Class in uk.ac.ebi.reactionblast.mapping.graph
-
- MDLFileReader - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
Class that reads MDL files (various versions).
- MDLFileReader(InputStream, IChemObjectReader.Mode) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLFileReader
-
Constructor for MDL file reader
- MDLFileReader(InputStream) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLFileReader
-
Constructor for MDL file reader
- MDLFileReader(Reader) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLFileReader
-
Constructor for MDL file reader
- MDLFileReader(Reader, IChemObjectReader.Mode) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLFileReader
-
Constructor for MDL file reader
- MDLReaderBase - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
- MDLReaderBase() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
-
- MDLRXNV2000Reader - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
Reads a molecule from an MDL RXN file {
- MDLRXNV2000Reader(Reader) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
-
Constructs a new MDLReader that can read AtomContainer from a given
Reader.
- MDLRXNV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
-
- MDLRXNV2000Reader(InputStream) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
-
- MDLRXNV2000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
-
- MDLRXNV2000Reader() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
-
- MDLV2000Reader - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
Reads content from MDL molfiles and SD files.
- MDLV2000Reader() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
- MDLV2000Reader(InputStream) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
Constructs a new MDLReader that can read Molecule from a given
InputStream.
- MDLV2000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
- MDLV2000Reader(Reader) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
Constructs a new MDLReader that can read Molecule from a given Reader.
- MDLV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
- MDLV2000RXNWriter - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
Writes a reaction to a MDL rxn or SDF file.
- MDLV2000RXNWriter(Writer) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
-
Constructs a new MDLWriter that can write an array of Molecules to a
Writer.
- MDLV2000RXNWriter(OutputStream) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
-
Constructs a new MDLWriter that can write an array of Molecules to a
given OutputStream.
- MDLV2000RXNWriter() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
-
- MDLV2000Writer - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
Writes MDL molfiles, which contains a single molecule (see {
- MDLV2000Writer(Writer) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
-
Constructs a new MDLWriter that can write an IAtomContainer
to
the MDL molfile format.
- MDLV2000Writer(OutputStream) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
-
Constructs a new MDLWriter that can write an IAtomContainer
to a
given OutputStream.
- MDLV2000Writer() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
-
- MDLV2000Writer.SPIN_MULTIPLICITY - Enum in uk.ac.ebi.reactionblast.tools.rxnfile
-
Enumeration of all valid radical values.
- MDLWriterBase - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
- MDLWriterBase() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
-
- merge(RootSystem) - Method in class uk.ac.ebi.reactionblast.graphics.direct.RootSystem
-
- metals - Static variable in class uk.ac.ebi.reactionblast.tools.inchi.CDKInChI
-
- METRXN_RXN - Static variable in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- minus(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
data = matrix - B
- minusEquals(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
matrix = matrix - B
- modifyMatrix(Holder) - Static method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
-
Refills Matrix with true similarity scores
- MolContainer - Class in uk.ac.ebi.reactionblast.containers
-
- molecule - Variable in class uk.ac.ebi.reactionblast.tools.inchi.CDKInChI
-
- MoleculeAligner - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
-
Aligns molecules to a line specified by a vector.
- moleculeAlignMethod - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- MoleculeCanonicalizationTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
-
Transform a molecule to make it canonical.
- MoleculeCanonicalizationTransformation(ICanonicalMoleculeLabeller) - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.MoleculeCanonicalizationTransformation
-
- MoleculeInitializer - Class in org.openscience.smsd.helper
-
- MoleculeInitializer() - Constructor for class org.openscience.smsd.helper.MoleculeInitializer
-
- MoleculeLabelDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
-
Draws a set of text labels for one or more molecules.
- MoleculeLabelDrawer(Axis, Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.MoleculeLabelDrawer
-
- moleculeLabelFontSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- MoleculeLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.awtlayout
-
'Layout' a molecule in the context of a Graphics object; NOTE - does not
re-position the atoms...
- MoleculeLayout(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.MoleculeLayout
-
- MoleculeLayout(AbstractAWTLayout, Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.MoleculeLayout
-
- MoleculeMoleculeMapping - Class in uk.ac.ebi.reactionblast.mapping.container
-
- MoleculeMoleculeMapping() - Constructor for class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
-
- MoleculeMoleculePair - Class in uk.ac.ebi.reactionblast.mechanism.helper
-
- MoleculeMoleculePair(ReactantProductPair, ReactantProductPair, ReactantProductPair, String) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- MolFingerprint - Class in uk.ac.ebi.reactionblast.fingerprints
-
- MolFingerprint() - Constructor for class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
- MolFingerprint(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
- MolFingerprint(BitSet) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
- MolFingerprint(int) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
- MolFingerprint(boolean[]) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
- MolFingerprint(MolFingerprint) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
- MolMapping - Class in uk.ac.ebi.reactionblast.mapping.container.helper
-
- MolMapping(String, String, Integer, Integer) - Constructor for class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
-
- mul(double) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Multiplies a scalar with this EBIMatrix.
- mul(List<Double>) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Multiplies a Vector with this EBIMatrix.
- mul(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Multiplies this EBIMatrix with another one.
- MutableDescriptor - Class in uk.ac.ebi.centres
-
Holds a mutable descriptor value that can be passed around and set.
- MutableDescriptor() - Constructor for class uk.ac.ebi.centres.MutableDescriptor
-