recalc_normal_mode_tolerance: float

__init__(self, mol, normal_modes=None): 

@classmethod
from_data(cls, mol, data): 

set_molecule(self, mol): 

get_modes(self, quiet=False, allow_compute=True): 

@property
modes(self): 

• :returns: MolecularVibrations

construct_normal_modes(self, modes): 

load(self): 

update(self, modes): 

• :returns: _

load_normal_modes(self, file=None, mode=None, rephase=True, recalculate=False, quiet=False): 

Loads potential derivatives from a file (or from source_file if set)

• file: Any

• rephase: bool

  whether to rephase FChk normal modes or not

• :returns: _

get_normal_modes(self, quiet=False, compute_force_constants=True, **kwargs): 

Loads normal modes from file or calculates from force constants

• kwargs: Any

• :returns: _

get_force_constants(self, compute_force_constants=True, quiet=False): 

@classmethod
get_dipole_derivative_based_rephasing(cls, modes, analytic_dipoles, numerical_dipoles, strict=True, allow_swaps=False): 

@classmethod
get_fchk_normal_mode_rephasing(cls, mol, modes, use_dipoles=False): 

Returns the necessary rephasing to make the numerical dipole derivatives agree with the analytic dipole derivatives as pulled from a Gaussian FChk file

• :returns: _

@classmethod
get_partial_cubic_based_rephasing(cls, modes, partial_cubics: numpy.ndarray, degenerate_freq_threshold=1e-06, equivalent_threshold=0.01, nonzero_threshold=4.5e-06, ignore_single_zeros=False, frequency_scale=True): 

apply_transformation(self, transf): 

insert_atoms(self, atoms, coords, where): 

Handles the insertion of new atoms into the structure

• atoms: tuple[str]

• coords: CoordinateSet

• where: tuple[int]

• :returns: _

delete_atoms(self, where): 

Handles the deletion from the structure

• atoms: tuple[str]

• coords: CoordinateSet

• where: tuple[int]

• :returns: _