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chembl_beaker 0.2.3

RDKit in the Bottle on Tornado

Latest Version: 0.4.13


What is Beaker?

This is chembl_beaker package developed at `Chembl <>`_ group, `EMBL-EBI <>`_, Cambridge, UK.

This is wrapper for `RDKit <>`_ and `OSRA <>`_, which exposes following RDKit functions:

 * Format convertion
 * Fingerprints
 * Descriptors

As a portable lightweight webserver, speaking REST. This particular implementation wraps RDKit in `Bottle <>`_ on `Tornado <>`_.

Where is it used?

Beaker is used in `Clippy <>`_ project but can be used as a standalone web server as well.

Software dependencies

 * `RDKit <>`_
 * `OSRA <>`_
 * `Bottle <>`_
 * `Tornado <>`_

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``)

If you want to play with beaker run ``python``
If you want to run beaker in production you should do this using virtualenv, uWSGI and NGINX as described `here <>`_. Other standard python deployment stacks will work as well.

More info and help

More information can be found in `web based presentation <>`_. You can always email the author:
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