Introduction
CGExplore is a Python library for for working with
coarse-grained models.
The library is built off of stk, which comes with the pip install.
Important
Warning: This package is still very much underdevelopment and many changes are expected.
Installation
To install CGExplore, you need to follow these steps:
Create a conda or mamba environment:
mamba create -n NAME python=3.11
Activate the environment:
conda activate NAME
Install CGExplore with pip:
pip install cgexplore
Install OpenMM docs:
mamba install openmm
or:
conda install -c conda-forge openmm
Install openmmtools docs:
mamba install openmmtools
or:
conda config --add channels omnia --add channels conda-forge
conda install openmmtools
Then, update directory structure in env_set.py if using example code.
The library implements some analysis that uses Shape 2.1. Follow the instructions to download and installed at Shape
Developer Setup
To develop with CGExplore, you should create a new environment as above, then:
Clone CGExplore from here
From CGExplore directory use just to
install a dev environment with:
just dev
And then follow the previous steps.
Examples
The main series of examples are in First Paper Example. In that page you will find all the information necessary to reproduce the work in 10.1039/D3SC03991A
With each pull request a test is run as a GitHub Action connected to this repository. This ensures that the results obtained for a subset of the original data set do not change with changes to this library.
Note
cg_model_test is a good example of usage too!
New works done with CGExplore:
TBC.
Acknowledgements
This work was completed during my time as a postdoc, and then research fellow in the Pavan group at PoliTO (https://www.gmpavanlab.com/).