Class CDKSubGraphHandler
java.lang.Object
org.openscience.cdk.smsd.interfaces.AbstractSubGraph
org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
- All Implemented Interfaces:
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 for
CDKMCS
algorithm.- Author:
- Syed Asad Rahman <asad@ebi.ac.uk>
- Source code:
- main
- Belongs to CDK module:
- smsd
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionDeprecated.Returns all plausible mappings between query and target molecules.Deprecated.Returns all plausible mappings between query and target molecules.Deprecated.Returns one of the best matches with atoms mapped.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.
-
Constructor Details
-
CDKSubGraphHandler
public CDKSubGraphHandler()Deprecated.
-
-
Method Details
-
set
Deprecated.Initialise the query and target molecule. -
set
Deprecated.Initialise the query and target molecule. -
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
-
getUncommon
protected IAtomContainerSet getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds) throws CDKException Deprecated.- Parameters:
mol
-mcss
-shouldMatchBonds
-- Returns:
- IMolecule Set
- Throws:
CDKException
-
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
-
getFirstMapping
Deprecated.Returns one of the best matches with atom indexes mapped.- Specified by:
getFirstMapping
in interfaceIMCSBase
- Returns:
- Best Mapping Index
-
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
-
getFirstAtomMapping
Deprecated.Returns one of the best matches with atoms mapped.- Specified by:
getFirstAtomMapping
in interfaceIMCSBase
- Returns:
- Best Atom Mapping
-