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_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()
# 4. Computing the bonding information for the molecule.
# 5. Generating and adding various molecular representaions to the scene.
scene = window.Scene()
scene.set_camera(position=(20, 10, 0),
focal_point=(0, 0, 0),
view_up=(0, 1, 0))
scene.zoom(0.8)
axes_actor = actor.axes()
scene.add(axes_actor)
molecule = mol.Molecule(atomic_numbers, atom_coords, atom_types, model,
residue_seq, chain, sheets, helix, is_hetatm)
mol.compute_bonding(molecule)
# stick representation
scene.add(mol.stick(molecule, bond_thickness=0.2))
# ribbon representation
scene.add(mol.ribbon(molecule))
# ball and stick representation
# scene.add(mol.ball_stick(molecule, atom_scale_factor=0.3,
# bond_thickness=0.2))
# bounding box
scene.add(mol.bounding_box(molecule, linewidth=0.4))
# sphere representation
# scene.add(mol.sphere_cpk(molecule))
###############################################################################