Package org.openscience.cdk.normalize

Class Normalizer

java.lang.Object
org.openscience.cdk.normalize.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 Summary

    Constructors
    Constructor
    Description
    Normalizer()
    Deprecated.
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static boolean
    normalize(IAtomContainer ac, Document doc)
    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.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • Normalizer

      public Normalizer()
      Deprecated.

  • Method Details

    • 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