Hi Curt,

On Tue, Apr 4, 2017 at 12:03 PM, Curt Fischer <curt.r.fisc...@gmail.com>
wrote:

>
> RDKit's default 2D-depictions of macrocycles are very "round".  I found
> some slides
> <https://www.slideshare.net/NextMoveSoftware/rdkit-ugm-2016-higher-quality-chemical-depictions>
>  from
> John Mayfield that come from a 2016 UK RDKit user group meeting that says
> the same thing.  (See in particular slide 31.)
>

Yes, they are indeed very round and non-chemical.


>
> I'm wondering, what is the best way of forcing RDKit's depictions of these
> types of molecules to be less round?  (And I'm aware that a possible answer
> is, "there isn't a good way yet".)
>

I'm afraid the answer is "there isn't a good way yet". I do really hope
that this answer will change in a not-too-distant release, but I cannot
promise anything.

In a Jupyter notebook, I (hopefully) illustrate three approaches: (i) just
> importing an .sdf of your molecules from somewhere else, (ii) aligning to a
> non-macrocyclic substructure, and (iii) using the TemplateAlign module.
> https://github.com/tentrillion/ipython_notebooks/blob/master/force_pretty_
> macrocycles.ipynb
>
>
I think you hit on everything that's currently possible here. Using a
template to organize the atoms of the macrocycle, like you do to produce
outputs 8 and 11, seems to me like the strategy that's most likely to work.
It's unfortunate that it doesn't. My normal answer to this kind of
situation is "it's a hard problem and the code does what it can. Changing
the algorithm is a lot of work.", but those particular pathologies almost
look like bugs, not algorithmic deficiencies. I will take a look to see I
can track down what's causing that.

-greg




> What approaches did I miss?  What should I be doing?
>
> Curt
>
>
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