diff --git a/README.md b/README.md index 8e3de35..7f26d7d 100644 --- a/README.md +++ b/README.md @@ -30,61 +30,57 @@ ## What is it? -Subpocket explorer (SubPEx) is a tool that uses weighted ensemble (WE) path -sampling, as implemented in WESTPA, to maximize pocket conformational search. -SubPEx's goal is to produce a diverse ensemble of protein conformations for use -in ensemble docking. +Subpocket explorer (SubPEx) is a tool that uses weighted ensemble (WE) path sampling, as implemented in [WESTPA](https://github.com/westpa/westpa), to maximize pocket conformational search. +SubPEx's goal is to produce a diverse ensemble of protein conformations for use in ensemble docking. -As with any WE implementation, SubPEx uses a progress coordinate to focus -computational power on sampling phase space. The available progress coordinates -are: +As with any WE implementation, SubPEx uses a progress coordinate to focus computational power on sampling phase space. +The available progress coordinates are: - composite RMSD (a linear combination of backbone and pocket heavy-atom RMSD) - pocket heavy atoms RMSD - backbone RMSD - Jaccard distance of pocket volumes (jd) -We highly recommend using the composite RMSD progress coordinate. Use of other -coordinates is not officially supported. +We highly recommend using the composite RMSD progress coordinate. +Use of other coordinates may have inadequate performance. -## SubPEx use - -### Downloading and installing SubPEx +## Installation The first step is to download, clone, or copy the repository. ```bash -git clone https://git.durrantlab.pitt.edu/erh91/SubPEx-Erich.git +git clone git@github.com:durrantlab/subpex.git ``` -The repository includes a `yaml` file to create a `conda` environment with all -the necessary dependencies. Simply run this command: +The repository includes lock files to build the same environment we use for development. +Simply run this command (after ensuring you have Makefile tools installed): ```bash -conda env create -f environment.yaml +make environment ``` To activate the new `conda` environment, run: ```bash -conda activate westpa +conda activate subpex-dev ``` -Some users may wish to create their own environments or to use an existing -WESTPA environment. If so, install the following packages so SubPEx can -calculate the progress coordinate: +Some users may wish to create their own environments or to use an existing WESTPA environment. +If so, install the following packages so SubPEx can calculate the progress coordinate: -- Westpa -- MDAnalysis -- NumPy -- SciPy +- loguru +- mdanalysis +- westpa +- numpy +- scipy - scikit-learn -- yaml +- jinja2 +- pydantic +- pydantic-settings -Note that installing SubPEx into an existing environment is not officially -supported. +## Usage -### Configuring a SubPEx run +TODO: Needs to be updated to new version Users should take advantage of our autobuilder (`wizard.py`) to setup their SubPEx simulations. In some cases, however, users may wish to manually set up @@ -285,3 +281,24 @@ the output in the `job_logs` directory. - __pcoord_istate.py__ calculates the progress coordinate for the initial states. - __pcoord.py__ calculates the progress coordinate for the production run. + +## Deploying + +We use [bump-my-version](https://github.com/callowayproject/bump-my-version) to release a new version. +This will create a git tag that is used by [poetry-dynamic-version](https://github.com/mtkennerly/poetry-dynamic-versioning) to generate version strings and update `CHANGELOG.md`. + +For example, to bump the `minor` version you would run the following command. + +```bash +poetry run bump-my-version bump minor +``` + +After releasing a new version, you need to push and include all tags. + +```bash +git push --follow-tags +``` + +## License + +This project is released under the MIT License as specified in `LICENSE.md`.