pypka 2.5.0

A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism

PypKa

A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism DOI: 10.1021/acs.jcim.0c00718

@article{reis2020jcim,
author = {Reis, Pedro B. P. S. and Vila-Viçosa, Diogo and Rocchia, Walter and Machuqueiro, Miguel},
title = {PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations},
journal = {Journal of Chemical Information and Modeling},
volume = {60},
number = {10},
pages = {4442-4448},
year = {2020},
doi = {10.1021/acs.jcim.0c00718}
}

Documentation & Basic Usage

Documentation can be found here

Starting templates for the the API and CLI usage can be found here while a online notebook is hosted at Google Colab

Installation & Dependencies

PypKa should be installed in a Linux-based system. In Windows please use the WSL.

• python2.6>= & python3.5>=
• libgfortran4
• gawk
• pytest
• numpy
• delphi4py
• pdbmender

  python3 -m pip install pypka
  apt install gawk gcc gfortran libgfortran4 python2

A docker image is also available. A simple way of using it would be to build the image from the Dockerfile and running it on a local directory which contains the cli parameters file and input structure.

docker build -t pypka/latest -f Dockerfile .
docker run -v ${PWD}:/home/ -w /home -t pypka:latest python3.9 -m pypka <PARAMETERS_FILE>

Functioning working examples of the API, CLI, docker and notebook can be found under /examples.

Contributing

Contributions are encouraged, and they are greatly appreciated!

You can contribute in many ways:

• Report Bugs
• Fix Bugs
• Implement Features
• Write Documentation
• Submit Feedback

For more info check CONTRIBUTING

License

pypka is distributed under a LGPL-3.0, however delphi4py depends on DelPhi which is proprietary. To use DelPhi the user is required to download the DelPhi license here

Contacts

Please submit a github issue to report bugs and to request new features. Alternatively you may find the developer here. Please visit ou website for more information.