Package chemaxon.util

Class MolAligner


  • @PublicAPI
    public class MolAligner
    extends Object
    Tool for aligning a target molecule to a pattern molecule. Can be used for 2D and 3D alignment as well.
    • Constructor Detail

      • MolAligner

        public MolAligner()
        Creates a new MolAligner object.
      • MolAligner

        public MolAligner​(Molecule patternMolecule,
                          Molecule targetMolecule)
        Creates a new MolAligner object while setting the pattern and target molecules
        Parameters:
        patternMolecule - the pattern molecule
        targetMolecule -
    • Method Detail

      • setPatternMolecule

        public void setPatternMolecule​(Molecule mol)
        Sets pattern molecule and calculates its dimension
        Parameters:
        mol - pattern molecule
      • setTargetMolecule

        public void setTargetMolecule​(Molecule mol)
        Sets target molecule and calculates its dimension
        Parameters:
        mol - molecule to align
      • getError

        public double getError()
        Get the error for the best alignment
        Returns:
        the root mean square deviation of the mapping atoms
      • calculate

        public void calculate​(int[] hit)
        Calculate best alignment based on the hit map
        Parameters:
        hit - hit map array, use -1 for no matching atom index
      • align

        public void align​(int[] hit)
        Calculates and performs the best alignment possible specified by the hit map array.
        Parameters:
        hit - hit map array, use -1 for no matching atom index
        See Also:
        calculate(int[]), align()