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docker-compose-lbdd

An enviroment for ligand-based drug discovery.

This repositry were forked form yamasakih/docker-compose-django-rdkit

Setup

git clone [email protected]:masahiro-mochizuki/docker-compose-lbdd.git
cd docker-compose-lbdd
docker-compose build

How to use

Launch Jupyter Notebook

docker-compose up default

After execution of the above command, the message below will be shown like this:

main_1  |     Copy/paste this URL into your browser when you connect for the first time,
main_1  |     to login with a token:
main_1  |         http://(c3a6946d1451 or 127.0.0.1):8888/

In this example, you can access jupyter via URL. `http://127.0.0.1:8888/ .

An example code of accessing PostgresSQL from jupyter is examples/db_example.ipynb.

Excecute a python code

you can execute a python code without PostgreSQL database:

docker-compose run default python examples/mw_from_smiles.py CCC

Services

default

  • Python (version 3.6.0)
    • RDKit (version 2019.03.1)
    • scikit-learn
    • lightGBM
    • chainer
    • optuna
    • PostgreSQL10
    • pandas
    • numpy
    • matplotlib
    • tqdm
    • ipython
    • Jupyter Notebook

nvidia

The same package as the default is installed, but this service supports CUDA10.0.