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

Class VFlibMCSHandler

  • All Implemented Interfaces:
    IMCSBase
    @Deprecated
public class VFlibMCSHandler
extends AbstractMCSAlgorithm
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 class should be used to find MCS between query graph and target graph. First the algorithm runs VF lib VFMCSMapper and reports MCS between run query and target graphs. Then these solutions are extended using McGregor McGregor algorithm where ever required.
    Author:
    Syed Asad Rahman <asad@ebi.ac.uk>
    Source code:
    main
    Belongs to CDK module:
    smsd

    • Constructor Detail

      • VFlibMCSHandler

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

    • Method Detail

      • searchMCS

        public void searchMCS​(boolean bondTypeMatch)
        Deprecated.
        Initialise the MCS search algorithm. Each MCS algorithm should contain this method.
        Specified by:
        searchMCS in class AbstractMCSAlgorithm
        Parameters:
        bondTypeMatch -

      • 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

      • isBondMatchFlag

        public boolean isBondMatchFlag()
        Deprecated.
        Returns:
        the shouldMatchBonds

      • setBondMatchFlag

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