ConfTopo

Explore topological changes across protein conformational changes.

Running the app

ConfTopo runs as a Streamlit app. The preferred method of running the application is within a Docker container. Optionally, instructions are provided for running locally on macOS.

Regardless of the execution modality, first clone this repository:

git clone https://github.com/maduprey/conftopo.git

Docker

Setup

1. Install Docker.
2. cd into the repository.

Usage

1. Start Docker. For example, on most Linux distros:

   systemctl start docker

2. Build the Docker image:

   docker build -f docker/Dockerfile -t conftopo .

3. Run the Docker container:

   docker run -p 8501:8501 conftopo

4. In your browser, navigate to the Streamlit app at http://localhost:8501/

Local

Setup

1. Download and install UCSF ChimeraX 1.5. If the ChimeraX executable is installed somewhere else, edit the path /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX in chimerax.py.

2. cd into this repository.

3. Using conda, create and activate a virtual environment conftopo with pip installed:

   conda create -n conftopo python=3.8
   y # Accept any new packages that will be installed
   conda activate conftopo

4. Install the required Python packages:

   poetry install
   pip install streamlit==1.16.0

Usage

1. Start the Streamlit app:

   streamlit run run_conftopo.py

2. In your browser, navigate to http://localhost:8502/

Contributing

Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

conftopo was created by Michael Duprey. It is licensed under the terms of the MIT license.

Credits

conftopo was created with cookiecutter and the py-pkgs-cookiecutter template.