Hi Dimitri, Here's a notebook demonstrating the extent of the problem (which you've already seen, but this maybe makes it easier for others): https://nbviewer.jupyter.org/gist/greglandrum/461c52169e51f9b9e742a5996832ab3c
To be fair to all depiction algorithms: when you turn on the Hs, this is a really, really crowded molecule. It's going to be very difficult to do anything at all here that doesn't end up looking like crap in one way or another. @Nic: how do you want people from the RDKit community to deal with things like this? Is it productive to add them as issues in the coordgen issue tracker or do you have some other way you'd prefer to collect particularly ugly results from coordgen? -greg On Wed, Aug 14, 2019 at 12:22 AM Dimitri Maziuk via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > PS I played with it a bit: the least ugly version is if you > MMFF94-optimize it after rdkit.Chem.rdCoordGen.AddCoords() > > It's still far from perfect. > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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