def screen_simple(request):
"""View to take a smiles and then screen against a known library"""
import urllib
# Take the smiles in the request object
# Now get the library
if "dump_out" in request.GET:
return HttpResponse(
json.dumps(str(request)) + "\nBODY:" + request.body)
mol_type, screen_lib, fp_method, sim_method, threshold, params = request_handler(
request)
if "structure_source" in request.GET:
smiles = request.GET["structure_source"]
scr_mols = CloseableQueue.CloseableQueue()
[
scr_mols.put({"RDMOL": Chem.MolFromSmiles(str(x))})
for x in str(smiles).split(".")
]
scr_mols.close()
else:
# TODO - work out how to throw this as 400 error - doing the obvious doesn't seem to work
print "No smiles specified as parameter structure_source"
return HttpResponse(
"You must specify a structure as SMILES with the parameter structure_source"
)
# Now handle this file upload
return process_input(fp_method,
sim_method,
screen_lib,
mol_type,
threshold,
params=None,
scr_mols=scr_mols)
def screen_simple(request):
"""View to take a smiles and then screen against a known library of actives"""
import urllib
# Take the smiles in the request object
# Now get the library
if "dump_out" in request.GET:
return HttpResponse(
json.dumps(str(request)) + "\nBODY:" + request.body)
mol_type, screen_lib, fp_method, sim_method, threshold, params = request_handler(
request)
if "smiles" in request.GET:
smiles = request.GET["smiles"]
scr_mols = CloseableQueue.CloseableQueue()
[
scr_mols.put({"RDMOL": Chem.MolFromSmiles(str(x))})
for x in str(smiles).split(".")
]
scr_mols.close()
else:
return HttpResponse("You must state a SMILES")
# Now handle this file upload
return process_input(fp_method,
sim_method,
screen_lib,
mol_type,
threshold,
params=None,
scr_mols=scr_mols)
def start_dock(request):
# Get the library -> either as an ID or as an upload
if "LIB" in request.GET:
lib_id = int(request.GET["LIB"])
else:
try:
mol_type, screen_lib, fp_method, sim_method, threshold, params = request_handler(
request)
except:
screen_lib = None
if not screen_lib:
return HttpResponse("NO LIB SPECIFIED")
else:
libm = LibMethods(screen_lib, mol_type)
my_mols = libm.get_mols()
my_lib = register_lib([x["RDMOL"] for x in my_mols])
lib_id = my_lib.pk
# Now process this libary -> save to disk
# Get the environment
if "ENV" in request.GET:
env_id = int(request.GET["ENV"])
my_env = DockingEnv.objects.filter(pk=env_id)
if not my_env:
return HttpResponse("INVALID ENV")
else:
return HttpResponse("ERROR DOCKING ENV NOT SPECIFIED")
my_lib = DockingLib.objects.filter(pk=lib_id)
if not my_lib:
return HttpResponse("INVALID LIBARAY")
run_id = register_docking(my_env[0], my_lib[0])
# Now set this opff running
response = start_docking.delay(run_id)
return HttpResponse(run_id)
def start_dock(request):
# Get the library -> either as an ID or as an upload
if "LIB" in request.GET:
lib_id = int(request.GET["LIB"])
else:
try:
mol_type, screen_lib, fp_method, sim_method, threshold, params = request_handler(request)
except:
screen_lib = None
if not screen_lib:
return HttpResponse("NO LIB SPECIFIED")
else:
libm = LibMethods(screen_lib, mol_type)
my_mols = libm.get_mols()
my_lib = register_lib([x["RDMOL"] for x in my_mols])
lib_id = my_lib.pk
# Now process this libary -> save to disk
# Get the environment
if "ENV" in request.GET:
env_id = int(request.GET["ENV"])
my_env = DockingEnv.objects.filter(pk=env_id)
if not my_env:
return HttpResponse("INVALID ENV")
else:
return HttpResponse("ERROR DOCKING ENV NOT SPECIFIED")
my_lib = DockingLib.objects.filter(pk=lib_id)
if not my_lib:
return HttpResponse("INVALID LIBARAY")
run_id = register_docking(my_env[0], my_lib[0])
# Now set this opff running
response = start_docking.delay(run_id)
return HttpResponse(run_id)
def cluster_simple(request):
# Read the mols
# Take the smiles in the request object
if "dump_out" in request.GET:
return HttpResponse(json.dumps(str(request))+"\nBODY:" + request.body)
mol_type, screen_lib, fp_method, sim_method, threshold, params = request_handler(request)
# Now return the process
return process_input(fp_method, sim_method, screen_lib, mol_type, threshold, params)
def gen_confs(request):
"""View to take a library of input molecules and generate conformations from them"""
mol_type, screen_lib, fp_method, sim_method, threshold, params = request_handler(request)
# Now handle this file upload
libm = LibMethods(screen_lib, mol_type)
my_mols = libm.get_mols()
my_lib = register_lib([x["RDMOL"] for x in my_mols])
my_pk = setup_conf_run(my_lib, num_mols=None)
response = start_conf_gen.delay(my_pk)
return HttpResponse(str(my_pk))
def screen_simple(request):
"""View to take a smiles and then screen against a known library of actives"""
import urllib
# Take the smiles in the request object
# Now get the library
if "dump_out" in request.GET:
return HttpResponse(json.dumps(str(request))+"\nBODY:" + request.body)
mol_type, screen_lib, fp_method, sim_method, threshold, params = request_handler(request)
if "smiles" in request.GET:
smiles = request.GET["smiles"]
scr_mols = CloseableQueue.CloseableQueue()
[scr_mols.put({"RDMOL": Chem.MolFromSmiles(str(x))}) for x in str(smiles).split(".")]
scr_mols.close()
else:
return HttpResponse("You must state a SMILES")
# Now handle this file upload
return process_input(fp_method, sim_method, screen_lib, mol_type, threshold, params=None, scr_mols=scr_mols)
def screen_simple(request):
"""View to take a smiles and then screen against a known library"""
import urllib
# Take the smiles in the request object
# Now get the library
if "dump_out" in request.GET:
return HttpResponse(json.dumps(str(request))+"\nBODY:" + request.body)
mol_type, screen_lib, fp_method, sim_method, threshold, params = request_handler(request)
if "structure_source" in request.GET:
smiles = request.GET["structure_source"]
scr_mols = CloseableQueue.CloseableQueue()
[scr_mols.put({"RDMOL": Chem.MolFromSmiles(str(x))}) for x in str(smiles).split(".")]
scr_mols.close()
else:
# TODO - work out how to throw this as 400 error - doing the obvious doesn't seem to work
print "No smiles specified as parameter structure_source"
return HttpResponse("You must specify a structure as SMILES with the parameter structure_source")
# Now handle this file upload
return process_input(fp_method, sim_method, screen_lib, mol_type, threshold, params=None, scr_mols=scr_mols)