annotate hbonds/hbonds.tcl @ 0:8aa5e465b043 draft default tip

"planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"

# hbonds - finds hydrogen bonds in a trajectory
# 
# Authors:
#     JC Gumbart ([e-mail])
#     with the detailed hbond calculations contributed by Dong Luo ([e-mail])
#     also with thanks to Leo Trabuco and Elizabeth Villa whose salt bridge plugin provided the foundation for this one
#
# $Id: hbonds.tcl,v 1.9 2013/04/15 15:50:16 johns Exp $
#

#
# TODO:
#
# - show hbonds in the gui?
#

package provide hbonds 1.2

namespace eval ::hbonds:: {
  namespace export hbonds

  variable defaultAng 20
  variable defaultDist 3.0
  variable defaultWrite 0
  variable defaultFrames "all"
  variable defaultOutdir
  variable defaultLogFile ""
  variable defaultUpdateSel 1
  variable defaultPlot 1
  variable defaultPolar 0
  variable debug 0
  variable currentMol none
  variable atomselectText1 "protein"
  variable atomselectText2 ""
  variable defaultDatFile "hbonds.dat"
  variable statusMsg ""

  variable defaultDetailFile "hbonds-details.dat" 
  variable defaultDetailType none
  variable defaultDA both
}

proc ::hbonds::hbonds_gui {} {
  variable defaultDist
  variable defaultAng
  variable defaultWrite
  variable defaultPlot
  variable defaultFrames
  variable defaultLogFile
  variable defaultUpdateSel
  variable defaultDatFile
  variable defaultDetailFile
  variable defaultDetailType
  variable defaultPolar
  variable w
  variable defaultDA
  
  variable nullMolString "none"
  variable currentMol
  variable molMenuButtonText

 trace add variable [namespace current]::currentMol write [namespace code {
    variable currentMol
    variable molMenuButtonText
    if { ! [catch { molinfo $currentMol get name } name ] } {
      set molMenuButtonText "$currentMol: $name"
    } else {
      set molMenuButtonText $currentMol
    }
  # } ]
  set currentMol $nullMolString
  variable usableMolLoaded 0
  
  variable atomselectText1 "protein"
  variable atomselectText2 ""

  # Add traces to the checkboxes, so various widgets can be disabled
  # appropriately
  if {[llength [trace info variable [namespace current]::atomselectText2]] == 0} {
    trace add variable [namespace current]::atomselectText2 write ::hbonds::sel2_state
  }

  if {[llength [trace info variable [namespace current]::guiWrite]] == 0} {
    trace add variable [namespace current]::guiWrite write ::hbonds::write_state
  }

  if {[llength [trace info variable [namespace current]::guiType]] == 0} {
    trace add variable [namespace current]::guiType write ::hbonds::write_state
  }

  
  # If already initialized, just turn on
  if { [winfo exists .hbonds] } {
    wm deiconify $w
    return
  }
  set w [toplevel ".hbonds"]
  wm title $w "Hydrogen Bonds"
  wm resizable $w 0 0

  variable statusMsg "Ready."
  variable guiDist $defaultDist
  variable guiAng $defaultAng
  variable guiWrite $defaultWrite
  variable guiPlot $defaultPlot
  variable guiFrames $defaultFrames
  variable guiLogFile $defaultLogFile
  variable guiUpdateSel $defaultUpdateSel
  variable guiDatFile $defaultDatFile
  variable guiPolar $defaultPolar
  variable guiType $defaultDetailType
  variable guiDetailFile $defaultDetailFile
  variable guiOutdir [pwd]
  variable guiDA $defaultDA

  # Add a menu bar
  frame $w.menubar -relief raised -bd 2
  pack $w.menubar -padx 1 -fill x

  menubutton $w.menubar.help -text Help -underline 0 -menu $w.menubar.help.menu
  # XXX - set menubutton width to avoid truncation in OS X
  $w.menubar.help config -width 5

  # Help menu
  menu $w.menubar.help.menu -tearoff no
  $w.menubar.help.menu add command -label "About" \
    -command {tk_messageBox -type ok -title "About Hbonds" \
    -message "The H Bonds plugin searches for hydrogen bonds (subject to user criteria) within one selection or between two selections and then outputs the number of bonds as a function of time."}
  $w.menubar.help.menu add command -label "Help..." \
    -command "vmd_open_url [string trimright [vmdinfo www] /]/plugins/hbonds"

  pack $w.menubar.help -side right

  ############## frame for input options #################
  labelframe $w.in -bd 2 -relief ridge -text "Input options" -padx 1m -pady 1m
  
