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 test_get_b64_smiles(self):
# Compress and encode
url_compressed = quote(compress_string('c1ccccc1'))
response = self.app.get(
'/v1/depict/structure/smiles?val={0}&debug=true&gz=true'.format(
url_compressed))
self.assertEqual("200 OK", response.status)
def test_get_b64_pdb(self):
with open(LIGAND_FILE, 'r') as f:
ligand = f.read()
# Compress and encode
url_compressed = quote(compress_string(ligand))
response = self.app.get('/v1/depict/structure/pdb?val={0}&debug=true&gz=true'.format(url_compressed))
self.assertEqual("200 OK", response.status)
def test_get_b64_pdb(self):
with open(LIGAND_FILE, 'r') as f:
ligand = f.read()
# Compress and encode
url_compressed = quote(compress_string(ligand))
response = self.app.get(
'/v1/depict/structure/pdb?val={0}&debug=true&gz=true'.format(
url_compressed))
self.assertEqual("200 OK", response.status)
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 test_pdb_gz_to_sdf_gz(self):
"""
Test PDB to SDF molecule conversion with gzipped and base64 encoded molecule in both input and output
"""
# First perform the conversion using the toolktis here
reference = OEGraphMol()
ifs = oemolistream(LIGAND_FILE)
OEReadMolecule(ifs, reference)
# Read the ligand as a string to POST
with open(LIGAND_FILE, 'r') as f:
target = f.read()
# Perform the conversion to SDF
response = self.app.post(
'/v1/convert/molecule',
data=json.dumps(
{
"molecule": {
"value": compress_string(target),
"input": {"format": "pdb", "gz": True},
"output": {"format": "sdf", "gz": True}
}
}
),
headers={"content-type": "application/json"}
)
# Test response status
self.assertEqual("200 OK", response.status)
# Test the output schema
payload = json.loads(response.data.decode('utf-8'))
self.assertIn('molecule', payload)
self.assertIn('value', payload['molecule'])
self.assertIn('gz', payload['molecule'])
# Test the validity of the output molecule
mol = OEGraphMol()
ifs = oemolistream()
ifs.SetFormat(OEFormat_SDF)
self.assertTrue(ifs.openstring(inflate_string(payload['molecule']['value'])))
self.assertTrue(ifs.IsValid())
self.assertTrue(OEReadMolecule(ifs, mol))
self.assertTrue(mol.IsValid())
# Test that the two molecule strings are equal
self.assertEqual(OECreateCanSmiString(reference), OECreateCanSmiString(mol))
def test_interaction_b64_protein(self):
"""
Test providing a gzipped and then base64 encoded receptor
"""
# Read the protein and ligand
with open(LIGAND_FILE, 'r') as f:
ligand = f.read()
with open(RECEPTOR_FILE, 'r') as f:
receptor = f.read()
# POST in JSON
response = self.app.post(
'/v1/depict/interaction?format=png&debug=true',
data=json.dumps(
{
"ligand": {"value": ligand, "format": "pdb"},
"receptor": {"value": compress_string(receptor), "format": "pdb", "gz": True}
}
),
headers={"content-type": "application/json"}
)
self.assertEqual("200 OK", response.status)
def test_get_b64_smiles(self):
# Compress and encode
url_compressed = quote(compress_string('c1ccccc1'))
response = self.app.get('/v1/depict/structure/smiles?val={0}&debug=true&gz=true'.format(url_compressed))
self.assertEqual("200 OK", response.status)