I have filed a fix that will hopefully appear in the next patch release.
In the meantime, I fear there is no workaround other than restarting the
script after the offending molecule, which will be a nuisance to automate.
Dave
On Mon, Sep 5, 2022 at 11:04 AM David Cosgrove <davidacosgrov...@gmail.com>
wrote:
>
> Thanks, Rüdiger. On my mac it crashes with a segmentation fault, due to
> it using a negative index into a vector. That's also consistent with
> your exception, since it has taken an unsigned integer below zero which
> wraps round to a very large number. Disappointingly, it is in my drawing
> code, so I will file it as a bug and attempt to fix it. Do you have any
> representation of what the drawing is supposed to look like?
>
> Dave
>
> On Mon, Sep 5, 2022 at 8:29 AM Rüdiger Lang <r.l...@abcr.com> wrote:
>
>> Hello Dave,
>>
>>
>>
>> Thanks! I use the version 2022.03.05 but you are of course right, I had
>> attached the wrong mol-file. Sorry for that. But now two files where it
>> actually does not work.
>>
>>
>>
>> Best Rüdiger
>>
>>
>>
>> *Von:* David Cosgrove <davidacosgrov...@gmail.com>
>> *Gesendet:* Samstag, 3. September 2022 09:12
>> *An:* Rüdiger Lang <r.l...@abcr.com>
>> *Cc:* rdkit-discuss@lists.sourceforge.net
>> *Betreff:* Re: [Rdkit-discuss] Draw.MolToFile catch programm termination
>>
>>
>>
>> Hi Rüdiger,
>>
>> That file works fine for me using 2022.03.5. What version are you using?
>>
>>
>>
>> Also, I note that your script reads 191131.mol, but the one you have
>> provided is 191133.mol. Can you check that this is the file that is
>> causing the problem.
>>
>>
>>
>> Dave
>>
>>
>>
>>
>>
>> On Fri, Sep 2, 2022 at 1:40 PM Rüdiger Lang <r.l...@abcr.com> wrote:
>>
>> Hello everybody,
>>
>>
>>
>> I am trying to convert a large amount of mol files to png. Some mol files
>> cause the following error with "Draw.MolToFile":
>>
>>
>>
>> <<
>>
>> Could not convert io integer: 3221225477. Path 'exitCode'.
>>
>> Der Wert für einen Int32 war zu groß oder klein.
>>
>> (The value for an Int32 was too large or small.)
>>
>> >>
>>
>>
>>
>> I would like to catch this error to simply omit these files but despite
>> "try" the program exits with the above error.
>>
>> I have attached a problematic mol-file as an example.
>>
>> The program code looks like this:
>>
>>
>>
>> from rdkit import Chem
>>
>> from rdkit.Chem import Draw
>>
>> from try_parse.utils import ParseUtils
>>
>>
>>
>> Testmol = Chem.MolFromMolFile('C:\\Struct\\191131.mol')
>>
>>
>>
>> try:
>>
>> print('now we test: ')
>>
>> Draw.MolToFile(Testmol,'C:\\Struct\\Test191131.png')
>>
>> # i also tried this:
>>
>>
>> #test=ParseUtils.try_parse_int(Draw.MolToFile(Testmol,'C:\\Struct\\Test191131.png'))
>>
>> #print(test)
>>
>> except:
>>
>> print('I never reach this except but the programm stopps')
>>
>>
>>
>> Many thanks!
>>
>>
>>
>> Rüdiger Lang
>>
>>
>>
>>
>>
>>
>> Freundliche Grüße / Kind regards
>>
>> Rüdiger Lang
>> Data Analyst
>>
>> *abcr GmbH*
>> Im Schlehert 10
>> 76187 Karlsruhe
>> Germany
>>
>> r.l...@abcr.com
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>>
>>
>> --
>>
>> David Cosgrove
>>
>> Freelance computational chemistry and chemoinformatics developer
>>
>> http://cozchemix.co.uk
>>
>
>
> --
> David Cosgrove
> Freelance computational chemistry and chemoinformatics developer
> http://cozchemix.co.uk
>
>
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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