#!/bin/awk
# Awk script to assign unique serial atom names to MOL2 files

BEGIN {
  ATOMSECTION="FALSE" 
} 

{

  if ( $0 ~ /@<TRIPOS>BOND/ ) { ATOMSECTION="FALSE" }

  if ( ATOMSECTION=="TRUE" && $2 ~ /[A..Z]*[a..z]*/ ) {
    atomname=$2; 

    # If this is the first time seeing "atomname", set count to 1
    if ( !(atomname in atomcount) )
    { 
      atomcount[atomname] = 1; 
    }

    # Create new atom name by concatenating atom name and number, e.g. C4 or S1
    $2 = (atomname atomcount[atomname])

    ++atomcount[atomname];
    printf("%2i   %3s     % 8.5f   % 8.5f   % 8.5f  %3s  \n", $1, $2, $3, $4, $5, $6)
  }
  else {
    print $0
  }

  if ( $0 ~ /@<TRIPOS>ATOM/ ) { ATOMSECTION="TRUE" }
}