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clustering.tcl
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clustering.tcl
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#
# Clustering Tool v2.0
#
# A clustering tool to represent clusters in VMD.
#
# http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/cluster
# Author
# ------
# Luis Gracia, PhD
#
# Scientific Software Specialist
# Department of Physiology & Biophysics
# Weill Cornell Medical College
# 1300 York Avenue, Rm LC-501F
# New York, NY 10065
#
# Documentation
# -------------
# See the index.html file distributed with this file. For more update documentation see
# http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/cluster
# ToDo:
# - control clusters of different molecules:
# - add a dimension to array cluster.
# - change in molecule, switches to the cluster.
# - delete data of a molecule if a molecule no longer exists.
# - better parse on import to remove extra blanks
package provide clustering 2.0
namespace eval ::clustering:: {
namespace export clustering
}
# Hook for vmd, start the GUI
proc clustering_tk_cb {} {
clustering::cluster
return $clustering::w
}
proc clustering::destroy {} {
# Delete traces
# Delete remaining selections
global vmd_initialize_structure
trace vdelete vmd_initialize_structure w [namespace code UpdateMolecules]
}
# Main window
proc clustering::cluster {} {
variable w; # TK window
variable webpage "http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/cluster"
variable cluster; # Array with all levels clustering (set on import)
variable cluster0; # Array with current selected level
variable clust_file; # File used to load clustering data
variable clust_mol; # Molecule use to show clustering
variable clust_list; # Listbox with clusters for selected level
variable level_list; # Listbox with available clustering levels
variable conf_list; # Listbox with conformations for a level
variable confs; # Array with reverse lookup for conformations
variable join_1members 1; # Join single member clusters in a separate cluster
variable bb_def "C CA N"; # Backbone definition (diferent from VMD's definition)
variable bb_only 0; # Selection modifier (only name CA C N)
variable trace_only 0; # Selection modifier (only name CA)
variable noh 1; # Selection modifier (no hydrogens)
# Variables for measure cluster
variable calc_num 5; # number of clusters
variable calc_cutoff 1.0; # cutoff
variable calc_first 0; # first frame
variable calc_last -1; # last frame
variable calc_step 1; # frame step
variable calc_distfunc "rmsd"; # distance function
variable calc_selupdate 0; # selection update
variable calc_weight "none"; # weighting factor
global vmd_initialize_structure
if {[molinfo num] > 0} {
set clust_mol [molinfo top get id]
}
# If already initialized, just turn on
if { [winfo exists .clustering] } {
wm deiconify $w
return
}
# GUI look
option add *clustering.*borderWidth 1
option add *clustering.*Button.padY 0
option add *clustering.*Menubutton.padY 0
# Main window
set w [toplevel ".clustering"]
wm title $w "Clustering Tool"
wm resizable $w 1 1
bind $w <Destroy> [namespace current]::destroy
# Menu
# -------------
frame $w.menubar -relief raised -bd 2
pack $w.menubar -fill x
# Import menu
menubutton $w.menubar.import -text "Import" -underline 0 -menu $w.menubar.import.menu
pack $w.menubar.import -side left
menu $w.menubar.import.menu -tearoff no
$w.menubar.import.menu add command -label "NMRcluster..." -command "[namespace current]::import nmrcluster"
$w.menubar.import.menu add command -label "Xcluster..." -command "[namespace current]::import xcluster"
$w.menubar.import.menu add command -label "Cutree (R)..." -command "[namespace current]::import cutree"
$w.menubar.import.menu add command -label "Gromacs (g_cluster)..." -command "[namespace current]::import gcluster"
$w.menubar.import.menu add command -label "Charmm..." -command "[namespace current]::import charmm"
$w.menubar.import.menu add command -label "Raw (index list)..." -command "[namespace current]::import raw"
# Menubar / Help menu
menubutton $w.menubar.help -text "Help" -menu $w.menubar.help.menu
pack $w.menubar.help -side right
menu $w.menubar.help.menu -tearoff no
$w.menubar.help.menu add command -label "Help" -command "vmd_open_url $webpage"
$w.menubar.help.menu add command -label "About" -command [namespace current]::about
# Use measure cluster
# -------------
labelframe $w.calc -text "Use measure cluster" -relief ridge -bd 2
pack $w.calc -side top -fill x -anchor nw
frame $w.calc.buttons
pack $w.calc.buttons -side left -anchor nw -fill y -expand 1
button $w.calc.buttons.cluster -text "Calculate" -command [namespace code calculate]
pack $w.calc.buttons.cluster -side top -anchor nw -fill y -expand 1
frame $w.calc.options
pack $w.calc.options -side left -anchor nw
frame $w.calc.options.1
pack $w.calc.options.1 -side top -anchor nw
frame $w.calc.options.1.mol
pack $w.calc.options.1.mol -side left -anchor nw
label $w.calc.options.1.mol.label -text "Mol:"
menubutton $w.calc.options.1.mol.value -relief raised -bd 2 -direction flush \
