molecule_similarities

Prerequisites

To run this project, you need to set up the following environment variables:

export DB_NAME='your_database_name'
export DB_USER='your_database_user'
export DB_PASSWORD='your_database_password'
export DB_HOST='your_database_host'
export DB_PORT='your_database_port'
export AWS_ACCESS_KEY_ID='your_aws_access_key_id'
export AWS_SECRET_ACCESS_KEY='your_aws_secret_access_key'
export AWS_REGION='your_aws_region'

Installation

To install the required dependencies, run:

pip install -r requirements.txt

Fetch Data

To fetch the molecules data run this scripts:

python fetch_lookups.py
python fetch_molecules.py

Data Ingestion into PostgreSQL

Run bash scripts from scripts/ingestion folder

Calculate Morgan Fingerprints

To calculate morgan fingerprints run script from scripts/morgan_fingerprint

Calculate Tanimoto Similarities

To calculate morgan fingerprints run script from scripts/tanimoto