Package | Description |
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org.openscience.cdk.isomorphism | |
org.openscience.cdk.isomorphism.mcss |
Modifier and Type | Method and Description |
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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. |
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.
|
Modifier and Type | Method and Description |
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RMap |
RNode.getRMap()
Gets the rMap attribute of the RNode object.
|
Modifier and Type | Method and Description |
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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).
|
Modifier and Type | Method and Description |
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void |
RNode.setRMap(RMap rMap)
Sets the rMap attribute of the RNode object.
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