def run_hotspot_calculation(self, method="ghecom"):
"""
Runs the hotspots calculation on the specified PDB structure
:return:
"""
h = Runner()
settings = h.Settings()
settings.nrotations = self.number_rotations
settings.apolar_translation_threshold = 15
settings.polar_translation_threshold = 15
settings.sphere_maps = self.spheres
# Check if SuperStar and Ghecom have already been run.
super_archive_path = Path(self.out_dir.parent, "superstar_grids.zip")
if super_archive_path.exists():
super_tmp_path = Path(self.out_dir.parent, super_archive_path.stem)
if not super_tmp_path.exists(): super_tmp_path.mkdir()
unpack_archive(super_archive_path, super_tmp_path, 'zip')
b_grid = Grid.from_file(
str(Path(super_tmp_path, 'buriedness.ccp4').resolve()))
result = h.from_superstar(
protein=self.prepare_protein(),
superstar_grids=self.create_atomic_hotspots(super_tmp_path),
buriedness=b_grid,
charged_probes=self.charged,
settings=settings,
clear_tmp=True)
rmtree(super_tmp_path)
else:
result = h.from_protein(protein=self.prepare_protein(),
charged_probes=self.charged,
probe_size=7,
buriedness_method=method,
cavities=None,
nprocesses=1,
settings=settings)
# Save and zip the SuperStar Grids:
self._save_superstar_grids(h)
# Save and zip the Results
with hs_io.HotspotWriter(str(self.out_dir.resolve()),
visualisation="pymol",
grid_extension=".ccp4",
zip_results=True) as writer:
writer.write(result)
print(f"out_file: {str(Path(self.out_dir, 'out.zip').resolve())}")
return Path(self.out_dir, 'out.zip')
def _get_hotspot(self, cav_id):
"""
calculate hotspot map from pre-calculated superstar and buriedness grids
:param cav_id:
:return:
"""
# inputs
prot = Protein.from_file(self.apo_prep)
sr = HotspotReader(path=os.path.join(self.superstar[cav_id], "out.zip")).read()
superstar = [_AtomicHotspotResult(identifier=ident, grid=grid, buriedness=None)
for ident, grid in sr.super_grids.items()]
buriedness = Grid.from_file(self.buriedness)
# tasks
start = time.time()
h = Runner()
s = h.Settings()
s.apolar_translation_threshold = 14
s.polar_translation_threshold = 14
s.polar_contributions = False
s.sphere_maps = False
s.nrotations = 3000
hr = h.from_superstar(prot, superstar, buriedness, settings=s, clear_tmp=True)
finish = time.time()
# output
if not os.path.exists(self.hotspot[cav_id]):
os.mkdir(self.hotspot[cav_id])
with open(self.hotspot_time[cav_id], 'w') as t:
t.write(str(finish - start))
with HotspotWriter(self.hotspot[cav_id], zip_results=True) as writer:
writer.write(hr)