
Show HN: Chemozart – molecule editor and visualizer with mechanics calculators - mohebifar
https://github.com/mohebifar/chemozart
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goldfeld
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.

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sonium
> 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.

~~~
mohebifar
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.

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StavrosK
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.

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gene-h
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.

~~~
mohebifar
Thanks for your suggestion. I'll consider it.

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samuell
Looks nice, with 3D visualization from the start!

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

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kordless
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.

~~~
mohebifar
Sorry, it went down. Up again.

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

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

