Package org.openscience.cdk.modeling.builder3d

Class TemplateExtractor

java.lang.Object

org.openscience.cdk.modeling.builder3d.TemplateExtractor

public class TemplateExtractor
extends Object

Helper class that help setup a template library of CDK's Builder3D.

Author:

Christian Hoppe

Source code:

main

Belongs to CDK module:

builder3dtools

Constructor Summary

Constructors

Constructor	Description
TemplateExtractor()

Method Summary

Modifier and Type	Method	Description
void	cleanDataSet(String dataFile)
IAtomContainer	createAnyAtomAtomContainer(IAtomContainer atomContainer)
void	extractUniqueRingSystemsFromFile(String dataFile)
static void	main(String[] args)
void	makeCanonicalSmileFromRingSystems(String dataFileIn, String dataFileOut)
void	makeFingerprintFromRingSystems(String dataFileIn, String dataFileOut, boolean anyAtom, boolean anyAtomAnyBond)
List<IBitFingerprint>	makeFingerprintsFromSdf(boolean anyAtom, boolean anyAtomAnyBond, Map<String,Integer> timings, BufferedReader fin, int limit)
void	PartitionRingsFromComplexRing(String dataFile)
void	ReadNCISdfFileAsTemplate(String dataFile)
IAtomContainer	removeLoopBonds(IAtomContainer molecule, int position)
IAtomContainer	resetFlags(IAtomContainer ac)
void	writeChemModel(IAtomContainerSet som, String file, String endFix)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TemplateExtractor

public TemplateExtractor()

Method Detail

cleanDataSet

public void cleanDataSet(String dataFile)

ReadNCISdfFileAsTemplate

public void ReadNCISdfFileAsTemplate(String dataFile)

PartitionRingsFromComplexRing

public void PartitionRingsFromComplexRing(String dataFile)

extractUniqueRingSystemsFromFile

public void extractUniqueRingSystemsFromFile(String dataFile)

writeChemModel

public void writeChemModel(IAtomContainerSet som,
                           String file,
                           String endFix)

makeCanonicalSmileFromRingSystems

public void makeCanonicalSmileFromRingSystems(String dataFileIn,
                                              String dataFileOut)

makeFingerprintsFromSdf

public List<IBitFingerprint> makeFingerprintsFromSdf(boolean anyAtom,
                                                     boolean anyAtomAnyBond,
                                                     Map<String,Integer> timings,
                                                     BufferedReader fin,
                                                     int limit)
                                              throws Exception

Throws:

Exception

makeFingerprintFromRingSystems

public void makeFingerprintFromRingSystems(String dataFileIn,
                                           String dataFileOut,
                                           boolean anyAtom,
                                           boolean anyAtomAnyBond)
                                    throws Exception

Throws:

Exception

removeLoopBonds

public IAtomContainer removeLoopBonds(IAtomContainer molecule,
                                      int position)

createAnyAtomAtomContainer

public IAtomContainer createAnyAtomAtomContainer(IAtomContainer atomContainer)
                                          throws Exception

Throws:

Exception

resetFlags

public IAtomContainer resetFlags(IAtomContainer ac)

main

public static void main(String[] args)