#!/usr/bin/perl
# the above is the standard linux/unix path for perl: change if your computer is nonstandard

sub print_help{
    print STDERR <<EOF;

Syntax:  xyz_1atom [options] file.xyz

keep or color a single atom from a xyz file
options:
	-i or -a select the atom index (default = $index)
	-c just color the selected atom, keep them all
						version 26/11/2021 by Nick
EOF
    return;
}

$BIG=9.999e200;

# defaults:
$color=0;
$index=1;
$filename="-";

while($p=shift(@ARGV)){
    if($p=~/^[^\-]/){ # all command line options start with "-", otherwise it a filename
	$filename=$p;
	next;
    }
    if($p eq "-a" || $p eq "-i"){
        $index=shift(@ARGV)+0;
        $index>0 or die "Invalid index $index\n";
        next;
    }
    if($p eq "-c"){ # color atom and print them all
	$color=1;
        next;
    }
    if($p eq "-h"){ # help
	print_help;
	die "\n";
    }
    print_help;
    die "invalid option $p\n";
}


$count=-1;
$actualframes=0;

open(INPUT,"$filename") || die "Cannot open $filename\n";

while(<INPUT>){
    s/^\s*//; @li = split('\s+');
    if($#li==0 && $li[0]+0==$li[0]){
	$count++;
	$natms = $li[0];
	$index <= $natms or die "index $index is not compatible with this xyz file, with $natms atoms only\n";
	$_=<INPUT>;
	$comment=$_;
	s/^\s*//; @li = split('\s+');
	$time=$li[1]+0.;
	if($time<=0){
	    $time=$count;
	}
	if($color){
	    print $natms."\n";
	    print $comment;
	    for($i=1;$i<=$natms;$i++){
		$_=<INPUT>;
		if($i == $index){
		    s/^\s*//; @li = split('\s+');
		    print "O","\t",$li[1],"\t",$li[2],"\t",$li[3],"\n",
		}
		else{
		    print;
		}
	    }
	}
	else{
	    for($i=1;$i<=$natms;$i++){
		$_=<INPUT>;
		if($i == $index){
		    s/^\s*//; @li = split('\s+');
		    print $time,"\t",$li[1],"\t",$li[2],"\t",$li[3],"\t",$li[0],"\n",
		}
	    }
	}
    }
}
close(INPUT);