How to pass integers to tcl procedure in vmd

Question

I am new in tcl programming and I need to write a script for vmd that calculates two distances between two couples of atoms and print them in an output file. I do not understand why measure can not take atom_1, etc. This is my script and thank you for your help

proc distance {distance_1 atom_1 atom_2 distance_2 atom_3 atom_4 output} {
    set outfile [open $output w]
    puts $outfile "frame, $distance_1, $distance_2"

    set nf [molinfo top get numframes]

    for {set i 0} {$i < $nf} {incr i} {
            set d1 [measure bond {$atom_1 $atom_2} frame $i]
            set d2 [measure bond {$atom_3 $atom_4} frame $i]
            puts $outfile "$i , $d1 , $d2"
    }
    close $outfile

    }

score 2 · Accepted Answer · answered Jun 09 '20 at 08:34

2

The problem here is:

measure bond {$atom_1 $atom_2} frame $i

The issue is that {…} in Tcl actually means “quote this exactly, with no substitutions at all”. Instead of sending a list of two numbers in, it passes a list of two non-numbers (the literal strings $atom_1 and $atom_2).

The fix is to replace {$atom_1 $atom_2} with [list $atom_1 $atom_2].

Yes, proc and for and if make use of this behaviour. It's just that they pass things back to the Tcl interpreter engine as part of their execution.

answered Jun 09 '20 at 08:34

Donal Fellows

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1

Technically, you could use `"$atom_1 $atom_2"`, but that is less efficient (it forces string interpretations) and can blow up strangely when the elements contain Tcl metacharacters. – Donal Fellows Jun 09 '20 at 08:38
1

You are a savior! Thank you! =D – Jonny_92 Jun 09 '20 at 08:38

How to pass integers to tcl procedure in vmd

1 Answers1