Interface PairwiseComparison

  • All Known Implementing Classes:
    PairwiseAlignment, PairwiseSimilarity3D

    @PublicAPI
    public interface PairwiseComparison
    This interface designed for comparing two molecules in 3D by various overlay methodologies. One of molecules is called the query and the other is the target. The comparison results in the best overlay: the orientation and the conformation. The shape Tanimoto and the overlay score may be retrieved. Example usage:
     PairwiseComparison pc = new PairwiseAlignment();
     pc.setQueryRigidForced(true);
     pc.setTargetRigidForced(false);
     pc.setCount(4);
     pc.setQuery(Molecule query);
     double score = pc.similarity(Molecule target);
     double tanimoto = pc.getShapeTanimoto();
     
    • Method Detail

      • setQuery

        void setQuery​(Molecule query)
               throws chemaxon.marvin.alignment.AlignmentException
        Throws:
        chemaxon.marvin.alignment.AlignmentException
      • similarity

        double similarity​(Molecule target)
                   throws chemaxon.marvin.alignment.AlignmentException
        Calculates the 3D similarity between the previously set query and the target.
        Parameters:
        target - target to calculate similarity
        Returns:
        the similarity value.
        Throws:
        chemaxon.marvin.alignment.AlignmentException
      • setQuery

        void setQuery​(AlignmentMolecule query)
               throws chemaxon.marvin.alignment.AlignmentException
        Throws:
        chemaxon.marvin.alignment.AlignmentException
      • similarity

        double similarity​(AlignmentMolecule target)
                   throws chemaxon.marvin.alignment.AlignmentException
        Throws:
        chemaxon.marvin.alignment.AlignmentException
      • getAlignedMoleculesAsFragments

        Molecule getAlignedMoleculesAsFragments()
        After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.
        Returns:
        the aligned molecules.
      • getAlignedTarget

        Molecule getAlignedTarget()
        Returns:
        the target molecule in the final orientation and conformation.
      • getAlignedQuery

        Molecule getAlignedQuery()
      • removeAllMolecules

        void removeAllMolecules()
      • setQueryRigidForced

        void setQueryRigidForced​(boolean forced)
        Set this molecule to be rigid in the input conformation even if it contains rotatable bonds
        Parameters:
        forced - if true than rigid.
      • setTargetRigidForced

        void setTargetRigidForced​(boolean forced)
        Set this molecule to be rigid in the input conformation even if it contains rotatable bonds
        Parameters:
        forced - if true than rigid.
      • addNodeColorWeight

        void addNodeColorWeight​(int t1,
                                int t2,
                                double w)
      • getShapeTanimoto

        double getShapeTanimoto()
                         throws chemaxon.marvin.alignment.AlignmentException
        Throws:
        chemaxon.marvin.alignment.AlignmentException
      • setLicenseEnvironment

        void setLicenseEnvironment​(String env)
      • setCount

        void setCount​(int count)