Isn't this patch already incorporated in the master branch? On Tue, 13 Nov 2018 at 12:35, Malgorzata Werner < malgorzata.wer...@molecularhealth.com> 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/ > > > > Best, > > Malgorzata > > ------------------------------ > *From:* Henrique Castro <henrique...@outlook.com> > *Sent:* 13 November 2018 11:57:34 > *To:* rdkit-discuss@lists.sourceforge.net > *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 > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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