def get_top_biocatdb_hits():
reaction_node = request.form['reaction_node']
network_id = request.form['network_id']
substrates = json.loads(request.form['parents'])
products = json.loads(request.form['children'])
label = request.form['label']
enzyme = request.form['enzyme']
reaction_smiles = f"{substrates[0]}"
if len(substrates) > 1:
reaction_smiles += f".{substrates[1]}"
reaction_smiles += f">>{products[0]}"
query_reaction_svg = smiles_rxn_to_svg(reaction_smiles, rxnSize=(600, 100))
data = json.loads(current_app.redis.get(network_id))
attr_dict = json.loads(data['attr_dict'])
if enzyme == 'selected_enzyme':
enzyme = attr_dict[reaction_node]['selected_enzyme']
node_info = attr_dict[reaction_node]['enzyme_info'][enzyme]
if node_info is False:
print('No similar reactions found')
result = {
'node_info': '',
'product_keys': [],
'query_reaction_svg': query_reaction_svg,
'reaction_name': label,
'enzyme_name': enzyme
}
return jsonify(result=result)
else:
print(f'Similar reactions found for {reaction_node}')
for product_key in node_info:
node_info[product_key]['formatted_info'] = format_enzyme_info(
node_info[product_key])
for product_key in node_info:
try:
node_info[product_key]['reaction_svg'] = smiles_rxn_to_svg(
node_info[product_key]['smiles_reaction'],
rxnSize=(400, 75))
except Exception as e:
print(str(e))
node_info[product_key]['reaction_svg'] = ''
result = {
'node_info': node_info,
'product_keys': sorted(list(node_info.keys()), reverse=True),
'query_reaction_svg': query_reaction_svg,
'reaction_name': label,
'enzyme_name': enzyme
}
return jsonify(result=result)
def get_reaction_svg(s1, s2, p):
if s2 == "":
smi_rxn = f"{s1}>>{p}"
else:
smi_rxn = f"{s1}.{s2}>>{p}"
svg = smiles_rxn_to_svg(smi_rxn, rxnSize=(500,200))
return svg
def generate_rxn_svg(activity, rxnSize=(300, 70)):
reaction_smiles = ""
if activity.substrate_1_smiles is not None:
reaction_smiles += f"{activity.substrate_1_smiles}"
if activity.substrate_2_smiles is not None:
reaction_smiles += f".{activity.substrate_2_smiles}>>"
if activity.product_1_smiles is not None:
reaction_smiles += f"{activity.product_1_smiles}"
reaction_svg = smiles_rxn_to_svg(reaction_smiles, rxnSize=rxnSize)
return reaction_svg
def load_reaction_issue_info():
substrates = json.loads(request.form['parents'])
products = json.loads(request.form['children'])
reaction_smiles = f"{substrates[0]}"
if len(substrates) > 1:
reaction_smiles += f".{substrates[1]}"
reaction_smiles += f">>{products[0]}"
query_reaction_svg = smiles_rxn_to_svg(reaction_smiles, rxnSize=(600, 150))
result = {'query_reaction_svg': query_reaction_svg}
return jsonify(result=result)
def get_reaction_svg():
substrates = json.loads(request.form['parents'])
products = json.loads(request.form['children'])
label = request.form['label']
reaction_smiles = f"{substrates[0]}"
if len(substrates) > 1:
reaction_smiles += f".{substrates[1]}"
reaction_smiles += f">>{products[0]}"
query_reaction_svg = smiles_rxn_to_svg(reaction_smiles, rxnSize=(600, 100))
result = {'query_reaction_svg': query_reaction_svg, 'reaction_name': label}
return jsonify(result=result)
def reaction_issue(issue_id):
if current_user.is_authenticated:
user = user_datastore.get_user(current_user.id)
else:
user = None
issue = Issue.objects(id=issue_id).select_related()[0]
reaction_svg = smiles_rxn_to_svg(issue.issue_reaction_smiles,
rxnSize=(600, 150))
if issue.public == True:
public = 'Public'
else:
public = 'Not public'
num_issues = len(
Issue.objects(db.Q(reaction=issue.reaction) & db.Q(status='Open')))
comments = []
for comment in issue.comments:
can_edit = False
can_delete = False
if current_user.has_role('rxn_rules_admin') or comment.owner == user:
can_edit = True
can_delete = True
new_comment = {
'user':
f"{comment.owner.first_name} {comment.owner.last_name}, {comment.owner.affiliation}",
'date': comment.date.strftime("%d/%m/%Y, %H:%M:%S"),
'comment': comment.text,
'comment_id': str(comment.id),
'can_edit': can_edit,
'can_delete': can_delete
}
comments.append(new_comment)
return render_template(
'reaction_issues/issue_page.html',
reaction_name=issue.reaction.name,
reaction_svg=reaction_svg,
reaction_smiles=issue.issue_reaction_smiles,
raised_by=
f"{issue.raised_by.first_name} {issue.raised_by.last_name}, {issue.raised_by.affiliation}",
date=issue.date.strftime("%d/%m/%Y"),
status=issue.status,
public=public,
num_issues=num_issues,
issue_id=str(issue.id),
comments=comments)
def submit_reaction_issue():
substrates = json.loads(request.form['parents'])
products = json.loads(request.form['children'])
reaction_name = request.form['reaction']
comment = request.form['comment']
public = bool(strtobool(request.form['public']))
if len(Reaction.objects(name=reaction_name)) == 0:
result = {
'status': 'danger',
'msg': 'Can not raise an issue for a non retrobiocat reaction',
'issues': []
}
return jsonify(result=result)
reaction_smiles = f"{substrates[0]}"
if len(substrates) > 1:
reaction_smiles += f".{substrates[1]}"
reaction_smiles += f">>{products[0]}"
query_reaction_svg = smiles_rxn_to_svg(reaction_smiles, rxnSize=(300, 70))
user = user_datastore.get_user(current_user.id)
reaction = Reaction.objects(name=reaction_name)[0]
comment_obj = Comment(owner=user, text=comment)
comment_obj.save()
issue = Issue(reaction=reaction,
issue_reaction_smiles=reaction_smiles,
issue_reaction_svg=query_reaction_svg,
raised_by=user,
status='Open',
comments=[comment_obj],
public=public)
issue.save()
print(f"Issue saved for {issue.reaction}")
result = {'status': 'success', 'msg': 'Issue raised', 'issues': []}
return jsonify(result=result)