def post(self):
"""
Render JSON that has been POST'ed to this resource
:return: A Flask Response with the rendered image
:rtype: Response
"""
# Parse the query options
args = interaction_arg_parser.parse_args()
try:
# We exepct a JSON object in request.data with the protein and ligand data structures
payload = json.loads(request.data.decode("utf-8"))
self.__validate_schema(payload)
# Try to read the ligand from the payload
try:
ligand = read_molecule_from_string(
payload['ligand']['value'],
payload['ligand']['format'],
payload['ligand']['gz'] if 'gz' in payload['ligand'] else False,
args['reparse']
)
except Exception as ex:
message = "Error reading ligand"
if args['debug']:
message += ": {0}".format(str(ex))
raise Exception(message)
# Try to read the receptor from the payload
try:
receptor = read_molecule_from_string(
payload['receptor']['value'],
payload['receptor']['format'],
payload['receptor']['gz'] if 'gz' in payload['receptor'] else False,
args['reparse']
)
except Exception as ex:
message = "Error reading receptor"
if args['debug']:
message += ": {0}".format(str(ex))
raise Exception(message)
# Render the image
return _render_image(receptor, ligand, args)
# On error render a PNG with an error message
except Exception as ex:
if args['debug']:
return Response(json.dumps({"error": str(ex)}), status=400, mimetype='application/json')
else:
return render_error_image(args['width'], args['height'], str(ex))
def post(self):
"""
Render JSON that has been POST'ed to this resource
:return: A Flask Response with the rendered image
:rtype: Response
"""
# Parse the query options
args = interaction_arg_parser.parse_args()
try:
# We exepct a JSON object in request.data with the protein and ligand data structures
payload = json.loads(request.data.decode("utf-8"))
self.__validate_schema(payload)
# Try to read the ligand from the payload
try:
ligand = read_molecule_from_string(
payload['ligand']['value'], payload['ligand']['format'],
payload['ligand']['gz']
if 'gz' in payload['ligand'] else False, args['reparse'])
except Exception as ex:
message = "Error reading ligand"
if args['debug']:
message += ": {0}".format(str(ex))
raise Exception(message)
# Try to read the receptor from the payload
try:
receptor = read_molecule_from_string(
payload['receptor']['value'],
payload['receptor']['format'], payload['receptor']['gz']
if 'gz' in payload['receptor'] else False, args['reparse'])
except Exception as ex:
message = "Error reading receptor"
if args['debug']:
message += ": {0}".format(str(ex))
raise Exception(message)
# Render the image
return _render_image(receptor, ligand, args)
# On error render a PNG with an error message
except Exception as ex:
if args['debug']:
return Response(json.dumps({"error": str(ex)}),
status=400,
mimetype='application/json')
else:
return render_error_image(args['width'], args['height'],
str(ex))
def post(self):
"""
Convert a molecule to another file format
:return: A Flask Response with the rendered image
:rtype: Response
"""
# Parse the query options
try:
# We exepct a JSON object in request.data with the protein and ligand data structures
payload = json.loads(request.data.decode("utf-8"))
# Checks to make sure we have everything we need in payload
self.__validate_schema(payload)
# Read the molecule
mol = read_molecule_from_string(
payload['molecule']['value'],
payload['molecule']['input']['format'],
payload['molecule']['input']['gz']
if 'gz' in payload['molecule']['input'] else False,
payload['molecule']['input']['reparse']
if 'reparse' in payload['molecule']['input'] else False)
# Prepare the molecule for writing
ofs = oemolostream()
if payload['molecule']['output']['format'] == "smiles":
ofs_format = OEFormat_SMI
else:
ofs_format = OEGetFileType(
to_utf8(payload['molecule']['output']['format']))
if ofs_format == OEFormat_UNDEFINED:
raise Exception("Unknown output file type: " +
payload['molecule']['output']['format'])
ofs.SetFormat(ofs_format)
ofs.openstring()
OEWriteMolecule(ofs, mol)
# Get molecule output stream
if 'gz' in payload['molecule']['output'] and payload['molecule'][
'output']['gz']:
output = compress_string(ofs.GetString().decode('utf-8'))
else:
output = ofs.GetString().decode('utf-8')
return Response(json.dumps({
'molecule': {
'value':
output,
'format':
payload['molecule']['output']['format'],
'gz':
payload['molecule']['output']['gz']
if 'gz' in payload['molecule']['output'] else False
}
}),
status=200,
mimetype='application/json')
except Exception as ex:
return Response(json.dumps({"error": str(ex)}),
status=400,
mimetype='application/json')
def get(self, fmt):
"""
Render an image with the molecule passed through the URL
:param fmt: The image format
:type fmt: str
:return: The rendered image
:rtype: Response
"""
# Parse the query options
args = depictor_arg_parser.parse_args()
try:
# Read the molecule
mol = read_molecule_from_string(args['val'], fmt, bool(args['gz']),
bool(args['reparse']))
# Render the image
return self.__render_image(mol, args)
# On error render a PNG with an error message
except Exception as ex:
if args['debug']:
return Response(json.dumps({"error": str(ex)}),
status=400,
mimetype='application/json')
else:
return render_error_image(args['width'], args['height'],
str(ex))
def post(self, fmt):
