Constructor and Description |
---|
CDKMCSHandler(org.openscience.cdk.interfaces.IAtomContainer source,
org.openscience.cdk.interfaces.IAtomContainer target) |
CDKMCSHandler(org.openscience.cdk.interfaces.IAtomContainer source,
org.openscience.cdk.interfaces.IAtomContainer target,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType) |
Modifier and Type | Method and Description |
---|---|
java.util.List<AtomAtomMapping> |
getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
AtomAtomMapping |
getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
protected org.openscience.cdk.interfaces.IAtomContainerSet |
getUncommon(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer mcss,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType) |
boolean |
isTimeout() |
void |
setTimeout(boolean timeout) |
public CDKMCSHandler(org.openscience.cdk.interfaces.IAtomContainer source, org.openscience.cdk.interfaces.IAtomContainer target, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType)
source
- target
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- public CDKMCSHandler(org.openscience.cdk.interfaces.IAtomContainer source, org.openscience.cdk.interfaces.IAtomContainer target)
source
- target
- protected org.openscience.cdk.interfaces.IAtomContainerSet getUncommon(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer mcss, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType) throws org.openscience.cdk.exception.CDKException
mol
- mcss
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- org.openscience.cdk.exception.CDKException
public java.util.List<AtomAtomMapping> getAllAtomMapping()
getAllAtomMapping
in interface IResults
public AtomAtomMapping getFirstAtomMapping()
getFirstAtomMapping
in interface IResults
public boolean isTimeout()
public void setTimeout(boolean timeout)
timeout
- the timeout to set