Package | Description |
---|---|
org.openscience.cdk.smsd.algorithm.rgraph |
Modifier and Type | Method and Description |
---|---|
CDKRMap |
CDKRNode.getrMap()
Deprecated.
Returns resolution Map
|
CDKRMap |
CDKRNode.getRMap()
Deprecated.
Gets the rMap attribute of the RNode object
|
Modifier and Type | Method and Description |
---|---|
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).
|
static List<CDKRMap> |
CDKMCS.checkSingleAtomCases(IAtomContainer sourceGraph,
IAtomContainer targetGraph)
Deprecated.
Checks for single atom cases before doing subgraph/isomorphism search
|
protected Stack<List<CDKRMap>> |
CDKRMapHandler.getAllMaximum(List<List<CDKRMap>> overlaps)
Deprecated.
|
static List<CDKRMap> |
CDKMCS.getIsomorphAtomsMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
|
static List<CDKRMap> |
CDKMCS.getIsomorphMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns the first isomorph mapping found or null.
|
static List<List<CDKRMap>> |
CDKMCS.getIsomorphMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns all the isomorph 'mappings' found between two
atom containers.
|
static List<CDKRMap> |
CDKMCS.getSubgraphAtomsMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
|
static List<List<CDKRMap>> |
CDKMCS.getSubgraphAtomsMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
|
static List<CDKRMap> |
CDKMCS.getSubgraphMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
|
static List<List<CDKRMap>> |
CDKMCS.getSubgraphMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.
|
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.
|
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.
|
protected List<CDKRMap> |
CDKRMapHandler.removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps)
Deprecated.
|
protected List<List<CDKRMap>> |
CDKRMapHandler.removeSubGraph(List<List<CDKRMap>> overlaps)
Deprecated.
|
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.
|
Modifier and Type | Method and Description |
---|---|
protected boolean |
CDKRMapHandler.isSameRMap(CDKRMap sourceRMap,
CDKRMap targetRMap)
Deprecated.
|
void |
CDKRNode.setrMap(CDKRMap rMap)
Deprecated.
Sets resolution map/graph
|
void |
CDKRNode.setRMap(CDKRMap rMap)
Deprecated.
Sets the rMap attribute of the RNode object
|
Modifier and Type | Method and Description |
---|---|
protected Stack<List<CDKRMap>> |
CDKRMapHandler.getAllMaximum(List<List<CDKRMap>> overlaps)
Deprecated.
|
protected void |
CDKRMapHandler.identifyMatchedParts(List<List<CDKRMap>> list,
IAtomContainer source,
IAtomContainer target)
Deprecated.
|
protected void |
CDKRMapHandler.identifySingleAtomsMatchedParts(List<CDKRMap> list,
IAtomContainer source,
IAtomContainer target)
Deprecated.
|
protected boolean |
CDKRMapHandler.isSubgraph(List<CDKRMap> rmaps1,
List<CDKRMap> rmaps2)
Deprecated.
|
protected boolean |
CDKRMapHandler.isSubgraph(List<CDKRMap> rmaps1,
List<CDKRMap> rmaps2)
Deprecated.
|
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.
|
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.
|
static IAtomContainer |
CDKMCS.project(List<CDKRMap> rMapList,
IAtomContainer graph,
int key)
Deprecated.
Projects atom list of CDKRMap on atom molecule.
|
static ArrayList<IAtomContainer> |
CDKMCS.projectList(List<List<CDKRMap>> rMapsList,
IAtomContainer graph,
int key)
Deprecated.
Projects atom list of RMapsList on atom molecule.
|
protected List<CDKRMap> |
CDKRMapHandler.removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps)
Deprecated.
|
protected List<List<CDKRMap>> |
CDKRMapHandler.removeSubGraph(List<List<CDKRMap>> overlaps)
Deprecated.
|
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