[Feature] Chemistry support (ChemFig?)

[YuukoShionji]

Chemistry support wold be great. Reaction formulas, Binding structures, Molecule structure ect...

it would be great if you could add support for chemfig somehow

[shd101wyy]

Hi @YuukoShionji ,

Can you provide me with some libraries or programs for drawing Chemistry figures?

Thanks

[YuukoShionji]

If we ware working with normal latex Chamfig would be great, however it requiers tikz wich is not supported by Mathjax or katex.

There is however a javascript library that can draw molecules rather nicely Kekule.js (Repo), which would be perfect atleast for the molecules if it wasnt for the fact it dosnt support any tex/tax nativly, So one would have to write a "wrapper" for it. Here is a page about molecule drawing in their docs

As far as programs go there is a lot im just gonna name the most popular

• https://avogadro.cc/
• https://www.chemdoodle.com/
• https://www.chemaxon.com/products/marvin/marvinsketch/
• http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html
• http://www.pymol.org/

I think the most ideal solution is to write a MathJax/Katex module to Kekule.js

[shd101wyy]

I think I will take a look at the Kekule.js or just try to support tikz.
I will notice you if I make any progress.
Thanks :)

[shd101wyy]

May I also ask what operating system are you using?

[YuukoShionji]

Laptop (i use it in school): https://www.archlinux.org/ Desktop (Home work and self studies): https://gentoo.org/

[shd101wyy]

@YuukoShionji I just did some researches and I decide to support the tikz graphs.
My current plan is to support latex code chunk.
For example:

```{latex} 
\documentclass{article}
... your latex code here
\end{document}
```

So this will compile latex => pdf => svg and display it in preview.

For tikz graph, we write it in this way

```{latex tike:true}
\begin{tikzpicture} --> this line is not necessary.  
... your tikz code
\end{tikzpicture}
```

I will try to get it done by the end of next weekend. I am developing this extension on Mac and the TeX on Mac is kinda broken. I can't install the standalone.cls, so I might need your help to test it on Linux.

Please tell me if you have any advice.

Thanks

[shd101wyy]

@YuukoShionji TikZ is now supported. Check this doc.
Cheers :)

[YuukoShionji]

@shd101wyy nice! ~Tough unfortunetly it dosnt seem to be working for me :/ I get an latex ID, but it dosn't seem to do anythingimage~ edit: didnt realise i had to click "run", anyways good work! but i noticed when i export it the latex code still shows in the final doc, might be a bug, or am i doing it wrong?

[shd101wyy]

You can set hide to be true.

```{python hide:true}
print('you can see this output message, but not this code')
```

Then use shortcut shift-enter to run.

[pkpkpk]

Is the md/latex src used to generate the circuit diagram available somewhere? Thanks

[trivial-zero]

This extension somewhat has the feature to draw molecules for the built-in markdown preview using SMILE mathpix. But the MPE could not recognize it, so I can not export it :(