  set f [frame $w.in.all]
  set row 0
  
  grid [label $f.mollable -text "Molecule: "] \
    -row $row -column 0 -sticky e
  grid [menubutton $f.mol -textvar [namespace current]::molMenuButtonText \
    -menu $f.mol.menu -relief raised] \
    -row $row -column 1 -columnspan 3 -sticky ew
  menu $f.mol.menu -tearoff no
  incr row
  
  fill_mol_menu $f.mol.menu
  trace add variable ::vmd_initialize_structure write [namespace code "
    fill_mol_menu $f.mol.menu
  # " ]

  grid [label $f.sellabel1 -text "Selection 1 (Required): "] \
    -row $row -column 0 -sticky e
  grid [entry $f.sel1 -width 50 \
    -textvariable [namespace current]::atomselectText1] \
    -row $row -column 1 -columnspan 3 -sticky ew
  incr row

  grid [label $f.sellabel2 -text "Selection 2 (Optional): "] \
    -row $row -column 0 -sticky e
  grid [entry $f.sel2 -width 50 \
    -textvariable [namespace current]::atomselectText2] \
    -row $row -column 1 -columnspan 3 -sticky ew
  incr row

  grid [label $f.selwarning -text "NOTE: if sel1 and sel2 overlap, hbonds output is unreliable!"] \
    -row $row -column 1 -columnspan 2 -sticky w
  incr row

  grid [label $f.frameslabel -text "Frames: "] \
    -row $row -column 0 -sticky e
  grid [entry $f.frames -width 10 \
    -textvariable [namespace current]::guiFrames] \
    -row $row -column 1 -sticky ew
  grid [label $f.framescomment -text "(now, all, b:e, or b:s:e)"] \
    -row $row -column 2 -columnspan 2 -sticky w
  incr row

###    -row $row -column 0 -columnspan 4 -sticky w

##    -row $row -column 1 -columnspan 4 -sticky e

  grid [checkbutton $f.check -text \
    "Update selections every frame?" \
    -variable [namespace current]::guiUpdateSel] \
    -row $row -column 0 -sticky w
  grid [checkbutton $f.check2 -text \
    "Only polar atoms (N, O, S, F)?" \
    -variable [namespace current]::guiPolar] \
    -row $row -column 1 -sticky e
  incr row

  pack $f -side top -padx 0 -pady 0 -expand 1 -fill none

  set f [frame $w.in.cutoffs]
  set row 0

  #### donor/acceptor check ####
  grid [label $f.typelabel1 -text "Selection 1 is the: "] \
    -row $row -column 0 -sticky e
  grid [radiobutton $f.type11 -text "Donor" -state disabled \
    -variable [namespace current]::guiDA -value "D"] \
    -row $row -column 1 -sticky w
  grid [radiobutton $f.type12 -text "Acceptor" -state disabled \
    -variable [namespace current]::guiDA -value "A"] \
    -row $row -column 2 -sticky w
  grid [radiobutton $f.type13 -text "Both" \
    -variable [namespace current]::guiDA -value "both"] \
    -row $row -column 3 -sticky w
  incr row

  grid [label $f.ondistlabel -text "Donor-Acceptor distance (A): "] \
    -row $row -column 0 -sticky e
  grid [entry $f.ondist -width 5 \
    -textvariable [namespace current]::guiDist] \
    -row $row -column 1 -columnspan 3 -sticky ew
  incr row

  grid [label $f.comdistlabel -text "Angle cutoff (degrees): "] \
    -row $row -column 0 -sticky e
  grid [entry $f.comdist -width 5 \
    -textvariable [namespace current]::guiAng] \
    -row $row -column 1 -columnspan 3 -sticky ew
  incr row

  #### hbonds type define ####
  grid [label $f.typelabel -text "Calculate detailed info for: "] \
    -row $row -column 0 -sticky e
  grid [radiobutton $f.type1 -text "None" \
    -variable [namespace current]::guiType -value "none"] \
    -row $row -column 1 -sticky ew
  grid [radiobutton $f.type2 -text "All hbonds" \
    -variable [namespace current]::guiType -value "all"] \
    -row $row -column 2 -sticky ew
  grid [radiobutton $f.type3 -text "Residue pairs" \
    -variable [namespace current]::guiType -value "pair"] \
    -row $row -column 3 -sticky ew
  grid [radiobutton $f.type4 -text "Unique hbond" \
    -variable [namespace current]::guiType -value "unique"] \
    -row $row -column 4 -sticky ew
  incr row

  pack $f -side top -padx 0 -pady 5 -expand 1 -fill x

  pack $w.in -side top -pady 5 -padx 3 -fill x -anchor w

  ############## frame for output options #################
  labelframe $w.out -bd 2 -relief ridge -text "Output options" -padx 1m -pady 1m

