Class MoleculeStandardizer


  • public class MoleculeStandardizer
    extends java.lang.Object
    MoleculeStandardizer

    Copyright: Actelion Ltd., Inc. All Rights Reserved This software is the proprietary information of Actelion Pharmaceuticals, Ltd. Use is subject to license terms.

    Version:
    1.0 Apr 5, 2012 MvK: Start implementation
    Author:
    Modest von Korff
    • Constructor Detail

      • MoleculeStandardizer

        public MoleculeStandardizer()
    • Method Detail

      • getStandardized

        public StereoMolecule getStandardized​(java.lang.String idcode,
                                              java.lang.String coordinates)
                                       throws java.lang.Exception
        Returns a fragment, no counter ion is given.
        Parameters:
        idcode -
        coordinates - if null the result may change.
        Returns:
        Throws:
        java.lang.Exception
      • getStandardized

        public StereoMolecule getStandardized​(StereoMolecule mol)
                                       throws java.lang.Exception
        Returns a fragment, no counter ion is given.
        Parameters:
        mol -
        Returns:
        Throws:
        java.lang.Exception
      • repairAndUnify

        public boolean repairAndUnify​(StereoMolecule mol)
        Repairs wrong charged quaternary nitrogen. Unifies carbonyl acid groups, sulfonic acid, phosphoric acid, phenolic oxygen. Means: negative charges are removed. Adds Na+ or Cl- for final charge equilibration. Calls ensure helper arrays at the end.
        Parameters:
        mol -
        Returns:
        true if an atom was added.