Hi RDKit community,
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.)
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".)
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
What approaches did I miss? What should I be doing?
Curt
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