... and yet another example, bis-mu-dichloro-bis(allyl)dipalladium(II), drawn according to ChemAxon's instructions: https://docs.chemaxon.com/display/docs/How+to+draw+coordination+compounds
Michal On Thu, 13 Sep 2018 at 14:45, Michal Krompiec <michal.kromp...@gmail.com> wrote: > 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 >>> >>
Pd_allyl_chloride_dimer.mol
Description: Binary data
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