multiple_threads_foldx_positionscan.py

import argparse

parser = argparse.ArgumentParser(description=
                                 'To run Foldx PositionScan with multiple threads, make sure' +
                                 ' that you have the foldx and your pdb in the same floder')
parser.add_argument("-s", '--pdbfile', help="The pdb file, the repiared one")
parser.add_argument("-nt", '--number_threads', help="How many threads to run the Foldx")
args = parser.parse_args()

pdbname = args.pdbfile
nt = args.number_threads

# nt = 20
# pdbname="6QG9_A_Repair.pdb"
import os

try:
    file = open("SO_" + pdbname.replace("pdb", "fxout"), "r")
except FileNotFoundError:
    os.system("./foldx --command=SequenceOnly --pdb=" + pdbname)
    file = open("SO_" + pdbname.replace("pdb", "fxout"), "r")
lst = []
for line in file:
    l = line.replace("\n", "").split("\t")
    if len(l) > 3:
        lst.append(l[3] + "a")

t = len(lst) // (int(nt) - 1)
n = 0
for i in range(0, len(lst), t):
    b = lst[i:i + t]
    l = ""
    for x in b:
        l = l + x + ","
    n = n + 1
    o = "command=PositionScan\npdb=" + pdbname + "\npositions=" + l
    of_name = "PS_" + str(n) + ".cfg"
    of = open(of_name, "w+")
    of = open(of_name, "a+")
    print(o[:-1], file=of)
    os.system("nohup ./foldx -f " + of_name + " &")