chembl-sqlalchemy 1.0.35

SQLAlchemy ORM schema for ChEMBL.

chembl-sqlalchemy

SQLAlchemy ORM models for the ChEMBL database, enabling programmatic access to ChEMBL data using Python.

This package allows you to query and explore ChEMBL bioactivity data using SQLAlchemy, without having to manually define the table schemas yourself.

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Installation

Install via pip:

pip install chembl-sqlalchemy

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Usage

from chembl_sqlalchemy import Activities
from sqlalchemy import create_engine, select, sessionmaker

# Connect to a local ChEMBL SQLite database
engine = create_engine("sqlite:///chembl_35.db")
Session = sessionmaker(bind=engine)
session = Session()

# Example query: Get first 1000 non-null pChEMBL values
query = (
    select(Activities.molregno, Activities.pchembl_value, Activities.standard_type)
    .where(Activities.pchembl_value.isnot(None))
    .limit(1000)
)

results = session.execute(query).fetchall()

for molregno, pchembl_value, standard_type in results:
    print(molregno, pchembl_value, standard_type)

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Versioning

The versioning scheme is:

MAJOR.MINOR.CHEMBL_VERSION

For example:

• 1.0.35 → First release of the ORM wrapper
• 1.1.35 → Minor enhancements to the ORM wrapper

Each package version explicitly corresponds to a specific ChEMBL database version to avoid compatibility issues.

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Database Files

The package does not include the ChEMBL database file itself. You can download the corresponding SQLite file from the ChEMBL downloads page.

Place it in your project directory or reference it by path when creating the SQLAlchemy engine.

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License

This project is licensed under the MIT License.