  set f [frame $w.out.all]
  set row 0

  grid [checkbutton $f.check1 -text \
    "Plot the data with MultiPlot?" \
    -variable [namespace current]::guiPlot] \
    -row $row -column 0 -columnspan 2 -sticky w
  incr row
  grid [label $f.label -text "Output directory: "] \
    -row $row -column 0 -columnspan 1 -sticky e
  grid [entry $f.entry -textvariable [namespace current]::guiOutdir \
    -width 35 -relief sunken -justify left -state readonly] \
    -row $row -column 1 -columnspan 1 -sticky e
  grid [button $f.button -text "Choose" -command "::hbonds::getoutdir"] \
    -row $row -column 2 -columnspan 1 -sticky e
  incr row
  grid [label $f.loglabel -text "Log file? "] \
    -row $row -column 0 -sticky e
  grid [entry $f.logname -width 30 \
    -textvariable [namespace current]::guiLogFile] \
    -row $row -column 1 -columnspan 2 -sticky ew
  incr row

  grid [checkbutton $f.check2 -text \
    "Write output to files?" \
    -variable [namespace current]::guiWrite] \
    -row $row -column 0 -columnspan 3 -sticky w
    incr row
  grid [label $f.fbdata -text "Frame/bond data? " -state disabled] \
    -row $row -column 0 -sticky e
  grid [entry $f.datname -width 30 \
    -textvariable [namespace current]::guiDatFile -state disabled] \
    -row $row -column 1 -columnspan 2 -sticky ew
    incr row
  grid [label $f.detdata -text "Detailed hbond data? " -state disabled] \
    -row $row -column 0 -sticky e
  grid [entry $f.detname -width 30 \
    -textvariable [namespace current]::guiDetailFile -state disabled] \
    -row $row -column 1 -columnspan 2 -sticky ew


  pack $f -side left -padx 0 -pady 5 -expand 1 -fill x
  pack $w.out -side top -pady 5 -padx 3 -fill x -anchor w

  ############## frame for status #################
  labelframe $w.status -bd 2 -relief ridge -text "Status" -padx 1m -pady 1m

  set f [frame $w.status.all]
  label $f.label -textvariable [namespace current]::statusMsg
  pack $f $f.label
  pack $w.status -side top -pady 5 -padx 3 -fill x -anchor w

  set f [frame $w.control]
  button $f.button -text "Find hydrogen bonds!" -width 20 \
  -command {::hbonds::hbonds -gui 1 -dist $::hbonds::guiDist -ang $::hbonds::guiAng -writefile $::hbonds::guiWrite -outdir $::hbonds::guiOutdir -frames $::hbonds::guiFrames -log $::hbonds::guiLogFile -upsel $::hbonds::guiUpdateSel -plot $::hbonds::guiPlot -outfile $::hbonds::guiDatFile -polar $::hbonds::guiPolar -type $::hbonds::guiType -detailout $::hbonds::guiDetailFile -DA $::hbonds::guiDA } 

  pack $f $f.button

}

# Adapted from pmepot gui
proc ::hbonds::fill_mol_menu {name} {

  variable usableMolLoaded
  variable currentMol
  variable nullMolString
  $name delete 0 end

  set molList ""
  foreach mm [array names ::vmd_initialize_structure] {
    if { $::vmd_initialize_structure($mm) != 0} {
      lappend molList $mm
      $name add radiobutton -variable [namespace current]::currentMol \
        -value $mm -label "$mm [molinfo $mm get name]"
    }
  }

  #set if any non-Graphics molecule is loaded
  if {[lsearch -exact $molList $currentMol] == -1} {
    if {[lsearch -exact $molList [molinfo top]] != -1} {
      set currentMol [molinfo top]
      set usableMolLoaded 1
    } else {
      set currentMol $nullMolString
      set usableMolLoaded  0
    }
  }

