def _write_pymol_isoslider(self, hr):
"""
generates the commands for an isoslider
:param hr: a hotspot result
:type hr: `hotspots.results.Results`
"""
# Isosurface obj's take the name: "surface_{probe ID}_{hotpsot ID}"
# e.g. "surface_apolar_hotspotA"
if not isinstance(hr, list):
hr = [hr]
# the hotspot grids are always output
surface_dic = {h.identifier: {'fhm': [f"surface_{g}_{h.identifier}" for g in h.super_grids.keys()]}
for h in hr}
surface_value_dic = {h.identifier: {"fhm": max([round(g.extrema[1], 1) for g in h.super_grids.values()])}
for h in hr}
for h in hr:
if self.settings.output_superstar and h.superstar:
surface_dic[h.identifier].update({'superstar': [f"surface_superstar_{g}_{h.identifier}"
for g in h.superstar.keys()]})
surface_value_dic[h.identifier].update({'superstar': max([round(g.extrema[1], 1)
for g in h.superstar.values()])})
if self.settings.output_weighted and h.weighted_superstar:
surface_dic[h.identifier].update({'weighted': [f"surface_weighted_superstar_{g}_{h.identifier}"
for g in h.weighted_superstar.keys()]})
surface_value_dic[h.identifier].update({'weighted': max([round(g.extrema[1], 1)
for g in h.weighted_superstar.values()])})
if self.settings.output_buriedness and h.buriedness:
surface_dic[h.identifier].update({'buriedness': [f"surface_buriedness_{h.identifier}"]})
surface_value_dic[h.identifier].update({'buriedness': 8})
min_value = 0
print(surface_dic)
print(surface_value_dic)
self.pymol_out.commands += PyMOLCommands.isoslider(surface_dic, surface_value_dic)
def pymol_visulisation(self, outdir=None, fname="pymol_file.py"):
if not outdir:
outdir = os.getcwd()
if not os.path.exists(outdir):
os.mkdir(outdir)
if self.ligands:
with MoleculeWriter(os.path.join(outdir, "ligands.mol2")) as w:
for ligand in self.ligands:
try:
w.write(ligand.molecule)
except AttributeError:
w.write(ligand)
if self.protein:
with MoleculeWriter(os.path.join(outdir, "protein.mol2")) as w:
w.write(self.protein.molecule)
self.pymol_out = PyMOLFile()
if self.ligands:
self.pymol_out.commands += PyMOLCommands.load(
"ligands.mol2", "ligands")
if self.protein:
self.pymol_out.commands += PyMOLCommands.load(
"protein.mol2", "protein")
# write out point spheres and projection sphere and lines if applicable
self.pymol_out.commands += self.features_to_pymol_strings(
self.detected_features)
if self.feature_point_grids:
for identifier, g in self.feature_point_grids.items():
g.write(os.path.join(outdir, f"{identifier}.grd"))
point_colour = rgb_to_decimal(
self.feature_definitions[identifier].colour)
self.pymol_out.commands += PyMOLCommands.set_color(
f"{identifier}_color", point_colour)
self.pymol_out.commands += PyMOLCommands.load(
f"{identifier}.grd", f"{identifier}_grid")
self.pymol_out.commands += PyMOLCommands.isosurface(
f"{identifier}_grid",
f"surface_{identifier}",
level=1,
color=f"{identifier}_color")
self.pymol_out.commands += PyMOLCommands.group(
"feature_grids", self.feature_point_grids.keys())
self.pymol_out.commands += PyMOLCommands.group(
"feature_grids",
[f"surface_{a}" for a in self.feature_point_grids])
min_value = 0
surface_dic = {
self.identifier: {
'feature_grids':
[f"surface_{g}" for g in self.feature_point_grids.keys()]
}
}
surface_value_dic = {
self.identifier: {
"feature_grids":
max([
round(g.extrema[1], 1)
for g in self.feature_point_grids.values()
])
}
}
self.pymol_out.commands += PyMOLCommands.isoslider(
surface_dic, surface_value_dic)
self.pymol_out.write(os.path.join(outdir, fname))