On 03/11/2018 04:27, Greg Landrum wrote:
Hi Eric,
On Fri, Nov 2, 2018 at 2:00 PM Eric Jonas <jo...@ericjonas.com> wrote:
Hello! I'm trying to figure out if there's any known or sane way to
automatically plot numerical values adjacent to atoms using the
rdkit drawing machinery. Ideally I'd like to annotate certain atoms
programmatically with values. I think the conventional way this is
done for publication is post-hoc editing in illustrator but it would
be great if there was an automatic or supported mechanism.
Hi Eric,
One hackish way is to export your molecules in 3D in the PDB format.
Then shove your numeric value into the B-factor field.
Then, color your molecules by B-factor using your favorite viewer
(Chimera, pymol, etc.).
For this to work correctly, you may have to scale your values so that
they become in the same
range than B-factors.
Wit a little programming, you could also export your molecules (in 3D,
still) directly
as balls in the BILD format of UCSF Chimera, and look at them into
Chimera.
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html
Regards,
Francois.
Doing this correctly is on the list of high-priority things to do, and
I really hope to have something done for the 2019.03 release, but
there's no way I can guarantee that (it's a hard problem).
In the meantime, there's a way to at least do something that is,
hopefully, better than nothing:
https://gist.github.com/greglandrum/8cf8ecc3253abf0a5139a776a5095163
[1]
displayed here:
https://nbviewer.jupyter.org/gist/greglandrum/8cf8ecc3253abf0a5139a776a5095163
[2]
Links:
------
[1]
https://gist.github.com/greglandrum/8cf8ecc3253abf0a5139a776a5095163
[2]
https://nbviewer.jupyter.org/gist/greglandrum/8cf8ecc3253abf0a5139a776a5095163
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