Hi David,
I think I already have a fix for this bug, I'll submit a PR later. If
you can create a ?GitHub issue it would be great so I can link my PR to
the bug.
Thanks, cheers
p.
On 06/04/19 12:10, David Cosgrove wrote:
Hi Paolo,
Many thanks for the speedy reply. I'll do as you suggest for now. Do
you want me to file an issue on github, or even, maybe, see if I can
fix it myself?
Cheers,
Dave
On Mon, Jun 3, 2019 at 5:32 PM Paolo Tosco <paolo.tosco.m...@gmail.com
<mailto:paolo.tosco.m...@gmail.com>> wrote:
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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--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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