Install MDAnalysis, pandas and their dependencies:
pip install pandas
pip install mdanalysis mdanalysistests
PROPKA 3.1 does not have official releases at the moment but we can pip-install the source directly from GitHub (you need to have git installed):
pip install git+https://github.com/jensengroup/propka-3.1.git@master#egg=propka-3.1
This should install the most recent version of PROPKA 3.1 that supports all required features for propkatraj.
Install from source with:
git clone https://github.com/Becksteinlab/propkatraj.git
cd propkatraj
pip install .
Use the --user flag for pip to install among your local user packages.
The following should then work (inside the python interpreter or in a Python script):
from propkatraj import get_propka
The propkatraj.get_propka() function contains all functionality.