public class CDKRMapHandler
extends java.lang.Object
Constructor and Description |
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CDKRMapHandler() |
Modifier and Type | Method and Description |
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java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> |
calculateIsomorphs(org.openscience.cdk.interfaces.IAtomContainer Molecule1,
org.openscience.cdk.interfaces.IAtomContainer Molecule2,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType)
This function calculates only one solution (exact) because we are looking
at the molecules which are exactly same in terms of the bonds and atoms
determined by the Fingerprint
|
java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> |
calculateOverlapsAndReduce(org.openscience.cdk.interfaces.IAtomContainer molecule1,
org.openscience.cdk.interfaces.IAtomContainer molecule2,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType)
This function calculates all the possible combinations of MCS
|
java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> |
calculateOverlapsAndReduce(org.openscience.cdk.interfaces.IAtomContainer molecule1,
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer molecule2)
This function calculates all the possible combinations of MCS
|
void |
calculateOverlapsAndReduceExactMatch(org.openscience.cdk.interfaces.IAtomContainer Molecule1,
org.openscience.cdk.interfaces.IAtomContainer Molecule2,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType)
This function calculates only one solution (exact) because we are looking
at the molecules which are exactly same in terms of the bonds and atoms
determined by the Fingerprint
|
java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> |
calculateSubGraphs(org.openscience.cdk.interfaces.IAtomContainer Molecule1,
org.openscience.cdk.interfaces.IAtomContainer Molecule2,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType)
This function calculates only one solution (exact) because we are looking
at the molecules which are exactly same in terms of the bonds and atoms
determined by the Fingerprint
|
protected java.util.Stack<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> |
getAllMaximum(java.util.List<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> overlaps) |
java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> |
getMappings()
Returns mapping solutions
|
protected java.util.List |
getMaximum(java.util.List overlaps) |
org.openscience.cdk.interfaces.IAtomContainer |
getSource()
Returns source molecule
|
org.openscience.cdk.interfaces.IAtomContainer |
getTarget()
Returns target molecule
|
protected void |
identifyMatchedParts(java.util.List<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> list,
org.openscience.cdk.interfaces.IAtomContainer source,
org.openscience.cdk.interfaces.IAtomContainer target) |
protected void |
identifySingleAtomsMatchedParts(java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> list,
org.openscience.cdk.interfaces.IAtomContainer source,
org.openscience.cdk.interfaces.IAtomContainer target) |
protected boolean |
isSameRMap(org.openscience.smsd.algorithm.rgraph.CDKRMap sourceRMap,
org.openscience.smsd.algorithm.rgraph.CDKRMap targetRMap) |
protected boolean |
isSubgraph(java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> rmaps1,
java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> rmaps2) |
boolean |
isTimeout() |
protected java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> |
removeRedundantMappingsForSingleAtomCase(java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> overlaps) |
protected java.util.List<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> |
removeSubGraph(java.util.List<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> overlaps) |
void |
setMappings(java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> mappings)
Set mapping solutions
|
void |
setSource(org.openscience.cdk.interfaces.IAtomContainer aSource)
Set source molecule
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void |
setTarget(org.openscience.cdk.interfaces.IAtomContainer aTarget)
Set target molecule
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void |
setTimeout(boolean timeout) |
public org.openscience.cdk.interfaces.IAtomContainer getSource()
public void setSource(org.openscience.cdk.interfaces.IAtomContainer aSource)
aSource
- the source to setpublic org.openscience.cdk.interfaces.IAtomContainer getTarget()
public void setTarget(org.openscience.cdk.interfaces.IAtomContainer aTarget)
aTarget
- the target to setpublic java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> calculateOverlapsAndReduce(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType) throws org.openscience.cdk.exception.CDKException
molecule1
- molecule2
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- org.openscience.cdk.exception.CDKException
public java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> calculateOverlapsAndReduce(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer molecule2) throws org.openscience.cdk.exception.CDKException
molecule1
- molecule2
- org.openscience.cdk.exception.CDKException
public void calculateOverlapsAndReduceExactMatch(org.openscience.cdk.interfaces.IAtomContainer Molecule1, org.openscience.cdk.interfaces.IAtomContainer Molecule2, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType) throws org.openscience.cdk.exception.CDKException
Molecule1
- Molecule2
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- org.openscience.cdk.exception.CDKException
public java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> calculateSubGraphs(org.openscience.cdk.interfaces.IAtomContainer Molecule1, org.openscience.cdk.interfaces.IAtomContainer Molecule2, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType) throws org.openscience.cdk.exception.CDKException
Molecule1
- Molecule2
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- org.openscience.cdk.exception.CDKException
public java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> calculateIsomorphs(org.openscience.cdk.interfaces.IAtomContainer Molecule1, org.openscience.cdk.interfaces.IAtomContainer Molecule2, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType) throws org.openscience.cdk.exception.CDKException
Molecule1
- Molecule2
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- org.openscience.cdk.exception.CDKException
protected java.util.List<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> removeSubGraph(java.util.List<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> overlaps)
overlaps
- protected java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> removeRedundantMappingsForSingleAtomCase(java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> overlaps)
overlaps
- protected java.util.List getMaximum(java.util.List overlaps)
overlaps
- protected java.util.Stack<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> getAllMaximum(java.util.List<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> overlaps)
overlaps
- protected void identifyMatchedParts(java.util.List<java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap>> list, org.openscience.cdk.interfaces.IAtomContainer source, org.openscience.cdk.interfaces.IAtomContainer target)
list
- source
- target
- protected void identifySingleAtomsMatchedParts(java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> list, org.openscience.cdk.interfaces.IAtomContainer source, org.openscience.cdk.interfaces.IAtomContainer target)
list
- source
- target
- protected boolean isSubgraph(java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> rmaps1, java.util.List<org.openscience.smsd.algorithm.rgraph.CDKRMap> rmaps2)
rmaps1
- rmaps2
- protected boolean isSameRMap(org.openscience.smsd.algorithm.rgraph.CDKRMap sourceRMap, org.openscience.smsd.algorithm.rgraph.CDKRMap targetRMap)
sourceRMap
- sourceAtomtargetRMap
- targetAtompublic java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> getMappings()
public void setMappings(java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> mappings)
mappings
- the mappings to setpublic boolean isTimeout()
public void setTimeout(boolean timeout)
timeout
- the timeout to set