Class MMPAlignmentResult

  • All Implemented Interfaces:
    chemaxon.marvin.alignment.AlignmentResult

    @PublicAPI
    public class MMPAlignmentResult
    extends Object
    implements chemaxon.marvin.alignment.AlignmentResult
    Results of the MMPAlignment process.
    • Method Detail

      • getMolecule1Aligned

        public Molecule getMolecule1Aligned()
        Specified by:
        getMolecule1Aligned in interface chemaxon.marvin.alignment.AlignmentResult
        Returns:
        the first (reference) molecule of the alignment with the new coordinates. If this molecule is set as rigid in AlignmentProperties.FlexibilityMode then the original coordinates are returned.
      • getMolecule2Aligned

        public Molecule getMolecule2Aligned()
        Specified by:
        getMolecule2Aligned in interface chemaxon.marvin.alignment.AlignmentResult
        Returns:
        the molecule "toAlign" with the modified coordinates.
      • getShapeScore

        public double getShapeScore()
        Returns:
        The shape overlay - atom type score, which is maximized during the alignment.
      • getShapeTanimoto

        public double getShapeTanimoto()
      • getRmsd

        public double getRmsd()
        Returns:
        coordinate RMSD of the MCS for the reference-toAlign atoms.
      • toMolecule

        public Molecule toMolecule()
        Creates a single two-fragment molecule from the reference and aligned molecule.
        Specified by:
        toMolecule in interface chemaxon.marvin.alignment.AlignmentResult
        Returns:
        a two-fragment molecule from the reference and aligned molecule the MCS rmsd, and Shape Tanimoto values are added as properties.