Uses of Class
org.openscience.cdk.isomorphism.mcss.RMap

Packages that use RMap

Package	Description
org.openscience.cdk.isomorphism
org.openscience.cdk.isomorphism.mcss

Uses of RMap in org.openscience.cdk.isomorphism

Methods in org.openscience.cdk.isomorphism that return types with arguments of type RMap

Modifier and Type	Method and Description
static List<RMap>	UniversalIsomorphismTester.checkSingleAtomCases(IAtomContainer g1, IAtomContainer g2) Checks for single atom cases before doing subgraph/isomorphism search.
List<RMap>	UniversalIsomorphismTester.getIsomorphAtomsMap(IAtomContainer g1, IAtomContainer g2) Returns the first isomorph 'atom mapping' found for g2 in g1.
List<RMap>	UniversalIsomorphismTester.getIsomorphMap(IAtomContainer g1, IAtomContainer g2) Returns the first isomorph mapping found or null.
List<List<RMap>>	UniversalIsomorphismTester.getIsomorphMaps(IAtomContainer g1, IAtomContainer g2) Returns all the isomorph 'mappings' found between two atom containers.
List<RMap>	UniversalIsomorphismTester.getSubgraphAtomsMap(IAtomContainer g1, IAtomContainer g2) Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure of g1.
List<List<RMap>>	UniversalIsomorphismTester.getSubgraphAtomsMaps(IAtomContainer g1, IAtomContainer g2) Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure of g1.
List<RMap>	UniversalIsomorphismTester.getSubgraphMap(IAtomContainer g1, IAtomContainer g2) Returns the first subgraph 'bond mapping' found for g2 in g1.
List<List<RMap>>	UniversalIsomorphismTester.getSubgraphMaps(IAtomContainer g1, IAtomContainer g2) Returns all the subgraph 'bond mappings' found for g2 in g1.
static List<RMap>	UniversalIsomorphismTester.makeAtomsMapOfBondsMap(List<RMap> l, IAtomContainer g1, IAtomContainer g2) This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
static List<List<RMap>>	UniversalIsomorphismTester.makeAtomsMapsOfBondsMaps(List<List<RMap>> l, IAtomContainer g1, IAtomContainer g2) This makes maps of matching atoms out of a maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
List<List<RMap>>	UniversalIsomorphismTester.search(IAtomContainer g1, IAtomContainer g2, BitSet c1, BitSet c2, boolean findAllStructure, boolean findAllMap) General RGraph parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input.

Method parameters in org.openscience.cdk.isomorphism with type arguments of type RMap

Modifier and Type	Method and Description
static List<RMap>	UniversalIsomorphismTester.makeAtomsMapOfBondsMap(List<RMap> l, IAtomContainer g1, IAtomContainer g2) This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
static List<List<RMap>>	UniversalIsomorphismTester.makeAtomsMapsOfBondsMaps(List<List<RMap>> l, IAtomContainer g1, IAtomContainer g2) This makes maps of matching atoms out of a maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
static IAtomContainer	UniversalIsomorphismTester.project(List<RMap> rMapList, IAtomContainer g, int id) Projects a list of RMap on a molecule.
static List<IAtomContainer>	UniversalIsomorphismTester.projectList(List<List<RMap>> rMapsList, IAtomContainer g, int id) Projects a list of RMapsList on a molecule.

Uses of RMap in org.openscience.cdk.isomorphism.mcss

Methods in org.openscience.cdk.isomorphism.mcss that return RMap

Modifier and Type	Method and Description
RMap	RNode.getRMap() Gets the rMap attribute of the RNode object.

Methods in org.openscience.cdk.isomorphism.mcss that return types with arguments of type RMap

Modifier and Type	Method and Description
List<RMap>	RGraph.bitSetToRMap(BitSet set) Converts a RGraph bitset (set of RNode) to a list of RMap that represents the mapping between to substructures in G1 and G2 (the projection of the RGraph bitset on G1 and G2).

Methods in org.openscience.cdk.isomorphism.mcss with parameters of type RMap

Modifier and Type	Method and Description
void	RNode.setRMap(RMap rMap) Sets the rMap attribute of the RNode object.