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

[Karol L. <kar...@gm...>]

Hi guys,

This is a good idea - let's create a GitHub issue for it lest we forget
about it. This has come up in the past when we talked about having
Z-matrices. I guess that would be the next step.

Regarding the coordinate-to-angle calculations - they'll be so fast for 99%
of the cases that it's not worthwhile to think about calculating things
on-the-fly.

- Karol


On Mon, Apr 2, 2018 at 3:44 PM, Eric Berquist <er...@pi...> wrote:

> Hi Tyler,
>
> I know you didn't ask this, but regarding the different implementations,
> I'll implement them and try them out. In general, I think that assuming
> performance doesn't vary too wildly, we're more interested in
> implementations that are close to the original intent (the equations),
> thought the "fast" one seems reasonable. A better timing test would compare
> both small molecules and very large ones, like MOFs or proteins, using
> `timeit`.
>
> > 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 I propose is a new method (see https://github.com/cclib/
> cclib/tree/master/src/cclib/method) that would take a `ccdata` instance
> and calculate all possible distances, angles, and torsions. In general,
> when we parse, we don't compute derived data; the only things we compute
> are quantities for attributes _if_ they can be computed from other
> attributes. The need for this is rare (see trickery for `coreelectrons` in
> Q-Chem). Once the `ccdata` is passed to the method, it is probably fine to
> precompute all values rather than on-the-fly, but this is not as important
> as keeping the calculation separate from the parsing. Eventually we could
> do both.
>
> See if you can write a method that would basically look like the
> `Molecule` but is initialized from a `ccdata` instance.
>
> Eric
>
> On Mon, Apr 2, 2018 at 10:10 AM, Tyler Josephson <jos...@um...> wrote:
>
>> 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
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F20305272%2Fdihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=LRIupf4KL2vU2HJH0SuJpkEdUie0rUOiSgEGq61VZv0%3D&reserved=0>
>> 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/ProgrammingProject
>>> s/tree/master/Project%2301
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCrawfordGroup%2FProgrammingProjects%2Ftree%2Fmaster%2FProject%252301&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=RVJgFfkFGATY7cQmozjV8zYWZuCOa2KWhxYBE5l3uC8%3D&reserved=0>
>>>
>>> Some of it is available (https://github.com/berquist/p
>>> rogramming_party/blob/master/eric/molecule.py
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fberquist%2Fprogramming_party%2Fblob%2Fmaster%2Feric%2Fmolecule.py&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=rHZe4h49qc4HM3Tow2VMDdfHYm9hWxlLEBr58Kk5zL4%3D&reserved=0>),
>>> 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
>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=bqoJnaPbbc1W%2BSq81RrBgbARpQHFmXsemHI2Sbi9eiY%3D&reserved=0>
>>>>
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>>>>
>>>
>>
>>
>> --
>> Tyler Josephson
>> PhD Chemical Engineering
>> Postdoctoral Research Associate, Siepmann Group
>> University of Minnesota, Twin Cities
>> 651-269-1433 |  | LinkedIn
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=qV%2BEiuoXrqlCNf9K8scXONaMiRvip5fImikj%2BYFdalc%3D&reserved=0>
>>
>
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