def add_bonds(self, bonds):
api.validate_sequence(bonds, tuple, "bonds",
((lambda p: len(p) == 3,
"must have length 3"),
(lambda p: (isinstance(p[0], str)
or isinstance(p[0], Atom))
and (isinstance(p[1], str)
or isinstance(p[1], Atom)),
"elements must be strings or atoms"),
(lambda p: p[2] in self._bond_orders,
"bond order must be one of "
+ str(self._bond_orders))))
for a1, a2, order in bonds:
atom1 = self._get_atom(a1)
atom2 = self._get_atom(a2)
if atom1 is atom2:
raise ValueError("bond between %s and itself"
% str(atom1.full_path()))
p = self.common_ancestor((atom1, atom2))
if p is self:
self._bonds.append((atom1, atom2, order))
else:
raise ValueError("bond %s-%s must be defined in fragment %s"
% (str(atom1.full_path()),
str(atom2.full_path()),
p._label))
def add_atoms(self, atoms):
api.validate_sequence(atoms, Atom, "atoms")
new_attrs = set()
for a in atoms:
self._check_child_obj(a, new_attrs)
for a in atoms:
self._add_child_obj(a)
self._atoms.extend(atoms)
def add_fragments(self, fragments):
api.validate_sequence(fragments, Fragment, "fragments")
new_attrs = set()
for f in fragments:
self._check_child_obj(f, new_attrs)
for f in fragments:
self._add_child_obj(f)
self._fragments.extend(fragments)
def __init__(self, universe, name, strings, label_type):
api.validate_type(universe, Universe, "universe")
api.validate_label(name, "name")
api.validate_sequence(strings, str, "strings")
api.validate_value(label_type, self._allowed_types, "label_type")
self._universe = universe
self._name = name
self._string_array = N.array(list('\0'.join(strings) + '\0'),
dtype='S')
self._type = label_type
def __init__(self, universe, name, strings):
api.validate_type(universe, Universe, "universe")
self._universe = universe
api.validate_label(name, "name")
self._name = name
api.validate_sequence(strings, str, "strings")
if len(strings) != self._number_of_values():
raise ValueError("incorrect number of strings")
for s in strings:
api.validate_ascii_string(s, "label")
self._strings = ImmutableTuple(strings)
def add_molecules(self, molecules):
api.validate_sequence(molecules, tuple, "molecules",
((lambda p: len(p) == 2, "must have length 2"),
(lambda p: isinstance(p[0], Fragment)
and isinstance(p[1], int),
"elements must be (fragment, count) pairs")))
self._molecules.extend(molecules)
self._templates.extend([f for f, c in molecules])
self._molecule_counts.extend([c for f, c in molecules])
self._atom_counts.extend([f.number_of_atoms for f, c in molecules])
self._site_counts.extend([f.number_of_sites for f, c in molecules])
self._bond_counts.extend([f.number_of_bonds for f, c in molecules])
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)
def symmetry_transformations(self, symmetry_transformations):
if self.cell_shape == "infinite" \
and len(symmetry_transformations) > 0:
raise ValueError("Symmetry transformations are allowed "
"only in periodic universes")
api.validate_sequence(symmetry_transformations, tuple,
"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,)"),))
self._symmetry_transformations = symmetry_transformations
def __init__(self, args):
species, fragments, atoms, bonds = args
api.validate_label(species, "species")
self.species = species
labels = set()
api.validate_sequence(fragments, ImmutableTuple, "fragments", ((lambda p: len(p) == 2, "must have length 2"),))
for label, fragment in fragments:
api.validate_label(label, "fragment label")
if label in labels:
raise ValueError("label %s occurs more than once" % label)
labels.add(label)
api.validate_type(fragment, Fragment, "fragment template")
self.fragments = fragments
api.validate_sequence(atoms, ImmutableTuple, "atoms", ((lambda p: len(p) == 2, "must have length 2"),))
for label, atom in atoms:
api.validate_label(label, "atom label")
if label in labels:
raise ValueError("label %s occurs more than once" % label)
labels.add(label)
api.validate_type(atom, Atom, "atom")
self.atoms = atoms
self.attrs = ImmutableDict(IT.chain(fragments, atoms))
api.validate_sequence(bonds, tuple, "bonds", ((lambda p: len(p) == 3, "must have length 3"),))
for a1, a2, order in bonds:
self._validate_bond_atom(a1)
self._validate_bond_atom(a2)
if a1.split(".")[0] == a2.split(".")[0]:
raise ValueError(
"bond between %s and %s must be defined " "in fragment %s" % (a1, a2, a1.split(".")[0])
)
api.validate_value(order, api.MosaicFragment._bond_orders, "bond order")
self.bonds = bonds