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Re: [cclib-devel] Distance, Angle, Dihedral
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From: Eric B. <er...@pi...> - 2018-04-05 00:24:54
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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 >> <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 >>> <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> >>>>> >>>>> ------------------------------------------------------------ >>>>> ------------------ >>>>> 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%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 >>> <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 >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%7Cerb74%40pitt.edu%7Cc7e776a577974aa5c75e08d59932ebeb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=PqD9nmeVymmkU2RsxQ%2BQsaYd%2BGi7rg4zECHuDRvgMcA%3D&reserved=0> >> _______________________________________________ >> cclib-devel mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-devel >> <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> >> >> > |
