1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
|
"""
Flask Documentation: http://flask.pocoo.org/docs/
Jinja2 Documentation: http://jinja.pocoo.org/2/documentation/
Werkzeug Documentation: http://werkzeug.pocoo.org/documentation/
"""
import os
from app import app
from flask import render_template, request, flash
from werkzeug.utils import secure_filename
from random import choice, shuffle
from string import digits, ascii_lowercase
# Note: that when using Flask-WTF we need to import the Form Class that we created
# in forms.py
from .forms import MyForm, curieForm, statusForm, generateSMILES
def gen_word(N, min_N_dig, min_N_low):
choose_from = [digits]*min_N_dig + [ascii_lowercase]*min_N_low
choose_from.extend([digits + ascii_lowercase] * (N-min_N_low-min_N_dig))
chars = [choice(bet) for bet in choose_from]
shuffle(chars)
return ''.join(chars)
def convertToBinaryData(filename):
# Convert digital data to binary format
with open(filename, 'rb') as file:
binaryData = file.read()
return binaryData
###
# Routing for your application.
###
@app.route('/')
def home():
"""Render website's home page."""
return render_template('home.html')
@app.route('/About')
def about():
"""Render about page."""
return render_template('about.html')
@app.route('/Visualise')
def visualise():
"""Render visualisation page."""
return render_template('visualise.html')
@app.route('/Status',methods=['GET','POST'])
def status():
taskStatusForm = statusForm()
if request.method == 'POST':
if taskStatusForm.validate_on_submit():
jobID = taskStatusForm.jobID.data
import mysql.connector as con
mycon = con.connect(host=app.config['DB_HOST'],user=app.config['DB_USER'],password=app.config['DB_PASSWORD'],port=app.config['DB_PORT'],database=app.config['DB_NAME'])
mycursor = mycon.cursor()
sqlQuery = 'select id, protein_name, ligand_name, date, description, done from curieweb where id="%s"' % (jobID)
mycursor.execute(sqlQuery)
records = mycursor.fetchall()
if records == []:
return render_template('job_status_error.html',job=jobID)
r = records[0]
protein_name = r[1]
ligand_name = r[2]
date = r[3]
description = r[4]
done = r[5]
if done==1:
done="Completed"
elif done==0:
done="Queued"
return render_template('job_status.html',ID=jobID,pn=protein_name,ln=ligand_name,subDate=date,desc=description,status=done)
flash_errors(taskStatusForm)
return render_template('job_status_form.html',form=taskStatusForm)
@app.route('/basic-form', methods=['GET', 'POST'])
def basic_form():
if request.method == 'POST':
firstname = request.form['firstname']
lastname = request.form['lastname']
email = request.form['email']
return render_template('result.html',
firstname=firstname,
lastname=lastname,
email=email)
return render_template('form.html')
@app.route('/wtform', methods=['GET', 'POST'])
def wtform():
myform = MyForm()
if request.method == 'POST':
if myform.validate_on_submit():
# Note the difference when retrieving form data using Flask-WTF
# Here we use myform.firstname.data instead of request.form['firstname']
firstname = myform.firstname.data
lastname = myform.lastname.data
email = myform.email.data
flash('You have successfully filled out the form', 'success')
return render_template('result.html', firstname=firstname, lastname=lastname, email=email)
flash_errors(myform)
return render_template('wtform.html', form=myform)
tfWorking = -1
try:
import tensorflow as tf
tfWorking = 1
except:
print("Could not load tensorflow model :/")
tfWorking = 0
if tfWorking == 1:
from lstm_chem.utils.config import process_config
from lstm_chem.model import LSTMChem
from lstm_chem.generator import LSTMChemGenerator
config = process_config("app/prod/config.json")
modeler = LSTMChem(config, session="generate")
gen = LSTMChemGenerator(modeler)
print("Testing Model")
gen.sample(1)
@app.route('/Generate', methods=['GET','POST'])
def generate():
"""Generate novel drugs"""
form = generateSMILES()
with open("./app/prod/config.json") as config:
import json
j = json.loads(config.read())
print("Model Name:", j["exp_name"])
if request.method == 'POST' and form.validate_on_submit():
result = gen.sample(form.n.data)
print(tfWorking)
if tfWorking == 0:
flash("Failed to initialise the model!","danger")
else:
return render_template('generate.html',expName=j["exp_name"],epochs=j["num_epochs"],optimizer=j["optimizer"].capitalize(), form=form,result=result)
return render_template('generate.html',expName=j["exp_name"],epochs=j["num_epochs"],optimizer=j["optimizer"].capitalize(), form=form)
@app.route('/Dock', methods=['GET', 'POST'])
def dock_upload():
form = curieForm()
if request.method == 'POST' and form.validate_on_submit():
print("Recieved task: ",form.description.data)
description = form.description.data
target = form.target.data
ligand = form.ligand.data
cx,cy,cz = str(form.center_x.data), str(form.center_y.data), str(form.center_z.data)
sx,sy,sz = str(form.size_x.data), str(form.size_y.data), str(form.size_z.data)
email = form.email.data
import mysql.connector as con
mycon = con.connect(host=app.config['DB_HOST'],user=app.config['DB_USER'],password=app.config['DB_PASSWORD'],port=app.config['DB_PORT'],database=app.config['DB_NAME'])
mycursor = mycon.cursor()
import tempfile
with tempfile.TemporaryDirectory() as directory:
os.chdir(directory)
target.save(secure_filename(target.filename))
ligand.save(secure_filename(ligand.filename))
buffer = "center_x="+cx+"\ncenter_y="+cy+"\ncenter_z="+cz+"\nsize_x="+sx+"\nsize_y="+sy+"\nsize_z="+sz
with open("config.txt","w") as f:
f.write(buffer)
ligandB = convertToBinaryData(secure_filename(ligand.filename))
receptor = convertToBinaryData(secure_filename(target.filename))
config = convertToBinaryData("config.txt")
ligandName = secure_filename(ligand.filename)
receptorName = secure_filename(target.filename)
sqlQuery = "insert into curieweb (id, email, protein, protein_name, ligand_pdbqt, ligand_name,date, description, config) values (%s,%s,%s,%s,%s,%s,CURDATE(),%s,%s) "
jobID = gen_word(16, 1, 1)
print("Submitted JobID: ",jobID)
insert_tuple = (jobID,email,receptor,receptorName,ligandB,ligandName,description,config)
mycursor.execute(sqlQuery,insert_tuple)
mycon.commit()
print("Description",description)
return render_template('display_result.html', filename="OwO", description=description,job=jobID)
flash_errors(form)
return render_template('dock_upload.html', form=form)
###
# The functions below should be applicable to all Flask apps.
###
# Flash errors from the form if validation fails
def flash_errors(form):
for field, errors in form.errors.items():
for error in errors:
flash(u"Error in the %s field - %s" % (
getattr(form, field).label.text,
error
), 'danger')
@app.route('/<file_name>.txt')
def send_text_file(file_name):
"""Send your static text file."""
file_dot_text = file_name + '.txt'
return app.send_static_file(file_dot_text)
@app.after_request
def add_header(response):
"""
Add headers to both force latest IE rendering engine or Chrome Frame,
and also to cache the rendered page for 10 minutes.
"""
response.headers['X-UA-Compatible'] = 'IE=Edge,chrome=1'
response.headers['Cache-Control'] = 'public, max-age=0'
return response
@app.errorhandler(404)
def page_not_found(error):
"""Custom 404 page."""
return render_template('404.html'), 404
if __name__ == '__main__':
app.run(debug=True, host="0.0.0.0", port="8080")
|
