def __init__(self):
super(self.__class__, self).__init__(description=__doc__)
# handle command line arguments
self.add_argument(
'path',
help='path to working directory'
)
self.add_argument(
'pdb',
help='PDB code for target'
)
self.add_argument(
'chemical_id',
help='PDB code for target'
)
self.add_argument(
'-hs', '--hotspot_guided',
default=True,
help='Use Hotspot insights to guide docking'
)
self.args = self.parse_args()
# create temp for output files
self.temp = tempfile.mkdtemp()
# calculate hotspot using Hotspots API
if self.args.hotspot_guided is True:
try:
self.hr = hs_io.HotspotReader(path=os.path.join(self.args.path, "out.zip")).read()
except IOError:
h = calculation.Runner()
settings = h.Settings()
settings.nrotations = 3000
settings.sphere_maps = True
self.hr = h.from_pdb(pdb_code=self.args.pdb,
charged_probes=True,
buriedness_method='ghecom',
nprocesses=5,
settings=settings)
with hs_io.HotspotWriter(path=os.path.join(self.args.path), zip_results=True) as hw:
hw.write(self.hr)
# generate molecule for docking
self.search_ligands = os.path.join(self.temp, self.args.chemical_id + ".mol2")
self.ligand = self.from_smiles(smiles=_Ligand.from_chemicalid(chemicalid=self.args.chemical_id).smiles,
path=self.search_ligands,
identifier=self.args.chemical_id)
# dock search ligands into hotspot protein
self.docked_ligands = self.dock()
if self.args.hotspot_guided is True:
self.rescored_ligands = self.rescore()
def calc_hr(self):
"""
runs the hotspot calculation and returns a `hotspots.calculation.Result`
:return: `hotspots.calculation.Result`
"""
h = calculation.Runner()
settings = calculation.Runner.Settings(sphere_maps=True)
cavs = Cavity.from_pdb_file(self._hs_fname)
return h.from_protein(protein=self.protein,
charged_probes=True,
buriedness_method='ghecom',
cavities=cavs,
nprocesses=5,
settings=settings)
from hotspots import calculation
from hotspots.hs_io import HotspotWriter
r = calculation.Runner()
result = r.from_pdb("3cqw", charged_probes=False, nprocesses=3)
with HotspotWriter("/home/pcurran/New folder/akt1/protoss") as w:
w.write(result)
print set([len(a.neighbours) for a in result.protein.atoms])