brs-libs 0.2.0

'libraries for rptools'

brs-libs

Libraries for rpTools:

• rpCache
• rpSBML

rpSBML

Defines SBML structure with additional fields relative to RetroPath2 objects.

Prerequisites

• Python 3 with the following modules:
  • python-libsbml
• RDKit

rpCache

Memory management

File mode

This is the default mode. All cache data are stored into files on disk and loaded in memory each time the tool is used. In this mode, fingerprint in memory is equal to the size of cache files loaded in memory multiplied by the number of processes which are running at the same time. Option can be specified by --store-mode file.

DB mode

In order to save memory space, cache data can be loaded once in a database (redis) so that the memory space taken is equal to one instance of the cache, whatever the number of processes whic are running. Option can be specified by --store-mode <db_host>, where db_host is the hostname on which redis server is running.

Install

rpCompletion requires RDKit which is not available through pip. It can be installed through Conda:

[sudo] conda install -c rdkit rdkit

From pip

[sudo] python -m pip install brs_libs

From Conda

[sudo] conda install -c brsynth brs_libs

Run

(Re-)generate the cache

From Python code

from brs_libs import rpCache

rpCache.generate_cache(outdir)

From CLI

After having installed brs_libs Python module:

python -m brs_libs --gen_cache <folder>

Test

Tests can be runned. To do so, please follow insructions below:

cd tests
./test-in-docker.sh

Authors

• Melchior du Lac
• Joan Hérisson

Acknowledgments

• Thomas Duigou

Licence

brs_libs is released under the MIT licence. See the LICENCE file for details.