Well since someone suggested hacking B factors and using Pymol... not using RDKit but
CCCOCC |$_AV:;;;3.14$| AV=Atom Value, round tripped through MOLfile and ChemAxon extended SMILES. [image: image.png] Live Depiction: https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=CCCOCC%20%7C%24_AV%3A%3B%3B%3B3.14%24%7C&abbr=on&hdisp=bridgehead&showtitle=false&zoom=1.6&annotate=atomvalue John On Tue, 6 Nov 2018 at 02:01, Francois Berenger <mli...@ligand.eu> wrote: > 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 > > > > _______________________________________________ > > 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 >
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