Class Normalizer


  • @Deprecated
    public class Normalizer
    extends Object
    Deprecated.
    The functionality provided by with class is better suited to SMIRKS
    Adjusts parts of an AtomContainer to the configuration of a fragment.
    Author:
    shk3
    Source code:
    main
    Belongs to CDK module:
    smiles
    Created on:
    2004-03-04
    • Constructor Detail

      • Normalizer

        public Normalizer()
        Deprecated.
    • Method Detail

      • normalize

        public static boolean normalize​(IAtomContainer ac,
                                        Document doc)
                                 throws CDKException
        Deprecated.
        The method takes an XML files like the following:
        <replace-set>
        <replace>O=N=O</replace>
        <replacement>[O-][N+]=O</replacement>
        </replace-set>
        All parts in ac which are the same as replace will be changed according to replacement. Currently the following changes are done: BondOrder, FormalCharge. For detection of fragments like replace, we rely on UniversalIsomorphismTester. doc may contain several replace-sets and a replace-set may contain several replace fragments, which will all be normalized according to replacement.
        Parameters:
        ac - The atomcontainer to normalize.
        doc - The configuration file.
        Returns:
        Did a replacement take place?
        Throws:
        InvalidSmilesException - doc contains an invalid smiles.
        CDKException