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

Class CDKRMapHandler

  • @Deprecated
public class CDKRMapHandler
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 algorithm derives from the algorithm described in [Tonnelier, C. and Jauffret, Ph. and Hanser, Th. and Jauffret, Ph. and Kaufmann, G., Machine Learning of generic reactions: 3. An efficient algorithm for maximal common substructure determination, Tetrahedron Comput. Methodol., 1990, 3:351-358] and modified in the thesis of T. Hanser [Unknown BibTeXML type: HAN93].
    Author:
    Syed Asad Rahman <asad@ebi.ac.uk>
    Source code:
    main
    Belongs to CDK module:
    smsd

    • Constructor Detail

      • CDKRMapHandler

        public CDKRMapHandler()
        Deprecated.

    • Method Detail

      • getSource

        public IAtomContainer getSource()
        Deprecated.
        Returns source molecule
        Returns:
        the source

      • setSource

        public void setSource​(IAtomContainer aSource)
        Deprecated.
        Set source molecule
        Parameters:
        aSource - the source to set

      • getTarget

        public IAtomContainer getTarget()
        Deprecated.
        Returns target molecule
        Returns:
        the target

      • setTarget

        public void setTarget​(IAtomContainer aTarget)
        Deprecated.
        Set target molecule
        Parameters:
        aTarget - the target to set

      • calculateOverlapsAndReduce

        public void calculateOverlapsAndReduce​(IAtomContainer molecule1,
                                       IAtomContainer molecule2,
                                       boolean shouldMatchBonds)
                                throws CDKException
        Deprecated.
        This function calculates all the possible combinations of MCS
        Parameters:
        molecule1 -
        molecule2 -
        shouldMatchBonds -
        Throws:
        CDKException

      • calculateOverlapsAndReduceExactMatch

        public void calculateOverlapsAndReduceExactMatch​(IAtomContainer molecule1,
                                                 IAtomContainer molecule2,
                                                 boolean shouldMatchBonds)
                                          throws CDKException
        Deprecated.
        This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
        Parameters:
        molecule1 -
        molecule2 -
        shouldMatchBonds -
        Throws:
        CDKException

      • calculateSubGraphs

        public void calculateSubGraphs​(IAtomContainer molecule1,
                               IAtomContainer molecule2,
                               boolean shouldMatchBonds)
                        throws CDKException
        Deprecated.
        This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
        Parameters:
        molecule1 -
        molecule2 -
        shouldMatchBonds -
        Throws:
        CDKException

      • calculateIsomorphs

        public void calculateIsomorphs​(IAtomContainer molecule1,
                               IAtomContainer molecule2,
                               boolean shouldMatchBonds)
                        throws CDKException
        Deprecated.
        This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
        Parameters:
        molecule1 -
        molecule2 -
        shouldMatchBonds -
        Throws:
        CDKException

      • removeRedundantMappingsForSingleAtomCase

        protected List<CDKRMap> removeRedundantMappingsForSingleAtomCase​(List<CDKRMap> overlaps)
        Deprecated.
        Parameters:
        overlaps -
        Returns:

      • getMaximum

        protected List getMaximum​(List overlaps)
        Deprecated.
        Parameters:
        overlaps -
        Returns:

      • identifySingleAtomsMatchedParts

        protected void identifySingleAtomsMatchedParts​(List<CDKRMap> list,
                                               IAtomContainer source,
                                               IAtomContainer target)
        Deprecated.
        Parameters:
        list -
        source -
        target -

      • isSubgraph

        protected boolean isSubgraph​(List<CDKRMap> rmaps1,
                             List<CDKRMap> rmaps2)
        Deprecated.
        Parameters:
        rmaps1 -
        rmaps2 -
        Returns:

      • isSameRMap

        protected boolean isSameRMap​(CDKRMap sourceRMap,
                             CDKRMap targetRMap)
        Deprecated.
        Parameters:
        sourceRMap - sourceAtom
        targetRMap - targetAtom
        Returns:

      • getMappings

        public List<Map<Integer,​Integer>> getMappings()
        Deprecated.
        Returns mapping solutions
        Returns:
        the mappings

      • setMappings

        public void setMappings​(List<Map<Integer,​Integer>> mappings)
        Deprecated.
        Set mapping solutions
        Parameters:
        mappings - the mappings to set

      • isTimeoutFlag

        public boolean isTimeoutFlag()
        Deprecated.
        Returns true if a time out occurred else false
        Returns:
        the timeoutFlag

      • setTimeoutFlag

        public void setTimeoutFlag​(boolean timeoutFlag)
        Deprecated.
        Set time out flag
        Parameters:
        timeoutFlag - the timeoutFlag to set