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.