else:
print('Error no activity category is suitable')
return None
def _log_time(self, msg):
if self.log_times == True:
print(msg)
def _log(self, msg):
if self.print_log == True:
print(msg)
if __name__ == '__main__':
from retrobiocat_web.mongo.default_connection import make_default_connection
make_default_connection()
t0 = time.time()
scorer = SubstrateSpecificityScorer(log_times=True)
t1 = time.time()
print(f"Time to load = {round(t1-t0,3)}")
reactionName = 'All'
enzyme = 'CAR'
product = 'CCc1ccc(C=O)cc1'
score, info, top_hits_json = scorer.scoreReaction(reactionName,
enzyme,
product,
None,
None,
sim_cutoff=0.5,
for rxn in query_result:
rxns[rxn.name] = []
for rxn_string in rxn.smarts:
rxns[rxn.name].append(rxn_string)
return rxns
def load_rules_by_type(query_result):
rules_by_type = {}
for rxn in query_result:
rule_type = rxn.type
if rule_type not in rules_by_type:
rules_by_type[rule_type] = []
rules_by_type[rule_type].append(rxn.name)
return rules_by_type
if __name__ == '__main__':
default_connection.make_default_connection()
t0 = time.time()
query_result = get_reactions()
rxns = load_rxns(query_result)
reactionEnzymeCofactorDict = load_cofactors(query_result)
reactions, enzymes, reaction_enzyme_map = load_reactions_and_enzymes(
query_result)
t1 = time.time()
print(f"Time to load rules = {round(t1-t0, 3)}")
print(reactions)
