def test_product_against_rules():
target_smiles = request.form['target_smiles']
smarts = request.form['smarts']
try:
smarts_list = yaml.load(smarts, Loader=yaml.FullLoader)
except:
return jsonify(result={'status': 'fail'})
try:
rxn_list = []
for sma in smarts_list:
rxn_list.append(rdchiralReaction(sma))
except:
return jsonify(result={'status': 'fail'})
try:
network = Network()
if request.form['combine_enantiomers'] == 'true':
network.settings['combine_enantiomers'] = True
else:
network.settings['combine_enantiomers'] = False
network.rxn_obj.rxns = {'test_smarts': rxn_list}
network.rxns = {'test_smarts': rxn_list}
network.generate(target_smiles, 1)
nodes, edges = network.get_visjs_nodes_and_edges()
print(nodes)
result = {'status': 'success', 'nodes': nodes, 'edges': edges}
except:
result = {'status': 'fail'}
return jsonify(result=result)
def load_rxns(query_result):
rxns = {}
for rxn in query_result:
rxns[rxn.name] = []
for rxn_string in rxn.smarts:
rxns[rxn.name].append(rdchiralReaction(rxn_string))
return rxns
def load_rxns(yaml_dict):
rxns = {}
for name in yaml_dict:
if name not in rxns:
rxns[name] = []
for rxn_string in yaml_dict[name]['smarts']:
try:
rxns[name].append(rdchiralReaction(rxn_string))
except:
print('Error loading reaction - ' + str(name))
return rxns
def get_rxns(self, smile):
if self.policy_model == None:
self.load_model()
reactions = self.get_actions(smile)
rxns = {}
metadata = {}
for reaction in reactions:
name = f"Chem_{reaction['metadata']['classification']}"
extra_string = ''
num = 1
while name + extra_string in rxns:
extra_string = f"_{num}"
num += 1
name = name + extra_string
rxns[name] = [rdchiralReaction(reaction['smarts'])]
metadata[name] = reaction['metadata']
return rxns, metadata
def _test_smarts(self, smarts):
try:
smarts_list = yaml.load(smarts, Loader=yaml.FullLoader)
except:
self.state = 'danger'
self.issues.append('Could not load smarts yaml')
return
try:
rxn_list = []
for sma in smarts_list:
rxn_list.append(rdchiralReaction(sma))
except:
self.state = 'danger'
self.issues.append('Could not load reactions')
return
return rxn_list
def visualise_smarts():
smarts_yaml = request.form['smarts_yaml']
try:
smarts_list = yaml.safe_load(smarts_yaml)
except:
result = {'status': 'fail', 'msg': 'Could not load yaml'}
return jsonify(result=result)
try:
rxn_list = []
for sma in smarts_list:
rxn_list.append(rdchiralReaction(sma))
list_imgs = rxntosvg(rxn_list, rxnSize=(450, 150))
except:
result = {'status': 'fail', 'msg': 'Could not load rxn imgs'}
return jsonify(result=result)
result = {'status': 'success', 'msg': '', 'list_imgs': list_imgs}
return jsonify(result=result)
def apply_reaction_rev():
p = request.form['p']
reaction_q = Reaction.objects(name=request.form['reaction'])
if len(reaction_q) == 0:
print(f"{request.form['reaction']} was not found in RetroBioCat")
result = {'status': 'danger',
'msg': 'No reaction on RetroBioCat with this name',
'issues': [f"{request.form['reaction']} was not found in RetroBioCat"]}
return jsonify(result=result)
rdkit_rxns = {'rdkit_rxns': []}
rdchiral_rxns = {'rd_chiral_rxns': []}
try:
for smarts in reaction_q[0].smarts:
rdkit_rxns['rdkit_rxns'].append(rdChemReactions.ReactionFromSmarts(smarts))
try:
rdchiral_rxns['rd_chiral_rxns'].append(rdchiralReaction(smarts))
except:
pass
except Exception as e:
print('Error parsing reaction SMARTS')
print(e)
result = {'status': 'danger',
'msg': 'Error parsing reaction SMARTS',
'issues': []}
return jsonify(result=result)
rule_applicator = RuleApplicator(None)
smi = p
try:
products = rule_applicator.apply_rules(smi, rdchiral_rxns)['rd_chiral_rxns']
except:
products = []
if products == []:
try:
products = rule_applicator.apply_rules_rdkit(smi, rdkit_rxns)['rdkit_rxns']
except:
products = []
no_dupl = []
for prod in products:
if prod not in no_dupl:
no_dupl.append(prod)
products = no_dupl
svg_dict = make_svg_dict(products)
reaction_svgs = []
for smi_list in products:
if len(smi_list) == 1:
reaction_svgs.append(get_reaction_svg(smi_list[0], '', p))
elif len(smi_list) == 2:
reaction_svgs.append(get_reaction_svg(smi_list[0], smi_list[1], p))
else:
reaction_svgs.append(get_reaction_svg('', '', p))
if len(products) == 0:
result = {'status': 'danger',
'msg': 'No products',
'issues': []}
return jsonify(result=result)
result = {'status': 'success',
'msg': '',
'products': products,
'reaction_svgs': reaction_svgs,
'svg_dict': svg_dict,
'issues': []}
return jsonify(result=result)