
Hack-a-Mol - breck
https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm
======
busyant
Funny.

I have recommended this website
([https://www.stolaf.edu/depts/chemistry/courses/toolkits/247/...](https://www.stolaf.edu/depts/chemistry/courses/toolkits/247/js/names/dnames.htm))
to many of my students to help them practice naming alkyl substituted alkanes.

The web-page has an "analyze" button that does a great job showing students
how to find the longest carbon chain, which is then used to help determine the
molecule's IUPAC name.

I've always wondered who was behind the site that I had recommended, but I was
never curious enough to poke around and answer my own question.

When I saw "hack-a-mol" and stolaf.edu, I thought, "okay, must be the same
person."

People like this (his name is Bob Hanson:
[https://www.stolaf.edu/people/hansonr/](https://www.stolaf.edu/people/hansonr/))
are hidden gems. He's probably not super-famous, but he's made many great
tools and I can only imagine that his students have benefited tremendously
from his passion and skills.

~~~
moron4hire
Reminds me of Paul Falstad and his excellent circuit simulator tool. He
originally wrote it as a Java applet, then gave permission to an Iian Sharp to
have it rewritten in HTML5:
[https://www.falstad.com/circuit/](https://www.falstad.com/circuit/)

------
theophrastus
This is a very impressive site for teaching molecular file formats indeed! If
there is one caveat that an old crystallographer might add...

    
    
      press ENTER, the 2D and 3D structures will update. 
    

When going from the 2d connectivity graph to 3d there arise essential emergent
properties, some of which can be specified, like stereochemistry (left or
right chirality), and some which can be estimated with a lot of theory and
additional calculation like multiple conformers (e.g. trans and cis), and
thermal preferences (staggered vs eclipsed along rotable bonds), and onwards
to intensive quantum chemistry for electron distribution which is so critical
for design for enzyme binding. That is, "3d" at this level is very much an
approximate single still image of a very dynamic system.

------
bluejellybean
What a neat and timely teaching tool! Literally just an hour ago today I was
reading an article in Chemical Review titled "Concepts of Artificial
Intelligence for Computer-Assisted Drug Discovery" [0]. There was a lot of
pretty standard stuff in there related to AI work but the real puzzle for me
was trying to come up with a clean way to store and work with these data sets.
I had come up with a few possible solutions that seemed decent but I knew
there had to be a more standardized format. After struggling to get the
correct search terms I decided to take a coffee break and then lo and behold,
I come across this post. Thank you Mr. Hansom, you have successfully kept me
busy the rest of the night :)

[0][https://pubs.acs.org/doi/10.1021/acs.chemrev.8b00728](https://pubs.acs.org/doi/10.1021/acs.chemrev.8b00728)

------
neiman
That's great!

How do you represent a chemical structure mathematically? Is it a graph? Or
something else? It seems more complicated than just a simple graph structure.

~~~
Reelin
Mathematically:
[https://en.wikipedia.org/wiki/Schr%C3%B6dinger_equation](https://en.wikipedia.org/wiki/Schr%C3%B6dinger_equation)

Is it a graph? Mostly yes - just ignore anything that's not covalent. It
depends a bit on how complicated an interaction you're willing to allow an
edge to represent, and how much of reality you're willing to ignore. A few
examples of complications are linked below. The depictions may seem trivial,
but for large molecules things quickly become ridiculous.

[https://en.wikipedia.org/wiki/Resonance_(chemistry)](https://en.wikipedia.org/wiki/Resonance_\(chemistry\))

[https://en.wikipedia.org/wiki/Pi_interaction](https://en.wikipedia.org/wiki/Pi_interaction)

[https://en.wikipedia.org/wiki/Antibonding_molecular_orbital](https://en.wikipedia.org/wiki/Antibonding_molecular_orbital)

------
rambojazz
Anyone knows if this program is open source?

~~~
HarryHirsch
There is Openbabel, which was open-sourced by the folks from Openeye in New
Mexico. Anthony Nichols is quite a character, and David Weininger was even
more so.

The CACTVS software used on that website is related to Gasteiger at Erlangen.

~~~
text70
I will second Openbabel as a reliable tool in my comp-chem pipeline.

------
chmod775
What is going on? This was actually submitted 11 hours ago, but now re-appears
under the _same HN URL_ on the front-page, saying it was submitted only 1 hour
ago?

On top of that all comments on it seem to have shifted by like 10 hours as
well (busyant's comment is actually half a day old by now, not 40 minutes).

You can see the timestamps don't match up here:
[https://news.ycombinator.com/submitted?id=breck](https://news.ycombinator.com/submitted?id=breck)
(says 11 hours ago).

Or here:
[https://news.ycombinator.com/threads?id=busyant](https://news.ycombinator.com/threads?id=busyant)
(says 10 hours ago on his comment on this submission).

~~~
dredmorbius
Likely the 2nd chance queue.

This is a process HN has devised to give selected submissions another chance
at the front page. See:

[https://news.ycombinator.com/item?id=11662380](https://news.ycombinator.com/item?id=11662380)

~~~
chmod775
It's kind of problematic that they roll back the time on user comments as
well. This kind of "rewriting history" can lead to all sorts of issues.

~~~
sbierwagen
How, specifically?

~~~
chmod775
You don't see how lying about when something was posted can lead to problems?
Just making sure I'm answering the right question.

The spectrum begins at me being slightly annoyed because I can't tell posts
that were posted just now from posts that were posted hours ago.

It probably ends at people arguing in court over such things as prior art in
patent cases, or someone trying to submit an online comment as evidence.
Imagine Facebook mucking with timestamps... Often _when_ is pretty important.

There's a lot of things in between there which I'll leave to your imagination.

In any case, changing meta information silently can be as bad as silently
changing the content of posts themselves and will hurt your credibility as a
platform. The reddit CEO did it as a _joke_ once, and that already caused a
massive shitstorm[1].

[1]:
[https://www.reddit.com/r/announcements/comments/5frg1n/tifu_...](https://www.reddit.com/r/announcements/comments/5frg1n/tifu_by_editing_some_comments_and_creating_an/)

