Package 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
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic 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.
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Constructor Details
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Normalizer
public Normalizer()Deprecated.
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Method Details
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normalize
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
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