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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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Python 3 compatibility for pdb2pqr #516

Closed speleo3 closed 4 years ago

speleo3 commented 6 years ago

Tested with Python 2.7, 3.6, 3.7 by running pdb2pqr with various parameters (including --apbs-input and --with-ph).

Based on @tonigi's first commit from PR #440, but excludes his additional changes like propka3.1 support (could be easily added in a separate PR).

This PR only covers pdb2pqr so far. I can send a separate PR for pdb2pka once this is merged.

speleo3 commented 6 years ago

For the record: This doesn't touch the SCons build system, it simply runs pdb2pqr from the source directory.

sobolevnrm commented 6 years ago

Wow -- thank you very much for doing this!

On Sat, Jul 28, 2018 at 12:02 AM Thomas Holder notifications@github.com wrote:

For the record: This doesn't touch the SCons build system, it simply runs pdb2pqr from the source directory.

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cowsandmilk commented 5 years ago

Are you missing changes to pdb2pqr.py.in ? That is, you might have modified pdb2pqr.py in your copy and not made the change to pdb2pqr.py.in for the fact that has_key has been removed.

speleo3 commented 5 years ago

You are right @cowsandmilk. I didn't notice because I'm not using the SCons build system.

speleo3 commented 4 years ago

@sobolevnrm do you have plans to merge this? Or should we use a fork like https://github.com/tonigi/apbs-pdb2pqr/tree/htmd-fixups/ instead?

sobolevnrm commented 4 years ago

Yes, we are planning to merge this. We are very short-staffed right now. Please do not fork the code.

Thank you,

Nathan

On Fri, Apr 3, 2020 at 5:07 AM Thomas Holder notifications@github.com wrote:

@sobolevnrm https://github.com/sobolevnrm do you have plans to merge this? Or should we use a fork like https://github.com/tonigi/apbs-pdb2pqr/tree/htmd-fixups/ instead?

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