Hi David,
a workaround could be adding a final check after the for loop:
#!/usr/bin/env python
from rdkit import Chem
suppl1 = Chem.SmilesMolSupplier('test1.smi', titleLine=False, nameColumn=1)
rec_num = 0
print("len(suppl1) = {0:d}".format(len(suppl1)))
for mol in suppl1:
rec_num += 1
if not mol:
print('Record {} not read.'.format(rec_num))
else:
print('Record {} read ok.'.format(rec_num))
if (rec_num == len(suppl1) - 1):
rec_num += 1
print('Record {} not read.'.format(rec_num))
suppl2 = Chem.SmilesMolSupplier('test2.smi', titleLine=False, nameColumn=1)
rec_num = 0
print("len(suppl2) = {0:d}".format(len(suppl2)))
for mol in suppl2:
rec_num += 1
if not mol:
print('Record {} not read.'.format(rec_num))
else:
print('Record {} read ok.'.format(rec_num))
if (rec_num == len(suppl2) - 1):
rec_num += 1
print('Record {} not read.'.format(rec_num))
This should work until what seems to be an issue in the SmilesSupplier
is fixed.
Cheers,
p.
On 06/03/19 16:49, David Cosgrove wrote:
Hi,
I'm trying to catch the line numbers of lines in a SMILES file that
aren't parsed by the SmilesMolSupplier. Example code is attached,
along with 2 SMILES files. When there is a bad SMILES string on the
last line, the error is not reported, as in test2.smi. I've tried
iterating through the file in a loop using next(suppl1) and catching
the StopIteration exception, but I have the same issue. Is there a
way to spot a last bad record in a file?
Thanks,
Dave
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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