PDBBank update and pypdb update

protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS

http://protocaller.readthedocs.io

GNU General Public License v3.0

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PDBBank update and pypdb update #12

Closed kexul closed 3 years ago

kexul commented 3 years ago

Today I ran the example of T4-lysozyme, It seems that the pypdb has been broken because the update of PDBBank.

kexul commented 3 years ago

New readme readed, seems like you guys have found it.

msuruzhon commented 3 years ago

The Protein Data Bank has been rather unstable in the past half a year, and the recent update completely broke pypdb, and therefore ProtoCaller. It seems that they have made their API servers fairly stable now and they are removing all backward compatibility, so I modified a chunk of the code to accommodate that. I have pushed the commit now and the updated build should be available from conda within 1 hour. All the tests now pass, as well as the T4-lysozyme example.