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Cache to dope the result retrieval from reaction rules, to be used with RetroPath 3.0

Project description

Database based cache to dope data retrieval for RetroPath 3

Here it is a two components cache system to dope the result retrieval from reaction rules results, to be used with RetroPath 3.0. The 2 components are:

  • A python module to be imported in RetroPath 3.0
  • A Mongo database, which should be started independently (see "How to run the database in the background")

Notice : at reading time, some of following information might be deprecated!

Needed components

Setting up python environment

Basically: one needs a conda environment with following packages:

  • rdkit
  • pymongo
  • pytest
conda create --name myenv python=3.6
source activate myenv
conda install --channel rdkit rdkit=2018.09.1.0
conda install --channel conda-forge pytest
conda install pytest
conda install pymongo
conda install pyyaml

Install as a packages

pip install -e .

How to run the database service in the background

docker-compose -f service/run/mongo.yml up  # Or 'up -d' to start in the background

Q&A

  • Where are stored the db files ? In a named docker data volume, see service/run/*yml file.

How to cite

Please cite: to be completed

License

See LICENSE file

Project details


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