def getCCDefObj(self, dataContainer, molBuildType="model-xyz", suppressHydrogens=False): """Build OE molecule from the input chemical component definition object.""" # oemf = OeMoleculeFactory() if not self.__verbose: oemf.setQuiet() ccId = oemf.setChemCompDef(dataContainer) oemf.build(molBuildType=molBuildType) if self.__verbose: logger.info(" CCId = %s", ccId) logger.info(" Title = %s", oemf.getTitle()) logger.info(" SMILES = %s", oemf.getCanSMILES()) logger.info(" SMILES (stereo) = %s", oemf.getIsoSMILES()) logger.info(" Formula (Hill) = %s", oemf.getFormula()) logger.info(" InChI key = %s", oemf.getInChIKey()) logger.info(" InChI = %s", oemf.getInChI()) fD = {} fD = {"Formula": oemf.getFormula(), "SMILES": oemf.getCanSMILES(), "SMILES_STEREO": oemf.getIsoSMILES(), "InChI": oemf.getInChI(), "InChIKey": oemf.getInChIKey()} if suppressHydrogens: tMol = oemf.getGraphMolSuppressH() else: tMol = oemf.getMol() fD["OEMOL"] = tMol fD["xyz"] = oemf.getAtomDetails(xyzType="model") return (ccId, tMol, fD)
def getCCDefFile(self, ccFilePath, molBuildType="model-xyz", suppressHydrogens=False): """Fetch the molecule definition (ccPath) and build OE molecules for comparison. """ # mU = MarshalUtil(workPath=self.__workPath) rdCcObjL = mU.doImport(ccFilePath, fmt="mmcif") oemf = OeMoleculeFactory() if not self.__verbose: oemf.setQuiet() ccId = oemf.setChemCompDef(rdCcObjL[0]) oemf.build(molBuildType=molBuildType) if self.__verbose: logger.info(" CCId = %s", ccId) logger.info(" Title = %s", oemf.getTitle()) logger.info(" SMILES = %s", oemf.getCanSMILES()) logger.info(" SMILES (stereo) = %s", oemf.getIsoSMILES()) logger.info(" Formula (Hill) = %s", oemf.getFormula()) logger.info(" InChI key = %s", oemf.getInChIKey()) logger.info(" InChI = %s", oemf.getInChI()) fD = {} fD = {"Formula": oemf.getFormula(), "SMILES": oemf.getCanSMILES(), "SMILES_STEREO": oemf.getIsoSMILES(), "InChI": oemf.getInChI(), "InChIKey": oemf.getInChIKey()} if suppressHydrogens: tMol = oemf.getGraphMolSuppressH() else: tMol = oemf.getMol() fD["OEMOL"] = tMol fD["xyz"] = oemf.getAtomDetails(xyzType="model") return (ccId, tMol, fD)