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): 

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