}

proc ::hbonds::getoutdir {} {
  variable guiOutdir

  set newdir [tk_chooseDirectory \
    -title "Choose output directory" \
    -initialdir $guiOutdir -mustexist true]

  if {[string length $newdir] > 0} {
    set guiOutdir $newdir 
  } 
}

proc hbonds { args } { return [eval ::hbonds::hbonds $args] }
proc hbondsgui { } { return [eval ::hbonds::hbonds_gui] }

proc ::hbonds::hbonds_usage { } {

  variable defaultDist
  variable defaultAng
  variable defaultWrite
  variable defaultPlot
  variable defaultFrames
  variable defaultDatFile
  variable defaultDetailType
  variable defaultDA

  puts "Usage: hbonds -sel1 <atom selection> <option1> <option2> ..."
  puts "Options:"
  puts "  -sel2 <atom selection> (default: none)"
  puts "    NOTE: if sel1 and sel2 overlap, hbonds output is unreliable!"
  if $defaultWrite {
     puts "  -writefile <yes|no> (default: yes)"
  } else {
     puts "  -writefile <yes|no> (default: no)"
  }

  puts "  -upsel <yes|no> (update atom selections every frame? default: yes)"
  puts "  -frames <begin:end> or <begin:step:end> or all or now (default: $defaultFrames)"
  puts "  -dist <cutoff distance between donor and acceptor> (default: $defaultDist)"
  puts "  -ang <angle cutoff> (default: $defaultAng)"
  puts "  -plot <yes|no> (plot with MultiPlot, default: yes)"
  puts "  -outdir <output directory> (default: current)"
  puts "  -log <log filename> (default: none)"
  puts "  -outfile <dat filename> (default: $defaultDatFile)"
  puts "  -polar <yes|no> (consider only polar atoms (N, O, S, F)? default: no)"
  puts "  -DA <D|A|both> (sel1 is the donor (D), acceptor (A), or donor and acceptor (both)?"  
  puts "        Only valid when used with two selections, default: $defaultDA)"
  puts "  -type: (default: $defaultDetailType)"
  puts "        none--no detailed bonding information will be calculated"
  puts "        all--hbonds in the same residue pair type are all counted"
  puts "        pair--hbonds in the same residue pair type are counted once"
  puts "        unique--hbonds are counted according to the donor-acceptor atom pair type"
  puts "  -detailout <details output file> (default: stdout)"
  return
}

proc ::hbonds::hbonds { args } {

  global tk_version
  variable hbondcount 
  variable hbondallframes
  variable multichain 
  variable molid
  variable detailType

  variable defaultDist
  variable defaultAng
  variable defaultFrames
  variable defaultWrite
  variable defaultPlot
  variable defaultFrames
  variable defaultUpdateSel
  variable defaultDatFile
  variable defaultPolar
  variable defaultDA
  variable currentMol
  variable atomselectText1
  variable atomselectText2
  variable debug
  variable log
  variable statusMsg
  variable plotHbonds
  
  variable defaultOutdir [pwd]

  variable defaultDetailFile 
  variable defaultDetailType  

  set nargs [llength $args]
  if { $nargs == 0 || $nargs % 2 } {
    if { $nargs == 0 } {
      hbonds_usage
      error ""
    }
    if { $nargs % 2 } {
      hbonds_usage
        error "error: odd number of arguments $args"
    }
  }

  foreach {name val} $args {
    switch -- $name {
      -sel1 { set arg(sel1) $val }
      -sel2 { set arg(sel2) $val }
      -upsel { set arg(upsel) $val }
      -frames { set arg(frames) $val }
      -dist { set arg(dist) $val }
      -ang { set arg(ang) $val }
      -writefile { set arg(writefile) $val }
      -outdir { set arg(outdir) $val }
      -log { set arg(log) $val }
      -gui { set arg(gui) $val }
      -debug { set arg(debug) $val }
      -plot {set arg(plot) $val}
      -outfile {set arg(outfile) $val}
      -type { set arg(type) $val }
      -detailout { set arg(detout) $val }
      -polar {set arg(polar) $val }
      -DA { set arg(DA) $val }

      default { error "unknown argument: $name $val" }
    }
  }

  # was I called by the gui?
  if [info exists arg(gui)] {
      set gui 1
  } else {
      set gui 0
  }

  # debug flag
  if [info exists arg(debug)] {
      set debug 1
  }

  # outdir
  if [info exists arg(outdir)] {
    set outdir $arg(outdir)
  } else {
    set outdir $defaultOutdir
  }
  if { ![file isdirectory $outdir] } {
    error "$outdir is not a directory."
  }

  # log file
  if { [info exists arg(log)] && $arg(log) != "" } {
    set log [open [file join $outdir $arg(log)] w]
  } else {
    set log "stdout"
  }

  # polar atoms only?
  if [info exists arg(polar)] {
    if { $arg(polar) == "no" || $arg(polar) == 0 } {
      set polar 0
    } elseif { $arg(polar) == "yes" || $arg(polar) == 1 } {
      set polar 1
    } else {
      error "error: bad argument for option -polar $arg(polar): acceptable arguments are 'yes' or 'no'"
    }
  } else {
    set polar $defaultPolar
  }

