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M

MACIE_RXN - Static variable in class uk.ac.ebi.reactionblast.tools.TestUtility
 
main(String[]) - Static method in class aamtool.rgroup.ECRgroupFrequency
 
main(String[]) - Static method in class uk.ac.ebi.aamtool.ReactionDecoder
 
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.Stereos 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
 
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