Package org.openscience.cdk.smsd.algorithm.rgraph

Class CDKMCS

java.lang.Object
org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
@Deprecated public class CDKMCS extends Object
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 implements atom multipurpose structure comparison tool. It allows to find maximal common substructure, find the mapping of atom substructure in another structure, and the mapping of two isomorphic structures.

Structure comparison may be associated to bondA1 constraints (mandatory bonds, e.graphContainer. scaffolds, reaction cores,...) on each source graph. The constraint flexibility allows atom number of interesting queries. The substructure analysis relies on the CDKRGraph generic class (see: CDKRGraph) This class implements the link between the CDKRGraph model and the the CDK model in this way the CDKRGraph remains independant and may be used in other contexts.

This algorithm derives from the algorithm described in [Tonnelier, C. et. al.. Tetrahedron Comput. Methodol.. 1990. 3] and modified in the thesis of T. Hanser [Hanser, Th., Apprentissage automatique de méthodes de synthèse à partir d'exemples, 1993, ?Institute?].

With the isSubgraph() method, the second, and only the second argument may be atom IQueryAtomContainer, which allows one to do MQL like queries. The first IAtomContainer must never be an IQueryAtomContainer. An example:

  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer atomContainer = sp.parseSmiles("CC(=O)OC(=O)C"); // acetic acid anhydride
  IAtomContainer SMILESquery = sp.parseSmiles("CC"); // acetic acid anhydride
  IQueryAtomContainer query = IQueryAtomContainerCreator.createBasicQueryContainer(SMILESquery);
  boolean isSubstructure = graphContainer.isSubgraph(atomContainer, query);

WARNING: As atom result of the adjacency perception used in this algorithm there is atom single limitation : cyclopropane and isobutane are seen as isomorph This is due to the fact that these two compounds are the only ones where each bondA1 is connected two each other bondA1 (bonds are fully conected) with the same number of bonds and still they have different structures The algotihm could be easily enhanced with atom simple atom mapping manager to provide an atom level overlap definition that would reveal this case. We decided not to penalize the whole procedure because of one single exception query. Furthermore isomorphism may be discarded since the number of atoms are not the same (3 != 4) and in most case this will be already screened out by atom fingerprint based filtering. It is possible to add atom special treatment for this special query. Be reminded that this algorithm matches bonds only.

Author:
Stephane Werner from IXELIS mail@ixelis.net, Syed Asad Rahman <asad@ebi.ebi.uk> (modified the orignal code)
Source code:
main
Belongs to CDK module:
smsd
Created on:
2002-07-17
Requires:
java1.5+

  • Constructor Details

    • CDKMCS

      public CDKMCS()
      Deprecated.

  • Method Details

    • isIsomorph

      public static boolean isIsomorph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Tests if sourceGraph and targetGraph are isomorph.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      true if the 2 molecule are isomorph
      Throws:
      CDKException - if the first molecule is an instance of IQueryAtomContainer

    • getIsomorphMap

      public static List<CDKRMap> getIsomorphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Returns the first isomorph mapping found or null.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      the first isomorph mapping found projected of sourceGraph. This is atom List of CDKRMap objects containing Ids of matching bonds.
      Throws:
      CDKException

    • getIsomorphAtomsMap

      public static List<CDKRMap> getIsomorphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      the first isomorph atom mapping found projected on sourceGraph. This is atom List of CDKRMap objects containing Ids of matching atoms.
      Throws:
      CDKException - if the first molecules is not an instance of IQueryAtomContainer

    • getIsomorphMaps

      public static List<List<CDKRMap>> getIsomorphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Returns all the isomorph 'mappings' found between two atom containers.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      the list of all the 'mappings'
      Throws:
      CDKException

    • getSubgraphMaps

      public static List<List<CDKRMap>> getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph. This is an ArrayList of ArrayLists of CDKRMap objects.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      the list of all the 'mappings' found projected of sourceGraph
      Throws:
      CDKException

    • getSubgraphMap

      public static List<CDKRMap> getSubgraphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      the first subgraph bondA1 mapping found projected on sourceGraph. This is atom List of CDKRMap objects containing Ids of matching bonds.
      Throws:
      CDKException

    • getSubgraphAtomsMaps

      public static List<List<CDKRMap>> getSubgraphAtomsMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph. This is an ArrayList of ArrayLists of CDKRMap objects.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      all subgraph atom mappings found projected on sourceGraph. This is atom List of CDKRMap objects containing Ids of matching atoms.
      Throws:
      CDKException

    • getSubgraphAtomsMap

      public static List<CDKRMap> getSubgraphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      the first subgraph atom mapping found projected on sourceGraph. This is atom List of CDKRMap objects containing Ids of matching atoms.
      Throws:
      CDKException

