molecule

Molecule module.

class daltonproject.molecule.Molecule(atoms: str | None = None, input_file: str | None = None, charge: int = 0, symmetry: bool = False, isotopes: Sequence[str] | None = None)

Molecule class.

analyze_symmetry() → None

Analyze the molecular symmetry. Note that this translates the molecule’s center of mass to the origin.

atoms(atoms: str) → None

Specify atoms.

Parameters

atoms – Atoms specified with elements and coordinates (and optionally labels).

property coordinates: ndarray

Atomic coordinates.

isotopes_assign(isotopes: Sequence[str]) → None

Assign isotope order according to abundance.

Parameters

isotopes – Isotopes of the nuclei.

mol(filename: str) → None

Read dalton mol file.

Parameters

filename – Name of mol file containing charge, atoms, and coordinates.

property num_atoms: int

Return the number of atoms in the molecule.

xyz(filename: str) → None

Read xyz file.

Parameters

filename – Name of xyz file containing atoms and coordinates.