def from_arrays(cls, atom_array, bond_array, fragment_array,
polymer_array, molecule_array, symbols,
symmetry_transformations, cell_shape, convention):
assert atom_array.dtype == atom_array_dtype
assert bond_array.dtype == bond_array_dtype
assert fragment_array.dtype == fragment_array_dtype
if polymer_array is None:
polymer_array = N.zeros((0,), dtype=polymer_array_dtype)
assert polymer_array.dtype == polymer_array_dtype
assert molecule_array.dtype == molecule_array_dtype
assert isinstance(symbols, tuple)
assert symmetry_transformations.dtype == st_array_dtype
assert isascii(cell_shape)
assert isascii(convention)
universe = cls.__new__(cls)
universe._atom_array = atom_array
universe._bond_array = bond_array
universe._fragment_array = fragment_array
universe._polymer_array = polymer_array
universe._molecule_array = molecule_array
universe._symbols = tuple(symbols)
universe._symmetry_transformations = symmetry_transformations
universe._cell_shape = cell_shape
universe._convention = convention
return universe
def __init__(self, args):
cell_shape, molecules, symmetry_transformations, convention = args
api.validate_type(cell_shape, str, "cell_shape")
api.validate_value(cell_shape, list(self._cell_parameter_array_shapes.keys()), "cell_shape")
api.validate_sequence(
molecules,
ImmutableTuple,
"molecules",
(
(lambda p: len(p) == 3, "must have length 3"),
(
lambda p: isinstance(p[0], Fragment) and isascii(p[1]) and isinstance(p[2], int),
"elements must be (fragment, label, count) " "triples",
),
),
)
api.validate_sequence(
symmetry_transformations,
ImmutableTuple,
"symmetry_transformations",
(
(lambda p: len(p) == 2, "must have length 2"),
(
lambda p: hasattr(p[0], "shape") and p[0].shape == (3, 3) and p[0].dtype == N.float64,
"rotation matrix must be float64 " "and have shape (3,3)",
),
(
lambda p: hasattr(p[1], "shape") and p[1].shape == (3,) and p[0].dtype == N.float64,
"translation vector must be float64 " "and have shape (3,)",
),
),
)
if cell_shape == "infinite" and len(symmetry_transformations) > 0:
raise ValueError("Symmetry transformations are allowed " "only in periodic universes")
api.validate_label(convention, "Universe.convention")
self._cell_shape = cell_shape
self._molecules = ImmutableTuple(
ImmutableTuple((FragmentRef(label, fragment), count)) for fragment, label, count in molecules
)
self._symmetry_transformations = symmetry_transformations
self._convention = convention
self._fragments = ImmutableTuple(ImmutableTuple((f, l)) for f, l, c in molecules)
self._molecule_counts = ImmutableTuple(c for f, l, c in molecules)
self._atom_counts = ImmutableTuple(f.number_of_atoms for f, l, c in molecules)
self._site_counts = ImmutableTuple(f.number_of_sites for f, l, c in molecules)
self._bond_counts = ImmutableTuple(f.number_of_bonds for f, l, c in molecules)
