List<CDKRMap> |
CDKRGraph.bitSetToRMap(BitSet set) |
Deprecated.
Converts a CDKRGraph bitset (set of CDKRNode)
to a list of CDKRMap that represents the
mapping between to substructures in G1 and G2
(the projection of the CDKRGraph bitset on G1
and G2).
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static List<CDKRMap> |
CDKMCS.checkSingleAtomCases(IAtomContainer sourceGraph,
IAtomContainer targetGraph) |
Deprecated.
Checks for single atom cases before doing subgraph/isomorphism search
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protected Stack<List<CDKRMap>> |
CDKRMapHandler.getAllMaximum(List<List<CDKRMap>> overlaps) |
Deprecated.
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static List<CDKRMap> |
CDKMCS.getIsomorphAtomsMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds) |
Deprecated.
Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
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static List<CDKRMap> |
CDKMCS.getIsomorphMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds) |
Deprecated.
Returns the first isomorph mapping found or null.
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static List<List<CDKRMap>> |
CDKMCS.getIsomorphMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds) |
Deprecated.
Returns all the isomorph 'mappings' found between two
atom containers.
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static List<CDKRMap> |
CDKMCS.getSubgraphAtomsMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds) |
Deprecated.
Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
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static List<List<CDKRMap>> |
CDKMCS.getSubgraphAtomsMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds) |
Deprecated.
Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
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static List<CDKRMap> |
CDKMCS.getSubgraphMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds) |
Deprecated.
Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
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static List<List<CDKRMap>> |
CDKMCS.getSubgraphMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds) |
Deprecated.
Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.
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static List<CDKRMap> |
CDKMCS.makeAtomsMapOfBondsMap(List<CDKRMap> list,
IAtomContainer sourceGraph,
IAtomContainer targetGraph) |
Deprecated.
This makes atom map of matching atoms out of atom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
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static List<List<CDKRMap>> |
CDKMCS.makeAtomsMapsOfBondsMaps(List<List<CDKRMap>> list,
IAtomContainer sourceGraph,
IAtomContainer targetGraph) |
Deprecated.
This makes maps of matching atoms out of atom maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
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protected List<CDKRMap> |
CDKRMapHandler.removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps) |
Deprecated.
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protected List<List<CDKRMap>> |
CDKRMapHandler.removeSubGraph(List<List<CDKRMap>> overlaps) |
Deprecated.
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static List<List<CDKRMap>> |
CDKMCS.search(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
BitSet sourceBitSet,
BitSet targetBitSet,
boolean findAllStructure,
boolean findAllMap,
boolean shouldMatchBonds) |
Deprecated.
General Rgraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input.
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