  # donor/acceptor?
  if [info exists arg(DA)] {
    if { $arg(DA) == "D" || $arg(DA) == "donor" } {
      set DA "D"
    } elseif { $arg(DA) == "A" || $arg(DA) == "acceptor" } {
      set DA "A"
    } elseif { $arg(DA) == "both" } {
      set DA "both"
    } else {
      error "error: bad argument for option -DA $arg(DA): acceptable arguments are 'D', 'A', or 'both'"
    }
  } else {
    set DA $defaultDA
  }

  # get selection
  if [info exists arg(sel1)] {
     set molid [$arg(sel1) molid]
     if { $polar } {
        set sel1 [atomselect $molid "([$arg(sel1) text]) and (name \"N.*\" \"O.*\" \"S.*\" FA F1 F2 F3)"]
     } else {
        set sel1 $arg(sel1)
     }
     if [info exists arg(sel2)] {
        if { $polar } {
           set sel2 [atomselect $molid "([$arg(sel2) text]) and (name \"N.*\" \"O.*\" \"S.*\" FA F1 F2 F3)"]
        } else {
           set sel2 $arg(sel2)
        }
     }

  } elseif $gui {
    if { $currentMol == "none" } {
      error "No molecules were found."
    } else {
       set molid $currentMol
       if { $polar } {
          set sel1 [atomselect $currentMol "($atomselectText1) and (name \"N.*\" \"O.*\" \"S.*\" FA F1 F2 F3)"]
       } else {
          set sel1 [atomselect $currentMol $atomselectText1]
       }
     if {$atomselectText2 != ""} {
       if { $polar } {
          set sel2 [atomselect $currentMol "($atomselectText2) and (name \"N.*\" \"O.*\" \"S.*\" FA F1 F2 F3)"]
       } else {
          set sel2 [atomselect $currentMol $atomselectText2]
       }
      }
    }
  } else {
    hbonds_usage
    error "No atomselection was given."
  }

  # update selections?
  if [info exists arg(upsel)] {
    if { $arg(upsel) == "no" || $arg(upsel) == 0 } {
      set updateSel 0
    } elseif { $arg(upsel) == "yes" || $arg(upsel) == 1 } {
      set updateSel 1
    } else {
      error "error: bad argument for option -upsel $arg(upsel): acceptable arguments are 'yes' or 'no'"
    }
  } else {
    set updateSel $defaultUpdateSel
  }

# SETTING FRAMES

  set nowframe [molinfo $molid get frame]
  set lastframe [expr [molinfo $molid get numframes] - 1]
  if { ! [info exists arg(frames)] } { set arg(frames) $defaultFrames }
  if [info exists arg(frames)] {
    set fl [split $arg(frames) :]
    switch -- [llength $fl] {
      1 {
        switch -- $fl {
          all {
            set frames_begin 0
            set frames_end $lastframe
          }
          now {
            set frames_begin $nowframe
          }
          last {
            set frames_begin $lastframe
          }
          default {
            set frames_begin $fl
          }
        }
      }
      2 {
        set frames_begin [lindex $fl 0]
        set frames_end [lindex $fl 1]
      }
      3 {
        set frames_begin [lindex $fl 0]
        set frames_step [lindex $fl 1]
        set frames_end [lindex $fl 2]
      }
      default { error "bad -frames arg: $arg(frames)" }
    }
  } else {
    set frames_begin 0
  }
  if { ! [info exists frames_step] } { set frames_step 1 }
  if { ! [info exists frames_end] } { set frames_end $lastframe }
    switch -- $frames_end {
      end - last { set frames_end $lastframe }
  }
  if { [ catch {
    if { $frames_begin < 0 } {
      set frames_begin [expr $lastframe + 1 + $frames_begin]
    }
    if { $frames_end < 0 } {
      set frames_end [expr $lastframe + 1 + $frames_end]
    }
    if { ! ( [string is integer $frames_begin] && \
      ( $frames_begin >= 0 ) && ( $frames_begin <= $lastframe ) && \
	  [string is integer $frames_end] && \
  	  ( $frames_end >= 0 ) && ( $frames_end <= $lastframe ) && \
  	  ( $frames_begin <= $frames_end ) && \
  	  [string is integer $frames_step] && ( $frames_step > 0 ) ) } {
        error
      }
  } ok ] } { error "bad -frames arg: $arg(frames)" }
  if $debug {
    puts $log "frames_begin: $frames_begin"
    puts $log "frames_step: $frames_step"
    puts $log "frames_end: $frames_end"
    flush $log
  }

