Re: [cclib-devel] Distance, Angle, Dihedral

[Tyler J. <jos...@um...>]

Thanks, Eric, this is helpful!

I did find a useful and simple implementation of dihedrals in Python on
this page: https://stackoverflow.com/questions/20305272/
dihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python
I especially like Praexolitic's careful evaluation of the different
equations in order to select the fastest one.

For my current application, I added this in a rather ad-hoc manner to a
copy of the ccget script, calling it from within an if statement to be
executed when attr == 'atomcoords' . So I have what I need for now. I would
be interested in helping add this to cclib in a more formal way. After
seeing your code, I realize the community should probably have a discussion
about what this should entail and how it should be organized - should one
calculate all bonds, angles, dihedrals automatically, or should the code
simply return specific bonds/angles/dihedrals that are requested by the
user (or both)?

What would you recommend? I'm rather new to collaborative code development.

Regards,
Tyler



On Sun, Apr 1, 2018 at 10:09 PM, Eric Berquist <er...@pi...> wrote:

> Hi Tyler,
>
> Nothing is present right now in the package to do that, though it may be a
> useful method in the future.
>
> For reference, if you're looking for the expressions, I've coded up
> distances, torsions, and angles in the past from this project:
> https://github.com/CrawfordGroup/ProgrammingProjects/tree/
> master/Project%2301
>
> Some of it is available (https://github.com/berquist/
> programming_party/blob/master/eric/molecule.py), though the torsions
> aren't present for some reason. I can find them if you're interested.
>
> Eric
>
> On Sat, Mar 31, 2018 at 7:14 AM, Tyler Josephson <jos...@um...> wrote:
>
>> Hi there!
>>
>> I'm new to cclib, and enjoying it so far! It's a powerful tool. I wanted
>> to ask the community if you've worked on functions that would extract
>> particular distance, angle, or dihedral measurements (I need dihedrals for
>> my particular problem). I could read in the atomcoords and calculate them
>> myself, but I wanted to check if something else is available.
>>
>> Regards,
>> Tyler
>>
>> --
>> Tyler Josephson
>> PhD Chemical Engineering
>> Postdoctoral Research Associate, Siepmann Group
>> University of Minnesota, Twin Cities
>> 651-269-1433 |  | LinkedIn
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-- 
Tyler Josephson
PhD Chemical Engineering
Postdoctoral Research Associate, Siepmann Group
University of Minnesota, Twin Cities
651-269-1433 |  | LinkedIn <https://www.linkedin.com/in/trjosephson/>