def change_reaction_options():
task_id = request.form['task_id']
data = json.loads(current_app.redis.get(task_id))
graph_dict = json.loads(data['graph_dict'])
attr_dict = json.loads(data['attr_dict'])
target_smiles = data['target_smiles']
network_options = json.loads(data['network_options'])
graph = nx.from_dict_of_lists(graph_dict, create_using=nx.DiGraph)
network = Network(graph=graph, target_smiles=target_smiles)
network.update_settings(network_options)
network.add_attributes(attr_dict)
network.update_settings(
{'max_reactions': int(request.form['max_reactions'])})
"""
if len(retrobiocat.retrorules_diameters) != 0:
network.settings['rr_min_diameter'] = int(request.form['rr_min_diameter'])
network.settings['rr_min_products'] = int(request.form['rr_min_products'])
network.settings['rr_max_reactions'] = int(request.form['rr_max_reactions'])
"""
data['network_options'] = json.dumps(network.settings)
current_app.redis.mset({task_id: json.dumps(data)})
time_to_expire = 15 * 60 #15 mins * 60 seconds
current_app.redis.expire(task_id, time_to_expire)
result = {'network_options': json.dumps(network.settings)}
return jsonify(result=result)
def change_enzyme():
selected_node = request.form['selected_node']
selected_enzyme = request.form['selected_enzyme']
task_id = request.form['task_id']
data = json.loads(current_app.redis.get(task_id))
graph_dict = json.loads(data['graph_dict'])
attr_dict = json.loads(data['attr_dict'])
target_smiles = data['target_smiles']
network_options = json.loads(data['network_options'])
graph = nx.from_dict_of_lists(graph_dict, create_using=nx.DiGraph)
network = Network(graph=graph, target_smiles=target_smiles)
network.settings = network_options
network.add_attributes(attr_dict)
network.calculate_scores()
network.graph.nodes[selected_node]['attributes']['selected_enzyme'] = selected_enzyme
data['attr_dict'] = json.dumps(network.attributes_dict())
current_app.redis.mset({task_id: json.dumps(data)})
time_to_expire = 15 * 60 # 15 mins * 60 seconds
current_app.redis.expire(task_id, time_to_expire)
successors = list(network.graph.successors(selected_node))
predecessors = list(network.graph.predecessors(selected_node))
subgraph = network.graph.subgraph([selected_node]+successors+predecessors)
nodes, edges = network.get_visjs_nodes_and_edges(graph=subgraph)
result = {'nodes': nodes,
'edges': edges}
return jsonify(result=result)
def delete_step():
reaction = request.form['reaction']
task_id = request.form['task_id']
data = json.loads(current_app.redis.get(task_id))
graph_dict = json.loads(data['graph_dict'])
attr_dict = json.loads(data['attr_dict'])
target_smiles = data['target_smiles']
network_options = json.loads(data['network_options'])
graph = nx.from_dict_of_lists(graph_dict, create_using=nx.DiGraph)
network = Network(graph=graph,
target_smiles=target_smiles,
print_log=not current_app.config['PRODUCTION'])
network.update_settings(network_options)
network.add_attributes(attr_dict)
to_delete = network.delete_reaction_node(reaction)
nodes = []
edges = []
data['graph_dict'] = json.dumps(nx.to_dict_of_lists(network.graph))
data['attr_dict'] = json.dumps(network.attributes_dict())
nodes = add_new(data['nodes'], nodes)
edges = add_new(data['edges'], edges)
nodes, edges = delete_nodes_and_edges(to_delete, nodes, edges)
data['nodes'] = nodes
data['edges'] = edges
current_app.redis.mset({task_id: json.dumps(data)})
time_to_expire = 15 * 60 # 15 mins * 60 seconds
current_app.redis.expire(task_id, time_to_expire)
result = {'to_delete': to_delete}
return jsonify(result=result)
def change_network_options():
reaction_colours = request.form['reaction_colours']
edge_colours = request.form['edge_colours']
task_id = request.form['task_id']
data = json.loads(current_app.redis.get(task_id))
graph_dict = json.loads(data['graph_dict'])
attr_dict = json.loads(data['attr_dict'])
target_smiles = data['target_smiles']
network_options = json.loads(data['network_options'])
graph = nx.from_dict_of_lists(graph_dict, create_using=nx.DiGraph)
network = Network(graph=graph, target_smiles=target_smiles)
network.update_settings(network_options)
network.add_attributes(attr_dict)
network.settings['colour_reactions'] = reaction_colours
network.settings["colour_arrows"] = edge_colours
nodes, edges = network.get_visjs_nodes_and_edges()
data['nodes'] = add_new(data['nodes'], nodes)
data['edges'] = add_new(data['edges'], edges)
data['network_options'] = json.dumps(network.settings)
current_app.redis.mset({task_id: json.dumps(data)})
time_to_expire = 15 * 60 #15 mins * 60 seconds
