pdb_file = open(sys.argv[2], 'r') #input file
out_file_protein = open(sys.argv[4], 'w') #output file
out_file_ligand = open(sys.argv[6], 'w')
pdb_code = str(sys.argv[2])[:-4] #changed to -4 by RB 13/07/10
out_file_cofactor = open(pdb_code + '_hetero.pdb', 'w')
out_file_protein_cofactor = open(
pdb_code + '_volume.pdb', 'w') # for contact area calculation with sybyl
db = str(sys.argv[8])
tb = str(sys.argv[10])
us = str(sys.argv[12])
pw = str(sys.argv[14])
wantedpacode = str(sys.argv[15]) # Added 02/07/2012 - Aurijit Sarkar
wantedpdb = str(sys.argv[16])
wantedlig = str(sys.argv[17])
conn = mysql.connect2server(pw, us, db)
cursor = conn.cursor()
#db = 'dataset_0709'
command = "select lig, cof, metal from " + tb + " where id = '" + wantedpdb + "' and pacode = '" + wantedpacode + "' and lig = '" + wantedlig + "' limit 1"
print command
cursor.execute(command)
rows = cursor.fetchall()
ligand = rows[0][0]
print ligand
cofactor = str(rows[0][1])
print cofactor
metal = str(rows[0][2])
print metal
#HETATM 4666 ZN ZN A 701 43.821 38.240 46.712 1.00 25.11 ZN
os.chdir(curr_dir)
files = os.listdir('./')
files.sort()
path = os.path.abspath(os.path.curdir)
for file_ in files:
if file_[-4:] == '.pdb':
os.chdir(path)
pdb_code = file_[:-4]
os.chdir(pdb_code) # cd in new directory and do docking stuff
newpath = os.path.abspath(os.path.curdir)
# Connect to the MySQL database
conn = mysql.connect2server(pword, uname, db)
cursor = conn.cursor()
# Get the name of the cofactor
command = "select lig, cof, metal from " + tb + " where id = '" + wantedpdb + "' and pacode = '" + pacode + "' and lig = '" + wantedlig + "' limit 1"
cursor.execute(command)
rows = cursor.fetchall()
conn.close()
cursor.close()
ligand = rows[0][0]
cofactor = str(rows[0][1])
metal = str(rows[0][2])
prediction = 'less_druggable' elif score > 0.59: prediction = 'druggable' # Upload descriptors into new format table db = str(sys.argv[4]) # Database tb = str(sys.argv[5]) # Table dt = str(sys.argv[6]) # Descriptor Table us = str(sys.argv[7]) # Username pw = str(sys.argv[8]) # Password wantedpacode = str(sys.argv[10]) # PA code for Pseudomonas protein wantedpdb = str(sys.argv[11]) # 4 letter code for PDB wantedlig = str(sys.argv[12]) # 3 letter code for ligand bound to protein conn=mysql.connect2server(pw, us, db) cursor = conn.cursor () command = "Select * from "+ dt +" where id = '" + wantedpdb +"' and pacode = '" + wantedpacode + "' and lig = '" + wantedlig + "'" cursor.execute(command) label_exists = cursor.fetchall() if len(label_exists) > 0: command = "UPDATE " + dt + " SET csa = " + str(csa) + " WHERE id = '" + wantedpdb +"' and pacode = '" + wantedpacode + "' and lig = '" + wantedlig + "'" cursor.execute(command) command = "UPDATE " + dt + " SET hsa_t = " + str(hsa_t) + " WHERE id = '" + wantedpdb +"' and pacode = '" + wantedpacode + "' and lig = '" + wantedlig + "'" cursor.execute(command) command = "UPDATE " + dt + " SET psa_r = " + str(psa_r) + " WHERE id = '" + wantedpdb +"' and pacode = '" + wantedpacode + "' and lig = '" + wantedlig + "'"
os.chdir(curr_dir)
files = os.listdir('./')
files.sort()
path = os.path.abspath(os.path.curdir)
for file_ in files:
if file_[-4:] == '.pdb':
os.chdir(path)
pdb_code = file_[:-4]
os.chdir(pdb_code) # cd in new directory and do docking stuff
newpath = os.path.abspath(os.path.curdir)
# Connect to the MySQL database
conn=mysql.connect2server(pword, uname, db)
cursor = conn.cursor ()
# Get the name of the cofactor
command = "select lig, cof, metal from "+tb+" where id = '" + wantedpdb +"' and pacode = '" + pacode + "' and lig = '" + wantedlig + "' limit 1"
cursor.execute(command)
rows = cursor.fetchall ()
conn.close()
cursor.close()
ligand = rows[0][0]
cofactor = str(rows[0][1])
metal = str(rows[0][2])
