Package org.openscience.cdk.smsd.interfaces

Class AbstractMCS

  • Direct Known Subclasses:
    Isomorphism
    @Deprecated
public abstract class AbstractMCS
extends Object
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    Interface for all MCS algorithms.
    Author:
    Syed Asad Rahman <asad@ebi.ac.uk>
    Source code:
    main
    Belongs to CDK module:
    smsd

    • Constructor Detail

      • AbstractMCS

        public AbstractMCS()
        Deprecated.

    • Method Detail

      • init

        public abstract void init​(IAtomContainer source,
                          IAtomContainer target,
                          boolean removeHydrogen,
                          boolean cleanAndConfigureMolecule)
                   throws CDKException
        Deprecated.
        initialize query and target molecules.
        Parameters:
        source - query mol
        target - target mol
        removeHydrogen - true if remove H (implicit) before mapping
        cleanAndConfigureMolecule - eg: percieveAtomTypesAndConfigureAtoms, detect aromaticity etc
        Throws:
        CDKException

      • init

        public abstract void init​(IQueryAtomContainer source,
                          IAtomContainer target)
                   throws CDKException
        Deprecated.
        initialize query and target molecules. Note: Here its assumed that hydrogens are implicit and user has called these two methods percieveAtomTypesAndConfigureAtoms and CDKAromicityDetector before initializing calling this method.
        Parameters:
        source - query mol
        target - target mol
        Throws:
        CDKException

      • setChemFilters

        public abstract void setChemFilters​(boolean stereoFilter,
                                    boolean fragmentFilter,
                                    boolean energyFilter)
        Deprecated.
        initialize query and target molecules.
        Parameters:
        stereoFilter - set true to rank the solutions as per stereo matches
        fragmentFilter - set true to return matches with minimum fragments
        energyFilter - set true to return matches with minimum bond changes based on the bond breaking energy

      • getEnergyScore

        public abstract Double getEnergyScore​(int key)
        Deprecated.
        Returns summation energy score of the disorder if the MCS is removed from the target and query graph. Amongst the solutions, a solution with lowest energy score is preferred.
        Parameters:
        key - Index of the mapping solution
        Returns:
        Total bond breaking energy required to remove the mapped part

      • getFragmentSize

        public abstract Integer getFragmentSize​(int key)
        Deprecated.
        Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph. Amongst the solutions, a solution with lowest fragment size is preferred.
        Parameters:
        key - Index of the mapping solution
        Returns:
        Fragment count(s) generated after removing the mapped parts

      • getProductMolecule

        public abstract IAtomContainer getProductMolecule()
        Deprecated.
        Returns modified target molecule on which mapping was performed.
        Returns:
        return modified product Molecule

      • getReactantMolecule

        public abstract IAtomContainer getReactantMolecule()
        Deprecated.
        Returns modified query molecule on which mapping was performed.
        Returns:
        return modified reactant Molecule

      • getStereoScore

        public abstract Integer getStereoScore​(int key)
        Deprecated.
        Returns a number which denotes the quality of the mcs. A solution with highest stereo score is preferred over other scores.
        Parameters:
        key - Index of the mapping solution
        Returns:
        true if no stereo mismatch occurs else false if stereo mismatch occurs

      • isStereoMisMatch

        public abstract boolean isStereoMisMatch()
        Deprecated.
        Returns true if mols have different stereo chemistry else false if no stereo mismatch.
        Returns:
        true if mols have different stereo chemistry else false if no stereo mismatch. true if stereo mismatch occurs else true if stereo mismatch occurs.

      • isSubgraph

        public abstract boolean isSubgraph()
        Deprecated.
        Checks if query is a subgraph of the target. Returns true if query is a subgraph of target else false
        Returns:
        true if query molecule is a subgraph of the target molecule

      • getTanimotoSimilarity

        public abstract double getTanimotoSimilarity()
                                      throws IOException
        Deprecated.
        Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
        Returns:
        Tanimoto Similarity between 0 and 1
        Throws:
        IOException

      • getEuclideanDistance

        public abstract double getEuclideanDistance()
                                     throws IOException
        Deprecated.
        Returns Euclidean Distance between query and target molecule.
        Returns:
        Euclidean Distance (lower the score, better the match)
        Throws:
        IOException

      • getAllAtomMapping

        public abstract 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.
        Returns:
        All possible MCS atom Mappings

      • getAllMapping

        public abstract 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.
        Returns:
        All possible MCS Mapping Index

      • getFirstAtomMapping

        public abstract Map<IAtom,​IAtom> getFirstAtomMapping()
        Deprecated.
        Returns one of the best matches with atoms mapped.
        Returns:
        Best Atom Mapping

      • getFirstMapping

        public abstract Map<Integer,​Integer> getFirstMapping()
        Deprecated.
        Returns one of the best matches with atom indexes mapped.
        Returns:
        Best Mapping Index

      • getBondSensitiveTimeOut

        public abstract double getBondSensitiveTimeOut()
        Deprecated.
        get timeout in mins for bond sensitive searches
        Returns:
        the bondSensitive TimeOut

      • setBondSensitiveTimeOut

        public abstract void setBondSensitiveTimeOut​(double bondSensitiveTimeOut)
        Deprecated.
        set timeout in mins (default 0.10 min) for bond sensitive searches
        Parameters:
        bondSensitiveTimeOut - the bond Sensitive Timeout in mins (default 0.30 min)

      • getBondInSensitiveTimeOut

        public abstract double getBondInSensitiveTimeOut()
        Deprecated.
        get timeout in mins for bond insensitive searches
        Returns:
        the bondInSensitive TimeOut

      • setBondInSensitiveTimeOut

        public abstract void setBondInSensitiveTimeOut​(double bondInSensitiveTimeOut)
        Deprecated.
        set timeout in mins (default 1.00 min) for bond insensitive searches
        Parameters:
        bondInSensitiveTimeOut - the bond insensitive