def test_sphere_cpk(interactive=False):
atomic_numbers, atom_coords = get_default_molecular_info()
molecule = mol.Molecule(atomic_numbers, atom_coords)
table = mol.PTable()
colormodes = ['discrete', 'single']
colors = np.array([[table.atom_color(1), table.atom_color(6)],
[[150/255, 250/255, 150/255]]], dtype=object)
scene = window.Scene()
for i, colormode in enumerate(colormodes):
test_actor = mol.sphere_cpk(molecule, colormode)
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.sphere_cpk, molecule, 'multiple')
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_periodic_table():
# Testing class PeriodicTable()
table = mol.PTable()
npt.assert_equal(table.atomic_number('C'), 6)
npt.assert_equal(table.element_name(7), 'Nitrogen')
npt.assert_equal(table.atomic_symbol(8), 'O')
npt.assert_allclose(table.atomic_radius(1, 'VDW'), 1.2, 0.1, 0)
npt.assert_allclose(table.atomic_radius(6, 'Covalent'), 0.75, 0.1, 0)
npt.assert_array_almost_equal(table.atom_color(1), np.array([1, 1, 1]))
# Test errors
npt.assert_raises(ValueError, table.atomic_radius, 4, "test")
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()
downloadurl = "https://files.rcsb.org/download/"
pdbfn = pdb_code + ".pdb"
flag = 0
if not os.path.isfile(pdbfn):
flag = 1
url = downloadurl + pdbfn
outfnm = os.path.join(pdbfn)
try:
urllib.request.urlretrieve(url, outfnm)
except Exception:
print("Error in downloading the file!")
###############################################################################
# Creating a `PeriodicTable()` object to obtain atomic numbers from names of
# elements
table = mol.PTable()
###############################################################################
# Creating empty lists which will be filled with atomic information as we
# parse the pdb file.
NumberOfAtoms = 0
atom_coords = []
atomic_numbers = []
atom_types = []
model = []
sheets = []
helix = []
residue_seq = []
chain = []
is_hetatm = []