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
# 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
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