Hello David, first of all thank you for your work on this great program. Attached is the drawing of how we think the mol files should look.
Best Rüdiger Von: David Cosgrove <davidacosgrov...@gmail.com> Gesendet: Montag, 5. September 2022 12:04 An: Rüdiger Lang <r.l...@abcr.com> Cc: rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] Draw.MolToFile catch programm termination 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<mailto: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<mailto:davidacosgrov...@gmail.com>> Gesendet: Samstag, 3. September 2022 09:12 An: Rüdiger Lang <r.l...@abcr.com<mailto:r.l...@abcr.com>> Cc: rdkit-discuss@lists.sourceforge.net<mailto: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<mailto: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<mailto:r.l...@abcr.com> _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto: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
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