how to merge two files using python

Question

I want to merge two files. The code should sum the second line of both files (input1.txt and input2.txt), write to a file (final.txt) the result of that summation, append all lines starting with "1MOL" in the input2.txt to the final.txt, and finally append all lines (except first two lines) in the input1.txt to the final.txt. My code only writes "18" (the sum of the second lines in both input files) to the final.txt. How can I fix my code?

input1.txt

Molecule in solvent
13
    1MET      N    1   4.761   6.470   2.128
    1MET     H1    2   4.749   6.567   2.153
    1MET     H2    3   4.833   6.430   2.184
    1MET     H3    4   4.785   6.464   2.031
    1MET     CA    5   4.636   6.399   2.152
    1MET     HA    6   4.567   6.442   2.093
    1MET     CB    7   4.651   6.250   2.113
    1MET    HB1    8   4.730   6.213   2.162
    1MET    HB2    9   4.667   6.244   2.015
    1MET     CG   10   4.530   6.163   2.147
    1MET    HG1   11   4.452   6.219   2.119
    1MET    HG2   12   4.532   6.156   2.247
    1MET     SD   13   4.524   5.998   2.070
 spc.itp

input2.txt:

Gallium Rubidium
   5
    1MOL     CL    1   2.131   2.473   6.188
    1MOL      P    2   1.714   2.422   6.273
    1MOL      O    3   1.839   2.324   6.306
    1MOL      O    4   1.783   2.542   6.188
    1MOL      O    5   1.682   2.491   6.416

My code:

search_string = 'MOL'
    #read the first input file
    with open("input1.txt", mode="r") as f1:
    #open a file to merge two files
        with open("final.txt", mode="a") as f: 
            #skip the first line of the input1.txt
            line=f1.readlines()
            #take the second line of input1.txt
            a=float(line[1])
            #read the second input file
            with open("input2.txt", mode="r") as f2:
                f2lines=f2.readlines()
                b=float(f2lines[1])
                result=float(a+b)
                f.write("%.f\n" % result)
                for f2lines in f2:
                if search_string in f2lines:
                    f.write(f2lines)

Desired final.txt:

18
    1MOL     CL    1   2.131   2.473   6.188
    1MOL      P    2   1.714   2.422   6.273
    1MOL      O    3   1.839   2.324   6.306
    1MOL      O    4   1.783   2.542   6.188
    1MOL      O    5   1.682   2.491   6.416
    1MET      N    1   4.761   6.470   2.128
    1MET     H1    2   4.749   6.567   2.153
    1MET     H2    3   4.833   6.430   2.184
    1MET     H3    4   4.785   6.464   2.031
    1MET     CA    5   4.636   6.399   2.152
    1MET     HA    6   4.567   6.442   2.093
    1MET     CB    7   4.651   6.250   2.113
    1MET    HB1    8   4.730   6.213   2.162
    1MET    HB2    9   4.667   6.244   2.015
    1MET     CG   10   4.530   6.163   2.147
    1MET    HG1   11   4.452   6.219   2.119
    1MET    HG2   12   4.532   6.156   2.247
    1MET     SD   13   4.524   5.998   2.070
 spc.itp

Answer 1

f2lines=f2.readlines() read all lines from f2. Then for f2lines in f2: will get nothing. Change for f2lines in f2: loop to

for f2line in f2lines:
    if search_string in f2line:
        f.write(f2line)

And you forget to append lines in line to final file. You need another for loop to do this:

for i in xrange(2, len(line)):
    f.write(line[i])

The code is:

search_string = 'MOL'
#read the first input file    
with open("input1.txt", mode="r") as f1:
    #open a file to merge two files
    with open("final.txt", mode="w") as f: 
        #skip the first line of the input1.txt
        line=f1.readlines()
        #take the second line of input1.txt
        a=float(line[1])
        #read the second input file
        with open("input2.txt", mode="r") as f2:
            f2lines=f2.readlines()
            b=float(f2lines[1])
            result=float(a+b)
            f.write("%.f\n" % result)
            for f2line in f2lines:
                if search_string in f2line:
                    f.write(f2line)
            for i in xrange(2,len(line)):
                f.write(line[i])