"""
Render a raw receptor-ligand that has been POST'ed to this resource by first searching for the ligand
:return: A Flask Response with the rendered image
:rtype: Response
"""
# Parse the query options
args = interaction_arg_parser.parse_args()
try:
# Try to read the receptor-ligand complex
try:
mol = read_molecule_from_string(request.data.decode("utf-8"),
fmt, args['gz'],
args['reparse'])
except Exception as ex:
message = "Error reading molecule file"
if args['debug']:
message += ": {0}".format(str(ex))
raise Exception(message)
# Generate the ligand selection functor
if args['chain'] or args['resi'] or args['resn']:
functor = generate_ligand_functor(args['chain'], args['resi'],
args['resn'])
else:
raise Exception("No ligand selection options given")
# Split the ligand from the complex
ligand = OEGraphMol()
OESubsetMol(ligand, mol, functor, False, False)
# Check the ligand
if not ligand or ligand.NumAtoms() == 0:
raise Exception("No atoms matched ligand selection")
# Delete the ligand from the complex
for atom in mol.GetAtoms(functor):
mol.DeleteAtom(atom)
# Error check receptor
if not mol or mol.NumAtoms() == 0:
raise Exception("No atoms in receptor")
return _render_image(mol, ligand, args)
except Exception as ex:
if args['debug']:
return Response(json.dumps({"error": str(ex)}),
status=400,
mimetype='application/json')
else:
return render_error_image(args['width'], args['height'],
str(ex))
def post(self, fmt):
"""
Render a raw receptor-ligand that has been POST'ed to this resource by first searching for the ligand
:return: A Flask Response with the rendered image
:rtype: Response
"""
# Parse the query options
args = interaction_arg_parser.parse_args()
try:
# Try to read the receptor-ligand complex
try:
mol = read_molecule_from_string(
request.data.decode("utf-8"),
fmt,
args['gz'],
args['reparse']
)
except Exception as ex:
message = "Error reading molecule file"
if args['debug']:
message += ": {0}".format(str(ex))
raise Exception(message)
# Generate the ligand selection functor
if args['chain'] or args['resi'] or args['resn']:
functor = generate_ligand_functor(args['chain'], args['resi'], args['resn'])
else:
raise Exception("No ligand selection options given")
# Split the ligand from the complex
ligand = OEGraphMol()
OESubsetMol(ligand, mol, functor, False, False)
# Check the ligand
if not ligand or ligand.NumAtoms() == 0:
raise Exception("No atoms matched ligand selection")
# Delete the ligand from the complex
for atom in mol.GetAtoms(functor):
mol.DeleteAtom(atom)
# Error check receptor
if not mol or mol.NumAtoms() == 0:
raise Exception("No atoms in receptor")
return _render_image(mol, ligand, args)
except Exception as ex:
if args['debug']:
return Response(json.dumps({"error": str(ex)}), status=400, mimetype='application/json')
else:
return render_error_image(args['width'], args['height'], str(ex))
def post(self):
"""
Convert a molecule to another file format
:return: A Flask Response with the rendered image
:rtype: Response
"""
# Parse the query options
try:
# We exepct a JSON object in request.data with the protein and ligand data structures
payload = json.loads(request.data.decode("utf-8"))
# Checks to make sure we have everything we need in payload
self.__validate_schema(payload)
# Read the molecule
mol = read_molecule_from_string(
payload['molecule']['value'],
payload['molecule']['input']['format'],
payload['molecule']['input']['gz'] if 'gz' in payload['molecule']['input'] else False,
payload['molecule']['input']['reparse'] if 'reparse' in payload['molecule']['input'] else False
)
# Prepare the molecule for writing
ofs = oemolostream()
if payload['molecule']['output']['format'] == "smiles":
ofs_format = OEFormat_SMI
else:
ofs_format = OEGetFileType(to_utf8(payload['molecule']['output']['format']))
if ofs_format == OEFormat_UNDEFINED:
raise Exception("Unknown output file type: " + payload['molecule']['output']['format'])
ofs.SetFormat(ofs_format)
ofs.openstring()
OEWriteMolecule(ofs, mol)
# Get molecule output stream
if 'gz' in payload['molecule']['output'] and payload['molecule']['output']['gz']:
output = compress_string(ofs.GetString().decode('utf-8'))
else:
output = ofs.GetString().decode('utf-8')
return Response(json.dumps(
{
'molecule': {
'value': output,
'format': payload['molecule']['output']['format'],
'gz': payload['molecule']['output']['gz'] if 'gz' in payload['molecule']['output'] else False
}
}
), status=200, mimetype='application/json')
except Exception as ex:
return Response(json.dumps({"error": str(ex)}), status=400, mimetype='application/json')
def post(self, fmt):
"""
Render an image with the molecule POST'ed to this resource
:param fmt: The molecule format
:type fmt: str
:return: The rendered image
:rtype: Response
"""
# Parse the query options
args = depictor_arg_parser.parse_args()
try:
# Read the molecule
mol = read_molecule_from_string(request.data.decode("utf-8"), fmt, bool(args['gz']), bool(args['reparse']))
# Render the image
return self.__render_image(mol, args)
# On error render a PNG with an error message
except Exception as ex:
if args['debug']:
return Response(json.dumps({"error": str(ex)}), status=400, mimetype='application/json')
else:
return render_error_image(args['width'], args['height'], str(ex))