def tractability_workflow(protein, tag):
"""
A very simple tractability workflow.
:param str protein: PDB identification code
:param str tag: Tractability tag: either 'druggable' or 'less-druggable'
:return: `pandas.DataFrame`
"""
# 1) calculate Fragment Hotspot Result
runner = Runner()
result = runner.from_pdb(pdb_code=protein,
nprocesses=1,
buriedness_method='ghecom')
# 2) calculate Best Continuous Volume
extractor = Extractor(hr=result)
bcv_result = extractor.extract_volume(volume=500)
# 3) find the median score
grid = Grid.get_single_grid(bcv_result.super_grids, mask=False)
values = grid.grid_values(threshold=5)
median = np.median(values)
# 4) return the data
return pd.DataFrame({
'scores': values,
'pdb': [protein] * len(values),
'median': [median] * len(values),
'tractability': [tag] * len(values),
})
def run(self):
h = Runner()
# hotspot calculation settings
s = h.Settings()
s.apolar_translation_threshold = 15
s.polar_translation_threshold = 15
s.polar_contributions = False
s.nrotations = 3000
s.sphere_maps = True
hr = h.from_pdb(pdb_code=self.pdb,
charged_probes=False,
buriedness_method='ghecom',
nprocesses=3,
settings=s,
cavities=None)
out_settings = HotspotWriter.Settings()
out_settings.charged = False
with HotspotWriter(os.path.dirname(self.output().path),
grid_extension=".grd",
zip_results=True,
settings=out_settings) as w:
w.write(hr)
def test_generate_real(self):
runner = Runner()
hr = runner.from_pdb(pdb_code="2vta", buriedness_method='ghecom')
settings = HotspotWriter.Settings()
settings.output_superstar = True
parent = "testdata/2vta"
with HotspotWriter(parent) as w:
w.write(hr)
def run(self):
"""from fragment hotspot calc from protein"""
h = Runner()
settings = Runner.Settings(sphere_maps=False)
result = h.from_pdb(pdb_code=self.args.pdb,
charged_probes=True,
buriedness_method=self.args.buriedness_method,
nprocesses=5,
settings=settings)
with HotspotWriter(path=self.args.out_dir,
zip_results=self.args.zipped) as writer:
writer.write(result)
