def test_write_pymol_isoslider(self):
# read in manually
path = "testdata/hs_io/minimal_all_grids/out.zip"
base = tempfile.mkdtemp()
with zipfile.ZipFile(path) as hs_zip:
hs_zip.extractall(base)
base = os.path.join(base, "hotspot")
interactions = ["donor", "acceptor", "apolar"]
super_grids = {p: Grid.from_file(os.path.join(base, f"{p}.grd")) for p in interactions}
superstar_grids = {p: Grid.from_file(os.path.join(base, f"superstar_{p}.grd")) for p in interactions}
prot = Protein.from_file(os.path.join(base, "protein.pdb"))
hr = Results(super_grids=super_grids,
protein=prot,
superstar=superstar_grids)
hr.identifier = "hotspot"
settings = HotspotWriter.Settings()
settings.output_superstar = True
writer = HotspotWriter("testdata/hs_io/minimal_all_grids", settings=settings) # we won't actually write
writer.pymol_out.commands += writer._write_pymol_isosurfaces(hr.super_grids,
"hotspot",
"hotspot",
"fhm")
writer.pymol_out.commands += writer._write_pymol_isosurfaces(hr.superstar,
"hotspot",
"hotspot",
"superstar")
writer._write_pymol_isoslider(hr)
writer.pymol_out.write("testdata/hs_io/minimal_all_grids/test_write_pymol_isoslider.py")
def calc(args):
prot_file, hotspot_file = args
prot = Protein.from_file(prot_file)
# pre prepared
runner = Runner()
settings = Runner.Settings()
settings.apolar_translation_threshold = 8
settings.polar_translation_threshold = 10
# pdb = os.path.basename(prot_file)[0][:4]
#
# mol_path = os.path.join(os.path.dirname(prot_file))
hr = runner.from_protein(prot,
nprocesses=3,
settings=settings,
probe_size=3)
for p, g in hr.super_grids.items():
hr.super_grids[p] = g.dilate_by_atom()
try:
e = Extractor(hr)
bv = e.extract_volume(volume=250)
except:
bv = Results(
protein=hr.protein.copy(),
super_grids={p: g.copy()
for p, g in hr.super_grids.items()})
hr.identifier = "hotspot"
bv.identifier = "bcv"
with HotspotWriter(hotspot_file) as w:
w.write([hr, bv])