Package org.openscience.cdk.smsd.algorithm.mcsplus

Class MCSPlusHandler

java.lang.Object
org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
All Implemented Interfaces:
IMCSBase
@Deprecated public class MCSPlusHandler 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 acts as a handler class for MCSPlus algorithm. MCSPlus
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd

  • Constructor Details

    • MCSPlusHandler

      public MCSPlusHandler()
      Deprecated.
      Constructor for the MCS Plus algorithm class

  • Method Details

    • set

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

    • set

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

    • searchMCS

      public void searchMCS(boolean shouldMatchBonds)
      Deprecated.
      Initialise the MCS search algorithm. Each MCS algorithm should contain this method. Function is called by the main program and serves as a starting point for the comparison procedure.
      Specified by:
      searchMCS in class AbstractMCSAlgorithm
      Parameters:
      shouldMatchBonds -

    • 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