> 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.
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