Package chemaxon.alignment

Class MMPAlignmentResult

java.lang.Object
chemaxon.alignment.MMPAlignmentResult
All Implemented Interfaces:
AlignmentResult
@PublicApi public class MMPAlignmentResult extends Object implements AlignmentResult
Results of the MMPAlignment process.

  • Method Details

    • getMolecule1Aligned

      public Molecule getMolecule1Aligned()
      Description copied from interface: AlignmentResult
      The molecule with coordinates changed to fulfill the alignment requested by the input parameters.
      Specified by:
      getMolecule1Aligned in interface 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()
      Description copied from interface: AlignmentResult
      The molecule with coordinates changed to fulfill the alignment requested by the input parameters.
      Specified by:
      getMolecule2Aligned in interface 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 AlignmentResult
      Returns:
      a two-fragment molecule from the reference and aligned molecule the MCS rmsd, and Shape Tanimoto values are added as properties.