Examples

All molecule objects are expected to be ASE Atoms objects.

These functions do not modify the input molecule.

Note

These examples use default tolerances and standard conventions. For details on geometric tolerance, eigenvalue tolerance, and internal data structures, see Concepts.

Symmetrize a molecule's geometry and detect its point group

An ASE Atoms object is passed to the function and a new symmetrized Atoms object is returned.

The returned object includes metadata such as the detected point group.

from ase import Atoms
import numpy as np
from minimalsym import symmetrize

## Set positions for molecule
theta = np.radians(104.5)

positions = np.array([
    [0.0, 0.0, 0.0],
    [0.958, 0.0, 0.0],
    [0.958 * np.cos(theta), 0.958 * np.sin(theta), 0.0]
])

## Create Atoms object
mol = Atoms(symbols=["O", "H", "H"], positions=positions)

## Symmetrize molecule
mol_symmetric = symmetrize(mol, geom_tol=0.05)

## Check output
print("Detected Point group: ", mol_symmetric.info["pg"])
# Example output: "Detected Point group: C2v"
# Symmetrized positions:
# [[ 0.     0.     0.066]
#  [-0.    -0.757 -0.521]
#  [ 0.     0.757 -0.521]]

For a deeper understanding of how symmetrization works internally, see the Symmetrize Algorithm Flowchart.

See: symmetrize API

---

Generate alternative symmetry candidates

An ASE Atoms object is passed to the function and a list of SymmetryResult is returned.

The data in SymmetryResult can be accessed through the attributes:

• mol
• pg
• rmsd

from minimalsym import generate_symmetry_candidates

## Get candidate symetries of mol
candidate_symmetries = generate_symmetry_candidates(mol, geom_tol=0.5)

for elem in candidate_symmetries:
    print(f"Symmetrized molecule: {elem.mol}")
    print(f"Point group: {elem.pg}")
    print(f"RMSD: {elem.rmsd}")

    # Example output:
    # Symmetrized molecule: Atoms(symbols='B12', pbc=False)
    # Point group: C3v
    # RMSD: 0.00011057236018531259

    # Symmetrized molecule: Atoms(symbols='B12', pbc=False)
    # Point group: C3
    # ...

See: generate_symmetry_candidates API

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Detecting a point group

An ASE Atoms object is passed to the function and a string with the point group of the molecule is returned.

from minimalsym import get_point_group

## Detect point group for molecule
pg_str = get_point_group(mol, geom_tol=0.05)

## Check output
print("Detected Point group: ", pg_str)
# Example output: "Detected Point group: C2v"

See: get_point_group API

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Checking planarity

An ASE Atoms object is passed to the function and a bool is returned. True if the molecule passed has planarity.

from minimalsym import is_planar

## Check planarity for molecule
mol_is_planar = is_planar(mol, geom_tol=0.05)

## Check output
print("Mol is planar: ", mol_is_planar)
# Example output: "Mol is planar: True"

See: is_planar API

---

Get symmetry-inequivalent atoms

Find symmetry-inequivalent atoms using all symmetry operations.

Two atoms are in the same equivalence class if any symmetry operation (proper or improper) maps one onto the other.

An ASE Atoms object is passed to the function and a tuple is returned.

Returns: (unique, parent)

    unique : sorted representative atom indices (one per equivalence class).

    parent : array where parent[i] gives the representative of atom i

from minimalsym import get_inequivalent

## Get symmetry-inequivalent atoms for molecule
atom_indices_list, parent_mapping = get_inequivalent(mol, geom_tol=0.3)

## Check output
print("Inequivalent indices list: ", atom_indices_list)
# Example output: "Inequivalent indices list: [0 1 2]"

print("Parent mapping: ", parent_mapping)
# Example output: Parent mapping: [0 1 2 0 0 1 1 1 1 2 2 1]"

See: get_inequivalent API

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See the API Public Reference for full documentation.