Package org.openscience.cdk.smsd.interfaces

Class AbstractMCS

java.lang.Object
org.openscience.cdk.smsd.interfaces.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>

  • Constructor Summary

    Constructors
    Constructor
    Description
    AbstractMCS()
    Deprecated.
     

  • Method Summary

    Modifier and Type
    Method
    Description
    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.
    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.
    abstract double
    getBondInSensitiveTimeOut()
    Deprecated.
    get timeout in mins for bond insensitive searches
    abstract double
    getBondSensitiveTimeOut()
    Deprecated.
    get timeout in mins for bond sensitive searches
    abstract Double
    getEnergyScore(int key)
    Deprecated.
    Returns summation energy score of the disorder if the MCS is removed from the target and query graph.
    abstract double
    getEuclideanDistance()
    Deprecated.
    Returns Euclidean Distance between query and target molecule.
    abstract Map<IAtom,IAtom>
    getFirstAtomMapping()
    Deprecated.
    Returns one of the best matches with atoms mapped.
    abstract Map<Integer,Integer>
    getFirstMapping()
    Deprecated.
    Returns one of the best matches with atom indexes mapped.
    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.
    abstract IAtomContainer
    getProductMolecule()
    Deprecated.
    Returns modified target molecule on which mapping was performed.
    abstract IAtomContainer
    getReactantMolecule()
    Deprecated.
    Returns modified query molecule on which mapping was performed.
    abstract Integer
    getStereoScore(int key)
    Deprecated.
    Returns a number which denotes the quality of the mcs.
    abstract double
    getTanimotoSimilarity()
    Deprecated.
    Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
    abstract void
    init(IAtomContainer source, IAtomContainer target, boolean removeHydrogen, boolean cleanAndConfigureMolecule)
    Deprecated.
    initialize query and target molecules.
    abstract void
    init(IQueryAtomContainer source, IAtomContainer target)
    Deprecated.
    initialize query and target molecules.
    abstract boolean
    isStereoMisMatch()
    Deprecated.
    Returns true if mols have different stereo chemistry else false if no stereo mismatch.
    abstract boolean
    isSubgraph()
    Deprecated.
    Checks if query is a subgraph of the target.
    abstract void
    setBondInSensitiveTimeOut(double bondInSensitiveTimeOut)
    Deprecated.
    set timeout in mins (default 1.00 min) for bond insensitive searches
    abstract void
    setBondSensitiveTimeOut(double bondSensitiveTimeOut)
    Deprecated.
    set timeout in mins (default 0.10 min) for bond sensitive searches
    abstract void
    setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter)
    Deprecated.
    initialize query and target molecules.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • AbstractMCS

      public AbstractMCS()
      Deprecated.

  • Method Details

    • 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