Show HN: Chemozart – molecule editor and visualizer with mechanics calculators | Hacker News Reader

Show HN: Chemozart – molecule editor and visualizer with mechanics calculators

github.com

34 pointsmohebifar17 comments

I've dreamed about this for so long! More generally, every time I've gotten really excited about: microbiology, chemistry, maybe geology and well, bioinformatics, I lost heart quickly because I could find no tools that were interactive, simulating and stimulating to use, preferably visual like this. Thanks! When I meet programmers who can have not one original idea about some side project to do, I think back to things I want like this, and wonder if those programmers could find ideas if other areas of life would interest them. I mean, there are SO many tools waiting to be built for every new field I barely study, it's still such a gold rush of software building opportunities if you're not tied to thinking only ideas "that scale".

Edit: The README ends saying there are other chemical apps like this. What are them? I'd actually really like one with just plaintext notation.

> I lost heart quickly because I could find no tools that were interactive, simulating and stimulating to use, preferably visual like this.

This is because there is no use-case for professional users.

When it comes to computational chemistry there are two possibilities:

The computational load is low, but also accuracy like the implemented force-field method. Now you can calculate molecular properties so fast that it feels interactive.

Or you use more accurate methods (hybrid density functionals). For decently sized molecules (>100 atoms) you now might want to consider using HPC (speak supercomputer). Now you have something which is state of the art, but it's not interactive anymore.

If you however use computationally cheap methods, you probably want to calculate properties of a LOT of molecules (high throughput calculations, screening). This means you must either use known structures, or generate them programmatically (using some genetic algorithm usually). Now you don't need anything interactive either.

You're right but this application is designed mostly for educational purposes. It's a web application so students and teachers can use their mobile device (iPad, iPhone, Android devices, etc.) to use the features this application offers. They can easily understand the stereochemistry of a molecule rather than using those modeling kits.

> This is because there is no use-case for professional users.

I don't know, it can still useful for generating your initial cells for complicated systems (defects, interfaces, etc.), and it can always be useful to test an idea qualitatively before you do a high-accuracy calculation.

https://en.wikipedia.org/wiki/Category:Computational_chemist... lists quite a few, and some of them are links to additional software lists, like https://en.wikipedia.org/wiki/List_of_molecular_graphics_sys... .

There is so much software because there are many different needs, each with specialist requirements. Most likely you want to look at PyMol. However, even though that's one of the more approachable packages it will require some domain knowledge.

Some colleagues of mine build a similar tool, http://molcalc.org/

It gives you access to a lot more properties of the molecule you build than just the energy: Thermodynamics, solvation energies, vibrational frequencies etc.

That is a great project but its back-end is written in php and it uses open babel via "shell_exec" function. All I wanted to do was making another powerful package completely written in JavaScript (Using node.js in back-end) which only requires a good knowledge of JavaScript to develop the application. I also ported Open Babel into Node.js so that you can use this library with native js codes. As far as I know there is no chemical application built on top of Node.js. This application can be extended and developed so fast as JavaScript is becoming more and more popular (Just take a look at this data visualization: githut.info) meaning that more developers and volunteers can contribute on this platform.

This would be sweet with an API so that I could embed the molecule editor in a nodejs app (like using Electron) and control some things from my app.

I don't know exactly what you mean by plaintext notation but Avogadro is pretty good. Nanoengineer is also pretty cool if you are willing to dig for it.

I don't have a use for this, but I do have a friendly piece of advice: I saw a demo of a molecule manipulator for the Leap Motion (which I have) and it was an amazingly intuitive way to manipulate 3D models. The Leap JS API is very simple to use (they really give you everything you need) and you can probably integrate it in an hour. I definitely recommend adding Leap support, it's a fantastic way to zoom and pan your model around with natural gestures.

You should implement energy minimization or rather use openbabel's energy minimization functions. Doing SteepestDescentTakeNSteps every couple of frames and updating atom positions should give you some neat behavior. Pretty cool to see openbabel running in the browser.

Thanks for your suggestion. I'll consider it.

Looks nice, with 3D visualization from the start!

(Forwarded to the Cheminformatics G+ community too: https://plus.google.com/communities/113690459303191514146)

What I want when I click through on these things is a working demo, or a way to launch a working demo. Occasionally you'll find a website demoing the software, less occasionally, a decent README on how to build and launch it. FWIW, their demo is currently down.

Sorry, it went down. Up again.

looks nice. Are you considering to add templates, eg. benzene ring etc?

Good idea! We will take your advice. We will also be happy to see you having a PR.

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