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MinimalSym

PyPI Python License

MinimalSym is a Python package for molecular symmetry analysis in Atomic Simulation Environment (ASE) Atoms objects, including structure symmetrization. It provides fast, geometry-based symmetry detection and manipulation, designed to integrate seamlessly into existing ASE workflows.

Internally, MinimalSym constructs symmetry operations and atom mappings, then projects atomic positions onto symmetry elements to enforce exact symmetry.

Installation

pip install minimalsym
See the Installation page for details.

Getting started

MinimalSym is a Python package that provides essential symmetry functionality for molecules represented as ASE Atoms objects.

Follow the steps below to quickly set up and use MinimalSym with ASE.

Install the necessary libraries

pip install minimalsym ase

Symmetrize a molecule

from ase.build import molecule
from minimalsym import symmetrize

## Create Atoms object.
mol = molecule("H2O")

## Symmetrize molecule.
mol_symmetric = symmetrize(mol)

## Check output
print(mol_symmetric.info["pg"])

For further examples and details on how to use MinimalSym, see the Usage and API pages.

Features

  • Point group detection: Detect common point groups for molecules based on their geometry.
  • Molecule symmetrization: Apply symmetry operations to molecules, aligning them to the detected point group.
  • Find symmetry-inequivalent atoms: Atoms are grouped if any symmetry operation (proper or improper) maps one onto the other.
  • ASE Atoms-native workflow: Directly integrates with ASE Atoms objects, enabling smooth use in existing workflows.

Scope and limitations

  • Works on finite molecules (no periodic structure support)
  • Uses geometric tolerance-based symmetry detection
  • Results depend on the chosen geom_tol

Supported point groups

Point groups are classifications of molecules based on their symmetry operations. MinimalSym can detect the following common molecular point groups:

  • C₁, Cₛ, Cᵢ
  • Cₙ, Cₙᵥ, Cₙₕ
  • Dₙ, Dₙₕ, Dₙd
  • Sₙ
  • T, T_h, T_d
  • O, O_h
  • I, I_h
  • C0v, D0h

Detection depends on the symmetry present in the input geometry and the tolerance used during symmetry detection.

API Overview

  • symmetrize(mol, geom_tol=...) -> Atoms
  • get_point_group(mol, geom_tol=...) -> str
  • is_planar(mol, geom_tol=...) -> bool
  • get_inequivalent(mol, geom_tol=...) -> (unique, parent)

See the full API Reference.

Acknowledgments

This package is based on and inspired by NASymmetry / MolSym, modified to focus on core symmetry functionality.

License

Distributed under the MIT License. See LICENSE for details.

Contributing

If you find MinimalSym useful or have suggestions for improvement, please feel free to open an issue or pull request on GitHub.