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])