org.openscience.cdk.normalize

Class Normalizer

java.lang.Object

org.openscience.cdk.normalize.Normalizer

Deprecated.

The functionality provided by with class is better suited to SMIRKS

@Deprecated
public class Normalizer
extends Object

Adjusts parts of an AtomContainer to the configuration of a fragment.

Author:

shk3

Source code:

master

Belongs to CDK module:

smiles

Created on:

2004-03-04

Constructor Summary

Constructors

Constructor and Description
Normalizer() Deprecated.

Method Summary

Modifier and Type	Method and 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 Detail

Normalizer

public Normalizer()

Deprecated.

Method Detail

normalize

public static boolean normalize(IAtomContainer ac,
                                Document doc)
                         throws InvalidSmilesException,
                                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