A simple Python library for analyzing and extracting information from free energy surfaces from molecular simulation.
- NumPy
- Pandas
- SciPy
- Matplotlib
- ImageMagick
- jupyter (just for the notebook example)
A YML file is provided: conda env create --file fes_tools.yml -n "fes_tools"
All can be installed via conda from scratch conda install pandas matplotlib imagemagick jupyter scipy
From the directory with setup.py: pip install -e ./ --user
import fes_tools into your python scripts and use the class based structure to analyze your simualtions.
fes_tools can extract the ∆G and of a reaction and the transition state energy of currently 1 and 2 dimension free energy surfaces, as well as plot them.
This can be done via the fes class for single surfaces or many sequential surfaces.
An example Jupyter Notebook is provided.