def from_increments(cls, increments, rep, deltas=None):
if deltas is None:
deltas = cls.get_default_deltas(rep)
if sanity_checking_enabled:
if isinstance(increments, np.ndarray) and len(increments.shape) != 1:
raise ValueError("'increments' should be 1-dimensional")
if isinstance(deltas, np.ndarray) and len(deltas.shape) != 1:
raise ValueError("'deltas' should be 1-dimensional")
if type_checking_enabled:
if not isinstance(increments, (np.ndarray, list, tuple)):
raise TypeError
if not isinstance(deltas, (np.ndarray, list, tuple)):
raise TypeError
if sanity_checking_enabled:
if len(increments) != len(rep):
raise ValueError("length of increments must match length of representation, but {0} != {1}".format(len(increments), len(rep)))
if len(increments) != len(deltas):
raise ValueError("length of increments must match deltas, but {0} != {1}".format(len(increments), len(deltas)))
disps = []
for inc, delta, coord in zip(increments, deltas, rep):
if hasunits(delta):
disps.append(inc * delta.in_units(coord.units))
else:
# Assume the default units for the genre
disps.append(inc * (delta * coord.units.genre.default).in_units(coord.units))
return Displacement(rep, disps, increments=increments, deltas=deltas)
def __array_wrap__(self, out_arr, context=None):
"""
See http://docs.scipy.org/doc/numpy/user/basics.subclassing.html#array-wrap for explanation
"""
if context is not None:
if context[0] is np.multiply:
if len(context[1]) == 2:
op1, op2 = context[1]
else:
_, op1, op2 = context[1]
if op1 is self:
tens = op1
other = op2
elif op2 is self:
tens = op2
other = op1
else:
raise Exception("something very enigmatic happened...")
#----------------------------------------#
if hasunits(other):
out_arr.units = self.__mul_units__(tens.units, other.units)
else:
out_arr.units = self.units
#--------------------------------------------------------------------------------#
return np.ndarray.__array_wrap__(self, out_arr, context)
def __array_wrap__(self, out_arr, context=None):
"""
See http://docs.scipy.org/doc/numpy/user/basics.subclassing.html#array-wrap for explanation
"""
if context is not None:
if context[0] is np.multiply:
if len(context[1]) == 2:
op1, op2 = context[1]
else:
_, op1, op2 = context[1]
if op1 is self:
tens = op1
other = op2
elif op2 is self:
tens = op2
other = op1
else:
raise Exception("something very enigmatic happened...")
#----------------------------------------#
if hasunits(other):
out_arr.units = self.__mul_units__(tens.units, other.units)
else:
out_arr.units = self.units
#--------------------------------------------------------------------------------#
return np.ndarray.__array_wrap__(self, out_arr, context)
def __init__(self, base_molecule_or_representation, differentiable, deltas=None, details=None):
if type_checking_enabled:
if not isinstance(base_molecule_or_representation, (Molecule, Representation)):
raise TypeError
if not isinstance(differentiable, type) and issubclass(differentiable, Differentiable):
raise TypeError
if sanity_checking_enabled:
if not issubclass(differentiable, MolecularProperty):
# TODO write this error
raise ValueError
self._differentiable = differentiable
if isinstance(base_molecule_or_representation, Molecule):
# Assume the first InternalRepresentation is the one we want
self._representation = base_molecule_or_representation.internal_representation
else:
self._representation = base_molecule_or_representation
self.displacements = {}
self.deltas = deltas
self.details = details
if deltas is not None:
if type_checking_enabled and not isinstance(deltas, Iterable):
raise TypeError
if sanity_checking_enabled and len(deltas) != len(self.representation):
raise ValueError("dimension mismatch. 'deltas' list (length {}) must be the same " \
"as the number of coordinates ({})".format(len(deltas), len(self.representation)))
self.deltas = []
for delta, coord in zip(deltas, self.representation):
if hasunits(delta):
if sanity_checking_enabled and not compatible_units(delta.units, coord.units):
raise IncompatibleUnitsError("{} is not in valid units for a displacement of a {}".format(
delta, coord.__class__.__name__
))
else:
delta = delta * coord.units
self.deltas.append(delta)
else:
self.deltas = Displacement.get_default_deltas(self.representation)
