pyMDMix --- http://mdmix.sourceforge.net

The program is distributed under GNU GPLv3 license. Find the license file under Licenses/ folder.

DOCUMENTATION

All documentation on program usage is online at http://mdmix.sourceforge.net

INSTALLATION

1- Dependencies

This version of pyMDMix depends on:

• ambertools>=12
• python>=2.7

make sure ambertools environment variables are set

2 - Installation process

it is advised to install pyMDMix in a virtual environment

there are three recommended ways to install pyMDMix:

1. from the repository by python -m pip install [insert address here]

2. from the project's local folder after cloning the repo by python -m pip install .

3. Use conda or mamba: we will first create the correct conda environment which will already contain ambertools. We will then set the AMBERHOME variable within the environment and finally proceed to install pymdmix from the local git cloned files. Make sure $CONDA_PREFIX points to the conda installation directory (it may happen when you activate the new environment this varaible is lost, in that case change the variable for the explicit path).

git clone https://github.com/CBDD/pyMDmix.git
cd pyMDMix
conda env create -f environment_p27.yml
conda activate mdmix-env
conda env config vars set AMBERHOME=$CONDA_PREFIX/envs/mdmix-env
pip install .

3 - Testing

You can test the package has been successfuly installed by activating the environment and, from a folder other than the cloned repository, running python -m pyMDMix if everything went fine, you will see something like Welcome to MDMix 2.6

The main script should have been installed correclty also. check it by running mdmix -h

Test the program works correctly: Move again to the package source directory and type: > python pyMDMix/test.py all This will run a series of source code checks. No test should fail.

4 - Using Docker

Build and run from a docker container using the provided Dockerfile.

• docker build -t pymdmix .
• docker run -v $PWD:/mnt pymdmix -h

The docker run command will mount the current working directory (windows users should replace $PWD by %cd%) so the container has access to the current location. Output will be also in the current working directory. s

4 - Enjoy!

Read program usage at online documentation.