def test_neighbourhood(self):
# check the catchment critera
neighbours = Grid.neighbourhood(i=0,
j=0,
k=0,
high=self.buriedness.nsteps,
catchment=1)
self.assertEqual(3, len(neighbours))
neighbours1 = Grid.neighbourhood(i=5,
j=5,
k=5,
high=self.buriedness.nsteps,
catchment=1)
self.assertEqual(6, len(neighbours1))
f = PyMOLFile()
for i, n in enumerate(neighbours + neighbours1):
f.commands += PyMOLCommands.sphere(f"sphere_{i}", (0, 0, 1, 1), n,
0.1)
f.commands += PyMOLCommands.load_cgo(f"sphere_{i}",
f"sphere_{i}_obj")
f.commands += PyMOLCommands.sphere("centre", (1, 0, 0, 1), (5, 5, 5),
0.1)
f.commands += PyMOLCommands.load_cgo("centre", "centre_obj")
f.commands += PyMOLCommands.sphere("centre1", (1, 0, 0, 1), (0, 0, 0),
0.1)
f.commands += PyMOLCommands.load_cgo("centre1", "centre1_obj")
f.write("testdata/grid_extension/neighbourhood.py")
def test_cylinder(self):
self.pymol_file.commands += PyMOLCommands.cylinder(
"_mycylinder", (0, 0, 0), (1, 1, 1), 2, (1, 0, 0, 0.5))
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_mycylinder", "mycylinder")
self.pymol_file.commands += PyMOLCommands.cylinder(
"_mycylinder2", (0, 0, 0), (10, 10, 10), 0.2, (1, 0, 0, 1),
(0.5, 0.5, 0))
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_mycylinder2", "mycylinder2")
self.pymol_file.write("testdata/wrapper_pymol/test_cylinder.py")
def test_arrow(self):
self.pymol_file.commands += PyMOLCommands.arrow(
"_myarrow", (1, 1, 0), (4, 5, 0), (1, 0, 0), (0, 0, 1))
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_myarrow", "myarrow")
self.pymol_file.write("testdata/wrapper_pymol/test_arrow.py")
def test_cone(self):
self.pymol_file.commands += PyMOLCommands.cone("_mycone", (0, 0, 0),
(10, 10, 10), 5,
(1, 0, 0))
self.pymol_file.commands += PyMOLCommands.load_cgo("_mycone", "mycone")
self.pymol_file.write("testdata/wrapper_pymol/test_cone.py")
def test_sphere(self):
self.pymol_file.commands += PyMOLCommands.sphere("_mysphere",
self.pomegranate,
(0, 0, 0),
radius=2)
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_mysphere", "mysphere")
self.pymol_file.commands += PyMOLCommands.sphere("_mysphere1",
self.pomegranate,
(1, 1, 1),
radius=1)
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_mysphere1", "mysphere1")
self.pymol_file.write("testdata/wrapper_pymol/test_sphere.py")
def visualise(g, gname, peaks):
# visualise
gobj_name = f"{gname}_grid"
surface_objname = f"surface_{gobj_name}"
vis = f"testdata/grid_extension/{gname}.py"
gpath = f"testdata/grid_extension/{gname}.grd"
g.write(gpath)
f = PyMOLFile()
f.commands += PyMOLCommands.load(fname=f"{gname}.grd",
objname=gobj_name)
f.commands += PyMOLCommands.isosurface(
grd_name=gobj_name,
isosurface_name=surface_objname,
level=5,
color="yellow")
for i, p in enumerate(peaks):
f.commands += PyMOLCommands.sphere(objname=f"peak_obj_{i}",
rgba=[1, 1, 1, 1],
coords=p,
radius=0.5)
f.commands += PyMOLCommands.load_cgo(obj=f"peak_obj_{i}",
objname=f"peak_{i}")
f.write(vis)
def test_edge_detection(self):
self.selected = Grid.from_file("testdata/result/molA.grd")
edge = self.selected.edge_detection()
self.assertLess(len(edge), self.selected.count_grid())
f = PyMOLFile()
for i, n in enumerate(edge):
f.commands += PyMOLCommands.sphere(f"sphere_{i}", (0, 0, 1, 1), n,
0.1)
f.commands += PyMOLCommands.load_cgo(f"sphere_{i}",
f"sphere_{i}_obj")
f.write("testdata/grid_extension/edge_detection.py")
def to_pymol_str(self):
pymol_out = ""
pymol_out += PyMOLCommands.sphere("peak_obj", (1, 1, 1, 1),
coords=self.point,
radius=1)
pymol_out += PyMOLCommands.load_cgo("peak_obj", "peak")
ligand_peak_features = []
for i, feat in enumerate(self.features):
pymol_out += feat.to_pymol_str(i=i)
ligand_peak_features.append(f"{feat.identifier}_{i}")
pymol_out += PyMOLCommands.group("ligand_peak_features",
ligand_peak_features)
return pymol_out
def to_pymol_str(self, i=0, label=True, transparency=0.6):
pymol_out = ""
point_colour = rgb_to_decimal(self.colour)
point_colour = utilities.Colour(point_colour[0], point_colour[1],
point_colour[2], transparency)
feat_ID = f"{self.identifier}_{i}"
group = []
coords = (self.point[0].centre[0], self.point[0].centre[1],
self.point[0].centre[2])
radius = self.point[0].radius
point_objname = f"{self.identifier}_point_{i}"
pymol_out += PyMOLCommands.sphere(point_objname,
point_colour,
coords,
radius=radius)
pymol_out += PyMOLCommands.load_cgo(point_objname,
f"{point_objname}_obj")
group.append(f"{point_objname}_obj")
if self.score != 0 and label:
score_name = f"{point_objname}_score"
pymol_out += PyMOLCommands.pseudoatom(
objname=score_name,
coords=coords,
label=f'{round(self.score, 1)}')
group.append(score_name)
rank_name = f"{self.identifier}_rank_{i}"
pymol_out += PyMOLCommands.pseudoatom(objname=rank_name,
coords=coords,
label=str(i + 1))
group.append(rank_name)
if self.projected:
proj_coords = (self.projected[0].centre[0],
self.projected[0].centre[1],
self.projected[0].centre[2])
projection_objname = f"{self.identifier}_projection_{i}"
line_objname = f"{self.identifier}_line_{i}"
group.extend([projection_objname, line_objname])
if self.projected_value != 0 and label:
proj_score_name = f"{point_objname}_proj_score"
pymol_out += PyMOLCommands.pseudoatom(
objname=proj_score_name,
coords=proj_coords,
label=f'{round(self.projected_value, 1)}')
group.append(proj_score_name)
projected_colour = adjust_lightness(self.colour, percentage=30)
projected_colour = utilities.Colour(projected_colour[0],
projected_colour[1],
projected_colour[2],
transparency)
projected_radius = self.projected[0].radius
pymol_out += PyMOLCommands.sphere(projection_objname,
projected_colour,
proj_coords,
radius=projected_radius)
pymol_out += PyMOLCommands.load_cgo(projection_objname,
f"{projection_objname}_obj")
pymol_out += PyMOLCommands.line(line_objname,
coords,
proj_coords,
rgb=projected_colour)
pymol_out += PyMOLCommands.group(feat_ID, group)
return pymol_out