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>
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
>
>
>
>
>
> _______________________________________________
> Rdkit-discuss mailing
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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