def test_write_fake_multi(self):
a = self.generate_fake(buriedness=True, superstar=True)
b = self.generate_fake(buriedness=True, superstar=True)
settings = HotspotWriter.Settings()
settings.output_superstar = True
with HotspotWriter("testdata/hs_io/minimal_multi_all_grids", settings=settings) as w:
w.write([a, b])
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):
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 run(self):
# create pharmacophore
ref = PharmacophoreModel.from_pdb(pdb_code=self.pdb,
chain=self.chain,
representatives=self.input().path,
identifier=self.pdb)
ref.rank_features(max_features=6, feature_threshold=5)
# write pymol file
ref.write(self.output()["pymol"].path)
# write Results file
temp = tempfile.mkdtemp()
PDBResult(self.pdb).download(temp)
result = Results(protein=Protein.from_file(
os.path.join(temp, "{}.pdb".format(self.pdb))),
super_grids=ref.dic)
out_settings = HotspotWriter.Settings()
out_settings.charged = False
with HotspotWriter(os.path.dirname(self.output()["grids"].path),
grid_extension=".grd",
zip_results=True,
settings=out_settings) as w:
w.write(result)
# write aligned molecules
with MoleculeWriter(self.output()['aligned_mols'].path) as w:
for l in ref.aligned_ligands:
w.write(l)
# points
points = ref._comparision_dict()
with open(self.output()['points'].path, 'wb') as w:
pickle.dump(points, w)
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):
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 to_grid(target, pdb):
out_dir = "Z:/patel_set/{}/{}".format(target, pdb)
mols = MoleculeReader(
join(out_dir, "reference_pharmacophore", "aligned_mols.mol2"))
p = PharmacophoreModel.from_ligands(ligands=mols, identifier="test")
result = Results(super_grids=p.dic,
protein=Protein.from_file(
join(out_dir, "hs", "{}.pdb".format(pdb))))
out = Helper.get_out_dir(join(out_dir, "reference_pharmacophore", "grids"))
settings = HotspotWriter.Settings()
settings.isosurface_threshold = [2, 5, 10]
with HotspotWriter(path=out, zip_results=True, settings=settings) as w:
w.write(result)
def test_write_real_single(self):
base = "testdata/1hcl"
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}
buriedness = Grid.from_file(os.path.join(base, "buriedness.grd"))
prot = Protein.from_file(os.path.join(base, "protein.pdb"))
hr = Results(super_grids=super_grids,
protein=prot,
buriedness=buriedness,
superstar=superstar_grids)
settings = HotspotWriter.Settings()
settings.output_superstar = True
with HotspotWriter("testdata/hs_io/minimal_all_grids_real", settings=settings) as w:
w.write(hr)
def test_write_pymol_isosurfaces(self):
# test out.zip prepared, generate minimal pymol commands to test isosurface gen code
settings = HotspotWriter.Settings()
writer = HotspotWriter("testdata/hs_io/minimal_all_grids", settings=settings) # we won't actually write
# pymol file initialised in the writer init function, therefore the unzip code is already in place
writer.pymol_out.commands += writer._write_pymol_isosurfaces({"apolar": None, "donor": None, "acceptor": None},
"hotspot",
"hotspot",
"fhm")
writer.pymol_out.commands += writer._write_pymol_isosurfaces({"apolar": None, "donor": None, "acceptor": None},
"hotspot",
"hotspot",
"superstar")
writer.pymol_out.write("testdata/hs_io/minimal_all_grids/test_write_pymol_isosurfaces.py")
def run(self):
hs = HotspotReader(self.input().path).read()
settings = Extractor.Settings()
settings.cutoff = 12
settings.mvon = False
extractor = Extractor(hs, settings)
best = extractor.extract_best_volume(volume=100)[0]
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(best)
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 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)
PDBResult(identifier=pdb).download(out_dir=dirname)
if os.path.exists(reps):
representatives = reps
else:
representatives = None
try:
result = HotspotReader(path=os.path.join(dirname, "out.zip")).read()
pharmacophore = result.get_pharmacophore_model()
pharmacophore.rank_features(max_features=5)
except:
pharmacophore = PharmacophoreModel.from_pdb(
pdb_code=pdb,
chain="H",
out_dir=dirname,
representatives=representatives)
pharmacophore.rank_features(max_features=5)
result = Results(super_grids=pharmacophore.dic,
protein=Protein.from_file(
os.path.join(dirname, pdb + ".pdb")))
pharmacophore.write(os.path.join(dirname, "crossminer.cm"))
pharmacophore.write(os.path.join(dirname, "pharmit.json"))
# write out Results object
settings = HotspotWriter.Settings()
settings.isosurface_threshold = [2, 5, 10]
with HotspotWriter(dirname, settings=settings) as w:
w.write(result)