https://github.com/brsynth/rp3_dcache
https://github.com/brsynth/rp3_dcache
Last synced: 6 months ago
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- Host: GitHub
- URL: https://github.com/brsynth/rp3_dcache
- Owner: brsynth
- License: mit
- Created: 2019-09-26T11:41:24.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2021-04-28T06:16:15.000Z (about 5 years ago)
- Last Synced: 2025-09-09T20:14:08.353Z (11 months ago)
- Language: Python
- Size: 17.6 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Database based cache to dope data retrieval for RetroPath RL
Here it is a two components cache system to dope the result retrieval from reaction rules
results, to be used with RetroPath RL. The 2 components are:
- A python module to be imported in RetroPath RL
- 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
- docker : https://docs.docker.com/install/
- docker-compose : https://docs.docker.com/compose/install/
- conda : https://docs.conda.io/projects/conda/en/latest/user-guide/install/
## Setting up python environment
Basically: one needs a conda environment with following packages:
- rdkit
- pymongo
- pytest
```bash
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
```bash
pip install -e .
```
## How to run the database service in the background
```bash
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: Koch M, Duigou T, Faulon JL. Reinforcement Learning for Bioretrosynthesis. ACS Synthetic Biology (2020). DOI: https://doi.org/10.1021/acssynbio.9b00447
## License
See LICENSE file