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

Class VFlibSubStructureHandler

java.lang.Object
org.openscience.cdk.smsd.interfaces.AbstractSubGraph
org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
All Implemented Interfaces:
IMCSBase
@Deprecated public class VFlibSubStructureHandler extends AbstractSubGraph 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 is an ultra fast method to report if query is a substructure for target molecule. If this case is true then it returns only all mapping. This is much faster than VFlibMCSHandler class as it only reports first match and backtracks. This class should only be used to report if a query graph is a substructure of the target graph.
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd

  • Constructor Details

    • VFlibSubStructureHandler

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

  • Method Details

    • 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

    • isSubgraph

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

    • isBondMatchFlag

      public boolean isBondMatchFlag()
      Deprecated.
      Returns:
      the shouldMatchBonds

    • setBondMatchFlag

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