def get_params(smiles, request):
try:
smiles = canon_input(smiles)
except:
smiles = ""
height = None
mol = None
bond_id_list = []
highlightBondColors = {}
if "height" in request.GET:
height = int(request.GET["height"])
width = None
if "width" in request.GET:
width = int(request.GET["width"])
if "atom_indices" in request.GET:
mol = Chem.MolFromSmiles(smiles)
bond_id_list, highlightBondColors, mol = parse_atom_ids(
request.GET["atom_indices"], mol)
if "Xe" in smiles:
bond_id_list, highlightBondColors, mol = parse_xenons(smiles)
img_type = request.GET.get("img_type", None)
get_mol = draw_mol(
smiles,
width=width,
height=height,
img_type=img_type,
highlightBonds=bond_id_list,
mol=mol,
bondcolors=highlightBondColors,
)
if type(get_mol) == HttpResponse:
return get_mol
return HttpResponse(get_mol)
def get_full_graph(smiles,
graph_url="neo4j",
graph_auth="neo4j/neo4j",
isomericSmiles=True):
"""
For the given smiles and graph credentials, query the Neo4j database
:param: smiles
:param: graph_url - note that for local Neo4j graphs, this can be set to 'localhost'
:param: graph_auth - username/password.
:param: isomericSmiles True/False
:return: Output dictionary - This is returned "as-is" from the Fragalysis-Backend api/graph query.
"""
msg = f"get_full_graph(\"{smiles}\", graph_url={graph_url}, isomericSmiles={isomericSmiles})"
smiles = canon_input(smiles, isomericSmiles)
msg += f" canon_smiles=\"{smiles}\""
driver = get_driver(graph_url, graph_auth)
records = []
with driver.session() as session:
debug_proximal_num_records = 0
for record in session.run(find_proximal_query(smiles)):
debug_proximal_num_records += 1
ans = define_proximal_type(record)
records.append(ans)
msg += f" n_proximals={debug_proximal_num_records}"
debug_double_edge_num_records = 0
for record in session.run(find_double_edge_query(smiles)):
debug_double_edge_num_records += 0
ans = define_double_edge_type(record)
records.append(ans)
msg += f" n_double_edge={debug_double_edge_num_records}"
for label in list(set([x.label for x in records])):
# Linkers are meaningless
if "." in label:
continue
if records:
orga_dict = organise(records, None)
orga_dict_len = len(orga_dict)
msg += f" orga_dict_len={orga_dict_len}"
logger.info(f"GRAPH -> {msg}")
return orga_dict
msg += f" (fall-through) ret=None"
logger.info(f"GRAPH -> {msg}")
return None
def get_full_graph(smiles, graph_url="neo4j"):
smiles = canon_input(smiles)
driver = get_driver(graph_url)
with driver.session() as session:
records = []
for record in session.read_transaction(find_proximal, smiles):
ans = define_proximal_type(record)
records.append(ans)
for record in session.read_transaction(find_double_edge, smiles):
ans = define_double_edge_type(record)
records.append(ans)
for label in list(set([x.label for x in records])):
# Linkers are meaningless
if "." in label:
continue
if records:
orga_dict = organise(records, None)
return orga_dict
else:
print("Nothing found for input: " + smiles)
def get_picks(smiles, num_picks, graph_url="neo4j", graph_auth="neo4j/neo4j"):
smiles = canon_input(smiles)
driver = get_driver(graph_url, graph_auth)
with driver.session() as session:
records = []
for record in session.run(find_proximal_query(smiles)):
ans = define_proximal_type(record)
records.append(ans)
for record in session.run(find_double_edge_query(smiles)):
ans = define_double_edge_type(record)
records.append(ans)
for label in list(set([x.label for x in records])):
# Linkers are meaningless
if "." in label:
continue
if records:
orga_dict = organise(records, num_picks)
return orga_dict
else:
print("Nothing found for input: " + smiles)