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)