Package org.openscience.cdk.smsd.algorithm.vflib

Class VFlibSubStructureHandler

  • All Implemented Interfaces:
    IMCSBase
    @Deprecated
public class VFlibSubStructureHandler
extends AbstractSubGraph
implements IMCSBase
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    This is an ultra fast method to report if query is a substructure for target molecule. If this case is true then it returns only all mapping. This is much faster than VFlibMCSHandler class as it only reports first match and backtracks. This class should only be used to report if a query graph is a substructure of the target graph.
    Author:
    Syed Asad Rahman <asad@ebi.ac.uk>
    Source code:
    main
    Belongs to CDK module:
    smsd

    • Constructor Detail

      • VFlibSubStructureHandler

        public VFlibSubStructureHandler()
        Deprecated.
        Constructor for an extended VF Algorithm for the MCS search

    • Method Detail

      • set

        public void set​(MolHandler reactant,
                MolHandler product)
        Deprecated.
        Initialise the query and target molecule. Set the VFLib MCS software
        Specified by:
        set in interface IMCSBase
        Parameters:
        reactant -
        product -

      • 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

      • 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

      • 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

      • 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

      • isSubgraph

        public boolean isSubgraph​(boolean shouldMatchBonds)
        Deprecated.
        Description copied from class: AbstractSubGraph
        Initialise the Subgraph search algorithm. Each Subgraph algorithm should contain this method.
        Specified by:
        isSubgraph in class AbstractSubGraph
        Returns:
        true if Query/reactant is a subgraph of Target/product else false

      • isBondMatchFlag

        public boolean isBondMatchFlag()
        Deprecated.
        Returns:
        the shouldMatchBonds

      • setBondMatchFlag

        public void setBondMatchFlag​(boolean shouldMatchBonds)
        Deprecated.
        Parameters:
        shouldMatchBonds - the shouldMatchBonds to set