This repository contains the scripts to create Docker images with the MCCS toolchain and all third-party software used in the MCCS protocol installed and configured.
To use scripts in this repository to install and configure the included third-party software, one must read and agree their licenses first:
- PROPKA: https://github.com/jensengroup/propka/blob/master/LICENSE
- Open Babel: https://github.com/openbabel/openbabel/blob/master/COPYING
- VEGA CLI: https://www.ddl.unimi.it/vega/
- UCSF Chimera: https://www.cgl.ucsf.edu/chimera/docs/licensing.html
| Folder | Root Image | OS |
|---|---|---|
| slim | debian:buster-slim | Debian GNU/Linux 10, code name Buster |
To build the image, one must first install Docker. The Docker Desktop is full-featured with GUI support and runs on Windows and macOS while on Linux platforms the command line Docker Engine is provided.
One can build the Docker image from a command line
docker build slim -t mccs
It usually takes a few minutes to build, varying by connection speed and computer performance.
With the Docker image successfully built, one can start a container with
docker run --rm -it -v "$(pwd):/data" mccs
The MCCS tools run with molecular models. Via the -v "$(pwd):/data" argument, docker maps the current working directory to the /data directory in the container. Once the container launched, one can navigate to /data and perform the computation.
# In the container
cd /data
# Now you can use the tools against the molecular models located in your physical hard drive.
# All MCCS related tools are immediately available and most can be invoked by name, e.g. jdock, mccsx.
# Third-party software are invoked by the following commands.
# Please refer to their official documentation for detailed usage.
propka3
obabel
vega
chimera --nogui
# The side chain fixing script is located at ~/incompleteSideChains.py