Make Every internal degree in Z-matrix a variable

ModifZmat.py

import pandas as pd
import numpy as np
import os
import sys

fname = sys.argv[1]

def ZmatRead(filename='OPLS_TMA.z'):
    zmat_part = []
    add_bonds = []
    for line in open(filename).readlines():
        if 'Geometry Variations follow' in line: break
        zmat_part.append(line)
    rline = False
    for line in open(filename).readlines():
        if 'Additional Bonds follow' in line: rline =True  
        elif 'Harmonic Constraints follow' in line: break  
        if rline: add_bonds.append(line)
    add_bonds = add_bonds[1:]
    return(zmat_part,add_bonds)

def PrinNewZmat(zmat,abonds,fname): 
    ofile = open('NEW_'+fname,'w')
    for line in zmat:   ofile.write('%s'%line) 
    ofile.write('''                    Geometry Variations
                    Variable Bonds follow         (I4)''')
    ofile.write('\n0004-%04d\n'%(len(zmat)-1))
    ofile.write('                    Additional Bonds follow       (2I4)\n')
    for line in abonds: ofile.write('%s'%line)
    ofile.write('''
                    Variable Bond Angles follow   (I4)
0005-%04d
                    Additional Bond Angles follow (3I4)
AUTO
                    Variable Dihedrals follow     (3I4,F12.6)
0006-%04d
                    Additional Dihedrals follow   (6I4)
AUTO
                    Domain Definitions follow     (4I4)
                    Final blank line'''%(len(zmat)-1,len(zmat)-1))
    ofile.close() 
    return None
zmat, abonds  = ZmatRead(fname)
PrinNewZmat(zmat,abonds,fname)
#print(len(zmat),len(abonds))
#print(ZmatRead(fname))