Hi Mohammad, thank you for your advice! I will have a look at that file.
With kind regards, Madeleine On 8 Jun 2021, at 14:34, Ghahremanpour, Mohammad <mohammad.ghahremanp...@yale.edu<mailto:mohammad.ghahremanp...@yale.edu>> wrote: Hi Madeleine, There is also a data file for ring types. That might help you fix the problem with small rings. openbabel/data/ringtyp.txt Best, Mohammad On Jun 8, 2021, at 8:15 AM, Marie-Madeleine Walz <marie-madeleine.w...@icm.uu.se<mailto:marie-madeleine.w...@icm.uu.se>> wrote: Hi David, thank you for your advice regarding using AssignTotalChargeToAtoms. Adding it resulted in less errors in the bond order assignment. Unfortunately, it did not remove e.g. the error with sulfite (SO3^2-) that is still getting three double bonds. Another issue is that some of the small rings (e.g. thiirene, C2H2S) are not recognised as rings. This is really confusing as the coordinates fullfil the requirement set in mol.cpp, ConnectTheDots(), lines 3027-3028: // bonded if closer than elemental Rcov + tolerance cutoff = SQUARE(rad[j] + rad[k] + 0.45); If you have any advice I would really appreciate it. With kind regards, Madeleine On 7 Jun 2021, at 15:34, David Koes <dk...@pitt.edu<mailto:dk...@pitt.edu>> wrote: There is AssignTotalChargeToAtoms which is called when parsing the gamess format, but not, apparently, gaussian. Again, if you could upload examples of failures to a GitHub Issue (or even better, start a pull request with failing tests added to the testing framework) that would be helpful. David Koes Associate Professor Computational & Systems Biology University of Pittsburgh On 6/7/21 8:22 AM, Marie-Madeleine Walz wrote: Hi David, thank you for your reply. I tested your code that assigns a sp2 hybridisation to a N as e.g. in azete (in mol.cpp), and it solves the incorrect bond orders. However, I think that this is a general problem: I have numerous compounds that get incorrect bond orders and that end up with a different charge than specified in the Gaussian output file (like e.g. sulfite and sulfur trioxide). I think it might be a good idea to have somewhere a general "charge check”. (Maybe there is and I miss to use it? I checked whether OB is getting the specified charge and it seems to get it.) For example, it would be great if there is a function that checks (i) the charge of the compound (or whether it is a radical) and (ii) the sum of bond orders to a certain atom (I guess that is done with GetExplicitValence()). If a compound is neutral (and not a radical) and ends up with e.g. a C that only has three single bonds, this should be somehow corrected. Is there any way to do this with the existing OB functions, i.e. without changing the code? With kind regards, Madeleine När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uu.se%2Fom-uu%2Fdataskydd-personuppgifter%2F&data=04%7C01%7Cmohammad.ghahremanpour%40yale.edu%7C3800a155cf7140cbbe9408d92a772244%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637587513460790622%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=unIJsWaCXbAz%2B0gRtvO25UCDGA6naxS8vigP3EEaaQw%3D&reserved=0 E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uu.se%2Fen%2Fabout-uu%2Fdata-protection-policy&data=04%7C01%7Cmohammad.ghahremanpour%40yale.edu%7C3800a155cf7140cbbe9408d92a772244%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637587513460790622%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Z2wEGiSarBatMRVsJniKLg6O23SWykeotgK0o7qt604%3D&reserved=0 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net<mailto:OpenBabel-Devel@lists.sourceforge.net> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fopenbabel-devel&data=04%7C01%7Cmohammad.ghahremanpour%40yale.edu%7C3800a155cf7140cbbe9408d92a772244%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637587513460790622%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=rJNJ1K5VEHB5LyW8Wu6h2jabAoyhLWaLLdLA%2F7Iv8JE%3D&reserved=0
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