def test_add_atom_bond_creation():
molecule = mol.Molecule()
mol.add_atom(molecule, 6, 0, 0, 0)
mol.add_atom(molecule, 6, 1, 0, 0)
mol.add_bond(molecule, 0, 1, 1)
npt.assert_equal(molecule.total_num_bonds, 1)
npt.assert_equal(molecule.total_num_atoms, 2)
def test_stick(interactive=False):
molecule = mol.Molecule()
mol.add_atom(molecule, 6, 0, 0, 0)
mol.add_atom(molecule, 6, 2, 0, 0)
# Test errors for inadequate bonding data
npt.assert_raises(ValueError, mol.stick, molecule)
mol.add_bond(molecule, 0, 1, 1)
colormodes = ['discrete', 'single']
bond_thickness = [0.1, 0.12]
table = mol.PTable()
colors = np.array([[table.atom_color(6)],
[[150/255, 150/255, 150/255],
[50/255, 50/255, 50/255]]], dtype=object)
scene = window.Scene()
for i, colormode in enumerate(colormodes):
test_actor = mol.stick(molecule, colormode, bond_thickness[i])
scene.add(test_actor)
scene.reset_camera()
scene.reset_clipping_range()
if interactive:
window.show(scene)
npt.assert_equal(scene.GetActors().GetNumberOfItems(), 1)
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr, colors=colors[i])
npt.assert_equal(report.objects, 1)
scene.clear()
# Testing warnings
npt.assert_warns(UserWarning, mol.stick, molecule, 'multiple')
def test_deep_copy_molecule():
molecule1 = mol.Molecule()
mol.add_atom(molecule1, 6, 0, 0, 0)
mol.add_atom(molecule1, 6, 1, 0, 0)
mol.add_bond(molecule1, 0, 1, 1)
molecule2 = mol.Molecule()
mol.deep_copy_molecule(molecule2, molecule1)
npt.assert_equal(molecule2.total_num_bonds, 1)
npt.assert_equal(molecule2.total_num_atoms, 2)
def test_atomic_number():
# Testing atomic number get/set functions
molecule = mol.Molecule()
mol.add_atom(molecule, 4, 0, 0, 0)
# Testing get_atomic_number
npt.assert_equal(mol.get_atomic_number(molecule, 0), 4)
# Testing set_atomic_number
mol.set_atomic_number(molecule, 0, 6)
npt.assert_equal(mol.get_atomic_number(molecule, 0), 6)
def test_atomic_position():
# Testing atomic position get/set functions
molecule = mol.Molecule()
mol.add_atom(molecule, 4, 0, 0, 0)
# Testing get_atomic_position
npt.assert_array_almost_equal(mol.get_atomic_position(molecule, 0),
np.array([0, 0, 0]))
# Testing set_atomic_number
mol.set_atomic_position(molecule, 0, 1, 1, 1)
npt.assert_array_almost_equal(mol.get_atomic_position(molecule, 0),
np.array([1, 1, 1]))
def test_bond_order():
# Testing bond order get/set functions
# Testing get_bond_order
molecule = mol.Molecule()
mol.add_atom(molecule, 6, 0, 0, 0)
mol.add_atom(molecule, 6, 1, 0, 0)
mol.add_bond(molecule, 0, 1, 3)
npt.assert_equal(mol.get_bond_order(molecule, 0), 3)
# Testing set_bond_order
mol.set_bond_order(molecule, 0, 2)
npt.assert_equal(mol.get_bond_order(molecule, 0), 2)
# Testing get_all_bond_orders
npt.assert_array_almost_equal(mol.get_all_bond_orders(molecule),
np.array([2]))
def test_bounding_box(interactive=False):
scene = window.Scene()
molecule = mol.Molecule()
mol.add_atom(molecule, 6, 0, 0, 0)
mol.add_atom(molecule, 6, 1, 1, 1)
mol.add_bond(molecule, 0, 1, 1)
molecule_actor = mol.stick(molecule)
test_box = mol.bounding_box(molecule, colors=(0, 1, 1), linewidth=0.1)
scene.add(molecule_actor)
scene.add(test_box)
if interactive:
window.show(scene)
npt.assert_equal(scene.GetActors().GetNumberOfItems(), 2)
table = mol.PTable()
colors = np.array([table.atom_color(1), table.atom_color(6)])
arr = window.snapshot(scene)
report = window.analyze_snapshot(arr, colors=colors)
npt.assert_equal(report.objects, 1)
scene.clear()
