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pierrepo / PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:
https://pbxplore.readthedocs.org/en/latest/
MIT License
28 stars 17 forks source link

Remove --phipsi option #120

Closed HubLot closed 8 years ago

HubLot commented 8 years ago

Fix the issue #118

I didn't remove write_phipsi and write_phipsi_entry function because they can be useful for the API user. I update the notebook to warn about the RAM issue and suggest an alternative.

Please check if I didn't miss a thing.

pierrepo commented 8 years ago

I would also remove both write_phipsi and write_phipsi_entry functions that are mostly subjectif formatting functons and rather provide a more free example in the Notebook file. For instance:

pdb_path = os.path.join(pbx.DEMO_DATA_PATH, '2LFU.pdb')

with open('output.phipsi', 'w') as outfile:
    for chain_name, chain in pbx.chains_from_files([pdb_path]):
        dihedral = chain.get_phi_psi_angles()
        for res in sorted(dihedral):
            print("{} {:6d} {} {} ".format(chain_name, res, dihedral[res]["phi"], dihedral[res]["psi"]))
HubLot commented 8 years ago

Done!

pierrepo commented 8 years ago

Wunderbar !

pierrepo commented 8 years ago

Fix #118

HubLot commented 8 years ago

maybe after these 2 PR, it is worth it to push a new version on Pypi?

pierrepo commented 8 years ago

Yep. Correct. I'll do it today.

jbarnoud commented 8 years ago

We should have a CHANGELOG somewhere to write down what changes between two versions.

pierrepo commented 8 years ago

Brilliant idea. I'll start one.