#!/usr/local/bin/nawk -f
# substitute numbers for atom names

# read carfile and generate associative array to map atom names to numbers
function atom_number_array(carfile,array,   nr,offset){
	# read carfile
	nr = 0
	offset = 1
	while ( getline <carfile == 1){
		++nr
		# subtract offset from line number of lines corresponding to atoms (header)
		if ( NF != 9 ||
			$2 !~ /^-?[0-9][0-9]*\.[0-9][0-9]*(E-?[0-9][0-9]*)?$/ ||
			$3 !~ /^-?[0-9][0-9]*\.[0-9][0-9]*(E-?[0-9][0-9]*)?$/ ||
			$4 !~ /^-?[0-9][0-9]*\.[0-9][0-9]*(E-?[0-9][0-9]*)?$/ ) ++offset
		else array[$6 ":" $1] = nr-offset
	}
	close(carfile)
}


BEGIN{
	if ( FILENAME == "-" || c == "" ) {
		print "usage: name2number.awk [-v] c=<car-file> <name-file>"
		exit
	}
	atom_number_array(c,numberarray)
}
{
	for ( i=1 ; i<= NF ; ++i ) 
		if ( $i in numberarray )
			$i = numberarray[$i]
	print
}