mda.fetch_pdb() to generate Universe from Protein Databank structures #4907
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I have downloading / fetching from PDB and AFDB in Molecular Nodes here: https://github.com/BradyAJohnston/MolecularNodes/blob/main/molecularnodes/download.py Would be happy to work on implementation for MDA. |
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I wouldn't mind working on this as a little side project. Are issues assigned to people for MDAnalysis, or is it just open a pull request and have everyone look at your code once you have a working implementation? |
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The latter - we only assign issues in specific cases where this has been planned. In general, put up a PR! We very much welcome new contributions. As a basic rule, you’ll need tests that cover your code and your tests need to run (and old tests should not fail). See https://userguide.mdanalysis.org/stable/contributing_code.html for more details on how to contribute. Feel free to ask questions on the PR for specifics. Just be aware that people are busy and it can take a day or two until people have time. |
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@BradyAJohnston given that you already have a working implementation under a reasonable license, could @jauy123 just get started with using yours and you could help with reviewing (as opposed to having to do all the work)? If this gets merged then we could put both your names on the contribution. (Disclosure: @jauy123 is working in my research group) |
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Yep I haven't got time to work on it anytime soon so that would be great. Happy to have them re-use the code! |
Is your feature request related to a problem?
We used to have
mda.fetch_mmtf()to get a structure from the PDB but with the demise of MMTF, this was removed around release 2.6 or so.Describe the solution you'd like
It would be very convenient to have
mda.fetch_pdb(PDB_ID)to create a Universe from the entry in the Protein Databank with IDPDB_ID.Describe alternatives you've considered
VMD (load molecule), pymol (fetch) and Chimera (fetch by ID) can do this.
Alternatively, keep using this bash script or
wget/curl.Additional context
We will need the mmcif reader #2367 .
See also #3377 (fetch from alphafold database).
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