1. Getting Started

sm_confgen is a Python package providing a method of generating ligand conformers from Temperature Replic Exchange Molecular Dynamics (TREMD) simulations in GROMACS.

2. Installation

2.1. Requirements

Before installing sm_confgen, one should have a working version of GROMACS. Please refer to the GROMACS documentation for full installation instructions. All other dependencies are either included in the provided conda environment or will be installed automatically by pip.

2.2. Installation from source

One can also install sm_confgen from the source code, which is available in our `GitHub repository`_. Specifically, one can execute the following commands:

git clone https://github.com/ajfriedman22/SM_ConfGen
cd sm_confgen/
mamba env create -n env.yaml
mamba activate sm_confgen
pip install .

If you would like to install the package in the editable mode, simply append the last command with the flag -e so that changes you make in the source code will take effect without re-installation of the package. This is particularly useful if you would like to contribute to the development of the package. (Pull requests and issues are always welcome!)