RDKit and OSRA in the Bottle on Tornado as a Docker Image
Dockerized version of the Chembl chembl-beaker webserver that exposes functions for transformation of molecular information into other formats as a REST service
This Docker container builds the chembl_beaker package developed at ChEMBL group, EMBL-EBI, Cambridge, UK.
Beaker is a wrapper for RDKit and OSRA, which exposes following methods:
- Format conversion
- Compound recognition
- Raster image (PNG) generation
- Vector image (SVG) generation
- HTML5 ready compound representation
- Fingerprints
- Descriptors
- Ring information
- Maximum Common Substructure
- Smiliarity maps
- ChEMBL standardisation process, consisting of neutralisation, bond breaking, salt removal and applying various rules.
- 3D coordinates generation, using Universal Force Field
- Various other calculations (for example kekulisation)
- Marvin 4 JS compilant webservices
As a portable, lightweight, CORS-ready, REST-speaking, SPORE-documented webserver. This particular Dockerfile allows you to deploy Beaker without compiling and installing sources or using the Chembl virtual machine image. It wraps RDKit in Bottle on Tornado.
Make sure your machine supports Docker, then (assuming Linux) type docker pull jjander/chembl_beaker to pull the Dockerfile from Docker-Hub and build it on your machine. Or git clone https://github.com/iSnow/chembl_beaker-docker.git && docker build -t chembl/beaker:1.1.14 . to pull the latest version from Github and build it on your machine.
(assuming Linux) type docker run -p 7655:8080 chembl/beaker:1.1.14 to start the image. Point your browser to http://:8080/docs (e.g. http://localhost:8080/docs) to start using Beaker.
- OCR for images of chemical structures - installation instruction for OSRA 2.0 which is used in this Beaker distribution. Dockerfile for OSRA
- myChembl 29 released - myChembl also contains Beaker if you'd rather use it via a VM and integrated with iPython notebooks. See also this description of the ChEMBL webservices update and the API description
- installing RDKit with Anaconda - Miniconda, a related version is used to install RDKit in this Beaker distribution. Compiling RDKit for Docker is described in this Dockerfile