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
|
import mysql.connector as con
import configparser
iniConfig = configparser.ConfigParser()
iniConfig.read('config.ini')
try:
iniConfig['DATABASE']
except KeyError:
iniConfig.read("../config.ini")
mycon = con.connect(host=iniConfig['DATABASE']['HOST'],user=iniConfig['DATABASE']['USER'],password=iniConfig['DATABASE']['PASSWORD'],port=iniConfig['DATABASE']['PORT'],database=iniConfig['DATABASE']['NAME'])
mycursor = mycon.cursor()
sql_select_Query = "select * from curieweb where done=0 LIMIT 1"
mycursor.execute(sql_select_Query)
records = mycursor.fetchall()
if records == []:
print("Empty Set 😳")
print("No active task, exitting gracefully")
exit(0)
def email(zipArchive):
import smtplib
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from email.mime.base import MIMEBase
from email import encoders
fromaddr = iniConfig['SMTP']['EMAIL']
toaddr = toEmail
msg = MIMEMultipart()
msg['From'] = fromaddr
msg['To'] = toaddr
msg['Subject'] = "Curie Web Results for Job ID " + str(jobID)
body = "Attached Zip contains the docked files, PLIP report and PyMOL Visualisations. If the ZIP file does not contain these files, please report this issue by replying to this email. Job was submitted on {} with the description {}".format(date, description)
msg.attach(MIMEText(body, 'plain'))
filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
p = MIMEBase('application', 'octet-stream')
with open((str(zipArchive) + ".zip"), "rb") as attachment:
p.set_payload((attachment).read())
encoders.encode_base64(p)
p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p)
s = smtplib.SMTP(iniConfig['SMTP']['SERVER'], iniConfig['SMTP']['PORT'])
s.starttls()
s.login(fromaddr, iniConfig['SMTP']['PASSWORD'])
text = msg.as_string()
s.sendmail(fromaddr, toaddr, text)
s.quit()
def get3DModel(protein,ligand):
try:
import pymol2
except ImportError:
print("🤭 PyMOL 2 has not been installed correctly")
return None
session = pymol2.PyMOL()
session.start()
cmd = session.cmd
cmd.load(protein,"target")
cmd.load(ligand,"ligand")
cmd.save("model.dae")
session.stop()
def CopyContentOfFolder(sauce,destination):
src_files = os.listdir(sauce)
for file_name in src_files:
full_file_name = os.path.join(sauce, file_name)
if os.path.isfile(full_file_name):
copy(full_file_name, destination)
def RemoveAllFilesMatching(directory,pattern):
print(directory+"/*"+pattern)
FileList = glob.glob(directory+"/*"+pattern)
for FilePath in FileList:
try:
os.remove(FilePath)
except:
print("Error in removing misc file")
receptor_name = "protein.pdbqt"
ligand_name = "ligand.pdbqt"
description = "Curie Web Task"
#print(records[0])
r = records[0]
jobID = r[0]
toEmail = r[1]
targetB = r[2]
if r[3] is not None:
receptor_name = str(r[3])
if r[6] is not None:
ligand_name = str(r[6])
ligandB = r[4]
configB = r[7]
date = r[8]
if r[9] is not None:
description = r[9]
import os,glob
cd = os.getcwd()
f = os.path.join(cd,"static/uploads")
reportDirectory = os.path.join(f,"reports")
scripts = os.path.join(cd,"scripts")
modelDirectory = os.path.join(f,"3DModels")
#t = os.path.join(f,"receptor",target)
#r = os.path.join(f,"ligands",ligand)
#c = os.path.join(f,"configs",config)
print(f)
import tempfile
from shutil import make_archive, copyfile,copy
with tempfile.TemporaryDirectory() as directory:
print('The created temporary directory is %s' % directory)
os.chdir(directory)
with open(receptor_name,"wb") as file:
file.write(targetB)
with open(ligand_name,"wb") as file:
file.write(ligandB)
with open("config.txt","wb") as file:
file.write(configB)
# Legacy Docker Curie-Cli Run
#os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
CopyContentOfFolder(scripts,directory)
os.system("./main.sh -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
RemoveAllFilesMatching(directory,".py")
RemoveAllFilesMatching(directory,".sh")
z = "Curie_Web_Result_"+str(jobID)
zi = os.path.join(f,z)
make_archive(zi, 'zip', directory)
copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf")))
get3DModel(receptor_name,ligand_name.replace(".pdbqt","_out.pdbqt"))
os.system("collada2gltf -i model.dae -o model.gltf")
try:
copyfile("model.gltf",os.path.join(modelDirectory,(str(jobID)+".gltf")))
except:
print("Does not have Collada2GLTF Installed")
email(zi)
mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
mycon.commit()
exit(0)
arch = os.popen("uname -m").read()
print("Generating 3D Model")
if "x86" in arch:
os.system("docker run -it --rm -v $(pwd):/usr/app leon/usd-from-gltf:latest model.gltf model.usdz")
elif "aarch64" in arch:
os.system("docker run -it --rm -v $(pwd):/usr/app navanchauhan/usd-from-gltf:latest model.gltf model.usdz")
try:
copyfile("model.usdz",os.path.join(modelDirectory,(str(jobID)+".usdz")))
except:
print("Could not generate USDZ file")
email(zi)
mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
mycon.commit()
|
