Metadata-Version: 2.1
Name: pypka
Version: 2.6.0
Summary: A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
Home-page: https://pypka.org
License: LGPLv3
Author: Pedro Reis
Author-email: pdreis@fc.ul.pt
Requires-Python: >=3.6,<4.0
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: Other/Proprietary License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering
Requires-Dist: delphi4py (>=1.0.1,<2.0.0)
Requires-Dist: numpy
Requires-Dist: pdbmender (>=0.3.0,<0.4.0)
Requires-Dist: psutil
Requires-Dist: pytest (>=6.2.5,<7.0.0)
Project-URL: Documentation, https://pypka.readthedocs.io/en/latest/
Project-URL: Repository, https://github.com/mms-fcul/PypKa
Description-Content-Type: text/markdown

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# PypKa

A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
DOI: <a href="https://doi.org/10.1021/acs.jcim.0c00718">10.1021/acs.jcim.0c00718</a>

```bibtex
@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](https://pypka.readthedocs.io/en/latest/)

  Starting templates for the the API and CLI usage can be found [here](https://pypka.readthedocs.io/en/latest/example.html) while a online notebook is hosted at [Google Colab](https://colab.research.google.com/github/mms-fcul/PypKa/blob/master/pypka/example/notebook/pypka.ipynb)

## Installation & Dependencies

PypKa should be installed in a Linux-based system. In Windows please use the [WSL](https://docs.microsoft.com/en-us/windows/wsl/install-win10).

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

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

A docker image is also [available](https://hub.docker.com/r/pedrishi/pypka). 
A simple way of using it would be to build the image from the [Dockerfile](./Dockerfile) and running it on a local directory which contains the cli parameters file and input structure.
```bash
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](./CONTRIBUTING.rst)

## License

  pypka is distributed under a [LGPL-3.0](./LICENSE), however delphi4py depends on
  DelPhi which is proprietary. To use DelPhi the user is required to
  download the DelPhi license
  [here](https://honiglab.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi)

## Contacts

  Please submit a github issue to report bugs and to request new features.
  Alternatively you may find the developer [here](mailto:pdreis@fc.ul.pt). Please visit ou [website](http://mms.rd.ciencias.ulisboa.pt/) for more information.

