skip to navigation
skip to content

Not Logged In

chembl_beaker 0.2.3

RDKit in the Bottle on Tornado

Latest Version: 0.4.13

chembl_beaker
======

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/>`_ and `OSRA <http://cactus.nci.nih.gov/osra/>`_, which exposes following RDKit functions:

 * Format convertion
 * Fingerprints
 * Descriptors

As a portable lightweight webserver, speaking REST. This particular implementation wraps RDKit in `Bottle <http://bottlepy.org/docs/dev/>`_ on `Tornado <http://www.tornadoweb.org/en/stable/>`_.

Where is it used?
--------

Beaker is used in `Clippy <https://github.com/madgpap/chembl_clippy>`_ project but can be used as a standalone web server as well.

Software dependencies
--------

 * `RDKit <http://www.rdkit.org/>`_
 * `OSRA <http://cactus.nci.nih.gov/osra/>`_
 * `Bottle <http://bottlepy.org/docs/dev/>`_
 * `Tornado <http://www.tornadoweb.org/en/stable/>`_

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 porn 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``)
 * **osra_binaries_location** - path to OSRA binary you want to use for compound recognition (string, default ``/usr/bin/osra``)

Running
--------
If you want to play with beaker run ``python run_beaker.py``
If you want to run beaker in production you should do this using virtualenv, uWSGI and NGINX as described `here <http://fclef.wordpress.com/2013/01/12/bottle-virtualenv-uwsgi-nginx-installation-on-ubuntu-12-04-1-lts/>`_. Other standard python deployment stacks will work as well.

More info and help
--------

More information can be found in `web based presentation <https://github.com/mnowotka/beaker-presentation>`_. You can always email the author: mmmnow@gmail.com
 
  • Downloads (All Versions):
  • 52 downloads in the last day
  • 459 downloads in the last week
  • 3832 downloads in the last month