# DONE SETTING FRAMES
    
  # get Dist
  if [info exists arg(dist)] {
    set dist $arg(dist)
  } else {
    set dist $defaultDist
  }

  # get Ang
  if [info exists arg(ang)] {
    set ang $arg(ang)
  } else {
    set ang $defaultAng
  }

  # write files?
  if [info exists arg(writefile)] {
     if { $arg(writefile) == "no" || $arg(writefile) == 0 } {
        set writefile 0
     } elseif { $arg(writefile) == "yes" || $arg(writefile) == 1 } {
        set writefile 1
        if [info exists arg(outfile)] {
           if {$arg(outfile) != ""} {
              set datfile $arg(outfile)
           } else {
              set datfile $defaultDatFile
           }
        } else {
           set datfile $defaultDatFile
        }

        if [info exists arg(detout)] {
           if {$arg(detout) != ""} {
              set detailFile $arg(detout)
           } else {
              set detailFile $defaultDetailFile
           }
        } else {
           set detailFile $defaultDetailFile
        }

     } else {
       error "error: bad argument for option -writefile $arg(writefile): acceptable arguments are 'yes' or 'no'"
     }

  } else {
    set writefile $defaultWrite
    set datfile $defaultDatFile
    set detailFile $defaultDetailFile
  }

  # Plot?
  if [info exists arg(plot)] {
    if { ($arg(plot) == "no" || $arg(plot) == 0) && $writefile } {
      set plotHbonds 0
    } elseif { ($arg(plot) == "yes" || $arg(plot) == 1) || !$writefile } {
      set plotHbonds 1
    } else {
      error "error: bad argument for option -plot $arg(plot): acceptable arguments are 'yes' or 'no'"
    }
  } else {
    set plotHbonds $defaultPlot
  }

  # Don't call multiplot in text mode
  if {![info exists tk_version]} {
    set plotHbonds 0
  }

  # calculate details?
  if [info exists arg(type)] {
    if { $arg(type) == "none" || $arg(type) == 0 } {
      set detailType "none"
    } elseif { $arg(type) == "unique" || $arg(type) == "all" || $arg(type) == "pair" } {
      set detailType $arg(type)
    } else {
      error "error: bad argument for option -type $arg(type): acceptable arguments are 'none', 'all', 'pair', or 'unique'"
    }
  } else {
      set detailType $defaultDetailType
  }

  # print name, version and date of plugin
  puts $log "H-Bonds Plugin, Version 1.1"
  puts $log "[clock format [clock scan now]]\n"
  puts $log "Parameters used in the calculation of hydrogen bonds:"
  puts $log "- Atomselection 1: [$sel1 text]"
  if [info exists sel2] {
      puts $log "- Atomselection 2: [$sel2 text]"
  }
  if $updateSel {
      puts $log "- Update selections every frame: yes"
  } else {
      puts $log "- Update selections every frame: no"
  }
  puts $log "- Initial frame: $frames_begin"
  puts $log "- Frame step: $frames_step"
  puts $log "- Final frame: $frames_end"
  puts $log "- Donor-Acceptor distance: $dist"
  puts $log "- Angle cutoff: $ang"
  puts $log "- Type: $detailType"
  if $writefile {
    puts $log "- Write a file with H bond/frame data: yes"
    puts $log "- Filename: $datfile"
    if {$detailType != "none"} {
       puts $log "- Details output file: $detailFile"
    }
  } else {
    puts $log "- Write a file with H bond/frame data: no"
  }
  puts $log ""
  flush $log

### CALCULATES HBONDS HERE

  # check if multiple chains/molecules exist in the two selections
  set chainlist [$sel1 get chain]
  if { [lsearch -not $chainlist [lindex $chainlist 0]] == -1 } {
     set multichain 0
  } else { set multichain 1 }
  if {[info exists sel2]} {
     set chainlist [$sel2 get chain]
  }
  if { [lsearch -not $chainlist [lindex $chainlist 0]] == -1 && $multichain == 0} {
     set multichain 0
  } else { set multichain 1 }

  set hbondallframes {}
  set hbondcount {}
  set numberofframes [expr { ($frames_end - $frames_begin) / $frames_step + 1 }]


  for { set f $frames_begin } { $f <= $frames_end } { incr f $frames_step } {

     $sel1 frame $f
     if {[info exists sel2]} {
        $sel2 frame $f
     }

     if $updateSel {
        $sel1 update
        if {[info exists sel2]} {
           $sel2 update
        }
     }

