That's a really nice presentation. -P.
On Fri, Nov 18, 2016 at 3:16 AM, Greg Landrum <greg.land...@gmail.com> wrote: > This is a very big topic, and one where I would very much like to improve > the RDKit. John Mayfield gave a great talk on the issues (and some ideas > about fixing them based on his work with the CDK) at the UGM that some of > you may find interesting : > https://github.com/rdkit/UGM_2016/blob/master/Presentations/JohnMayfield_ > Depiction.pdf > > Fixing the larger problems is a *lot* of work and not something that is > likely to happen quickly, but there is some low-hanging fruit (like cutting > crossed bonds) that I ought to be able to do something about.[1] > > -greg > [1] the trick is to avoid, as much as possible, creating drawings that > look like Möbius strips. > _____________________________ > From: Peter S. Shenkin <shen...@gmail.com> > Sent: Thursday, November 17, 2016 11:23 PM > Subject: Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a > bit off-topic) > To: <rdkit-discuss@lists.sourceforge.net> > > > > > On 17 Nov 2016, at 4:12 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > > Philosophically speaking, there must exist molecules for which a legible > 2D projection is simply not possible. > > > Hi, > > I don't think that 2D projection of a 3D structure is an appropriate > paradigm for 2D depiction, in general. I think of it as being more about 2D > construction. I don't think camphor is a particularly difficult example, > though, and I think that the hidden-line elimination (for lack of a better > term) that Marvin does gives it a leg up on RDKit's representation. > > By the way, I do not think that Marvin is the best there is out there; > it's just what I happen to have available for comparison. > > Stereochemistry adds complications, because 3D information has to be > encoded in some way. Camphor (your suggestion) has a little of this. I gave > Marvin a non-stereo SMILES and it picked an enantiomer. I drew the same > enantiomer. I did not specify stereochemistry to RDKit, so, despite the > visual confusion of the bond crossings, I suppose it's good that it didn't > depict an explicit enantiomer. > > And labels add further complications. The two approaches I've seen for > labels are using them as the atomic vertices, as RDKit does, and adding > them adjacent to the vertices. I personally prefer the latter, because to > my eye, it's easier to see the connectivity without being distracted by the > labels. > > But my philosophical point was that different forms of 2D depiction work > better for different purposes. Stéphane wants to see sugars drawn as > carbohydrate chemists are used to seeing them. I would like to see the 2D > connectivity as clearly as possible and would sacrifice some conventions > for that purpose. And so on. > > -P. > > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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