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
>
>
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to