Openbabel

OpenBabel — Chemical Format Conversion & Manipulation

OpenBabel 3.1.1. Two interfaces: pybel (Python API, high-level) and obabel (CLI, batch processing). Supports 146 formats, MMFF94/UFF/GAFF force fields.

When to Use This Skill

• Converting between molecular formats: SMILES ↔ SDF ↔ MOL2 ↔ PDB ↔ InChI ↔ CIF ↔ XYZ ↔ 100+ others
• Generating 3D coordinates from SMILES (quick alternative to RDKit ETKDGv3)
• Conformer searching with force field scoring
• Protonation state at given pH
• Computing molecular descriptors (LogP, TPSA, MR) and fingerprints
• SMARTS substructure filtering of large libraries
• Batch library processing (split, deduplicate, filter)
• Converting formats unsupported by RDKit (CIF, VASP POSCAR, XYZ, etc.)

Quick Start

from openbabel import pybel

# Read SMILES → generate 3D → write SDF
mol = pybel.readstring('smi', 'CC(=O)Oc1ccccc1C(=O)O')   # aspirin
mol.make3D(forcefield='mmff94', steps=500)
mol.write('sdf', 'aspirin.sdf', overwrite=True)

# Read SDF → SMILES
for mol in pybel.readfile('sdf', 'library.sdf'):
    print(mol.write('can').strip())   # canonical SMILES

Router — What to Read

| Task | Reference | |------|-----------| | pybel Python API: read, write, 3D, descriptors, fingerprints, SMARTS | references/pybel-python.md | | obabel CLI: conversion, --gen3d, --conformer, filtering, pH, split | references/obabel-cli.md | | Format codes, fingerprint types, descriptors, Tanimoto | references/formats-fingerprints.md |

Two Interfaces

| | pybel | obabel CLI | |---|---|---| | Use case | Scripted workflows, per-molecule logic | Batch conversion, library filtering | | Import | from openbabel import pybel | subprocess or shell | | Speed | Moderate | Fast (C++ core) | | Flexibility | High (per-atom access) | Moderate (flags) |

Installation

conda install -c conda-forge openbabel   # recommended (includes C++ libs)
pip install openbabel                     # Linux/macOS only

# Verify
python -c "from openbabel import pybel; print(pybel.readstring('smi','C').molwt)"
obabel --version

Key Global Variables

from openbabel import pybel

pybel.informats    # dict: {'sdf': 'MDL MOL format', 'smi': 'SMILES format', ...}
pybel.outformats   # dict of writable formats
pybel.fps          # list of fingerprint types: ['FP2', 'FP3', 'FP4', 'MACCS']
pybel.descs        # list of descriptor names
pybel.forcefields  # list of available force fields

Relation to RDKit

| Task | Prefer | |------|--------| | Drug-like 3D (ETKDGv3) | RDKit | | Non-organic / unusual atoms | OpenBabel (UFF) | | Format not in RDKit (CIF, XYZ, etc.) | OpenBabel | | SMARTS filtering (speed) | OpenBabel CLI | | Fingerprints (ECFP) | RDKit | | Fingerprints (FP2/FP3/MACCS) | OpenBabel |

Related Skills

• rdkit — complementary: ETKDGv3 conformers, ECFP fingerprints, reactions
• ase — ASE reads XYZ/CIF; OpenBabel converts to those formats
• scientific-skills:datamol — fast preprocessing, also wraps RDKit

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: Kdevos12
• Source: Kdevos12/ALKYL
• License: MIT

Install and usage instructions live in the source repository linked above.