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authorNavan Chauhan <navanchauhan@gmail.com>2020-09-11 18:37:16 +0530
committerNavan Chauhan <navanchauhan@gmail.com>2020-09-11 18:37:16 +0530
commitd55ef146e83a5a975cecc67183781eed25858242 (patch)
tree08248846eb8dee63099e0000d6a974bf8edd77ff
parent7381e25ef4bb2e9363f61f31712a2d5cbacf4d60 (diff)
fixed variable name clash
-rw-r--r--app/dock-single.py18
-rw-r--r--app/dock_docker.py16
2 files changed, 18 insertions, 16 deletions
diff --git a/app/dock-single.py b/app/dock-single.py
index daf920c..e9ef9b2 100644
--- a/app/dock-single.py
+++ b/app/dock-single.py
@@ -9,15 +9,15 @@ from collections import namedtuple
import mysql.connector as con
import configparser
-config = configparser.ConfigParser()
-config.read('config.ini')
+iniConfig = configparser.ConfigParser()
+iniConfig.read('config.ini')
try:
- config['DATABASE']
+ iniConfig['DATABASE']
except KeyError:
- config.read("../config.ini")
+ iniConfig.read("../config.ini")
-mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
+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 id,email,pdb,ligand_smile,ligand_name,description,date FROM curieweb WHERE pdb IS NOT NULL AND done=0 LIMIT 1"
@@ -183,7 +183,7 @@ def email(zipArchive):
from email.mime.base import MIMEBase
from email import encoders
- fromaddr = config['SMTP']['EMAIL']
+ fromaddr = iniConfig['SMTP']['EMAIL']
msg = MIMEMultipart()
msg['From'] = fromaddr
@@ -200,9 +200,9 @@ def email(zipArchive):
p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p)
- s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT'])
+ s = smtplib.SMTP(iniConfig['SMTP']['SERVER'], iniConfig['SMTP']['PORT'])
s.starttls()
- s.login(fromaddr, config['SMTP']['PASSWORD'])
+ s.login(fromaddr, iniConfig['SMTP']['PASSWORD'])
text = msg.as_string()
s.sendmail(fromaddr, toaddr, text)
@@ -245,6 +245,8 @@ with tempfile.TemporaryDirectory() as directory:
with open("config.txt","w") as file:
file.write(configuration)
os.system('obabel -:"%s" --gen3d -opdbqt -O%s.pdbqt' % (records[3],records[4]))
+ print("Ligand:",records[4])
+ print(str(records[4]+".pdbqt"))
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" % (pdbqt,str(records[4]+".pdbqt")))
z = "Curie_Web_Result_"+str(jobID)
zi = os.path.join(f,z)
diff --git a/app/dock_docker.py b/app/dock_docker.py
index bd6f053..712e725 100644
--- a/app/dock_docker.py
+++ b/app/dock_docker.py
@@ -1,15 +1,15 @@
import mysql.connector as con
import configparser
-config = configparser.ConfigParser()
-config.read('config.ini')
+iniConfig = configparser.ConfigParser()
+iniConfig.read('config.ini')
try:
- config['DATABASE']
+ iniConfig['DATABASE']
except KeyError:
- config.read("../config.ini")
+ iniConfig.read("../config.ini")
-mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
+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"
@@ -28,7 +28,7 @@ def email(zipArchive):
from email.mime.base import MIMEBase
from email import encoders
- fromaddr = config['SMTP']['EMAIL']
+ fromaddr = iniConfig['SMTP']['EMAIL']
toaddr = toEmail
msg = MIMEMultipart()
@@ -46,9 +46,9 @@ def email(zipArchive):
p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p)
- s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT'])
+ s = smtplib.SMTP(iniConfig['SMTP']['SERVER'], iniConfig['SMTP']['PORT'])
s.starttls()
- s.login(fromaddr, config['SMTP']['PASSWORD'])
+ s.login(fromaddr, iniConfig['SMTP']['PASSWORD'])
text = msg.as_string()
s.sendmail(fromaddr, toaddr, text)