Hi Greg, Thanks for your fast reply. I've got two examples of ferrocene MOLfiles, generated by MarvinSketch in KNIME, from ferrocene.cdxml (found somewhere in the rdkit github repo), the other one from the ferrocene template in Marvin. But actually they are almost the same. The third example is Pd(dba)2 (also from Marvin's template library). As you can see, the attachment is made via a dummy atom placed where the bond is drawn (middle of Cp ring or middle of double bond). Best regards, Michal
On Thu, 13 Sep 2018 at 14:14, 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 >> >
fecp_from_mrv.sdf
Description: Binary data
pd_dba2.mol
Description: Binary data
fecp_from_cdx.sdf
Description: Binary data
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