Adds mmCIF downloading feature for `fetch`

julie-forman-kay-lab / IDPConformerGenerator

Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space

https://idpconformergenerator.readthedocs.io/

Apache License 2.0

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Adds mmCIF downloading feature for `fetch` #196

Closed menoliu closed 2 years ago

menoliu commented 2 years ago

idpconfgen fetch can now prioritize PDBx/mmCIF formatted files instead of only PDB files.

joaomcteixeira commented 2 years ago

Thanks. I want to add this also to the pdbdl client, and correct what you said about downloading cifs as pdbs.

joaomcteixeira commented 2 years ago

Added the mmcif priority to pdbdl. The other issue you said I won't change it. It is by design that pdbdl saves the resulting chains in PDB format.

joaomcteixeira commented 2 years ago

I need to inspect tests before merging

joaomcteixeira commented 2 years ago

Thanks @menoliu for the input on your previous commit. However, I rewrote it, okay? Why?

your implementation didn't scale properly, you assumed there will always be only two possible download links, what if there are 10? :wink:
the ext parameter became dependent on the priority parameter. You need to handle priority 3 times and created a three layer if-clause. I believe there's no need for that.
you made an abstract partial function depend on two specific types of input. If the function is abstract it shouldn't specify. Again, why only two? :wink:

I tested this locally and seemed to work. Can you confirm that PDB and mmCIFS are downloading as intended, please?

menoliu commented 2 years ago

Aha! I didn't think of that, I just assumed if the download would go though, it would be a valid one. Thanks for catching that :) I will do the tests.

Edit: I have tried fetch with the PDBIDs that only had the PDBx/mmCIF format and they all downloaded as .cif even though I prioritized .pdb! Things are working as intended :)