Add highlighting support

[bjonnh]

Can be used with pybel (or anything that sets the "color" property of atoms).

mol = pybel.readstring("smi","CCN(CC)CC") # triethylamine
pybel._operations['highlight'].Do(mol.OBMol, "[#7][#6][#1] #00FF00") 
imolecule.draw(mol, shader="lambert",format="pybel")

For now, only green is supported, I have to check openbabel source for a list of colors they allow.

[patrickfuller]

Looks useful! I use imolecule as a front end to some crystallography software. I wrote an all-js interactive highlighter there:

What's your use case? Would it be more useful to highlight in Python notebook code, or to do it interactively with the output?

Either way, I like the idea. Regarding OB colors, I'd rather convert them to hex python side. It saves us from having to duplicate color data.

[bjonnh]

I use that to highlight substructures in compounds. I have a series of filters (smarts) and apply them to each molecules then display them. That said if you made the highlighter already, I may just tweak it.

[patrickfuller]

Sounds like python functionality is the way to go.

Let's either add in a full list of color options, or edit this openbabel function to convert "green" to hex before sending to js. I like the idea of supporting arbitrary hex values, but either way works.

[bjonnh]

I made a better highlighter, now you can give the highlights with hex codes.

import pybel
import imolecule
mol = pybel.readstring("smi","OCN(CC)CCS")
pybel._operations['highlight'].Do(mol.OBMol, "[#6][#7] #FF0000") 
pybel._operations['highlight'].Do(mol.OBMol, "[#1][#8] #0000FF") 
pybel._operations['highlight'].Do(mol.OBMol, "[#16][#6] #00FF00") 
imolecule.draw(mol, shader="phong",format="pybel")

[patrickfuller]

This is cool!

The only things left are to revert the display_html patch and remove all the whitespace edits (they gunk up commit history).

• If you want to remove that display_html commit, you can just chop it off of your history with git reset --hard HEAD^ && git push -f origin develop.
• Regarding whitespace, it looks like your editor isn't replacing tabs with spaces or trimming the end of lines. You can search and replace with vim commands like %s/\t/ /g and %s/\s\+$//g. You may need to go in and make sure everything lines up after removing tabs - shouldn't take more than a minute.

[bjonnh]

Should be ok, I rewrote history (bad I know…) but everything is fine now.