Package com.actelion.research.chem
Class MoleculeStandardizer
- java.lang.Object
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- com.actelion.research.chem.MoleculeStandardizer
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public class MoleculeStandardizer extends java.lang.Object
MoleculeStandardizerCopyright: Actelion Ltd., Inc. All Rights Reserved This software is the proprietary information of Actelion Pharmaceuticals, Ltd. Use is subject to license terms.
- Version:
- 1.0 Apr 5, 2012 MvK: Start implementation
- Author:
- Modest von Korff
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Constructor Summary
Constructors Constructor Description MoleculeStandardizer()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static MoleculeStandardizer
getInstance()
StereoMolecule
getStandardized(StereoMolecule mol)
Returns a fragment, no counter ion is given.StereoMolecule
getStandardized(java.lang.String idcode, java.lang.String coordinates)
Returns a fragment, no counter ion is given.boolean
repairAndUnify(StereoMolecule mol)
Repairs wrong charged quaternary nitrogen.
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Method Detail
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getStandardized
public StereoMolecule getStandardized(java.lang.String idcode, java.lang.String coordinates) throws java.lang.Exception
Returns a fragment, no counter ion is given.- Parameters:
idcode
-coordinates
- if null the result may change.- Returns:
- Throws:
java.lang.Exception
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getStandardized
public StereoMolecule getStandardized(StereoMolecule mol) throws java.lang.Exception
Returns a fragment, no counter ion is given.- Parameters:
mol
-- Returns:
- Throws:
java.lang.Exception
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repairAndUnify
public boolean repairAndUnify(StereoMolecule mol)
Repairs wrong charged quaternary nitrogen. Unifies carbonyl acid groups, sulfonic acid, phosphoric acid, phenolic oxygen. Means: negative charges are removed. Adds Na+ or Cl- for final charge equilibration. Calls ensure helper arrays at the end.- Parameters:
mol
-- Returns:
- true if an atom was added.
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getInstance
public static MoleculeStandardizer getInstance()
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