#!/usr/bin/env python

#######################################################################
# Script to add the missing substructure fields to MOL2 format files  #
# Usage:  python fix_substructure.py  inputfile.mol2  outputfile.mol2 #
# Demetri Moustakas  7/15/2002                                        #
#######################################################################

import sys
import string

fin = open(sys.argv[1],"r")
fout = open(sys.argv[2], "w")

line = " "

while line:
  line = fin.readline()

  if line == "@<TRIPOS>MOLECULE\n":
   fout.write(line)
   line = fin.readline()
   fout.write(line)
   temp_line = fin.readline()
   num_bonds = string.atoi(string.split(temp_line)[1])
   line = ""
   line = line + " " + string.split(temp_line)[0] + " " + string.split(temp_line)[1]
   line = line + " 1 " + string.split(temp_line)[3] + " " + string.split(temp_line)[4] + "\n"
   fout.write(line)
  elif line == "@<TRIPOS>BOND\n":
   fout.write(line)
   for i in range(num_bonds):
    line = fin.readline()
    fout.write(line)
   fout.write("@<TRIPOS>SUBSTRUCTURE\n")
   fout.write("1   ****   1     TEMP       0   ****  ****\n")
  else:
   fout.write(line)


fin.close()
fout.close()