Hi RDKit gurus.
I noted that compound 4 in the sdf, a poorly represented aryl system fails
with this error.
Any ideas on how to try/catch this error, or skip the molecule with an
error, as the script dies painfully when it gets this far. Snippet enclosed
of the python call.
Best - and thanks,
mike
def calc_SDF(file_name_list):
print("")
print("SDF Chunking Completed")
print("")
calc_values = []
calc_values.append(str("ORIG_SMI SMILES InChi HAC HBD HBA molWt nRotB nAr
TPSA nChr"))
for j in range(len(file_name_list)):
assert os.path.isfile(file_name_list[j]), "File %s does not exist!" %
file_name_list[j]
mols = file_name_list[j]
suppl = Chem.SDMolSupplier(mols)
lensuppl = len(suppl)
remover = SaltRemover()
for i in range(lensuppl):
if suppl[i] is None:
with open('.//test_out.csv', 'w', newline='') as csvfile:
output = csv.writer(csvfile, delimiter=',', quoting =
csv.QUOTE_ALL)
output.writerow(['Compound: ', i, ' failed.'])
else:
orig = Chem.MolToSmiles(suppl[i])
Chem.rdmolops.SanitizeMol(suppl[i],268435455)
y = Chem.MolToSmiles(remover.StripMol(suppl[i]))
HAC = Chem.Lipinski.HeavyAtomCount(Chem.MolFromSmiles(y))
HBD = Chem.Lipinski.NumHDonors(Chem.MolFromSmiles(y))
HBA = Chem.Lipinski.NumHAcceptors(Chem.MolFromSmiles(y))
molwt = Chem.Descriptors.MolWt(Chem.MolFromSmiles(y))
nRotB = Chem.Lipinski.NumRotatableBonds(Chem.MolFromSmiles(y))
nAr = Chem.Lipinski.NumAromaticRings(Chem.MolFromSmiles(y))
InChi = Chem.MolToInchi(Chem.MolFromSmiles(y))
TPSA = Chem.Descriptors.TPSA(Chem.MolFromSmiles(y))
nChr =
len(Chem.FindMolChiralCenters(Chem.MolFromSmiles(y),includeUnassigned=True))
calc_values.append(str('{} {} {} {} {} {} {:.2f} {} {} {:.0f}
{}'.format(orig, y, InChi, HAC, HBD, HBA, molwt, nRotB, nAr, TPSA, nChr)))
print(j, i)
now = datetime.datetime.now()
print("")
print("Job ended at", now.strftime("%H:%M"), "on",
now.strftime("%Y-%m-%d"))
log.close()
sys.stderr = save_std_err
return calc_values
enamine_fail.sdf
Description: Binary data
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