Class CDKSubGraphHandler

  • 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 for CDKMCS algorithm.
    Author:
    Syed Asad Rahman <asad@ebi.ac.uk>
    Source code:
    main
    Belongs to CDK module:
    smsd
    • Constructor Detail

      • CDKSubGraphHandler

        public CDKSubGraphHandler()
        Deprecated.
    • Method Detail

      • set

        public void set​(MolHandler source,
                        MolHandler target)
        Deprecated.
        Initialise the query and target molecule.
        Specified by:
        set in interface IMCSBase
        Parameters:
        source -
        target -
      • isSubgraph

        public boolean isSubgraph​(boolean shouldMatchBonds)
        Deprecated.
        Initialise the Subgraph search algorithm. Each Subgraph algorithm should contain this method.
        Specified by:
        isSubgraph in class AbstractSubGraph
        Parameters:
        shouldMatchBonds -
        Returns:
        true if Query/reactant is a subgraph of Target/product else false
      • 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 interface IMCSBase
        Returns:
        All possible MCS Mapping Index
      • getFirstMapping

        public Map<Integer,​Integer> getFirstMapping()
        Deprecated.
        Returns one of the best matches with atom indexes mapped.
        Specified by:
        getFirstMapping in interface IMCSBase
        Returns:
        Best Mapping Index
      • 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 interface IMCSBase
        Returns:
        All possible MCS atom Mappings
      • getFirstAtomMapping

        public Map<IAtom,​IAtom> getFirstAtomMapping()
        Deprecated.
        Returns one of the best matches with atoms mapped.
        Specified by:
        getFirstAtomMapping in interface IMCSBase
        Returns:
        Best Atom Mapping