def test_subsystem_from_atoms(self):
mols = self._make_molecules()
system = System(mols)
sub = subsystem_from_atoms(system, np.array([True, True, False,
False, False, False,
False, False, False]))
assert_equals(sub.n_mol, 1)
def test_subsystem_from_atoms(self):
mols = self._make_molecules()
system = System(mols)
sub = subsystem_from_atoms(
system,
np.array(
[True, True, False, False, False, False, False, False, False]))
assert_equals(sub.n_mol, 1)
def delete():
s = current_system()
s = subsystem_from_atoms(s, ~current_selection().atom_selection_mask)
# Fix also trajectory
coords = current_trajectory()
for i, c in enumerate(coords):
coords[i] = c[~current_selection().atom_selection_mask]
display(s)
def delete():
s = current_system()
s = subsystem_from_atoms(s, ~current_selection().atom_selection_mask)
# Fix also trajectory
coords = current_trajectory()
for i, c in enumerate(coords):
coords[i] = c[~current_selection().atom_selection_mask]
display(s)
def test_system():
wat = Molecule([Atom("O", [-4.99, 2.49, 0.0]),
Atom("H", [-4.02, 2.49, 0.0]),
Atom("H", [-5.32, 1.98, 1.0])], export={'hello': 1.0})
wat.r_array *= 0.1
# Initialization from empty
s = System.empty(4, 4*3)
mols = []
for i in xrange(s.n_mol):
wat.r_array += 0.1
s.add(wat)
m = wat.copy()
mols.append(wat.copy())
# Printing just to test if there aren't any exception
print "Init from Empty"
print "*" * 72
_print_sysinfo(s)
print "Init Normal"
print "*" * 72
s = System(mols)
_print_sysinfo(s)
# 3 water molecules
r_array = np.random.random((9, 3))
type_array = ['O', 'H', 'H', 'O', 'H', 'H', 'O', 'H', 'H']
mol_indices = [0, 3, 6]
mol_n_atoms = [3, 3, 3]
s2 = System.from_arrays(r_array=r_array, type_array=type_array,
mol_indices=mol_indices, mol_n_atoms=mol_n_atoms)
print 'bonds', s2._mol_bonds
sub2 = subsystem_from_molecules(s2, np.array([0, 2]))
assert sub2.n_mol == 2
sub = subsystem_from_atoms(s2, np.array([True, True, False,
False, False, False,
False, False, False]))
assert sub.n_mol == 1
