I generated a table of images & info of the premade NCAA params in the database

This topic has 4 replies, 3 voices, and was last updated 4 years, 9 months ago by Anonymous.

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- February 16, 2020 at 2:27 pm #3347
  Anonymous
  I don’t have a problem*, I just wanted to link to a possibly useful resource. Namely, I was playing around with primeval genetic codes and I wanted to to know what the 3-letter code was for one amino acid. As a result I wrote a small script to make a table of images, filenames and three letter codes.
  
  https://github.com/matteoferla/Display-of-preset-Rosetta-NCAAs
  
  *) Unless I have added the wrong licence (MIT as me as author). On another repo, I made a 2to3 port of mol_to_params and added a MIT with Rosetta (Ian W. Davis) as author —I can do the same here.
- February 17, 2020 at 4:32 pm #15154
  Anonymous
  That’s cool! I think that’s potentially a very useful resource for people.
  
  Regarding licensing, I think you’re fine with the Display-of-preset-Rosetta-NCAAs repo. Items made with Rosetta are your own creation, and (though I’m not a licensing lawyer and can’t speak officially for RosettaCommons or University of Washington CoMotion) I think what you’ve presented is enough of a “use of” (rather than “modification of”) to be fine and considered your own work.
  
  —
  
  Your mol_to_params.py repo, though, is a violation of the Rosetta licensing terms. Though I beleive the licensing terms allow you to make modifications to Rosetta for your own use, publicly redistributing Rosetta code is against the licensing terms. I think (though again, not a licensing lawyer and not speaking officially) you’re okay to redistribute your modifications, but only so long as you don’t redistribute the Rosetta code itself. (For example, if you just redistributed patch files that might be alright.) It’s certainly an issue if you are claiming that the whole content of that repo is MIT licensed. (New code that you write can be MIT licensed, but the code from Rosetta that you didn’t write can’t be MIT relicensed, and simply modifying parts of a file doesn’t allow you to relicense the entire file.)
  
  As such, we’d appreciate it if you would remove the mol_to_params.py repo from public distribution. Feel free to make it a private repo for your own personal use, but please don’t publicly distribute Rosetta code (especially if you’re incorrectly implying that such code is MIT licensed).
  
  On a slightly happier note, though, I will mention that changes to make molfile_to_params work with Python3 have recently been merged into Rosetta master, and should be availible in recent weekly releases, and will be availible with the upcoming Rosetta 3.12 release.
- February 18, 2020 at 3:31 pm #15158
  Anonymous
  Ops. I assumed it was okay as it was just a script that is publically downloadable off http://www.pyrosetta.org/scripts and contains none of the main Rosetta code. I’ve switched it to private.
  
  That is good that a py3 version will be there. If I may ask or humbly suggest… will there be a wrapper to the `core` method of the `mol_to_param.py` file to make it usable as a python module without having to use SimpleNamespace/namedtuple? This is a bit of a pain as it obviously does not allow any IDE suggestions without having to read the argparse options, which are not always perfect.
- February 25, 2020 at 11:37 pm #15170
  Anonymous
  Holy cow — that’s super useful! Thank you for doing that!
  
  Thanks also for releasing your script to do this under a permissive licence. Would you be okay with it if we distributed your script with Rosetta (with your name on it as the original author)? The licence that you’ve given it permits this, but I wanted to confirm that this was something that you’ve thought about / would be okay with.
  - March 21, 2020 at 4:14 pm #15218
    Anonymous
    That is totally fine and I would be delighted.
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