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protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
43 stars 15 forks source link

Version update with new updated conda dependencies #21

Closed tsenapathi closed 3 years ago

tsenapathi commented 3 years ago

Hello @msuruzhon, We have updated some package dependencies for protocaller in conda-forge.

  1. PDB2PQR (https://anaconda.org/conda-forge/pdb2pqr)- This version dropped the PDB2PKA/APBS support from within PDB2PQR (temporarily) to get the independent conda install.
  2. pypdb (https://anaconda.org/conda-forge/pypdb)
  3. propka (https://anaconda.org/conda-forge/propka) And some more...

Especially we need to change htmd-pdb2pqr to the officially supported pdb2pqr package. So can we update the dependencies, run the tests and release a new version?

msuruzhon commented 3 years ago

Hi @tsenapathi, this is very good! Since ProtoCaller doesn't depend on pypdb anymore, this is no longer a requirement, but changing htmd-pdb2pqr to pdb2pqr requires some work. The tests for the tentative 1.2.0 version seem to pass now on my own laptop, but strangely enough I can't get the build to work, so there is no conda package yet. I am not exactly sure what is going wrong, I will try to take a look in the next few days, but it might be worth trying to relax the pdb2pqr requirements, as they seem to be clashing with the other dependencies.

tsenapathi commented 3 years ago

@msuruzhon Great!! Let me know if there is anything I can do to assist.

msuruzhon commented 3 years ago

The conda package is up and running and I have committed to master. I have also created two releases: 1.1.2, which covers the changes since the overhaul of the Protein Data Bank, and 1.2.0, where the only change relative to 1.1.2 is the pdb2pqr dependency. Both of them should be installable from conda and both of them should be functional. Feel free to test them and reopen if there are any issues.

tsenapathi commented 3 years ago

@msuruzhon Should we update the README.rst as well?

msuruzhon commented 3 years ago

Yes, I forgot to do that, I have edited it now.