### CHECK DA HERE!!!

     if {[info exists sel2]} {
        
        set count1 0
        set count2 0

        if {$DA == "D" || $DA == "both"} {
            set hbondsingleframe1 [measure hbonds $dist $ang $sel1 $sel2]
            set count1 [llength [lindex $hbondsingleframe1 0]]
        }
        if {$DA == "A" || $DA == "both"} {
            set hbondsingleframe2 [measure hbonds $dist $ang $sel2 $sel1]
            set count2 [llength [lindex $hbondsingleframe2 0]]
        }

        lappend framecount $f     
        lappend numHbonds [expr $count1 + $count2]

        if {$detailType != "none"} {
           if {$DA == "D" || $DA == "both"} {
              hbonds::hbonddetails $hbondsingleframe1
           }
           if {$DA == "A" || $DA == "both"} {
              hbonds::hbonddetails $hbondsingleframe2
           }
        }
     } else {
        set hbondsingleframe1 [measure hbonds $dist $ang $sel1]
        set count1 [llength [lindex $hbondsingleframe1 0]]

        lappend framecount $f     
        lappend numHbonds $count1

        if {$detailType != "none"} {
           hbonds::hbonddetails $hbondsingleframe1
        }

     }
  }


  # delete the selection if it was created here
  if { ![info exists arg(sel1)] } {
    $sel1 delete
  }

  if {[info exists sel2]} {
     if { ![info exists arg(sel2)] } {
        $sel2 delete
     }
  }

  if { $writefile } {

     set statusMsg "Printing frame/hbond data to file... "
     update
     puts -nonewline $log $statusMsg
     flush $log

     set outfile [open [file join $outdir $datfile] w]
     if $debug {
       puts $log "Printing to file $datfile"
     }
     
     foreach fr $framecount hb $numHbonds {
        puts $outfile "$fr $hb"
     }
     unset fr hb
     close $outfile
     
     append statusMsg "Done."
     update
     puts $log "Done."
     flush $log
  }

  if {$detailType != "none"} {
     if { $writefile } {
        set outfile [open [file join $outdir $detailFile] w]
        if $debug {
          puts $log "Printing detailed hbond info to file $detailFile"
        }
     } else { set outfile "stdout" }
     set statusMsg "Printing results ... "
     update
     puts $outfile "Found [llength $hbondcount] hbonds."
     if { $multichain } {
        puts -nonewline $outfile "donor \t\t\t "
     } else { puts -nonewline $outfile "donor \t\t " }
     if { $multichain } {
        puts $outfile "acceptor \t\t occupancy"
     } else { puts $outfile "acceptor \t occupancy" }
     foreach { h } $hbondallframes { o } $hbondcount {
         set occupancy [expr { 100*$o/($numberofframes+0.0) } ]
         set i -1
         if { $multichain } { puts -nonewline $outfile "Seg[lindex $h [incr i]]-" }
###         if { $multichain } { puts -nonewline $outfile "Chain[lindex $h [incr i]]-" }
         if { $detailType != "unique" } {
            puts -nonewline $outfile [format "%s%s%s \t " \
            [lindex $h [incr i]] [lindex $h [incr i]] [lindex $h [incr i]]]
         } else {
            puts -nonewline $outfile [format "%s%s%s%s \t " \
            [lindex $h [incr i]] [lindex $h [incr i]] [lindex $h [incr i]] [lindex $h [incr i]]]
         }
         if { $multichain } { puts -nonewline $outfile "Seg[lindex $h [incr i]]-" }
###         if { $multichain } { puts -nonewline $outfile "Chain[lindex $h [incr i]]-" }
         if { $detailType != "unique" } {
            puts $outfile [format "%s%s%s \t %.2f%%" \
            [lindex $h [incr i]] [lindex $h [incr i]] [lindex $h [incr i]] $occupancy]
          } else {
            puts $outfile [format "%s%s%s%s \t %.2f%%" \
            [lindex $h [incr i]] [lindex $h [incr i]] [lindex $h [incr i]] [lindex $h [incr i]] $occupancy]
         }
     }
     if { $outfile != "stdout" } {
        close $outfile
     }
   


  }


  if { $plotHbonds } {

     set title [format "%s %s %s: %s" Molecule $molid, [molinfo $molid get name]  "H-Bonds vs. Frame"]

     # feed everything to the plotter
     set plothandle [multiplot -title $title -xlabel "Frame " -ylabel "No. Bonds"]

     $plothandle add $framecount $numHbonds -lines -linewidth 1 -linecolor black -marker none 
     $plothandle replot
  }

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

  set statusMsg "Done."
  update

  return

}


# This gets called by VMD the first time the menu is opened.
proc hbonds_tk_cb {} {
  hbondsgui   ;# start the PDB Tool
  return $::hbonds::w
}


proc ::hbonds::sel2_state {args} {
  variable w
  variable atomselectText2
  variable guiDA
  variable defaultDA

