Class CDKSubGraphHandler

java.lang.Object
org.openscience.cdk.smsd.interfaces.AbstractSubGraph
org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
All Implemented Interfaces:
IMCSBase

@Deprecated public class CDKSubGraphHandler extends AbstractSubGraph implements IMCSBase
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. 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 CDKMCS algorithm.
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd
  • Constructor Details

    • CDKSubGraphHandler

      public CDKSubGraphHandler()
      Deprecated.
  • 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 -
    • isSubgraph

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

      protected IAtomContainerSet getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Parameters:
      mol -
      mcss -
      shouldMatchBonds -
      Returns:
      IMolecule Set
      Throws:
      CDKException
    • 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