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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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How to effectively process multiple .pdb files? #225

Closed zyang20 closed 2 years ago

zyang20 commented 2 years ago

Hi all, does anyone know how to do a batch processing of multiple .pdb files? the web server only allows one at a time. Thanks

sobolevnrm commented 2 years ago

I would recommend downloading the PB2PQR binary with pip install pdb2pqr and using that.

zyang20 commented 2 years ago

I did that in Jupyer notebook. But I couldn't figure out how to launch the software. There are no clear instructions. Anyone could give me instructions step by step? Thanks a lot.

sobolevnrm commented 2 years ago

Pip installs the command-line program pdb2pqr30 that you can use to run PDB2PQR--that is the preferred mode of execution (not via a notebook). However, pip also installs the pdb2pqr module from which you could import main_driver and manually pass the desired argument namespace returned by build_parser.

I'm going to convert this issue to a discussion since others may have the same question.