IAtomContainer parsedContent = inchiTool.processFormula( cf.getBuilder().newInstance(IAtomContainer.class), formula); if (connections != null)
@Override public void endElement(String uri, String local, String raw) { logger.debug("end element: ", raw); if ("identifier".equals(local)) { if (tautomer != null) { // ok, add tautomer setOfMolecules.addAtomContainer(tautomer); chemModel.setMoleculeSet(setOfMolecules); chemSequence.addChemModel(chemModel); } } else if ("formula".equals(local)) { if (tautomer != null) { logger.info("Parsing <formula> chars: ", currentChars); tautomer = inchiTool.processFormula(setOfMolecules.getBuilder().newInstance(IAtomContainer.class), currentChars); } else { logger.warn("Cannot set atom info for empty tautomer"); } } else if ("connections".equals(local)) { if (tautomer != null) { logger.info("Parsing <connections> chars: ", currentChars); inchiTool.processConnections(currentChars, tautomer, -1); } else { logger.warn("Cannot set dbond info for empty tautomer"); } } else { // skip all other elements } }