Package org.openscience.cdk.normalize
Class Normalizer
- java.lang.Object
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- org.openscience.cdk.normalize.Normalizer
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@Deprecated public class Normalizer extends Object
Deprecated.The functionality provided by with class is better suited to SMIRKSAdjusts 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 Constructor Description Normalizer()
Deprecated.
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Method Summary
All Methods Static Methods Concrete Methods Deprecated Methods 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.
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Method Detail
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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
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