Looks good, but maybe too slow for production use... (?)
-P.
On Thu, Dec 15, 2016 at 3:38 PM, Chris Swain <sw...@mac.com> wrote:
> At first glance this looks an interesting approach.
>
> Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram
> Generation of Complex Molecules and Ligand–Protein Interactions
> DOI: http://dx.doi.org/10.1021/acs.jcim.6b00391
>
> On 27 Sep 2016, at 05:38, rdkit-discuss-requ...@lists.sourceforge.net
> wrote:
>
> 2D drawing code is tough. The 90/10 rule applies: the last 10% of
> correctness takes 90% of the effort.
>
> I like Dmitri Agrafiotis's method, but IIRC it's patented; also, though
> it's good for rough work, it doesn't produce "beautiful" structural
> diagrams.
>
> Some of the 2D drawing methods that do produce "pretty" pictures have a
> large number of templates built in that match the most common (and even
> somewhat uncommon) motifs, and they fall down when they hit something they
> can't get a close enough match for. And then, the IUPAC has a whole list of
> "desirable" features in 2D diagrams (as in, "Don't show it this way, but
> rather show it that way."). So even if you produce what might appear to be
> an acceptable drawing, it might not match the IUPAC list of desirables.
>
> I think for the present purposes what we need is something correct, robust
> and legible, and of course the example shown does not exhibit that. (But I
> don't know what the starting SMILES is, so I don't know whether the
> 7-bonded C is due to a bad SMILES, in which case all bets are off.)
>
> In addition, I think some discussion earlier indicated that the RDKit 2D
> structures look much worse when H's are included.
>
> I actually wrote a code one time (while at Schr?dinger) to give a "badness"
> score to 2D structures. When our 2D depiction development was in progress,
> we created 2D SD files for many thousands of structures. I could put these
> through the program and sort with the worst on top. That allowed the most
> severe problems to be identified more quickly than, say, looking at
> thousands of 2D diagrams. The program looked at three things: Number of
> bonds that crossed, Number of atoms that were too close together, and Large
> disparity of bond lengths within the same molecule. (The checking code
> didn't deal with labels.)
>
> Writing the checker was a fun project, but I'm glad I didn't have to write
> the 2D depiction code. As Mark Twain said, "Improving oneself is good.
> Improving others is better ? and easier."
>
> -P.
>
>
>
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