def make_opsin_input():
seen = set()
with open('opsin_input.txt', 'w') as op_out:
result_dir = '../examples/mp/results'
for filename in os.listdir(result_dir):
if not filename.endswith('.json'):
continue
patent_id = filename[:-9]
print(patent_id)
tetko_file = '../examples/mp/tetko/%s.json' % patent_id
if not os.path.isfile(tetko_file):
continue
with open('%s/%s' % (result_dir, filename)) as fin:
results = json.loads(fin.read().decode('utf8'))
with open(tetko_file) as tin:
tetko_results = json.loads(tin.read().decode('utf8'))
for result in results:
if 'names' not in result:
continue
for name in result['names']:
in_tetko = False
for tetko_result in tetko_results:
if excess_normalize(name) == excess_normalize(
tetko_result['name']):
in_tetko = True
break
if not in_tetko and name not in seen:
seen.add(name)
op_out.write(('%s\n' % name).encode('utf8'))
def _get_standardized_result(result, tetko_results, n2s):
names = sorted(result['names'], key=len, reverse=True)
fv = float_value(standardize_value(result['melting_points'][0]['value']))
if not fv:
print('INVALID')
print(names)
print(result['melting_points'][0]['value'])
return
for name in names:
for tetko_result in tetko_results:
if excess_normalize(name) == excess_normalize(
tetko_result['name']):
return {
'name': name,
'smiles': tetko_result['smiles'],
'inchikey': tetko_result['inchikey'],
'value': result['melting_points'][0]['value'],
'float_value': fv
}
for name in names:
if name not in n2s:
print('MISSING: %s' % name)
continue
# results = cirpy.query(name.encode('utf8'), 'smiles', ['name_by_opsin', 'name_by_cir'])
# print(name)
# print([(r.value, r.resolver) for r in results])
# n2s[name] = [(r.value, r.resolver) for r in results]
# with open('n2s.pickle', 'w') as fout:
# pickle.dump(n2s, fout)
smiles = n2s[name]
if smiles:
if '.' in smiles:
continue
mol = Chem.MolFromSmiles(smiles)
if mol:
inchikey = Chem.InchiToInchiKey(Chem.MolToInchi(mol))
return {
'name': name,
'smiles': smiles,
'inchikey': inchikey,
'value': result['melting_points'][0]['value'],
'float_value': fv
}