Hi Greg, yeah, coordgen issues are probably the best way to keep track of where we perform poorly.
btw here’s that same structure when opened in maestro (coordinates generated with coordgen) > On 14 Aug 2019, at 06:02, Greg Landrum <greg.land...@gmail.com> wrote: > > 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 > > <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 > <mailto: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 > <http://www.bmrb.wisc.edu/> > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > <mailto:Rdkit-discuss@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
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