current_app.redis.expire(task_id, time_to_expire)
result = {
'nodes': nodes,
'edges': edges,
}
return jsonify(result=result)
def package_visjs_pathways(task_id, max_vis=100):
network_data = json.loads(current_app.redis.get(task_id + '__network'))
graph = nx.from_dict_of_lists(json.loads(network_data['graph_dict']),
create_using=nx.DiGraph)
network = Network(graph=graph,
target_smiles=network_data['target_smiles'],
print_log=not current_app.config['PRODUCTION'])
network.update_settings(json.loads(network_data['network_options']))
network.add_attributes(json.loads(network_data['attr_dict']))
evaluated_pathways = json.loads(
current_app.redis.get(f"{task_id}__evaluated_pathways"))
for i, pathway_varients in enumerate(evaluated_pathways):
if i > max_vis:
break
pathway_vis_js_data = []
max_var = len(pathway_varients)
for nodes in pathway_varients:
pathway = Pathway(nodes, network, calc_scores=False)
nodes, edges = pathway.get_visjs_nodes_and_edges()
pathway_vis_js_data.append((nodes, edges, max_var))
current_app.redis.mset(
{f"{task_id}__{i+1}": json.dumps(pathway_vis_js_data)})
current_app.redis.expire(f"{task_id}__{i+1}", 60 * 60)
def aizynth_step():
clicked_node = request.form['smiles']
x = request.form['x']
y = request.form['y']
task_id = request.form['task_id']
max_reactions = request.form['max_reactions']
aizynth_reaction_mode = request.form['aizynth_reaction_mode']
data = json.loads(current_app.redis.get(task_id))
graph_dict = json.loads(data['graph_dict'])
attr_dict = json.loads(data['attr_dict'])
target_smiles = data['target_smiles']
network_options = json.loads(data['network_options'])
graph = nx.from_dict_of_lists(graph_dict, create_using=nx.DiGraph)
network = Network(graph=graph,
target_smiles=target_smiles,
print_log=not current_app.config['PRODUCTION'])
network.update_settings(network_options)
network.add_attributes(attr_dict)
network.update_settings({
'max_reactions': int(max_reactions),
'aizynth_reaction_mode': aizynth_reaction_mode
})
new_substrate_nodes, new_reaction_nodes = network.add_chemical_step(
clicked_node)
all_new_nodes = [clicked_node] + new_substrate_nodes + new_reaction_nodes
subgraph = network.graph.subgraph(all_new_nodes)
nodes, edges = network.get_visjs_nodes_and_edges(graph=subgraph)
for i, node in enumerate(nodes):
nodes[i].update({'x': x, 'y': y})
result = {'nodes': nodes, 'edges': edges}
data['graph_dict'] = json.dumps(nx.to_dict_of_lists(network.graph))
data['attr_dict'] = json.dumps(network.attributes_dict())
nodes = add_new(data['nodes'], nodes)
edges = add_new(data['edges'], edges)
nodes, edges = delete_nodes_and_edges([], nodes, edges)
data['nodes'] = nodes
data['edges'] = edges
current_app.redis.mset({task_id: json.dumps(data)})
time_to_expire = 15 * 60 #15 mins * 60 seconds
current_app.redis.expire(task_id, time_to_expire)
return jsonify(result=result)
def task_add_retrorule_step(form_data, network_id):
job = get_current_job()
job.meta['progress'] = 'started'
job.save_meta()
clicked_node = form_data['smiles']
x = form_data['x']
y = form_data['y']
data = json.loads(current_app.redis.get(network_id))
graph_dict = json.loads(data['graph_dict'])
attr_dict = json.loads(data['attr_dict'])
target_smiles = data['target_smiles']
network_options = json.loads(data['network_options'])
graph = nx.from_dict_of_lists(graph_dict, create_using=nx.DiGraph)
network = Network(graph=graph, target_smiles=target_smiles)
network.update_settings(network_options)
network.add_attributes(attr_dict)
network.retrorules.retrorules_rxns = current_app.retrorules_rxns
network.retrorules.retrorule_db = current_app.retrorules_db
new_substrate_nodes, new_reaction_nodes = network.retrorules.add_step(
clicked_node)
all_new_nodes = [clicked_node] + new_substrate_nodes + new_reaction_nodes
subgraph = network.graph.subgraph(all_new_nodes)
nodes, edges = network.get_visjs_nodes_and_edges(graph=subgraph)
for i, node in enumerate(nodes):
nodes[i].update({'x': x, 'y': y})
result = {
'nodes': nodes,
'edges': edges,
'to_delete': [],
}
data['graph_dict'] = json.dumps(nx.to_dict_of_lists(network.graph))
data['attr_dict'] = json.dumps(network.attributes_dict())
data['nodes'] = add_new(data['nodes'], nodes)
data['edges'] = add_new(data['edges'], edges)
current_app.redis.mset({network_id: json.dumps(data)})
current_app.redis.expire(network_id, 5 * 60)
return result
def node_info():
if 'node' in request.form:
node = str(request.form['node'])
else:
result = {'name': 'error',
'type': 'error',
'data': {},
'html': ''}
return jsonify(result=result)
