Class CDKSubGraphHandler
- java.lang.Object
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- org.openscience.cdk.smsd.interfaces.AbstractSubGraph
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- org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
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- All Implemented Interfaces:
IMCSBase
@Deprecated public class CDKSubGraphHandler extends AbstractSubGraph implements IMCSBase
Deprecated.This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.This class acts as a handler class forCDKMCS
algorithm.- Author:
- Syed Asad Rahman <asad@ebi.ac.uk>
- Source code:
- main
- Belongs to CDK module:
- smsd
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Constructor Summary
Constructors Constructor Description CDKSubGraphHandler()
Deprecated.
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description List<Map<IAtom,IAtom>>
getAllAtomMapping()
Deprecated.Returns all plausible mappings between query and target molecules.List<Map<Integer,Integer>>
getAllMapping()
Deprecated.Returns all plausible mappings between query and target molecules.Map<IAtom,IAtom>
getFirstAtomMapping()
Deprecated.Returns one of the best matches with atoms mapped.Map<Integer,Integer>
getFirstMapping()
Deprecated.Returns one of the best matches with atom indexes mapped.protected IAtomContainerSet
getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)
Deprecated.boolean
isSubgraph(boolean shouldMatchBonds)
Deprecated.Initialise the Subgraph search algorithm.void
set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule.void
set(MolHandler source, MolHandler target)
Deprecated.Initialise the query and target molecule.
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Method Detail
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set
public void set(MolHandler source, MolHandler target)
Deprecated.Initialise the query and target molecule.
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set
public void set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule.
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isSubgraph
public boolean isSubgraph(boolean shouldMatchBonds)
Deprecated.Initialise the Subgraph search algorithm. Each Subgraph algorithm should contain this method.- Specified by:
isSubgraph
in classAbstractSubGraph
- Parameters:
shouldMatchBonds
-- Returns:
- true if Query/reactant is a subgraph of Target/product else false
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getUncommon
protected IAtomContainerSet getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds) throws CDKException
Deprecated.- Parameters:
mol
-mcss
-shouldMatchBonds
-- Returns:
- IMolecule Set
- Throws:
CDKException
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getAllMapping
public List<Map<Integer,Integer>> getAllMapping()
Deprecated.Returns all plausible mappings between query and target molecules. Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule- Specified by:
getAllMapping
in interfaceIMCSBase
- Returns:
- All possible MCS Mapping Index
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getFirstMapping
public Map<Integer,Integer> getFirstMapping()
Deprecated.Returns one of the best matches with atom indexes mapped.- Specified by:
getFirstMapping
in interfaceIMCSBase
- Returns:
- Best Mapping Index
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getAllAtomMapping
public List<Map<IAtom,IAtom>> getAllAtomMapping()
Deprecated.Returns all plausible mappings between query and target molecules. Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule- Specified by:
getAllAtomMapping
in interfaceIMCSBase
- Returns:
- All possible MCS atom Mappings
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getFirstAtomMapping
public Map<IAtom,IAtom> getFirstAtomMapping()
Deprecated.Returns one of the best matches with atoms mapped.- Specified by:
getFirstAtomMapping
in interfaceIMCSBase
- Returns:
- Best Atom Mapping
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