def test_shader_callback():
cone = ConeSource()
coneMapper = PolyDataMapper()
coneMapper.SetInputConnection(cone.GetOutputPort())
actor = Actor()
actor.SetMapper(coneMapper)
test_values = []
def callbackLow(_caller, _event, calldata=None):
program = calldata
if program is not None:
test_values.append(0)
id_observer = fs.add_shader_callback(actor, callbackLow, 0)
with pytest.raises(Exception):
fs.add_shader_callback(actor, callbackLow, priority='str')
mapper = actor.GetMapper()
mapper.RemoveObserver(id_observer)
scene = window.Scene()
scene.add(actor)
arr1 = window.snapshot(scene, size=(200, 200))
assert len(test_values) == 0
test_values = []
def callbackHigh(_caller, _event, calldata=None):
program = calldata
if program is not None:
test_values.append(999)
def callbackMean(_caller, _event, calldata=None):
program = calldata
if program is not None:
test_values.append(500)
fs.add_shader_callback(actor, callbackHigh, 999)
fs.add_shader_callback(actor, callbackLow, 0)
id_mean = fs.add_shader_callback(actor, callbackMean, 500)
# check the priority of each call
arr2 = window.snapshot(scene, size=(200, 200))
assert np.abs(
[test_values[0] - 999, test_values[1] - 500,
test_values[2] - 0]).sum() == 0
# check if the correct observer was removed
mapper.RemoveObserver(id_mean)
test_values = []
arr3 = window.snapshot(scene, size=(200, 200))
assert np.abs([test_values[0] - 999, test_values[1] - 0]).sum() == 0
def ribbon(molecule):
"""Create an actor for ribbon molecular representation.
Parameters
----------
molecule : Molecule
The molecule to be rendered.
Returns
-------
molecule_actor : vtkActor
Actor created to render the rubbon representation of the molecule to be
visualized.
References
----------
Richardson, J.S. The anatomy and taxonomy of protein structure
`Advances in Protein Chemistry, 1981, 34, 167-339.
<https://doi.org/10.1016/S0065-3233(08)60520-3>`_
"""
coords = get_all_atomic_positions(molecule)
all_atomic_numbers = get_all_atomic_numbers(molecule)
num_total_atoms = molecule.total_num_atoms
secondary_structures = np.ones(num_total_atoms)
for i in range(num_total_atoms):
secondary_structures[i] = ord('c')
resi = molecule.residue_seq[i]
for j, _ in enumerate(molecule.sheet):
sheet = molecule.sheet[j]
if molecule.chain[i] != sheet[0] or resi < sheet[1] or \
resi > sheet[3]:
continue
secondary_structures[i] = ord('s')
for j, _ in enumerate(molecule.helix):
helix = molecule.helix[j]
if molecule.chain[i] != helix[0] or resi < helix[1] or \
resi > helix[3]:
continue
secondary_structures[i] = ord('h')
output = PolyData()
# for atomic numbers
atomic_num_arr = nps.numpy_to_vtk(num_array=all_atomic_numbers,
deep=True,
array_type=VTK_ID_TYPE)
# setting the array name to atom_type as vtkProteinRibbonFilter requires
# the array to be named atom_type
atomic_num_arr.SetName("atom_type")
output.GetPointData().AddArray(atomic_num_arr)
# for atom names
atom_names = StringArray()
# setting the array name to atom_types as vtkProteinRibbonFilter requires
# the array to be named atom_types
atom_names.SetName("atom_types")
atom_names.SetNumberOfTuples(num_total_atoms)
for i in range(num_total_atoms):
atom_names.SetValue(i, molecule.atom_names[i])
output.GetPointData().AddArray(atom_names)
# for residue sequences
residue_seq = nps.numpy_to_vtk(num_array=molecule.residue_seq,
deep=True,
array_type=VTK_ID_TYPE)
residue_seq.SetName("residue")
output.GetPointData().AddArray(residue_seq)
# for chain
chain = nps.numpy_to_vtk(num_array=molecule.chain,
deep=True,
array_type=VTK_UNSIGNED_CHAR)
chain.SetName("chain")
output.GetPointData().AddArray(chain)
# for secondary structures
s_s = nps.numpy_to_vtk(num_array=secondary_structures,
deep=True,
array_type=VTK_UNSIGNED_CHAR)
s_s.SetName("secondary_structures")
output.GetPointData().AddArray(s_s)
# for secondary structures begin
newarr = np.ones(num_total_atoms)
s_sb = nps.numpy_to_vtk(num_array=newarr,
deep=True,
array_type=VTK_UNSIGNED_CHAR)
s_sb.SetName("secondary_structures_begin")
output.GetPointData().AddArray(s_sb)
# for secondary structures end
newarr = np.ones(num_total_atoms)
s_se = nps.numpy_to_vtk(num_array=newarr,
deep=True,
array_type=VTK_UNSIGNED_CHAR)
s_se.SetName("secondary_structures_end")
output.GetPointData().AddArray(s_se)
# for is_hetatm
is_hetatm = nps.numpy_to_vtk(num_array=molecule.is_hetatm,
deep=True,
array_type=VTK_UNSIGNED_CHAR)
is_hetatm.SetName("ishetatm")
output.GetPointData().AddArray(is_hetatm)
# for model
model = nps.numpy_to_vtk(num_array=molecule.model,
deep=True,
array_type=VTK_UNSIGNED_INT)
model.SetName("model")
output.GetPointData().AddArray(model)
table = PTable()
# for colors and radii of hetero-atoms
radii = np.ones((num_total_atoms, 3))
rgb = np.ones((num_total_atoms, 3))
for i in range(num_total_atoms):
radii[i] = np.repeat(table.atomic_radius(all_atomic_numbers[i], 'VDW'),
3)
rgb[i] = table.atom_color(all_atomic_numbers[i])
Rgb = nps.numpy_to_vtk(num_array=rgb,
deep=True,
array_type=VTK_UNSIGNED_CHAR)
Rgb.SetName("rgb_colors")
output.GetPointData().SetScalars(Rgb)
Radii = nps.numpy_to_vtk(num_array=radii, deep=True, array_type=VTK_FLOAT)
Radii.SetName("radius")
output.GetPointData().SetVectors(Radii)
# setting the coordinates
points = numpy_to_vtk_points(coords)
output.SetPoints(points)
ribbonFilter = ProteinRibbonFilter()
ribbonFilter.SetInputData(output)
ribbonFilter.SetCoilWidth(0.2)
ribbonFilter.SetDrawSmallMoleculesAsSpheres(0)
mapper = PolyDataMapper()
mapper.SetInputConnection(ribbonFilter.GetOutputPort())
molecule_actor = Actor()
molecule_actor.SetMapper(mapper)
return molecule_actor