cclib-devel Mailing List for cclib

Hi all,

I just published v1.5.3 in GitHub, merged it into master and uploaded to
PyPI. We'll now be working to fix as many additional things for v1.5.4 and
get that out before GSOC 2018 starts in May.

Best,
Karol

I've made an issue to track this: https://github.com/cclib/cclib/issues/489

On Tue, Apr 3, 2018 at 3:17 AM, Karol Langner <kar...@gm...>
wrote:

> 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
>> <)" rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Ftree%2Fmaster%2Fsrc%2Fcclib%2Fmethod&data=01%7C01%7Cerb74%40pitt.edu%7Cc7e776a577974aa5c75e08d59932ebeb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=0jscbsSZPM18PtDpSaGf6nSX26m%2BOAsvSYOwn3RGrz4%3D&reserved=0>)
>> 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
>>> <" rel="nofollow">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
>>>> <" rel="nofollow">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
>>>> <)," rel="nofollow">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
>>>>> <" rel="nofollow">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>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>>>> 1%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271
>>>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%2FUMc6h6
>>>>> 5RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%3D&reserved=0
>>>>> _______________________________________________
>>>>> cclib-devel mailing list
>>>>> ccl...@li...
>>>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%
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>>>>> data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596
>>>>> fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=vtaWqxXd
>>>>> aJ13NDCnSkApw%2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Tyler Josephson
>>> PhD Chemical Engineering
>>> Postdoctoral Research Associate, Siepmann Group
>>> University of Minnesota, Twin Cities
>>> 651-269-1433 |  | LinkedIn
>>> <" rel="nofollow">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>
>>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
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>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>> <" rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&data=01%7C01%7Cerb74%40pitt.edu%7Cc7e776a577974aa5c75e08d59932ebeb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9CvlgA4PZCkSvuIusHvwYL3LsxOxgoHLsLhYEdeICtk%3D&reserved=0>
>>
>>
>

I have noticed that Q-Chem 5.1 is very broken, but it won't be released
until May, so it's not worth rushing that.

On Wed, Apr 4, 2018 at 10:33 AM, Karol Langner <kar...@gm...>
wrote:

> I think it's a good idea to accelerate v1.5.3 and get it out in the next
> 2-3 days. We can do another release before GSOC starts in May, if there are
> any interesting changes/fixes.
>
> On Fri, Mar 30, 2018 at 5:20 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Nothing in particular comes to mind. We can try to narrow down what we
>> think is possible to do in 3 weeks, and move everything else to 1.5.4. We
>> should also take a look if it's time to go to v1.6. - typically this
>> happens if there is a new parser or major addition to methods or similar
>> thing.
>>
>> On Fri, Mar 30, 2018 at 4:41 PM, Eric Berquist <er...@pi...> wrote:
>>
>>> The timing is convenient for me, since I have a lot more free time.
>>> Aside from the general 1.5.3 label, is there anything that should be
>>> prioritized?
>>>
>>> On Wed, Mar 28, 2018 at 1:56 AM, Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Hi all,
>>>>
>>>> It's been a while since the last release again, and I want to get it
>>>> out before GSOC starts. I've set the release to April 22 (just before
>>>> announcing who the students are). The release might be off of that by a day
>>>> or two, but I'd like to finalize it around that time.
>>>>
>>>> So, let's try to get as much in as we can for v1.5.3!
>>>>
>>>> Karol
>>>>
>>>> P. S. And, of course, I want to do another release right after GSOC
>>>> ends, assuming there is a student.
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>>> 1%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05ea3f08d59470b584
>>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ynrjNxlL51L5ou
>>>> 5%2BprRiTswTVAFhsl%2BZ0ZOMm935OQc%3D&reserved=0
>>>> _______________________________________________
>>>> cclib-devel mailing list
>>>> ccl...@li...
>>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%
>>>> 2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&
>>>> data=01%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05ea3f08d594
>>>> 70b584%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=uwRN0SaL
>>>> W%2FMfnVBJ32jEw01u8eMtqP7jiZ1c5oxxTx0%3D&reserved=0
>>>>
>>>>
>>>
>>
>

I think it's a good idea to accelerate v1.5.3 and get it out in the next
2-3 days. We can do another release before GSOC starts in May, if there are
any interesting changes/fixes.

