rr_cache

RetroRules and MetaNetX cache

Name	Downloads	Version	Platforms

Description

rr_cache provides a cache for RetroRules and MetaNetX compounds and reactions

Requirements

rr_cache has the following dependencies:

• brs_utils
• requests
• rdkit
• colored

These dependencies can be installed through conda package manager with:

conda install -c conda-forge brs_utils requests rdkit colored

or by creating a dedicated environment:

conda env create -f environment.yaml

Install

From Conda

[sudo] conda install -c conda-forge rr_cache

Use

All cache data are stored into files on disk and loaded in memory each time the tool is used. Memory fingerprint is equal to the size of cache files loaded in memory multiplied by the number of processes which are running at the same time.

If the cache is present in the current working directory, it will be used. Otherwise, it will be downloaded from the remote repository. If it not possible to download the cache, either because it is not possible to reach it remotely or because the option --do-not-dwnl-cache is set, it will be generated from scratch.

Load rrCache in memory

from rr_cache import rrCache

cache = rrCache()
print(cache.cid_strc)

A part of cache For less loading time and memory footprint, a part of the cache can be loaded:

from rr_cache import rrCache

cache = rrCache(['cid_strc'])
cache.get_compound('MNXM2')

From CLI

python -m rr_cache --reaction-rules <RuleID_1> <RuleID_2>...

If RuleID_i is(are) set, prints out the reaction rule(s) or all reaction rules if nothing is specified.

python -m rr_cache --reactions <RxnID_1> <RxnID_2>...

If RxnID_i is(are) set, prints out the reaction(s) or all reactions if nothing is specified.

python -m rr_cache --compounds <CmpdID_1> <CmpdID_2>...

If CmpdID_i is(are) set, prints out the compound(s) or all compounds if nothing is specified.

python -m rr_cache --data-type <DataType>

If DataType is set, set the data type of the cache (default is mnx3.1).

(Re-)build the cache

From Python code

from rr_cache import rrCache

rrCache.Build(outdir)

From CLI

python -m rr_cache --build <folder>

Test

Please follow instructions below ti run tests:

cd tests
pytest -v

For further tests and development tools, a CI toolkit is provided in ci folder (see ci/README.md).

Authors

• Joan Hérisson
• Melchior du Lac

Acknowledgments

• Thomas Duigou

Licence

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