I would suggest that all coordination bonds to metal that exceed the accepted valence of an atom could be mark as zero-ordered. This is what happens in recent PDB reader changes and fixed a lot of problems with sanitization. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl
czw., 13 wrz 2018 o 18:16 Jan Halborg Jensen <jhjen...@chem.ku.dk> napisał(a): > 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> 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> 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 >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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