automol

automol is a Python library for working with molecular geometries. It centers on a single Geometry model (atomic symbols, Cartesian coordinates, charge, and spin) and provides:

• Geometries — creating, reading/writing (xyz), and transforming Geometry objects, plus geometric properties like distance matrices and connectivity.

• Molecular identity — generating and comparing molecular identifiers (InChI, SMILES) from a Geometry, and back.

• Visualization — interactive 3D viewing and static/animated rendering.

• Interoperability — converting to and from RDKit, ASE, and StereoMolGraph representations.

New here? Start with Installation, then Geometries.

User guide

• Installation
  • As a dependency
  • For development
• Geometries
  • Creating a Geometry
  • Reading and writing xyz
  • Molecular formula
  • Geometric properties
  • Transformations
  • Next steps
• Molecular identity
  • Generating an identity from a Geometry
  • Going back to a Geometry
  • kind
  • How algorithms are implemented
• Visualization
  • Interactive viewing
  • Rendering to files
• Interoperability
  • RDKit
  • ASE
  • StereoMolGraph
  • Adding a new conversion

Reference

• API Reference
  • automol