stcmz/mccs-docker

Docker image with the MCCS toolchain and all third-party software used in the MCCS protocol pre-configured and installed.

MCCS Docker Image

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.

Disclaimer

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

What's Included

• MCCS toolchain
  • gpcrn
  • mccsx
  • pdbget
  • pdbm
  • pdbqtf
  • jdock
  • pdbrn
• PROPKA
• Open Babel
• VEGA CLI
• UCSF Chimera
• Side Chain Fixing Script

Platforms

Folder	Root Image	OS
slim	debian:buster-slim	Debian GNU/Linux 10, code name Buster

How to Build

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.

Usage

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

Author

Maozi Chen