Here’s a modest step in the right direction https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/
Best regards, Jan On 13 Sep 2018, at 15:14, Greg Landrum <greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote: Hi Michal, Though the RDKit theoretically has many of the infrastructure pieces required to handle organometallics (though there's not a lot you can do with them once you've loaded them), the difficult part almost always ends up being finding input files that have reasonably machine-readable structures in them. If you have some examples you can share, I'd be happy to take a look to see if I can suggest ways to read them in. Best, -greg On Wed, Sep 12, 2018 at 10:30 PM Michal Krompiec <michal.kromp...@gmail.com<mailto:michal.kromp...@gmail.com>> wrote: Hello, I've been asked to analyze a dataset of organometallic compounds (provided in SDF), but it turns out that most of them are not compatible with RDKit (due to having pi-alkene, pi-allyl, cyclopentadienyl et al. ligands). The structures can be correctly represented in Marvin, though. Can anybody point me to a toolkit (or RDKit hack) that can handle these? Best, Michal ==== Dr. Michal Krompiec Adjunct Professor School of Chemistry, University of Southampton Highfield, Southampton SO17 1BJ, UK and Head of Computational Modelling | Performance Materials | Early Research and Business Development Merck _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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