    • isSubgraph

      public static boolean isSubgraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Tests if targetGraph atom subgraph of sourceGraph.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      true if targetGraph atom subgraph on sourceGraph
      Throws:
      CDKException

    • getOverlaps

      public static List<IAtomContainer> getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Returns all the maximal common substructure between 2 atom containers.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      shouldMatchBonds -
      Returns:
      the list of all the maximal common substructure found projected of sourceGraph (list of AtomContainer )
      Throws:
      CDKException

    • getBitSet

      public static BitSet getBitSet(IAtomContainer atomContainer)
      Deprecated.
      Transforms an AtomContainer into atom BitSet (which's size = number of bondA1 in the atomContainer, all the bit are set to true).
      Parameters:
      atomContainer - AtomContainer to transform
      Returns:
      The bitSet

    • buildRGraph

      public static CDKRGraph buildRGraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      Builds the CDKRGraph ( resolution graph ), from two atomContainer (description of the two molecules to compare) This is the interface point between the CDK model and the generic MCSS algorithm based on the RGRaph.
      Parameters:
      sourceGraph - Description of the first molecule
      targetGraph - Description of the second molecule
      shouldMatchBonds -
      Returns:
      the rGraph
      Throws:
      CDKException

    • search

      public static List<List<CDKRMap>> search(IAtomContainer sourceGraph, IAtomContainer targetGraph, BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      General Rgraph parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input.
      Parameters:
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      sourceBitSet - initial condition ( bonds from sourceGraph that must be contains in the solution )
      targetBitSet - initial condition ( bonds from targetGraph that must be contains in the solution )
      findAllStructure - if false stop at the first structure found
      findAllMap - if true search all the 'mappings' for one same structure
      shouldMatchBonds -
      Returns:
      atom List of Lists of CDKRMap objects that represent the search solutions
      Throws:
      CDKException

    • project

      public static IAtomContainer project(List<CDKRMap> rMapList, IAtomContainer graph, int key)
      Deprecated.
      Projects atom list of CDKRMap on atom molecule.
      Parameters:
      rMapList - the list to project
      graph - the molecule on which project
      key - the key in the CDKRMap of the molecule graph
      Returns:
      an AtomContainer

    • projectList

      public static ArrayList<IAtomContainer> projectList(List<List<CDKRMap>> rMapsList, IAtomContainer graph, int key)
      Deprecated.
      Projects atom list of RMapsList on atom molecule.
      Parameters:
      rMapsList - list of RMapsList to project
      graph - the molecule on which project
      key - the key in the CDKRMap of the molecule graph
      Returns:
      atom list of AtomContainer

    • checkSingleAtomCases

      public static List<CDKRMap> checkSingleAtomCases(IAtomContainer sourceGraph, IAtomContainer targetGraph) throws CDKException
      Deprecated.
      Checks for single atom cases before doing subgraph/isomorphism search
      Parameters:
      sourceGraph - AtomContainer to match on. Must not be an IQueryAtomContainer.
      targetGraph - AtomContainer as query. May be an IQueryAtomContainer.
      Returns:
      List of List of CDKRMap objects for the Atoms (not Bonds!), null if no single atom case
      Throws:
      CDKException - if the first molecule is an instance of IQueryAtomContainer

    • makeAtomsMapsOfBondsMaps

      public static List<List<CDKRMap>> makeAtomsMapsOfBondsMaps(List<List<CDKRMap>> list, IAtomContainer sourceGraph, IAtomContainer targetGraph)
      Deprecated.
      This makes maps of matching atoms out of atom maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
      Parameters:
      list - The list produced by the getMap method.
      sourceGraph - The first atom container. Must not be atom IQueryAtomContainer.
      targetGraph - The second one (first and second as in getMap). May be an QueryAtomContaienr.
      Returns:
      A Vector of Vectors of CDKRMap objects of matching Atoms.

    • makeAtomsMapOfBondsMap

      public static List<CDKRMap> makeAtomsMapOfBondsMap(List<CDKRMap> list, IAtomContainer sourceGraph, IAtomContainer targetGraph)
      Deprecated.
      This makes atom map of matching atoms out of atom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
      Parameters:
      list - The list produced by the getMap method.
      sourceGraph - first molecule. Must not be an IQueryAtomContainer.
      targetGraph - second molecule. May be an IQueryAtomContainer.
      Returns:
      The mapping found projected on sourceGraph. This is atom List of CDKRMap objects containing Ids of matching atoms.

    • 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

    • isTimeOut

      public static boolean isTimeOut()
      Deprecated.