MDStudio Structures

Molecular structure based microservice for the MDStudio workflow environment. This service combines the functionality of 9 popular cheminformatics packages through a common interface using Cinfony:

• webel
• silverwebel
• OpenBabel
• CDK
• RDkit
• Opsin
• Indigo
• JChem
• PyDPI

Installation Quickstart

MDStudio structures can be used in the MDStudio environment as Docker container or as standalone service.

Install option 1 Pre-compiled Docker container

MDStudio structures can be installed quickly from a pre-compiled docker image hosted on DockerHub by:

docker pull mdstudio/mdstudio_structures
docker run (-d) mdstudio/mdstudio_structures

In this mode you will first need to launch the MDStudio environment itself in order for the MDStudio structures service to connect to it. You can unify this behaviour by adding the MDStudio structures service to the MDStudio service environment as:

MDStudio/docker-compose.yml:

    services:
       mdstudio_structures:
          image: mdstudio/mdstudio_structures
          links:
            - crossbar
          environment:
            - CROSSBAR_HOST=crossbar
          volumes:
            - ${WORKDIR}/mdstudio_structures:/tmp/mdstudio/mdstudio_structures

And optionally add mdstudio_structures to MDStudio/core/auth/settings.dev.yml for automatic authentication and authorization at startup.

Install option 2 custom build Docker container

You can custom build the MDStudio structures Docker container by cloning the MDStudio_structures GitHub repository and run:

docker build MDStudio_structures/ -t mdstudio/mdstudio_structures

After successful build of the container follow the steps starting from docker run in install option 1.

Install option 3 standalone deployment of the service

If you prefer a custom installation over a (pre-)build docker container you can clone the MDStudio_structures GitHub repository and install mdstudio_structures locally as:

pip install (-e) mdstudio_structures/

Followed by:

./entry_point_mdstudio_structures.sh

or

export MD_CONFIG_ENVIRONMENTS=dev,docker
python -u -m mdstudio_structures