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

Class VFlibMCSHandler

java.lang.Object
org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
org.openscience.cdk.smsd.algorithm.vflib.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 Details

    • VFlibMCSHandler

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

  • Method Details

    • 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 -

    • set

      public void set(IQueryAtomContainer source, IAtomContainer target)
      Deprecated.
      Initialise the query and target molecule.
      Specified by:
      set in interface IMCSBase
      Parameters:
      source -
      target -

    • 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