def run(self):
prot = Protein.from_file(self.input().path)
mol = io.MoleculeReader('ligands/{}.sdf'.format(self.pdb))[0]
h = Runner()
s = h.Settings()
s.apolar_translation_threshold = 15
s.polar_translation_threshold = 15
s.polar_contributions = False
s.sphere_maps = True
s.nrotations = 3000
hr = h.from_protein(prot,
buriedness_method='ghecom',
nprocesses=1,
settings=s,
cavities=mol)
out_settings = HotspotWriter.Settings()
out_settings.charged = False
w = HotspotWriter(os.path.dirname(self.output().path),
grid_extension=".grd",
zip_results=True,
settings=out_settings)
w.write(hr)
def run(self):
hr = HotspotReader(self.input().path).read()
bcv = hr.tractability_map(volume=self.volume)
out_settings = HotspotWriter.Settings()
out_settings.charged = False
w = HotspotWriter(os.path.dirname(self.output().path),
grid_extension=".grd",
zip_results=True,
settings=out_settings)
w.write(bcv)
def run(self):
prot = Protein.from_file(self.input().path)
cavs = Cavity.from_pdb_file(self.input().path)
h = Runner()
s = h.Settings()
s.apolar_translation_threshold = 15
s.polar_translation_threshold = 15
s.polar_contributions = False
s.nrotations = 1000
hr = h.from_protein(prot,
buriedness_method='ghecom',
nprocesses=1,
settings=s,
cavities=cavs)
out_settings = HotspotWriter.Settings()
out_settings.charged = False
w = HotspotWriter(os.path.dirname(self.output().path),
grid_extension=".grd",
zip_results=True,
settings=out_settings)
w.write(hr)
