def test_line(self):
self.pymol_file.commands += PyMOLCommands.line("myline", (1, 1, 1),
(2, 2, 2),
self.pomegranate,
width=4)
self.pymol_file.commands += PyMOLCommands.line("myline2", (1, 1, 1),
(0, 0, 0),
self.pomegranate,
width=10)
self.pymol_file.write("testdata/wrapper_pymol/test_line.py")
def test_group(self):
self.pymol_file.commands += PyMOLCommands.line("myline1", (0, 0, 0),
(1, 1, 1),
self.pomegranate,
width=10)
self.pymol_file.commands += PyMOLCommands.pseudoatom(
"mypseudoatom1", (0, 0, 0), self.pomegranate)
self.pymol_file.commands += PyMOLCommands.pseudoatom(
"mypseudoatom2", (1, 1, 1), self.pomegranate)
self.pymol_file.commands += PyMOLCommands.group(
"mygroup", ["myline1", "mypseudoatom1", "mypseudoatom2"])
self.pymol_file.write("testdata/wrapper_pymol/test_group.py")
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