pypka 0.0.3

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

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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

# Contacts

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

# 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