Metadata-Version: 2.0
Name: pypka
Version: 0.0.1
Summary: A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
Home-page: https://github.com/mms-fcul/PypKa
Author: Pedro Reis
Author-email: pdreis@fc.ul.pt
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Cython
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3) 
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 3 - Alpha
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: pytest
Requires-Dist: coverage

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# PypKa

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


# Dependencies 

  - delphi4py #1.0.0
  - libgfortran4
  - gawk 
  - pytest
  - numpy


# 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](https://honiglab.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi)

# Documentation

  Documentation can be found [here](https://pypka.readthedocs.io/en/latest/). (Under development)

# Installation

  pip install pypka

  apt install gawk gcc gfortran libgfortran4

# Change Log

## v0.4
  - API development
  - code level documentation improvement
  - documentation wiki developement with tutorial
  - test suite implementation

## v0.3
  - integration with delphi4py
  - integration with PDB2PQR
  - additional testing

## v0.2
  - DelPhi is now divided into two python modules imported by delphiT.py
  - input arguments are defined in delphiT.py

  - DelPhi routines for reading input files are bundled in delphi1_module
  - delphi1_module returns DelPhi's internal data structure

  - delphi2_module does not do any I/O
  - delphi2_module returns solvation energies and potential map

  - delphiT.py calculates intrinsic pka and interactions energies
  - delphiT.py supports multiprocessing and Nanoshaper usage
  - delphiT.py supports membrane systems
  - delphiT.py supports double/single precision

## v0.1
  - migration from DelPhi 5.0 to DelPhi 5.1_Patched
  - delphiT calls delphiT.py
  - delphiT.py calls DelPhi 5.1_Patched
  - added benchmark process and small test set

## original version
  - delphiT calls directly DelPhi 5.0