try:
task_id = request.form['task_id']
data = json.loads(current_app.redis.get(task_id))
graph_dict = json.loads(data['graph_dict'])
attr_dict = json.loads(data['attr_dict'])
target_smiles = data['target_smiles']
network_options = json.loads(data['network_options'])
graph = nx.from_dict_of_lists(graph_dict, create_using=nx.DiGraph)
network = Network(graph=graph, target_smiles=target_smiles)
network.settings = network_options
network.add_attributes(attr_dict)
network.get_node_types()
if node in network.substrate_nodes:
result = get_substrate_info(node)
elif node in network.reaction_nodes:
if 'retrorule' not in network.graph.nodes[node]['attributes']:
result = get_reaction_info(node, network)
else:
result = get_retrorule_info(node, network)
else:
print('Error node not in substrates or reactions')
result = {'name': 'error',
'type': 'error',
'data' : {},
'html' : ''}
return jsonify(result=result)
except:
result = {'name': 'error',
'type': 'error',
'data': {},
'html': ''}
return jsonify(result=result)
def task_reorder_pathways(weights, pathways_id):
job = get_current_job()
job.meta['progress'] = 'started'
job.save_meta()
pathway_settings = json.loads(
current_app.redis.get(pathways_id + '__pathway_settings'))
pathway_settings.update({
'weight_num_enzymes': weights[0],
'weight_complexity': weights[1],
'weight_starting': weights[2],
'weight_known_enzymes': weights[3],
'weight_diversity': weights[4]
})
current_app.redis.mset(
{f"{pathways_id}__pathway_settings": json.dumps(pathway_settings)})
current_app.redis.expire(pathways_id, 60 * 60)
network_data = json.loads(current_app.redis.get(pathways_id + '__network'))
graph = nx.from_dict_of_lists(json.loads(network_data['graph_dict']),
create_using=nx.DiGraph)
network = Network(graph=graph,
target_smiles=network_data['target_smiles'],
print_log=not current_app.config['PRODUCTION'])
network.update_settings(json.loads(network_data['network_options']))
network.add_attributes(json.loads(network_data['attr_dict']))
all_pathways_nodes, all_scores = json.loads(
current_app.redis.get(f"{pathways_id}__all_pathways"))
pathways = load_pathways(all_pathways_nodes, all_scores, network)
pathway_evaluator = evaluate_pathways(pathways, weights)
print(weights)
package_evaluated_pathways(pathway_evaluator.df, pathways_id)
package_visjs_pathways(pathways_id)
job = get_current_job()
job.meta['progress'] = 'complete'
job.save_meta()
result = {}
return result
def get_visjs_pathway(task_id, pathway_id, varient):
network_data = json.loads(current_app.redis.get(task_id + '__network'))
pathway_data = json.loads(
current_app.redis.get(task_id + f'__{pathway_id}'))
pathway_nodes = pathway_data[varient - 1]
graph = nx.from_dict_of_lists(json.loads(network_data['graph_dict']),
create_using=nx.DiGraph)
network = Network(graph=graph,
target_smiles=network_data['target_smiles'],
print_log=not current_app.config['PRODUCTION'])
network.update_settings(json.loads(network_data['network_options']))
network.add_attributes(json.loads(network_data['attr_dict']))
pathway = Pathway(pathway_nodes, network, calc_scores=False)
nodes, edges = pathway.get_visjs_nodes_and_edges()
max_var = len(pathway_data)
return nodes, edges, max_var
def custom_reaction():
product_smiles = str(request.form['product'])
substrate_smiles = str(request.form['substrate'])
reaction_name = str(request.form['name'])
task_id = request.form['task_id']
data = json.loads(current_app.redis.get(task_id))
graph_dict = json.loads(data['graph_dict'])
attr_dict = json.loads(data['attr_dict'])
target_smiles = data['target_smiles']
network_options = json.loads(data['network_options'])
graph = nx.from_dict_of_lists(graph_dict, create_using=nx.DiGraph)
network = Network(graph=graph, target_smiles=target_smiles)
network.update_settings(network_options)
network.add_attributes(attr_dict)
new_substrate_nodes, new_reaction_nodes = network.custom_reaction(
product_smiles, substrate_smiles, reaction_name)
all_new_nodes = new_substrate_nodes + new_reaction_nodes
subgraph = network.graph.subgraph(all_new_nodes)
nodes, edges = network.get_visjs_nodes_and_edges(graph=subgraph)
result = {
'nodes': nodes,
'edges': edges,
}
data['graph_dict'] = json.dumps(nx.to_dict_of_lists(network.graph))
data['attr_dict'] = json.dumps(network.attributes_dict())
nodes = add_new(data['nodes'], nodes)
edges = add_new(data['edges'], edges)
data['nodes'] = nodes
data['edges'] = edges
current_app.redis.mset({task_id: json.dumps(data)})
current_app.redis.expire(task_id, 5 * 60)
return jsonify(result=result)
