chembl/beaker repository overview

⁠chembl_beaker

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⁠What is Beaker?

This is chembl_beaker package developed at ChEMBL <https://www.ebi.ac.uk/chembl/>_ group, EMBL-EBI <https://www.ebi.ac.uk/>_, Cambridge, UK.

This is wrapper for RDKit <http://www.rdkit.org/>_ which exposes following methods:

• Format convertion <https://github.com/chembl/chembl_beaker/blob/master/src/chembl_beaker/beaker/core_apps/conversions/views.py>_
• Vector image (SVG) generation, including Similarity Maps <https://github.com/chembl/chembl_beaker/blob/master/src/chembl_beaker/beaker/core_apps/svgImages/views.py>_
• Descriptors <https://github.com/chembl/chembl_beaker/blob/master/src/chembl_beaker/beaker/core_apps/descriptors/views.py>_
• Maximum Common Substructure <https://github.com/chembl/chembl_beaker/blob/master/src/chembl_beaker/beaker/core_apps/mcs/views.py>_
• Structural alerts <https://github.com/chembl/chembl_beaker/blob/master/src/chembl_beaker/beaker/core_apps/structuralAlerts/views.py>_
• ChEMBL Structure Pipeline <https://github.com/chembl/ChEMBL_Structure_Pipeline>_
• Marvin 4 JS compilant webservices <https://marvin4js.chemaxon.com/marvin4js-latest/docs/dev/webservices.html>_

As a portable, lightweight, CORS <https://en.wikipedia.org/wiki/Cross-origin_resource_sharing>-ready, REST <https://en.wikipedia.org/wiki/Representational_state_transfer>-speaking, SPORE <https://github.com/SPORE/specifications>-documented webserver. This particular implementation wraps RDKit in Bottle <http://bottlepy.org/docs/dev/> on Tornado <http://www.tornadoweb.org/en/stable/>_.

⁠Where is it used?

It can be used as web service backend for Marvin For Java Script <http://www.chemaxon.com/products/marvin/marvin-for-javascript/>_ as it exposes methods compatible with it's webservice specification <https://marvinjs-demo.chemaxon.com/latest/docs/dev/webservices.html>_. To do this you need to configure marvin sketcher instance:

::

marvin.sketcherInstance = new marvin.Sketch("sketch");
marvin.sketcherInstance.setServices(getDefaultServices({
    'clean2dws' : <url of  Beaker clean webservice>,
    'molconvertws' : <url of Beaker molExport webservice>,
    "stereoinfows" : <url of Beaker cipStereoInfo>
}));

⁠Usage

The best way is to use Docker::

docker run -p 5000:5000 chembl/beaker

open http://127.0.0.1:5000/docs⁠

⁠Configuration

By default configuration is stored in beaker.conf file, located in current directory. You can specify location of configuration file using --config (-c) parameter when running beaker. Configuration file format is standard *.ini. Beaker is distributed with example configuration file named beaker.conf.sample.

• debug - run bottle server in debug mode (True/False, default True)
• bottle_port - number of port on which Bottle server is listening for connections (integer, default 8080)
• bottle_host - hostname of Bottle server (string, default localhost)
• server_middleware - networking middleware library used by Bottle (string, default tornado)
• enable_cors - enable CORS plugin and respect all header settings below (True/False, default True)
• access_control_allow_origin - content of 'Access-Control-Allow-Origin' header send with every response (string, default *)
• access_control_allow_methods - content of 'Access-Control-Allow-Methods' header send with every response (string, default GET, POST, PUT, OPTIONS)
• installed_apps - apps installed in beaker, default to [ "beaker", "beaker.core_apps.autoDocs", "beaker.core_apps.conversions", "beaker.core_apps.descriptors", "beaker.core_apps.marvin", "beaker.core_apps.mcs", "beaker.core_apps.rasterImages", "beaker.core_apps.svgImages", "beaker.core_apps.similarityMaps", "beaker.core_apps.standardisation", ]

⁠Documentation

Like every good software written in Python, beaker is self-documented. When you run beaker, open your browser and go to URL: BEAKER_ROOT/docs. You will see live documentation genrated on the fly from all available webservices, exposed by beaker. You can immediately try them and see results return by the server. Every webservice should be documented - documentation is generated automatically as well, from docstring of every exposed webservice, interpreted as markdown.

⁠Development - writing your own extentions

Developing new app should be easy. The only required file is views.py where you should define your botte routes.