Writing efficient Tcl scripts in VMD

This page attempts to provide some advice for writing efficient Tcl visualization and analysis scripts in VMD.

Coding Style

• Main Tcl/Tk web site,
• Tcl Style Guide
• Tcl Wiki: tips on writing good Tcl/Tk scripts and packages.

Performance and Good Coding Practices

• Measuring performance (Tcl Wiki)
• Performance (Tcl Wiki)
• Performance: catch vs. info (Tcl Wiki)
• Elegance vs. performance (Tcl Wiki)
• Always delete atom selections when you're finished with them
• Use '$sel update' and '$sel frame $i' rather than creating entirely new atom selections when iterating over trajectory frames.
• Remember to close open files, or you'll lose data
• Use the built-in 'measure' and vector commands rather than hand-coded Tcl for better performance. (i.e. 'measure center $sel weight mass')
• Keep in mind that the result of a [$sel get {x y}] is a list wrapped in another list, even if the selection contains only one item. So if you parse the result with:

    foreach vec [$sel get { x y }] {
      # do stuff with $vec 
    }
  

  it will work no matter how many atoms are in $sel. If you know that you will only have one item in the list you can also use:

    set vec [lindex [$sel get {x y}] 0]
  

  is to use lindex to get the first element of the returned list which contains the vector you expect.
• When using functions that depend on using selections, make them able to handle the case of the selection not containing any atoms. If you don't, the subrouting will simply abort and return control to the main loop. e.g. see the use of 'catch' in the following example:

       # make a list of CoM coordinates of a selection over a trajectory
       # uses the previous coordinates if the selection is empty...
       set num_frames [molinfo $gr_mol get numframes]
       set coords {}
       if [ catch {
              set lastco [measure center $selection weight mass] 
            } errmsg ]  {
          set lastco {0.0 0.0 0.0}
       }
      
       for {set i 0} {$i < $num_frames} {incr i} {
          $selection frame $i
          if {$update} { $selection update }
          # compute the center of mass ...
          if [ catch {
                 set tmp [measure center $selection weight mass]
               } errmsg ] {
             set tmp $lastco
          }
          # ... and append it to the list.
          lappend coords $tmp
          set lastco $tmp
       }
  

• Use braces around expr expressions to get peak performance, see the Tcl performance wiki page for examples