VMD-L Mailing List

From: Mi Yang (drmiyang2019_at_gmail.com)
Date: Wed Oct 20 2021 - 00:57:01 CDT

Dear Colleagues,
We are trying to run the script of contact Vs Freq in the VMD command
prompt but it is not running and also not giving any error message...This
is strange! Any helpful comments will be highly appreciated.
We have tried different strategies to run it like after loading PSF and PBD
files or merging with other scripts...Is there a prerequisite input file
which we need to add?
Dr. Shabbir
=============script=====
proc contactFreq { {sel1} {sel2} {percent 0} {outFile stdout} {mol top} } {
  if { $outFile != "stdout" } {
     set outFile [open $outFile w]
  }
  puts $outFile "[clock format [clock scan now]] Search started."

  set allAtoms {}
  set allCount {}
  set numberOfFrames [molinfo $mol get numframes]
  for { set i 0 } { $i < $numberOfFrames } { incr i } {
      molinfo $mol set frame $i

      set frameCount {}
      set frameAtoms [atomselect $mol "$sel1 and noh and within 4 of ($sel2
and noh)"]
      foreach {segid} [$frameAtoms get segid] {resname} [$frameAtoms get
resname] {resid} [$frameAtoms get resid] {name} [$frameAtoms get name] {
 set atom [list $resid $resname $segid]
 if {[lsearch $frameCount $atom] != -1} continue
 lappend frameCount $atom
 set loc [lsearch $allAtoms $atom]
          if { $loc == -1 } {
             lappend allAtoms $atom
             lappend allCount 1
          } else {
             lset allCount $loc [expr { [lindex $allCount $loc] + 1 } ]
          }
     }
     $frameAtoms delete
  }

  puts $outFile "[clock format [clock scan now]] Search finished."

  puts $outFile "Find interactions:"
  puts $outFile "Residue \t\tfraction"
  #print count after sorting
  set outData {}
  foreach { a } $allAtoms { c } $allCount {
      lappend outData [concat $c $a]
  }
  foreach { data } [lsort -integer -index 1 $outData] {
      set c [lindex $data 0]
      set fraction [expr { 100*$c/($numberOfFrames+0.0) }]
      if { $fraction >= $percent } {
puts $outFile [format "%s-%s-%s \t\t %.2f%%" [lindex $data 3] [lindex $data
2] [lindex $data 1] $fraction]
      }
      #set beta according to the fraction, this is optional
      set atom [atomselect $mol "segid [lindex $data 3] and resname [lindex
$data 2] and resid [lindex $data 1]"]
      $atom set beta $fraction
      $atom delete
  }

  if { $outFile != "stdout" } {
      close $outFile
  }

}