Class TemplateExtractor
java.lang.Object
org.openscience.cdk.modeling.builder3d.TemplateExtractor
Helper class that help setup a template library of CDK's Builder3D.
- Author:
- Christian Hoppe
- Source code:
- main
- Belongs to CDK module:
- builder3dtools
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
cleanDataSet
(String dataFile) createAnyAtomAtomContainer
(IAtomContainer atomContainer) void
extractUniqueRingSystemsFromFile
(String dataFile) static void
void
makeCanonicalSmileFromRingSystems
(String dataFileIn, String dataFileOut) void
makeFingerprintFromRingSystems
(String dataFileIn, String dataFileOut, boolean anyAtom, boolean anyAtomAnyBond) makeFingerprintsFromSdf
(boolean anyAtom, boolean anyAtomAnyBond, Map<String, Integer> timings, BufferedReader fin, int limit) void
PartitionRingsFromComplexRing
(String dataFile) void
ReadNCISdfFileAsTemplate
(String dataFile) removeLoopBonds
(IAtomContainer molecule, int position) void
writeChemModel
(IAtomContainerSet som, String file, String endFix)
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Constructor Details
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TemplateExtractor
public TemplateExtractor()
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Method Details
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cleanDataSet
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ReadNCISdfFileAsTemplate
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PartitionRingsFromComplexRing
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extractUniqueRingSystemsFromFile
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writeChemModel
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makeCanonicalSmileFromRingSystems
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makeFingerprintsFromSdf
public List<IBitFingerprint> makeFingerprintsFromSdf(boolean anyAtom, boolean anyAtomAnyBond, Map<String, Integer> timings, BufferedReader fin, int limit) throws Exception- Throws:
Exception
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makeFingerprintFromRingSystems
public void makeFingerprintFromRingSystems(String dataFileIn, String dataFileOut, boolean anyAtom, boolean anyAtomAnyBond) throws Exception - Throws:
Exception
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removeLoopBonds
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createAnyAtomAtomContainer
- Throws:
Exception
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resetFlags
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main
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