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("")))
