public class TemplateExtractor extends Object
Constructor and Description |
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TemplateExtractor() |
Modifier and Type | Method and Description |
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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<BitSet> |
makeFingerprintsFromSdf(boolean anyAtom,
boolean anyAtomAnyBond,
Map<String,Integer> timings,
BufferedReader fin,
int limit) |
void |
PartitionRingsFromComplexRing(String dataFile) |
void |
ReadNCISdfFileAsTemplate(String dataFile) |
IMolecule |
removeLoopBonds(IMolecule molecule,
int position) |
IAtomContainer |
resetFlags(IAtomContainer ac) |
void |
writeChemModel(IMoleculeSet som,
String file,
String endFix) |
public void cleanDataSet(String dataFile)
public void ReadNCISdfFileAsTemplate(String dataFile)
public void PartitionRingsFromComplexRing(String dataFile)
public void extractUniqueRingSystemsFromFile(String dataFile)
public void writeChemModel(IMoleculeSet som, String file, String endFix)
public void makeCanonicalSmileFromRingSystems(String dataFileIn, String dataFileOut)
public List<BitSet> makeFingerprintsFromSdf(boolean anyAtom, boolean anyAtomAnyBond, Map<String,Integer> timings, BufferedReader fin, int limit) throws Exception
Exception
public void makeFingerprintFromRingSystems(String dataFileIn, String dataFileOut, boolean anyAtom, boolean anyAtomAnyBond) throws Exception
Exception
public IAtomContainer createAnyAtomAtomContainer(IAtomContainer atomContainer) throws Exception
Exception
public IAtomContainer resetFlags(IAtomContainer ac)
public static void main(String[] args)