def _get_smiles(inchi_term):
'''Get smiles.'''
try:
mol = inchi.MolFromInchi(inchi_term, treatWarningAsError=True)
return rdmolfiles.MolToSmiles(mol)
except Exception:
return None
def parse_f(f):
names = ['']
cid = -1
CAS = f.split('/')[1] if '/' in f else f
CAS = CAS.split('.')[0]
if CAS in ignored_CASs:
return None
failed_mol = False
try:
if CAS in syn_data:
d = syn_data[CAS]
if 'pubchem' in d:
raise Exception(
'Pubchem specified, not trying to use the mol file')
elif 'formula' in d:
raise Exception(
'Formula specified, not trying to use the mol file')
try:
mol = Chem.MolFromMolFile(f)
assert mol is not None
except:
print('Cannot read %s' % f)
1 / 0
try:
inchi_val = inchi.MolToInchi(mol)
except:
print('BAILING ON %s' % f)
1 / 0
mol = inchi.MolFromInchi(inchi_val) # Works better for ions
if mol is None:
print('BAILING ON reconversion to mol %s' % f)
1 / 0
except:
failed_mol = True
if CAS in syn_data:
d = syn_data[CAS]
if 'pubchem' in d:
if str(d['pubchem']) in mycache:
cid, iupac_name, names, mw, smi, inchi_val, inchikey, formula = mycache[
str(d['pubchem'])]
else:
pc = Compound.from_cid(d['pubchem'])
cid = pc.cid
iupac_name = pc.iupac_name
names = pc.synonyms
mw = pc.molecular_weight
smi = pc.canonical_smiles
inchi_val = pc.inchi
inchikey = pc.inchikey
formula = pc.molecular_formula
mycache[str(d['pubchem'])] = (cid, iupac_name, names, mw,
smi, inchi_val, inchikey,
formula)
else:
cid = -1
names = d['synonyms'] if 'synonyms' in d else ['']
mw = float(d['MW'])
smi = d['smiles'] if 'smiles' in d else ''
formula = d['formula'] if 'formula' in d else ''
inchi_val = d['inchi'] if 'inchi' in d else ''
inchikey = d['inchikey'] if 'inchikey' in d else ''
iupac_name = ''
else:
print('FAILED on %s and no custom data was available either' % CAS)
return None
if not failed_mol:
smi = Chem.MolToSmiles(mol, True)
inchi_val = inchi.MolToInchi(mol)
inchikey = inchi.InchiToInchiKey(inchi_val)
mw = Descriptors.MolWt(mol)
# for i in mol.GetAtoms():
# if i.GetIsotope():
# mw = Descriptors.ExactMolWt(mol)
# break
formula = CalcMolFormula(mol, True, True)
iupac_name = ''
try:
if not failed_mol:
if str(inchikey) in mycache:
cid, iupac_name, names = mycache[str(inchikey)]
else:
try:
pc = get_compounds(inchikey, 'inchikey')[0]
cid = pc.cid
iupac_name = pc.iupac_name
names = pc.synonyms
mycache[str(inchikey)] = (cid, iupac_name, names)
except:
mycache[str(inchikey)] = (-1, '', [''])
except:
cid = -1
iupac_name = ''
names = ['']
other_CAS = []
if CAS in pdf_data:
d = pdf_data[CAS]
name = d['Name']
if 'Other Names' in d:
syns = d['Other Names']
else:
syns = []
if not iupac_name:
iupac_name = name
else:
syns.insert(0, name)
if 'Deleted CAS' in d:
other_CAS.extend(d['Deleted CAS'])
if 'Alternate CAS' in d:
other_CAS.extend(d['Alternate CAS'])
syns = [i for i in syns if i not in dup_names]
names = syns + [i for i in names if i not in all_names] + other_CAS
actual_names = []
for name in names:
if name in all_user_names:
# If the name is in the user db, only add it if it corresponds to this CAS number
if CAS in syn_data and 'synonyms' in syn_data[
CAS] and name in syn_data[CAS]['synonyms']:
actual_names.append(name)
else:
# Discard it otherwise
pass
else:
# If the name is not in the user db we're all good
actual_names.append(name)
if CAS in syn_data and 'synonyms' in syn_data[CAS]:
# If the user has any syns for this cas number, add those names if the name hasn't already been aded
for n in syn_data[CAS]['synonyms']:
if n not in actual_names:
actual_names.append(n)
actual_names = [i for i in actual_names if i]
if inchi_val is not None:
inchi_val = inchi_val.replace('InChI=1S/', '')
formula = serialize_formula(formula)
s = '%d\t%s\t%s\t%g\t%s\t%s\t%s\t%s\t' % (cid, CAS, formula, mw, smi,
inchi_val, inchikey, iupac_name)
s += '\t'.join(actual_names)
print(s)
return None
for lig in chembl_help:
if chembl[i][0] == lig[0] or chembl[i][0] == None or str(
chembl[i][0]) == '':
delete = True
if delete == True:
i = i + 1
continue
chembl_help.append(list(chembl[i]))
i = i + 1
#pprint (chembl_help)
#Chembl standardize
for lig in range(0, len(chembl_help)):
#print ('Now I do this from Chembl: ' + chembl_help[lig][0])
mol = inchi.MolFromInchi(chembl_help[lig][0], sanitize=False)
try:
rdmolops.RemoveStereochemistry(mol)
except Exception:
print("Not able to remove stereochemistry. Chembl.")
try:
mol = standardise.run(mol)
except standardise.StandardiseException as e:
logging.warn(e.message)
try:
mol = s.standardize(mol)
except Exception:
print("Not able to standardize. Chembl.")
try:
mol = s.tautomer_parent(mol, skip_standardize=True)
except Exception:
curs2.execute("select receptor_id, uniprot_name from receptor")
receptor_dict = dict(curs2.fetchall())
curs3 = conn.cursor()
curs3.execute("select source_id, article_doi from source")
source_dict = dict(curs3.fetchall())
global similar_dict
similar_dict = {}
#drawing and saving picture of ligand, if not exists
for i in ligand_d:
exists = os.path.isfile(
'/home/adam/django_database/web/static/web/inchi/ligand_' + str(i[0]) +
'.png')
if not exists:
m = inchi.MolFromInchi(i[1], sanitize=False)
if m != None and m != '':
Draw.MolToFile(
m, '/home/adam/django_database/web/static/web/inchi/ligand_' +
str(i[0]) + '.png')
class ActivityList(ListView):
model = Activity
def get_context_data(self, **kwargs):
context = super(ActivityList, self).get_context_data(**kwargs)
return context
class ReceptorList(ListView):