How to change atom color ?

[gVallverdu]

Hi

I would like to change the default color of one atom (element). I think there might be a kind of parameters of the view where this is defined but I do not found where.

I can add a sphere or something like that as a workaround but this does not change the color of the bond in a ball+stick representation for example.

Thanks

python -c 'import nglview; print(nglview.__version__)'
2.7.7
python -c 'import ipywidgets; print(ipywidgets.__version__)'
7.5.1

[hainm]

@gVallverdu may be try to add your own color scheme?

#839

The selection language is here: http://nglviewer.org/ngl/api/manual/usage/selection-language.html

[gVallverdu]

Hi
Looking at #839 Yes I can do something. However, I have some difficulties reading the doc here: http://nglviewer.org/ngl/api/globals.html

I am looking for the class from which the atom variable is an instance. Can you help me about this point ?

The following works but If I want to change the color of one atom I must redefine all element... That's why I would like to read the doc to find a way to get the default color maybe ?

cm = ColormakerRegistry
cm.add_scheme_func('my_sel','''
 this.atomColor = function (atom) {
     if (atom.element == "C") {
       return 0x34495e // C
     } else if (atom.element == "H") {
       return 0xecf0f1
     } else if (atom.element == "S") {
       return 0xf1c40f
     } else if (atom.element == "N") {
       return 0x2980b9
     }
 }
''')

Thanks

[hainm]

@gVallverdu Oh, I think we are making thing complicated. See my example below, just use the selection language.

[vhorvath]

@hainm, I keep getting mentions, but I am not in this thread. Did you mean to add @gVallverdu instead? :)

[hainm]

hi @vhorvath I am terribly sorry. Yes, I meant @gVallverdu

[gVallverdu]

@hainm yes this is simpler but the bond are not colored correctly

But for one specific atom or a molecule/fragment not bonded to the whole system it is ok.

[hainm]

@arose any idea? thanks.

[dominiquesydow]

Hi @hainm,

I found this issue while trying to figure out how to recolor all C atoms in an atom selection.
Do you have any new ideas how the coloring could be extended also to the bonds with non-C atoms?

Minimal code example:

view = nglview.show_pdbid("3w32")
view.clear_representations()
view.add_representation("hyperball", selection="ligand")
view.add_representation("hyperball", selection="ligand and _C", color="magenta")
view.center()
view

Grey bonds should optimally also be magenta.

---

If this is not easily possible, I might go for the alternative and define element colors using the ColormakerRegistry as proposed above:

cm = ColormakerRegistry
cm.add_scheme_func('my_sel','''
 this.atomColor = function (atom) {
     if (atom.element == "C") {
       return 0x34495e // C
     } else if (atom.element == "H") {
       return 0xecf0f1
     } else if (atom.element == "S") {
       return 0xf1c40f
     } else if (atom.element == "N") {
       return 0x2980b9
     }
 }
''')

Could you maybe link me to the code where the nglview-default element colors are defined (for elements other than C, H, S, N, P)? My keyword searches in https://github1s.com/nglviewer/nglview/ where unsuccessful unfortunately, sorry.

[hainm]

Could you maybe link me to the code where the nglview-default element colors are defined (for elements other than C, H, S, N, P)? My keyword searches in https://github1s.com/nglviewer/nglview/ where unsuccessful unfortunately, sorry.

Hi @dominiquesydow: I am sorry that I don't know the answer.
Please search the code in NGL repo: https://github.com/nglviewer/ngl

And/or ask the usage of color in that repo since there are many experts there. Good luck.

[hainm]

For the color, you can search to JS code here: https://github.com/nglviewer/ngl/tree/master/src/color

[dominiquesydow]

@hainm, thanks a lot for the pointers!

[dominiquesydow]

In case anyone ends up in this issue searching for

Could you maybe link me to the code where the nglview-default element colors are defined (for elements other than C, H, S, N, P)?

Here is a the list of element-color mappings:
https://github.com/nglviewer/ngl/blob/1ec4a8c3a6a7a33c0c92f6d4eac01efde8ec4240/src/color/element-colormaker.ts#L13

[gVallverdu]

Following my question at the beginning, here is how I finally did. It is a simple loop over atoms. It is thus not so adapted in case of huge number of atoms. But, I haven't found any way to do it using another way.
https://github.com/gVallverdu/pychemcurv/blob/974aed913bdf2cfb9dd2598e536cf5332bba2dcd/pychemcurv/vis.py#L207

[hainm]

Thank you all. I go ahead closing this issue. Do feel free to open others if needed.

[hainm]

By the way, I've added

dynophores: Dynamic pharmacophore modeling of molecular interactions
pychemcurv: Discrete and local curvature applied to chemistry and chemical reactivity

to here: https://github.com/nglviewer/nglview/blob/master/README.md#projects-integrating-nglview