def test_bond_orders():
# Get a molecule with some bonds
wat = _make_water()
wat_o = wat.copy()
# 0,1 0,2
assert_npequal(wat.bond_orders, np.array([0, 0]))
# Remove a bond
wat.bonds = np.array([[0, 1]])
assert_npequal(wat.bond_orders, np.array([0]))
wat.bond_orders = np.array([2])
# Try with a system
s = System()
s.add(wat_o)
s.add(wat)
assert_npequal(s.bond_orders, np.array([0, 0, 2]))
s.reorder_molecules([1, 0])
# Bonds get sorted accordingly
assert_npequal(s.bond_orders, np.array([2, 0, 0]))
s.bonds = np.array([[0, 1], [0, 2], [3, 4], [3, 5]])
assert_npequal(s.bond_orders, np.array([2, 0, 0, 0]))
def test_reorder_molecules(self):
mols = self._make_molecules()
system = System(mols)
system.bonds = np.array([[0, 1], [3, 5]])
# Reordering
system.reorder_molecules([1, 0, 2, 3])
assert_eqbonds(system.bonds, [[0, 2], [3, 4]])
def test_bonds():
# TODO: deprecate this shit
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([Atom('O', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]), ])
# Adding bonds
s = System()
with s.batch() as b:
b.append(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(s.type_array, ['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
'C', 'C', 'C'])
eq_(s.dimensions['atom'], 12)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7)))
# Reordering
s.bonds = np.array([[0, 1], [6, 8]])
s.reorder_molecules([1, 0])
assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
def test_reorder_molecules(self):
mols = self._make_molecules()
system = System(mols)
system.bonds = np.array([[0, 1], [3, 5]])
# Reordering
system.reorder_molecules([1, 0, 2, 3])
assert_eqbonds(system.bonds, [[0, 2], [3, 4]])
def test_bond_orders():
# Get a molecule with some bonds
wat = _make_water()
wat_o = wat.copy()
# 0,1 0,2
assert_npequal(wat.bond_orders, np.array([0, 0]))
# Remove a bond
wat.bonds = np.array([[0, 1]])
assert_npequal(wat.bond_orders, np.array([0]))
wat.bond_orders = np.array([2])
# Try with a system
s = System()
s.add(wat_o)
s.add(wat)
assert_npequal(s.bond_orders, np.array([0, 0, 2]))
s.reorder_molecules([1, 0])
# Bonds get sorted accordingly
assert_npequal(s.bond_orders, np.array([2, 0, 0]))
s.bonds = np.array([[0, 1], [0, 2], [3, 4], [3, 5]])
assert_npequal(s.bond_orders, np.array([2, 0, 0, 0]))
def test_bonds():
# TODO: deprecate this shit
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([
Atom('O', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
])
# Adding bonds
s = System()
with s.batch() as b:
b.append(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(
s.type_array,
['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C'])
eq_(s.dimensions['atom'], 12)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7)))
# Reordering
s.bonds = np.array([[0, 1], [6, 8]])
s.reorder_molecules([1, 0])
assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
def get_system(self):
self.coordinates = self.interaction_manager.get_coordinates()
atoms = []
for index in range(len(self.interaction_manager.atoms)):
atom = self.interaction_manager.atoms[index]
type = atom.atom_type
if type.upper() == "C":
if atom.get_free_valency()!=0:
type = "Ne"
pos = 3.5 * self.coordinates[index]
atoms.append(Atom(type,pos))
mol = Molecule(atoms, self.interaction_manager.get_bonds_array())
system = System([mol])
system.bonds = np.array(self.interaction_manager.get_bonds_array())
return system
