text .t -width 50
frame .f1
label .f1.l1 -text "Delta" -width 15
entry .f1.t1 -width 20 -textvariable delta
pack .f1.l1 .f1.t1 -side left
pack configure .t .f1 -pady 5

set array x1
set array y1
set array z1

set array x2
set array y2
set array z2

proc parse_coord { sz px py pz } {
    upvar $px x $py y $pz z

    set sz_length [string length $sz]
    set comma1 [string first "," $sz]
    set x [string range $sz 0 [expr $comma1 - 1] ]
    set x [string trimleft $x]

    #set print $x
    #append print "\n"
    # .t insert insert $print

    set comma2 [string last "," $sz]
    set y [string range $sz  [expr $comma1 + 1] [expr $comma2 - 1] ]
    set y [string trimleft $y]

    #set print $y
    #append print "\n"
    # .t insert insert $print

    set z [string range $sz [expr $comma2 + 1] $sz_length ]
    set z [string trimleft $z]

    #append z "\n"
    #set print $z
    #append print "\n"
    # .t insert insert $print
}

proc distance { p1 p2 } {
    global x1 y1 z1
    global x2 y2 z2

    set dx [expr $x1($p1) - $x2($p2)]
    set dy [expr $y1($p1) - $y2($p2)]
    set dz [expr $z1($p1) - $z2($p2)]

    return [expr sqrt($dx * $dx + $dy * $dy + $dz * $dz)]
}

button .b -text "Select Atoms" -command {
    global x1 y1 z1
    global x2 y2 z2

    hcExec "query-response-has-tag false"

    set natoms1 [hcQuery "atom-count 1"]
    set print $natoms1
    append print "\n"
     .t insert insert $print

    set i 0
    while { $i < $natoms1 } {
        incr i 1

        set sz [hcQuery "coordinates($i,1)"]
        parse_coord $sz x1($i) y1($i) z1($i)
    }

    set natoms2 [hcQuery "atom-count 2"]
    set print $natoms2
    append print "\n"
     .t insert insert $print

    set i 0
    while { $i < $natoms2 } {
        incr i 1

        set sz [hcQuery "coordinates($i,2)"]
        parse_coord $sz x2($i) y2($i) z2($i)

        hcExec "select-atom $i 2"
    }

    #set delta 2

    set i 0
    while { $i < $natoms1 } {
        incr i 1

        set j 0
        while { $j < $natoms2 } {
            incr j 1

            set d [distance $i $j]
            if { $d < $delta } {
                set print "distance    1($i)\t  2($j)\t =   $d\n"
                 .t insert insert $print
                hcExec "select-atom $i 1"
            }
        }

    }
}

pack .b