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

Class VFMCSMapper

java.lang.Object
org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
All Implemented Interfaces:
IMapper
@Deprecated public class VFMCSMapper extends Object implements IMapper
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 finds MCS between query and target molecules using VF2 algorithm.
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd

  • Constructor Details

    • VFMCSMapper

      public VFMCSMapper(IQuery query)
      Deprecated.
      Parameters:
      query -

    • VFMCSMapper

      public VFMCSMapper(IAtomContainer queryMolecule, boolean bondMatcher)
      Deprecated.
      Parameters:
      queryMolecule -
      bondMatcher -

  • Method Details

    • getTimeout

      protected static double getTimeout()
      Deprecated.
      Returns:
      the timeout

    • getTimeManager

      protected static TimeManager getTimeManager()
      Deprecated.
      Returns:
      the timeManager

    • setTimeManager

      protected static void setTimeManager(TimeManager aTimeManager)
      Deprecated.
      Parameters:
      aTimeManager - the timeManager to set

    • hasMap

      public boolean hasMap(IAtomContainer targetMolecule)
      Deprecated.
      checks if a map exits for a molecule.
      Specified by:
      hasMap in interface IMapper
      Parameters:
      targetMolecule - targetMolecule graph
      Returns:
      true/false.

    • getMaps

      public List<Map<INode,IAtom>> getMaps(IAtomContainer target)
      Deprecated.
      Returns all solution map.
      Specified by:
      getMaps in interface IMapper
      Parameters:
      target - molecule.
      Returns:
      get maps.

    • getFirstMap

      public Map<INode,IAtom> getFirstMap(IAtomContainer target)
      Deprecated.
      Returns first solution map.
      Specified by:
      getFirstMap in interface IMapper
      Parameters:
      target -
      Returns:
      get first map.

    • countMaps

      public int countMaps(IAtomContainer target)
      Deprecated.
      Returns solution map count.
      Specified by:
      countMaps in interface IMapper
      Parameters:
      target - target molecule.
      Returns:
      map count.

    • hasMap

      public boolean hasMap(TargetProperties targetMolecule)
      Deprecated.
      checks if a map exits for a molecule.
      Specified by:
      hasMap in interface IMapper
      Parameters:
      targetMolecule - targetMolecule graph
      Returns:
      true/false.

    • getMaps

      public List<Map<INode,IAtom>> getMaps(TargetProperties targetMolecule)
      Deprecated.
      Returns all solution map.
      Specified by:
      getMaps in interface IMapper
      Parameters:
      targetMolecule -
      Returns:
      get maps.

    • getFirstMap

      public Map<INode,IAtom> getFirstMap(TargetProperties targetMolecule)
      Deprecated.
      Returns first solution map.
      Specified by:
      getFirstMap in interface IMapper
      Parameters:
      targetMolecule -
      Returns:
      get first map.

    • countMaps

      public int countMaps(TargetProperties targetMolecule)
      Deprecated.
      Returns solution map count.
      Specified by:
      countMaps in interface IMapper
      Parameters:
      targetMolecule -
      Returns:
      map count.

    • isTimeOut

      public static boolean isTimeOut()
      Deprecated.