On Fri, Mar 30, 2018 at 5:20 PM, Karol Langner <kar...@gm...>
wrote:

> Nothing in particular comes to mind. We can try to narrow down what we
> think is possible to do in 3 weeks, and move everything else to 1.5.4. We
> should also take a look if it's time to go to v1.6. - typically this
> happens if there is a new parser or major addition to methods or similar
> thing.
>
> On Fri, Mar 30, 2018 at 4:41 PM, Eric Berquist <er...@pi...> wrote:
>
>> The timing is convenient for me, since I have a lot more free time. Aside
>> from the general 1.5.3 label, is there anything that should be prioritized?
>>
>> On Wed, Mar 28, 2018 at 1:56 AM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Hi all,
>>>
>>> It's been a while since the last release again, and I want to get it out
>>> before GSOC starts. I've set the release to April 22 (just before
>>> announcing who the students are). The release might be off of that by a day
>>> or two, but I'd like to finalize it around that time.
>>>
>>> So, let's try to get as much in as we can for v1.5.3!
>>>
>>> Karol
>>>
>>> P. S. And, of course, I want to do another release right after GSOC
>>> ends, assuming there is a student.
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>> 1%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05ea3f08d59470b584
>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ynrjNxlL51L5ou
>>> 5%2BprRiTswTVAFhsl%2BZ0ZOMm935OQc%3D&reserved=0
>>> _______________________________________________
>>> cclib-devel mailing list
>>> ccl...@li...
>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%
>>> 2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&
>>> data=01%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05ea3f08d5
>>> 9470b584%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=
>>> uwRN0SaLW%2FMfnVBJ32jEw01u8eMtqP7jiZ1c5oxxTx0%3D&reserved=0
>>>
>>>
>>
>

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
>> <" rel="nofollow">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
>>> <" rel="nofollow">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
>>> <)," rel="nofollow">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
>>>> <" rel="nofollow">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>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>>> 1%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271
>>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%2FUMc6h6
>>>> 5RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%3D&reserved=0
>>>> _______________________________________________
>>>> cclib-devel mailing list
>>>> ccl...@li...
>>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%
>>>> 2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&
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>>>> fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=vtaWqxXd
>>>> aJ13NDCnSkApw%2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>>>>
>>>>
>>>
>>
>>
>> --
>> Tyler Josephson
>> PhD Chemical Engineering
>> Postdoctoral Research Associate, Siepmann Group
>> University of Minnesota, Twin Cities
>> 651-269-1433 |  | LinkedIn
>> <" rel="nofollow">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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>

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
> <" rel="nofollow">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
>> <" rel="nofollow">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
>> <)," rel="nofollow">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
>>> <" rel="nofollow">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>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>> 1%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271
>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%2FUMc6h6
>>> 5RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%3D&reserved=0
>>> _______________________________________________
>>> cclib-devel mailing list
>>> ccl...@li...
>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%
>>> 2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&
>>> data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d5
>>> 96fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=
>>> vtaWqxXdaJ13NDCnSkApw%2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>>>
>>>
>>
>
>
> --
> Tyler Josephson
> PhD Chemical Engineering
> Postdoctoral Research Associate, Siepmann Group
> University of Minnesota, Twin Cities
> 651-269-1433 |  | LinkedIn
> <" rel="nofollow">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>
>

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
>> <" rel="nofollow">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>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=
>> 01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb627
>> 1%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%2FUMc6h
>> 65RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%3D&reserved=0
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://na01.safelinks.protection.outlook.com/?url=https%3A%
>> 2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-
>> devel&data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3f
>> a1d08d596fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&
>> sdata=vtaWqxXdaJ13NDCnSkApw%2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>>
>>
>


-- 
Tyler Josephson
PhD Chemical Engineering
Postdoctoral Research Associate, Siepmann Group
University of Minnesota, Twin Cities
651-269-1433 |  | LinkedIn <" rel="nofollow">https://www.linkedin.com/in/trjosephson/>

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
> <" rel="nofollow">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>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! https://na01.safelinks.
> protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%
> 7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271%
> 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%
> 2FUMc6h65RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%3D&reserved=0
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.
> sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&data=
> 01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271%
> 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=vtaWqxXdaJ13NDCnSkApw%
> 2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>
>