def insert_g3testset(coll): for f in glob.glob("g*.txt"): print("Parsing " + f) for (m, charge, spin) in parse_file(f): try: clean_sites = [] for site in m: if Element.is_valid_symbol(site.specie.symbol): clean_sites.append(site) clean_mol = Molecule.from_sites(clean_sites, charge=charge, spin_multiplicity=spin) xyz = XYZ(clean_mol) bb = BabelMolAdaptor.from_string(str(xyz), "xyz") pbmol = pb.Molecule(bb.openbabel_mol) smiles = pbmol.write("smi").split()[0] can = pbmol.write("can").split()[0] inchi = pbmol.write("inchi") svg = pbmol.write("svg") d = {"molecule": clean_mol.as_dict()} comp = clean_mol.composition d["pretty_formula"] = comp.reduced_formula d["formula"] = comp.formula d["composition"] = comp.as_dict() d["elements"] = list(comp.as_dict().keys()) d["nelements"] = len(comp) d["charge"] = charge d["spin_multiplicity"] = spin d["smiles"] = smiles d["can"] = can d["inchi"] = inchi # d["names"] = get_nih_names(smiles) d["svg"] = svg d["xyz"] = str(xyz) d["tags"] = ["G305 test set"] coll.update( { "inchi": inchi, "charge": charge, "spin_multiplicity": spin }, {"$set": d}, upsert=True) except Exception as ex: print("Error in {}".format(f)) exc_type, exc_value, exc_traceback = sys.exc_info() traceback.print_exception(exc_type, exc_value, exc_traceback, limit=2, file=sys.stdout) print("{} parsed!".format(f))
print(fe.thermal_conductivity) # html print(fe.boiling_point) # html print(fe.melting_point) # html print(fe.critical_temperature) # html print(fe.superconduction_temperature) # html print(fe.liquid_range) # html print(fe.bulk_modulus) # html print(fe.youngs_modulus) # html print(fe.brinell_hardness) # html print(fe.rigidity_modulus) # html print(fe.mineral_hardness) # html print(fe.vickers_hardness) # html print(fe.density_of_solid) # html print(fe.coefficient_of_linear_thermal_expansion) # html print(fe.average_ionic_radius) print(fe.ionic_radii) print(fe.is_valid_symbol("Fe")) # dir print(fe.from_Z(26)) # dir print(fe.as_dict()) # dir print(fe.from_dict(fe.as_dict())) # dir print(fe.from_row_and_group(4, 8)) # dir print(fe.ground_state_term_symbol) # dir print(fe.icsd_oxidation_states) # dir print(fe.name) # dir print(fe.print_periodic_table()) # dir print(fe.term_symbols) # dir print(fe.valence) # dir print(fe.value) # dir print(fe.boiling_point) print(float(fe.boiling_point.to("")))