コード例 #1
0
 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);
   }
 }
コード例 #2
0
 /** @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);
   }
 }