  # Disable the prefix file field
  if {$atomselectText2 == ""} {
    if {[winfo exists $w.in.cutoffs]} {
      $w.in.cutoffs.type11 configure -state disabled
      $w.in.cutoffs.type12 configure -state disabled
      set guiDA $defaultDA
    }
  } else {
    if {[winfo exists $w.in.cutoffs]} {
      $w.in.cutoffs.type11 configure -state normal
      $w.in.cutoffs.type12 configure -state normal
    }
  }

}

proc ::hbonds::write_state {args} {
  variable w
  variable guiWrite
  variable guiType

  # Disable the prefix file field
  if {$guiWrite == 0} {
    if {[winfo exists $w.out.all]} {
      $w.out.all.fbdata configure -state disabled
      $w.out.all.datname configure -state disabled
    }
  } else {
    if {[winfo exists $w.out.all]} {
      $w.out.all.fbdata configure -state normal
      $w.out.all.datname configure -state normal
    }
  }
  if {$guiWrite == 0 || $guiType == "none"} {
    if {[winfo exists $w.out.all]} {
      $w.out.all.detdata configure -state disabled
      $w.out.all.detname configure -state disabled
    }
  } else {
    if {[winfo exists $w.out.all]} {
      $w.out.all.detdata configure -state normal
      $w.out.all.detname configure -state normal
    }
  }

}




proc hbonds::hbonddetails {hbondlist} {
   
   variable molid
   variable hbondcount 
   variable hbondallframes
   variable multichain 
   variable detailType

   set framehbond {}

      foreach { d } [lindex $hbondlist 0] { a } [lindex $hbondlist 1] {
          set newhbond_donor {}
          set donor [atomselect $molid "index $d"]
          if $multichain { lappend newhbond_donor [$donor get segname] }
###          if $multichain { lappend newhbond_donor [$donor get chain] }

          lappend newhbond_donor [$donor get resname] [$donor get resid]
          set atomname [$donor get name]
          if { [ lsearch { "N" "CA" "C" "O" } $atomname ] != -1 } {
             lappend newhbond_donor "-Main"
          } else {
             lappend newhbond_donor "-Side"
          }
          if { $detailType == "unique" } {
#             if { [lsearch { "OD1" "OD2" "OE1" "OE2" "OT1" "OT2" "NH1" "NH2" } $atomname] != -1 } {
#                lappend newhbond_donor "-[string range $atomname 0 1]"
#             } else { lappend newhbond_donor "-$atomname" }
              lappend newhbond_donor "-$atomname" 
          }
          # add support for water molecule here
          if { [$donor get chain] == "W" } {
             set newhbond_donor {}
             if $multichain { lappend newhbond_donor "W" }
             lappend newhbond_donor "water" "" "-O  "
             if { $detailType == "unique" } { lappend newhbond_donor " " }
          }
          $donor delete

          set newhbond_acceptor {}
          set acceptor [atomselect $molid "index $a"]
          if $multichain { lappend newhbond_acceptor [$acceptor get segname] }
###          if $multichain { lappend newhbond_acceptor [$acceptor get chain] }
          lappend newhbond_acceptor [$acceptor get resname] [$acceptor get resid]
          set atomname [$acceptor get name]
          if { [ lsearch { "N" "CA" "C" "O" } $atomname ] != -1 } {
             lappend newhbond_acceptor "-Main"
          } else {
             lappend newhbond_acceptor "-Side"
          }
          if { $detailType == "unique" } {
#             if { [lsearch { "OD1" "OD2" "OE1" "OE2" "OT1" "OT2" "NH1" "NH2" } $atomname] != -1 } {
#                lappend newhbond_acceptor "-[string range $atomname 0 1]"
#             } else { lappend newhbond_acceptor "-$atomname" }
              lappend newhbond_acceptor "-$atomname"
          }
          # add support for water molecule here
          if { [$acceptor get chain] == "W" } {
             set newhbond_acceptor {}
             if $multichain { lappend newhbond_acceptor "W" }
             lappend newhbond_acceptor "water" "" "-O  "
             if { $detailType == "unique" } { lappend newhbond_acceptor " " }
          }
          $acceptor delete

          set newhbond [concat $newhbond_donor $newhbond_acceptor]
          if { [lsearch $framehbond $newhbond] == -1 } {
             if { $detailType != "all" } { lappend framehbond $newhbond }
             set hbondexist [lsearch $hbondallframes $newhbond]
             if { $hbondexist == -1 } {
                lappend hbondallframes $newhbond
                lappend hbondcount 1
             } else {
                lset hbondcount $hbondexist [expr { [lindex $hbondcount $hbondexist] + 1 } ]
             }
          }
     }
return

}