Upload sprint results to fragalysis

[glass-w]

Description

Provides uploads to Fragalysis

Todos

Notable points that this PR has either accomplished or will accomplish.

• [x] Setup new function to push to Fragalysis.
• [x] Ensure formatting is correct for Fragalysis files.

Status

• [x] Ready to go

[glass-w]

This now uses a fragalysis_config.json file to specify parameters needed by the fragalysis API (see here and here).

An example of this type of file:

{
        "run": true,
        "ligands_filename": "reliable-transformations-final-ligands.sdf",
        "proteins_filename": "reliable-transformations-final-proteins.pdb",
        "fragalysis_sdf_filename": "compound-set_foldingathome-sprint-5.sdf",
        "ref_url": "https://discuss.postera.ai/t/folding-home-sprint-5/2423",
        "ref_mols": "x12073",
        "ref_pdb": "x12073",
        "target_name": "Mpro",
        "submitter_name": "Folding@home",
        "submitter_email": "first.last@choderlab.org",
        "submitter_institution": "MSKCC",
        "method": "Sprint 5",
        "upload_key": "<key number>",
        "new_upload": true 
}

[glass-w]

Currently this doesn't appear to upload results to the Fragalysis site but runs without errors. For now this can safely be put into production as long as either a) the fragalysis-config flag isn't specified or b) run is set to false in the fragalysis_config.json file (as described above).

[glass-w]

@jchodera I'm going to see if I can fix the zipped PDB files first. If this takes too long we can merge anyway and just disable the upload.

[glass-w]

Zipped PDB files now fixed and upload to Fragalysis is working.