Open Babel - The Universal Chemical Translator

Open Babel (and its Python wrapper pybel) is the essential tool for chemical data interoperability. It allows researchers to seamlessly move data between formats like SMILES, PDB, SDF, CIF, and Gaussian input/output.

When to Use

• Converting chemical files between different formats (e.g., SDF to PDB).
• Generating 3D coordinates from 2D structures or SMILES.
• Searching for substructures using SMARTS patterns.
• Performing fast molecular docking preparation (e.g., adding hydrogens, calculating charges).
• Running basic force field minimizations (UFF, GAFF, MMFF94).
• Calculating molecular fingerprints and Tanimoto coefficients.
• Batch processing large chemical databases (millions of molecules).

Reference Documentation

Official docs: https://openbabel.org/docs/dev/
Python API (Pybel): https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html
Search patterns: openbabel.OBMol, pybel.readfile, pybel.readstring, mol.make3D