Thank you for the tips. In a loooong and dumb workflow, I was able to load a sample molecule.
* Downloaded a sample .cif structure from CCDC https://www.ccdc.cam.ac.uk/structures/search?id=doi:10.5517/ccdc.csd.cc1m9hgw&sid=DataCite * Used OpenBabel to convert my .cif to .mol V3000 (the converted .mol fails to load in RDKit) * I was only able to load the molecule getting the .mol2 file provided in the same CCDC link and converting such .mol2 to .mol V3000 using OpenBabel (the .mol2 itself wasn't read by RDKit). Attached is my converted .mol V3000 -- Henrique C. S. Junior ________________________________ From: Michal Krompiec <[email protected]> Sent: Tuesday, November 13, 2018 11:16 To: [email protected] Cc: [email protected]; RDKit Discuss Subject: Re: [Rdkit-discuss] RDKit and organometallics Isn't this patch already incorporated in the master branch? On Tue, 13 Nov 2018 at 12:35, Malgorzata Werner <[email protected]<mailto:[email protected]>> wrote: Hi Henrique, You could try using v3000 sd files. Here's a blog about this: https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wildcardconsulting.dk%2Fuseful-information%2Fhow-to-solve-problems-with-coordinate-bonds-in-rdkit%2F&data=02%7C01%7C%7C3da7193ebdb349b124fa08d6496a30e9%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636777117763691235&sdata=hUC0cFUlbd6sEATeJ3Ma7SR9%2BXIA5PXc6rJLWb6VnXo%3D&reserved=0> Best, Malgorzata ________________________________ From: Henrique Castro <[email protected]<mailto:[email protected]>> Sent: 13 November 2018 11:57:34 To: [email protected]<mailto:[email protected]> Subject: [Rdkit-discuss] RDKit and organometallics Dear colleagues, I know that this is probably a dumb question, but since my searches showed no clarifying results I'm asking here anyway. I'm planning to use RDKit on my Ph.D. thesis, but my field of research is inorganic chemistry and molecular magnetism. That means that I'm dealing with organometallics (transition metals, lanthanides, actinides...). So far I was unable to import even a single structure to my RDKit test with different error messages like those (they are all the same structure, that is attached here): m = Chem.MolFromMolFile('st1.pdb') RDKit WARNING: [08:36:40] CTAB version string invalid at line 4 m = Chem.MolFromMolFile('st1.sdf') RDKit ERROR: [08:51:30] Explicit valence for atom # 1 N, 4, is greater than permitted m = Chem.MolFromMolFile('st1.mol2') RDKit WARNING: [08:52:15] Counts line too short: 'SMALL' on line4 Based on this, I'd like to as for hints on how to deal with molecules with "unusual" valences like the ones we deal in inorganic chemistry. Thanks in advance -- Henrique C. S. Junior _______________________________________________ Rdkit-discuss mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=02%7C01%7C%7C3da7193ebdb349b124fa08d6496a30e9%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636777117763691235&sdata=Z1%2BuqLQu7OvAkLN7v5iPIlty3TR1%2FU3S58sqWXjvSCU%3D&reserved=0>
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