Re: [Rdkit-discuss] Plotting values next to atoms

[John Mayfield]

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  wrote:

> On 03/11/2018 04:27, Greg Landrum wrote:
> > Hi Eric,
> >
> > On Fri, Nov 2, 2018 at 2:00 PM Eric Jonas  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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> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
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Re: [Rdkit-discuss] Docs intentionally broken?

[Greg Landrum]

I think the doc-generation system is now fixed - that was this PR:
https://github.com/rdkit/rdkit/pull/2161 - but I still need to re-generate
the documentation on the website. This is unlikely to happen before I get
back to Basel next week, but we'll see...

On Mon, Nov 5, 2018 at 6:04 PM Greg Landrum  wrote:

> The change from epydoc to sphinx/autodoc for the python documentation led
> to some URL changes (most of which I fixed with redirects) and some missing
> modules. Looks like the rdGeometry module is missing. I will see if I can
> add it back, but this may take a bit since I'm traveling this week and the
> beginning of next.
>
>
> -greg
>
>
> On Mon, Nov 5, 2018 at 1:23 PM Brian Cole  wrote:
>
>> My google search for 'rdkit python point3d' yielded the following as the
>> top result:
>>
>> https://rdkit.org/docs/api/rdkit.Geometry.rdGeometry-module.html
>>
>> Which unfortunately now has a 404, page not found.
>>
>> Was this an intentional reorganization of the documentation?
>>
>> -Brian
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>
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