public String getInChIKey(net.bioclipse.core.domain.IMolecule.Property urgency)
throws BioclipseException {
switch (urgency) {
case USE_CACHED:
return cachedInchi == null ? "" : cachedInchi.getKey();
case USE_CACHED_OR_CALCULATED:
if (cachedInchi != null) {
return cachedInchi.getKey();
}
case USE_CALCULATED:
calculateInchi();
return cachedInchi.getKey();
default:
throw new IllegalArgumentException("Unrecognized Property:" + urgency);
}
}
/** @throws BioclipseException */
private void calculateInchi() throws BioclipseException {
try {
IAtomContainer clone = (IAtomContainer) getAtomContainer().clone();
// remove aromaticity flags
for (IAtom atom : clone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : clone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
if (factory == null) {
factory = InChIGeneratorFactory.getInstance();
}
InChIGenerator gen = factory.getInChIGenerator(clone);
INCHI_RET status = gen.getReturnStatus();
if (status == INCHI_RET.OKAY || status == INCHI_RET.WARNING) {
InChI inchi = new InChI();
inchi.setValue(gen.getInchi());
inchi.setKey(gen.getInchiKey());
cachedInchi = inchi;
} else {
throw new InvalidParameterException(
"Error while generating InChI (" + status + "): " + gen.getMessage());
}
} catch (Exception e) {
throw new BioclipseException("Could not create InChI: " + e.getMessage(), e);
}
}