MolecularEmbedding
internal_fd_defaults: dict
cart_fd_defaults: dict
cartesian_by_internals_method: str
__init__(self, masses, coords, internals, internal_fd_opts=None, cartesian_fd_opts=None):
get_direct_converter(self, target):
get_inverse_converter(self, target):
register(self):
@property
coords(self):
@property
masses(self):
@classmethod
canonicalize_internal_coordinate_spec(cls, spec):
@property
internals(self):
@property
zmatrix(self):
@classmethod
convert_to_internals(cls, coords, masses, spec):
internal_coordinates_from_spec(self, spec: dict):
@property
internal_coordinates(self):
strip_embedding_coordinates(self, coords):
strip_derivative_embedding(self, derivs):
restore_embedding_coordinates(self, coords):
restore_derivative_embedding(self, derivs):
get_internals(self, *, coords=None, strip_embedding=True):
get_cartesians(self, *, coords=None, strip_embedding=True):
@property
redundant_internal_transformation(self):
@property
embedding_coords(self):
get_cartesians_by_internals(self, order=None, strip_embedding=False, reembed=True, method=None, coords=None, **fd_opts):
get_internals_by_cartesians(self, order=None, strip_embedding=False, coords=None, **opts):
embed_coords(self, coords, sel=None, in_paf=False, planar_ref_tolerance=None):
unembed_derivs(self, coords, derivs, sel=None, in_paf=False, planar_ref_tolerance=None):
@property
inertia_tensor(self):
@property
inertial_frame(self):
Provides the inertial axis frame
:returns:_
inertial_frame_derivatives(self):
@property
translation_rotation_modes(self):
get_translation_rotation_invariant_transformation(self, order=0, mass_weighted=True, strip_embedding=True, coords=None):