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.
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