chemease 0.2.0

A professional cheminformatics library built on RDKit.

ChemEase 🧪

ChemEase is a multi-purpose cheminformatics library built on top of RDKit, PubChem, and ChEMBL.

🇰🇷 한국어 문서(Korean Readme) 읽기

Features

• Database Integration: Fetch molecules, targets, and bioactivities easily from PubChem and ChEMBL.
• Advanced Descriptors: Calculate physicochemical properties and advanced fingerprints (e.g., MACCS Keys) for machine learning.
• 3D Structure & Optimization: Generate 3D conformers using ETKDG and optimize them with MMFF94 force fields.
• Clustering & Analysis: Perform Butina clustering and PCA on large chemical libraries.
• Virtual Synthesis: Simulate chemical reactions (e.g., Amide coupling) using SMIRKS/SMARTS patterns.
• CLI Support: Run major workflows directly from your terminal.

Installation

pip install chemease

Quick Start (CLI)

# Fetch a molecule and save it as SDF
chemease fetch --name "aspirin" -o aspirin.sdf

# Calculate advanced descriptors
chemease descriptors library.sdf -o features.csv

# Cluster a library
chemease cluster library.sdf --cutoff 0.6

Quick Start (Python)

from chemease import get_mol_from_chembl, calculate_advanced_descriptors_df, generate_conformers

# Load from ChEMBL
mol = get_mol_from_chembl("CHEMBL25") # Aspirin

# Calculate ML Features
df_features = calculate_advanced_descriptors_df([mol])

# Generate 3D Conformers
mol_3d = generate_conformers(mol, num_confs=5, optimize=True)

Contributing

Contributions are welcome! Please run black, isort, flake8, and pytest before submitting a pull request.