For what it's worth, I think I fixed this (and cleared up some other
problems) in this PR:
https://github.com/rdkit/rdkit/pull/2482
On Tue, Jun 4, 2019 at 1:44 PM Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> 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>
> 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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> Rdkit-discuss@lists.sourceforge.net
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>
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