public class BaseMCS
extends java.lang.Object
org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
and reports
MCS between run source and target graphs. Then these solutions are extended
using McGregor org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
algorithm where ever required.Modifier and Type | Field and Description |
---|---|
protected int |
countP |
protected int |
countR |
protected org.openscience.cdk.interfaces.IAtomContainer |
source |
protected org.openscience.cdk.interfaces.IAtomContainer |
target |
protected java.util.List<java.util.Map<INode,org.openscience.cdk.interfaces.IAtom>> |
vfLibSolutions |
Modifier and Type | Method and Description |
---|---|
protected void |
extendCliquesWithMcGregor(java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> refinedMCSSeeds) |
protected org.openscience.cdk.interfaces.IAtomContainer |
getProductMol() |
protected org.openscience.cdk.interfaces.IAtomContainer |
getReactantMol() |
protected boolean |
hasClique(java.util.Map<java.lang.Integer,java.lang.Integer> cliqueMap,
java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> mapGlobal) |
protected boolean |
isBondMatchFlag() |
protected boolean |
isCliquePresent(java.util.Map<java.lang.Integer,java.lang.Integer> cliqueMap,
java.util.Collection<java.util.Map<java.lang.Integer,java.lang.Integer>> mapGlobal) |
protected boolean |
isExtensionRequired() |
protected boolean |
isExtensionRequired(java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> mcsSeeds) |
boolean |
isMatchAtomType() |
protected boolean |
isMatchRings() |
protected void |
setVFMappings(boolean RONP,
IQuery query) |
protected int countR
protected int countP
protected final org.openscience.cdk.interfaces.IAtomContainer source
protected final org.openscience.cdk.interfaces.IAtomContainer target
protected final java.util.List<java.util.Map<INode,org.openscience.cdk.interfaces.IAtom>> vfLibSolutions
protected boolean hasClique(java.util.Map<java.lang.Integer,java.lang.Integer> cliqueMap, java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> mapGlobal)
cliqueMap
- mapGlobal
- protected boolean isCliquePresent(java.util.Map<java.lang.Integer,java.lang.Integer> cliqueMap, java.util.Collection<java.util.Map<java.lang.Integer,java.lang.Integer>> mapGlobal)
cliqueMap
- mapGlobal
- protected void extendCliquesWithMcGregor(java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> refinedMCSSeeds) throws org.openscience.cdk.exception.CDKException, java.io.IOException
refinedMCSSeeds
- org.openscience.cdk.exception.CDKException
java.io.IOException
protected void setVFMappings(boolean RONP, IQuery query)
RONP
- query
- protected org.openscience.cdk.interfaces.IAtomContainer getReactantMol()
protected org.openscience.cdk.interfaces.IAtomContainer getProductMol()
protected boolean isMatchRings()
protected boolean isBondMatchFlag()
protected boolean isExtensionRequired(java.util.List<java.util.Map<java.lang.Integer,java.lang.Integer>> mcsSeeds)
mcsSeeds
- protected boolean isExtensionRequired()
public boolean isMatchAtomType()