What languages do you recommend to create your own molecular drawing

Question

hi,
As a former hacker there was a certain server politics and because developing a probe enables scientists do make use of server less telemetry which is way easier then measuring the end of the reaction by manual TLC plates. Here I suppose the temperature of the mixture will at a certain point at their lowest. Esterification reactions can easily be followed by the E.C values and so on. This looks interesting so you can work on several projects and have the end point of many reactions. There is telemetry in mobile devices, the latest Windows and their software but I find little to nothing about their code. Any ideas how this works and the total price for such a chemical resistant telemetry device would be too high at the moment.

There is Chemsketsch for Windows but for the more exotic molecules you have to buy the licence

There is Marvin Sketch for Linux but how secure is this for novel molcules.

Another page is Chemspider.org and if you go to structure then there are 3 different molecular drawing software.

Java might be another interesting language to learn to see these molecules who they are and that's in 3D

- Any idea's how and where to get started and tips (how many hours each day, software or articles about this specific software) ?
- What languages must I study here to understand what I'm doing ?

All feedback is really appreciated!

btw: I use Linux OS

Answer 1

I don't know much about chemistry but I've developed a few applications using 3D graphics.

If you want to visualize molecules on a website, the fastest approach seems to be learning a little JavaScript and using a library like JSmol. If you don't know of other tools that generate .mol files, you could study that file format and write the files in a text editor like notepad.

If you need a graphics library for 3D visualizations in Linux, I recommend either OpenGL or WebGL. WebGL would be great if you want to publish visualizations on websites. OpenGL would be great if you want a visualization in a graphical user interface with an installed application that you're writing.

For programming languages, OpenGL is available in a lot of languages including Python, and c++. WebGL is best used with JavaScript and only useful within websites. I get the sense you're best off with Python in the long run because it is easier to learn than c++ and is widely used by non-computer science scientists.

You typed chemspider.org but I think you meant chemspider.com. I inspected chemspider.com enough to see that the 3D visualization on http://www.chemspider.com/Chemical-Structure.115651.html was made using a JavaScript library named jsmol. More detail on JSmol is at https://sourceforge.net/projects/jsmol/

I tried to find out more about JSmol and how it works. It looks heavily inspired by Jmol, an old Java applet. Modern browsers don't usually run Java applets, though. If something like that was made now, it should be made using WebGL.

The .mol file format could be useful if you want to create molecular models and reuse an existing tool like JSmol.
The .mol file format looks fairly simple except it defines some properties I've never heard of before. The .mol file format is described here:
https://chem.libretexts.org/Courses/University_of_Arkansas_Little_Rock/ChemInformatics_(2017)%3A_Chem_4399_5399/2.2%3A_Chemical_Representations_on_Computer%3A_Part_II/2.2.2%3A_Anatomy_of_a_MOL_file