A central task in drug discovery is searching, screening, and organizing large chemical databases. Here, we implement clustering on molecular similarity. We compute Morgan circular fingerprints, cluster using k-means, and perform dimensionality reduction using UMAP. Distributed GPU-accelerated algorithms enable real-time interactive exploration of chemical space.
A launch script, launch.sh, is provided to perform all tasks.
The environment can be customized for control of the container, to create your own repo, or to store the data in a custom location. However, if this is not needed, skip to Getting Started to use the defaults.
To customize your local environment, edit the appropriate section of launch.sh or provide a ~/.cheminf_local_environment file with the following information below.
To generate a template for .cheminf_local_environment, just run ./launch.sh with no arguments.
If .cheminf_local_environment does not exist, then a template will be written for you.
CONT=gitlab-master.nvidia.com:5005/<path_to_your_repo>
REGISTRY=gitlab-master.nvidia.com:5005
REGISTRY_USER='$oauthtoken'
REGISTRY_ACCESS_TOKEN=$(cat <path_to_your_access_token>)
PROJECT_PATH=/path/to/local/repo/dir
JUPYTER_PORT=8888
DATA_PATH=/path/to/scratch/space
Once your environment is setup, the following commands should be all you need.
Build your container:
./launch.sh build
Download the ChEMBL database:
./launch.sh dbSetup
Launch the dash interactive ChEMBL exploration tool:
./launch.sh dash
Navigate a browser to:
https://0.0.0.0:5000