def __short_str__(self):
tyname = self.__class__.__name__
if not self.is_orphaned():
return "{} for atom indices {}".format(tyname,
andjoin(self.atom_indices))
else:
return "(orphaned) {} with atoms {}".format(
tyname, andjoin(self.atom_indices))
def __str__(self):
"""
"""
tyname = self.__class__.__name__
if self.is_orphaned():
return "(orphaned) {} for atoms {}".format(tyname, andjoin([str(atom) for atom in self.atoms]))
else:
mol_short_name = short_str(self.molecule)
return "{} for atom indices {} of {}".format(tyname, andjoin(self.atom_indices), mol_short_name)
def __str__(self):
"""
"""
tyname = self.__class__.__name__
if self.is_orphaned():
return "(orphaned) {} for atoms {}".format(
tyname, andjoin([str(atom) for atom in self.atoms]))
else:
mol_short_name = short_str(self.molecule)
return "{} for atom indices {} of {}".format(
tyname, andjoin(self.atom_indices), mol_short_name)
def b_tensor_element(self, *cart_coords_or_indices):
"""
Retrieve an element of the Coordinate's B tensor using CartesianCoordinate instances
and/or integer indices *in the molecule's indexing scheme*.
"""
if self._btensor is None:
self._init_btensor()
if all(isinstance(c, CartesianCoordinate) for c in cart_coords_or_indices):
idxs = cart_coords_or_indices
elif all(isinstance(c, int) for c in cart_coords_or_indices):
try:
idxs = self.internal_indices_for(cart_coords_or_indices)
except CoordinateDependencyError:
#TODO raise an error here instead?
raise
#return 0.0
else:
raise TypeError(
"arguments to b_tensor_element must be all integers (in the molecule's"
" indexing scheme) or all CartesianCoordinate instances."
" Mixing of CartesianCoordinates and integers in b_tensor_element"
" arguments is confusing and thus no longer allowed."
" indices were ('{}')".format(
"', '".join(str(c) for c in cart_coords_or_indices)
)
)
if not self.is_orphaned():
try:
if self._btensor.has_order(len(cart_coords_or_indices)):
return self._btensor[idxs]
else:
self.fill_b_tensor_analytically(order=len(cart_coords_or_indices))
return self._btensor[idxs]
except CoordinateDependencyError:
#TODO raise an error here instead?
raise
#return 0.0
else:
if sanity_checking_enabled:
if not all(isinstance(cart, int) for cart in cart_coords_or_indices):
raise ValueError(
"b_tensor elements may not be retrieved for orphaned coordinates by"
" anything but integer indices (got indices of types {})".format(
andjoin("'" + type(item).__name__ + "'" for item in cart_coords_or_indices)
)
)
order = len(idxs)
if not self._btensor.has_order(order):
response = self.fill_b_tensor_analytically(order=order)
if response is NotImplemented:
self._btensor[...] = self.finite_difference_b_tensor(order=order)
try:
return self._btensor.for_order(order)[idxs]
except IndexError:
raise
def __short_str__(self):
tyname = self.__class__.__name__
if not self.is_orphaned():
return "{} for atom indices {}".format(tyname, andjoin(self.atom_indices))
else:
return "(orphaned) {} with atoms {}".format(tyname, andjoin(self.atom_indices))