from sys import argv
import argparse

script,infile,outfile, reference = argv
Ter = []
res = []


def get_Ter(reference):
    reference_1 = open(reference,"r")
    for line in reference_1:
        contents = line.split(" ")
        if contents[0] == "TER":
        resnum = line[22:27]
        resname = line[17:20]
        chain = line[21]
        Ter.append(resnum)

        def find_TER(infile,outfile):
            with open(infile, "r") as infile_1:
                content = infile_1.readlines()
            with open(outfile, "w+") as outfile_1:
                outfile_1.write(content)
                if line[0:6] == "ATOM  ":
                    resnum_1 = line[22:27]
                    res.append(resnum_1)
                    if resnum_1 in res == resnum in Ter:
                        outfile_1.write(line + "nTER")

        find_TER(infile,outfile)
get_Ter(reference)