def test_viewer_with_poses(self, local_dir=workdir):
pdbfiles = glob.glob(os.path.join(local_dir, "*.pdb"))
packed_poses = [io.pose_from_file(pdbfile) for pdbfile in pdbfiles]
poses = [io.to_pose(p) for p in packed_poses]
viewer.presets.coreBoundarySurface(packed_poses, delay=0)
viewer.presets.ligandsAndMetals(packed_poses,
continuous_update=True,
window_size=(100., 100.))
modules = [
viewer.setBackgroundColor("grey"),
viewer.setStyle(style="sphere",
colorscheme="greenCarbon",
radius=1.)
]
view = sum([viewer.init(poses)] + modules)
view()
self.assertEqual(view.poses, poses)
self.assertEqual(len(view.modules), 2)
view.reinit()
self.assertEqual(view.poses, poses)
self.assertEqual(len(view.modules), 0)
view.modules = modules
self.assertEqual(len(view.modules), len(modules))
view.reset()
self.assertIsNone(view.poses)
self.assertIsNone(view.pdbstrings)
view = viewer.init(poses, modules=modules)
self.assertEqual(len(view.modules), len(modules))
view.reset()
self.assertIsNone(view.modules)
def ligandsAndMetals(packed_and_poses_and_pdbs=None, *args, **kwargs):
"""
Display residues with ResidueProperty.LIGAND as 'brownCarbon' sticks with opaque surface,
and ResidueProperty.METAL as 'chainHetatm' spheres, with 'spectrum' cartoon representation,
disulfide bonds, polar hydrogens, and dashed hydrogen bonds.
@klimaj
"""
metals_selector = pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector(
pyrosetta.rosetta.core.chemical.ResidueProperty(31))
ligands_selector = pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector(
pyrosetta.rosetta.core.chemical.ResidueProperty(2))
view = viewer.init(packed_and_poses_and_pdbs=packed_and_poses_and_pdbs, *args, **kwargs) \
+ viewer.setBackgroundColor("lightgrey") \
+ viewer.setStyle(style="stick", colorscheme="lightgreyCarbon", radius=0.15) \
+ viewer.setStyle(residue_selector=ligands_selector, style="stick", colorscheme="brownCarbon", radius=0.5, label=True) \
+ viewer.setStyle(residue_selector=metals_selector, style="sphere", colorscheme="chainHetatm", radius=1.5, label=True) \
+ viewer.setHydrogenBonds() \
+ viewer.setDisulfides(radius=0.15) \
+ viewer.setHydrogens(color="white", radius=0.033, polar_only=True) \
+ viewer.setSurface(residue_selector=ligands_selector, surface_type="VDW", opacity=0.5, colorscheme="brownCarbon") \
+ viewer.setZoomTo(residue_selector=ligands_selector)
return view()
def templatePreset(packed_and_poses_and_pdbs=None, *args, **kwargs):
"""
Add a description of the preset Viewer here
@author
"""
view = viewer.init(packed_and_poses_and_pdbs=packed_and_poses_and_pdbs,
*args,
**kwargs)
# Add custom Viewer commands here
return view()
def test_viewer_with_pdbfiles(self, local_dir=workdir):
pdbfiles = glob.glob(os.path.join(local_dir, "*.pdb"))
viewer.presets.coreBoundarySurface(pdbfiles,
continuous_update=True)
viewer.presets.ligandsAndMetals(pdbfiles,
window_size=(200.01, 200.01))
view = viewer.init(pdbfiles, (1600, 400), delay=0.1234567890) \
+ viewer.setBackgroundColor("black") \
+ viewer.setStyle(style="line", colorscheme="blueCarbon")
view.show()
self.assertEqual(view.poses, [None] * len(pdbfiles))
self.assertEqual(len(view.modules), 2)
view.reinit()
self.assertEqual(view.poses, [None] * len(pdbfiles))
self.assertEqual(len(view.modules), 0)
view.reset()
self.assertIsNone(view.poses)
self.assertIsNone(view.pdbstrings)
def coreBoundarySurface(packed_and_poses_and_pdbs=None, *args, **kwargs):
"""
Display core residues as 'blackCarbon' sticks, boundary residues as 'greyCarbon' sticks, and surface residues
as 'whiteCarbon' sticks, with 'spectrum' cartoon representation, using the default arguments in
pyrosetta.rosetta.core.select.residue_selector.LayerSelector() to select layers.
@klimaj
"""
core_selector = pyrosetta.rosetta.core.select.residue_selector.LayerSelector(
)
core_selector.set_layers(True, False, False)
boundary_selector = pyrosetta.rosetta.core.select.residue_selector.LayerSelector(
)
boundary_selector.set_layers(False, True, False)
surface_selector = pyrosetta.rosetta.core.select.residue_selector.LayerSelector(
)
surface_selector.set_layers(False, False, True)
view = viewer.init(packed_and_poses_and_pdbs=packed_and_poses_and_pdbs,
*args,
**kwargs)
view.add(viewer.setStyle())
view.add(
viewer.setStyle(residue_selector=core_selector,
style="stick",
colorscheme="blackCarbon",
radius=0.25,
label=False))
view.add(
viewer.setStyle(residue_selector=boundary_selector,
style="stick",
colorscheme="greyCarbon",
radius=0.25,
label=False))
view.add(
viewer.setStyle(residue_selector=surface_selector,
style="stick",
colorscheme="whiteCarbon",
radius=0.25,
label=False))
view.add(viewer.setDisulfides(radius=0.25))
return view.show()