Package chemaxon.marvin.alignment

Class MolAligner

java.lang.Object
chemaxon.marvin.alignment.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 Summary

    Constructors
    Constructor
    Description
    MolAligner()
    Creates a new MolAligner object.
    MolAligner(Molecule patternMolecule, Molecule targetMolecule)
    Creates a new MolAligner object while setting the pattern and target molecules

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    align()
    Executes the best alignment based on hit map provided earlier
    void
    align(int[] hit)
    Calculates and performs the best alignment possible specified by the hit map array.
    static void
    align(Molecule pattern, Molecule target, int[] hit)
    Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.
    static void
    align(Molecule pattern, Molecule target, int[][] groupHit)
    Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.
    void
    calculate(int[] hit)
    Calculate best alignment based on the hit map
    double
    getError()
    Get the error for the best alignment
    void
    setPatternMolecule(Molecule mol)
    Sets pattern molecule and calculates its dimension
    void
    setTargetMolecule(Molecule mol)
    Sets target molecule and calculates its dimension

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • 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

  • Method Details

    • 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()
      Executes the best alignment based on hit map provided earlier
      See Also:

    • 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:

    • align

      public static void align(Molecule pattern, Molecule target, int[] hit)
      Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping. Possibly in the same position or optimally close to it.
      Parameters:
      pattern - the pattern molecule for alignment
      target - the target molecule that should be aligned to the pattern
      hit - mapping of the atom IDs of the pattern molecule to the atom IDs of the target molecule, returned by a search. Its size must be equal to the atom count of the pattern molecule, and for each ID i,
      invalid @link 
      {@link hit[i]
      } must be the mapped target atom ID or -1 if the atom is not mapped

    • align

      public static void align(Molecule pattern, Molecule target, int[][] groupHit)
      Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping. Possibly in the same position or optimally close to it.
      Parameters:
      pattern - the pattern molecule for alignment
      target - the target molecule that should be aligned to the pattern
      groupHit - mapping of the atom IDs of the pattern molecule to the atom IDs of the target molecule, returned by a search. Its size must be equal to the atom count of the pattern molecule, and for each ID i,
      invalid @link 
      {@link groupHit[i]
      } must be the array of mapped target atom IDs (usually exactly one)