VMD-L Mailing List

From: Teletchéa Stéphane (steletch_at_biomedicale.univ-paris5.fr)
Date: Thu Nov 20 2003 - 06:53:21 CST

Le jeu 20/11/2003 à 09:54, Teletchéa Stéphane a écrit :
Here a corrected version of the script :
1 - molecules ID are now taken correctly into account
2 - bond/angle/dihedral number are correct (before only the first
bond/angle/dihedral was correctly labelled)
3 - the extra '- ' is removed, thanks to Justin.

I've tested it with one or two molecules, DNA and/or protein.
It should work completely by now.

Can i make it available via my website ?

Stef

The modified script :

############################################################################
#cr
#cr (C) Copyright 1995-2003 The Board of Trustees of
the
#cr University of
Illinois
#cr All Rights
Reserved
#cr
############################################################################

# Callback for plotting values of labels. Triggered by the "graph"
button
# on the Labels menu.

# This callback sends data to xmgr, one dataset at a time. If xmgrace
is
# not found, it reverts to the save dialog.
proc vmd_labelcb_xmgr { args } {
  global vmd_graph_label
  foreach item $vmd_graph_label {
    foreach { type id } $item { break }
    set data [label graph $type $id]
    set info [label list $type]
    set ind [lindex $item 1]

    switch [lindex $item 0] {
        "Bonds" {
            set fin 2
            }
        "Angles" {
            set fin 3
            }
        "Dihedrals" {
            set fin 4
            }
    }

    set input "@type xy\n@ title \""
    
    for {set deb 0} { $deb < $fin } {incr deb 1} {
    
    set atom [lindex [lindex [lindex $info $ind] $deb] 1]
    set mol [lindex [lindex [lindex $info $ind] $deb] 0]
    set sel [atomselect $mol "index $atom"]
    set atomname [$sel get name]
    set resid [$sel get resid]
    set resname [$sel get resname]
    append input "$resname $resid:$atomname - "
    }
    
    set input [string trimright $input "- "]
    append input "\"\n"

    set i 0
    foreach elem $data {
      append input " $i $elem\n"
      incr i
    }
    set rc [catch {exec xmgrace -pipe << $input &} msg]
    if { $rc } {
      vmd_labelcb_save
    }
  }
}

# This callback simply saves the data to a file of the user's choice
using
# the Tk dialog box if available, otherwise through the text interface.
proc vmd_labelcb_save { args } {
  global vmd_graph_label tk_version
  foreach item $vmd_graph_label {
    foreach { type id } $item { break }
    set data [label graph $type $id]
    set title "Enter filename to save label data for $item"
    if [info exists tk_version] {
      set fname [tk_getSaveFile -title $title]
    } else {
      puts $title
      gets stdin fname
    }
    if { [string length $fname] } {
      set fd [open $fname w]
      foreach elem $data { puts $fd $elem }
      close $fd
    }
  }
}

# Choose a callback based on the platform: xmgr for unix, save for
everyone
# else (for now). Exception: if a command named vmd_labelcb_user is
defined,
# use that one instead of the default.
proc vmd_labelcb { args } {
  global tcl_platform
  if { [llength [info commands vmd_labelcb_user]] } {
    vmd_labelcb_user $args
  } else {
    switch $tcl_platform(platform) {
      unix {
        # Set the display variable to :0.0, unless it's already been set
        global env
        if { ![info exists env(DISPLAY)] } {
          puts "Setting DISPLAY environment variable to :0.0."
          set env(DISPLAY) :0.0
        }
        vmd_labelcb_xmgr $args
      }
      default {
        vmd_labelcb_save $args
      }
    }
  }
}

trace variable vmd_graph_label w vmd_labelcb 

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Linux 2.4.21-0.25mdk #1 Thu Jul 24 13:10:52 MDT 2003