Package chemaxon.marvin.alignment

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 Details

    • 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()

    • setProgressBar

      void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)

    • 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)