def test_structure_file():
for fn in [get_fn('tz2.pdb'), nv.datafiles.GRO]:
content = open(fn, 'r').read()
fs1 = nv.FileStructure(fn)
assert content == fs1.get_structure_string()
# gz
fn = get_fn('tz2_2.pdb.gz')
fs2 = nv.FileStructure(fn)
content = gzip.open(fn).read()
assert content == fs2.get_structure_string()
def test_structure_file():
for fn in ['data/tz2.pdb', nv.datafiles.GRO]:
content = open(fn, 'rb').read()
fs1 = nv.FileStructure(fn)
nt.assert_equal(content, fs1.get_structure_string())
# gz
fn = 'data/tz2_2.pdb.gz'
fs2 = nv.FileStructure(fn)
content = gzip.open(fn).read()
nt.assert_equal(content, fs2.get_structure_string())
def test_loaded_attribute():
traj = pt.datafiles.load_tz2()
structure = nv.FileStructure(nv.datafiles.PDB)
# False, empty constructor
view = nv.NGLWidget()
view.loaded = False
view.add_structure(structure)
view.add_trajectory(traj)
view
# False, constructor with a single Structure
view = nv.NGLWidget(structure)
view.loaded = False
view.add_trajectory(traj)
view
# True
view = nv.NGLWidget()
view.loaded = True
view.add_structure(structure)
view.add_trajectory(traj)
view
# False then True, empty constructor
view = nv.NGLWidget()
view.loaded = False
view.add_structure(structure)
view.loaded = True
view.add_trajectory(traj)
view
# False then True, constructor with a Trajectory
view = nv.NGLWidget(nv.PyTrajTrajectory(traj))
view.loaded = False
view.add_structure(structure)
view.loaded = True
view.add_trajectory(traj)
view
def test_get_name():
fn = nglview.datafiles.PDB
assert_equal(py_utils.get_name(object, dict(name='hello')), 'hello')
assert_equal(py_utils.get_name(nglview.FileStructure(fn), dict()),
'nglview.adaptor.FileStructure')
def test_adaptor_raise():
with pytest.raises(ValueError):
nv.FileStructure('hellotheredda.pdb')
def add_to_view(self, view):
view.add_component(nglview.FileStructure(self.export()))
def nglview_multimodel_ACV(biomol_filename, volume1_filename,
volume2_filename):
"""Create a nglview multi-model structure scene with donor and acceptor accessible-contact volumes (ACV)
Parameters
----------
structure_filename : str
multi-model PDB of the biomolecule
volume1_filename, volume2_filename : str
multi-model PDB of the donor and acceptor accessible-contact volume
Returns
-------
view : nglview.NGLWidget
n_model : int
"""
global view
view = nglview.NGLWidget()
struct = nglview.FileStructure(biomol_filename)
acv_D = nglview.FileStructure(volume1_filename)
acv_A = nglview.FileStructure(volume2_filename)
struct_str = struct.get_structure_string()
n_models = struct_str.count("MODEL")
view.add_component(struct)
view.add_component(acv_D)
view.add_component(acv_A)
view.clear_representations(component=0)
view.clear_representations(component=1)
view.clear_representations(component=2)
view.add_simplified_base(component=0,
selection="/0",
disablePicking=True,
colorScheme="atomindex")
view.add_cartoon(component=0,
selection="/0",
aspectRatio=4,
disablePicking=True,
colorScheme="atomindex")
view.add_surface(color="#6cb381",
wireframe=False,
opacity=0.4,
isolevel=0,
component=1,
disablePicking=True,
selection="CV")
view.add_surface(color="#c25449",
wireframe=False,
opacity=0.4,
isolevel=0,
component=2,
disablePicking=True,
selection="CV")
view.add_surface(color="#6cb381",
wireframe=True,
opacity=0.4,
isolevel=0,
component=1,
disablePicking=True,
selection="all")
view.add_surface(color="#c25449",
wireframe=True,
opacity=0.4,
isolevel=0,
component=2,
disablePicking=True,
selection="all")
view.stage.set_parameters(mouse_preset="pymol")
return view, n_models
def view_nglview(molecule, label=False):
"""!@brief Display molecules using the NGLView viewer.
A function to view molecules using the NGLView project (https://github.com/arose/nglview).
It is used to display the geometry of the backbone with atom index labels. It is
also used to display accepted nucleic acid candidates generated after
the search. For backbone molecules, the number of atoms in the backbone
is computed here and returned to be used for bounding the displayed atomic
indices in backbone widgets.
@param molecule (str) Path to a file containing the 3D structure of the molecule
@param label (bool) Whether to display atom index labels
@return number of atoms in @a molecule if @a label is True, else None
@attention If the molecules are not displayed correctly, you may need to execute
@code{.sh} jupyter-nbextension enable nglview --py --sys-prefix @endcode
@sa jupyter_widgets.path
@sa jupyter_widgets.single_result
"""
import openbabel
import nglview
# Check if the file exists
if not os.path.isfile(molecule):
return 0
# If a label is requested, then this is a backbone or base molecule
if label:
# Read the molecule and convert it to a pdb format
mol = openbabel.OBMol()
conv = openbabel.OBConversion()
fmt = conv.FormatFromExt(molecule)
conv.SetInAndOutFormats(fmt.GetID(), 'pdb')
conv.ReadFile(mol, molecule)
# Extract the number of atoms
num_atoms = mol.NumAtoms()
mol = conv.WriteString(mol)
# Display the molecule
struct = nglview.TextStructure(mol)
view = nglview.NGLWidget(struct, defaultRepresentation=False)
view.camera = 'orthographic'
view.add_representation('licorice')
view.add_representation('label', labelType='serial', backgroundColor='black', showBackground=True)
view.center()
display(view.display(gui=True))
# Return the number of atoms to be used for the backbone or base widgets
return num_atoms
# Show accepted candidates
else:
struct = nglview.FileStructure(molecule)
view = nglview.NGLWidget(struct, defaultRepresentation=False)
view.camera = 'orthographic'
view.add_representation('licorice')
view.center()
display(view.display(gui=True))
