mdw-zhong 0.1.0

Internal molecular dynamics workflow utilities for MD Workbench.

MD Workbench

Internal molecular dynamics workflow utilities.

The PyPI package name is mdw-zhong; the Python import package is md_workbench.

Install

The full runtime depends on conda-forge scientific packages and command-line tools such as OpenMM, RDKit, AmberTools, AutoDock Vina, Meeko, and PyMOL. For a working environment, install the conda environment first:

mamba env create -f environment.yml
mamba activate mdw
pip install mdw-zhong

Automated install or update from a checkout:

bash scripts/install_mdw_env.sh

Automated install on a machine without this repository checked out:

bash -c "$(curl -fsSL https://raw.githubusercontent.com/GeraltZeroZhong/mdw/main/scripts/install_mdw_env.sh)"

For local development from a checkout:

pip install -e .

Commands

mdw init-config
mdw self-check --config default_config.json
mdw gui
mdw run --config default_config.json
mdw plot --config default_config.json
mdw report --config default_config.json

Compatibility command names are also installed, including mdw-run, mdw-plot, mdw-report, mdw-mmgbsa, and mdw-self-check.

Packaging Note

pip install mdw-zhong installs the MD Workbench Python package and console commands. It intentionally does not try to install or create the full conda environment.