-textvariable [namespace current]::clust_mol -menu $w.calc.options.1.mol.value.menu
menu $w.calc.options.1.mol.value.menu -tearoff no
pack $w.calc.options.1.mol.label $w.calc.options.1.mol.value -side left
frame $w.calc.options.1.first
pack $w.calc.options.1.first -side left -anchor nw
label $w.calc.options.1.first.label -text "First:"
entry $w.calc.options.1.first.value -width 5 -textvariable [namespace current]::calc_first
pack $w.calc.options.1.first.label $w.calc.options.1.first.value -side left -anchor nw
frame $w.calc.options.1.last
pack $w.calc.options.1.last -side left -anchor nw
label $w.calc.options.1.last.label -text "Last:"
entry $w.calc.options.1.last.value -width 5 -textvariable [namespace current]::calc_last
pack $w.calc.options.1.last.label $w.calc.options.1.last.value -side left -anchor nw
frame $w.calc.options.1.step
pack $w.calc.options.1.step -side left -anchor nw
label $w.calc.options.1.step.label -text "Step:"
entry $w.calc.options.1.step.value -width 5 -textvariable [namespace current]::calc_step
pack $w.calc.options.1.step.label $w.calc.options.1.step.value -side left -anchor nw
frame $w.calc.options.2
pack $w.calc.options.2 -side top -anchor nw -fill x -expand 1
frame $w.calc.options.2.ncluster
pack $w.calc.options.2.ncluster -side left -anchor nw
label $w.calc.options.2.ncluster.label -text "Num:"
entry $w.calc.options.2.ncluster.value -width 3 -textvariable [namespace current]::calc_num
pack $w.calc.options.2.ncluster.label $w.calc.options.2.ncluster.value -side left -anchor nw
frame $w.calc.options.2.cutoff
pack $w.calc.options.2.cutoff -side left -anchor nw
label $w.calc.options.2.cutoff.label -text "Cutoff:"
entry $w.calc.options.2.cutoff.value -width 5 -textvariable [namespace current]::calc_cutoff
pack $w.calc.options.2.cutoff.label $w.calc.options.2.cutoff.value -side left -anchor nw
frame $w.calc.options.2.distfunc
pack $w.calc.options.2.distfunc -side left -anchor nw -fill x -expand 1
label $w.calc.options.2.distfunc.label -text "Function:"
menubutton $w.calc.options.2.distfunc.value -relief raised -bd 2 -direction flush \
-textvariable [namespace current]::calc_distfunc -menu $w.calc.options.2.distfunc.value.menu
menu $w.calc.options.2.distfunc.value.menu -tearoff no
foreach distfunc [list rmsd fitrmsd rgyrd] {
$w.calc.options.2.distfunc.value.menu add radiobutton -value $distfunc -label $distfunc -variable [namespace current]::calc_distfunc
}
pack $w.calc.options.2.distfunc.label -side left
pack $w.calc.options.2.distfunc.value -side left -fill x -expand 1
frame $w.calc.options.3
pack $w.calc.options.3 -side top -anchor nw
frame $w.calc.options.3.weight
pack $w.calc.options.3.weight -side left -anchor nw
label $w.calc.options.3.weight.label -text "Weight:"
menubutton $w.calc.options.3.weight.value -width 10 -relief raised -bd 2 -direction flush \
-textvariable [namespace current]::calc_weight -menu $w.calc.options.3.weight.value.menu
menu $w.calc.options.3.weight.value.menu -tearoff no
foreach field [list none user user2 user3 user4 radius mass charge beta occupancy] {
$w.calc.options.3.weight.value.menu add radiobutton -value $field -label $field -variable [namespace current]::calc_weight
}
pack $w.calc.options.3.weight.label $w.calc.options.3.weight.value -side left
checkbutton $w.calc.options.3.selupdate -text "Selupdate" -variable [namespace current]::calc_selupdate
pack $w.calc.options.3.selupdate -side left
# Selection frame
# -------------
labelframe $w.sel -text "Selection" -relief ridge -bd 2
pack $w.sel -side top -fill x
# Selection
frame $w.sel.left
pack $w.sel.left -side left -fill both -expand yes
text $w.sel.left.sel -height 3 -width 25 -highlightthickness 0 -selectborderwidth 0 -exportselection yes -wrap word -relief sunken -bd 1
pack $w.sel.left.sel -side top -fill both -expand yes
$w.sel.left.sel insert end "protein"
# Selections options
frame $w.sel.right
pack $w.sel.right -side right
checkbutton $w.sel.right.bb -text "Backbone" -variable [namespace current]::bb_only -command "[namespace current]::ctrlbb bb"
checkbutton $w.sel.right.tr -text "Trace" -variable [namespace current]::trace_only -command "[namespace current]::ctrlbb trace"
checkbutton $w.sel.right.noh -text "noh" -variable [namespace current]::noh -command "[namespace current]::ctrlbb noh"
pack $w.sel.right.bb $w.sel.right.tr $w.sel.right.noh -side top -anchor nw
# Results
# -------------
labelframe $w.result -text "Results" -relief ridge -bd 2
pack $w.result -side top -fill both -expand 1
# Options
frame $w.result.options
pack $w.result.options -side top -fill x
button $w.result.options.update -text "Update Views" -command [namespace code UpdateSel]
pack $w.result.options.update -side left
checkbutton $w.result.options.join -text "Join 1 member clusters" -variable clustering::join_1members -command [namespace code UpdateLevels]
pack $w.result.options.join -side right
# Data
frame $w.result.data
pack $w.result.data -fill both -expand 1
# Data / Level
frame $w.result.data.level
label $w.result.data.level.label -text "Levels:"
pack $w.result.data.level.label -side top -anchor nw
set level_list [listbox $w.result.data.level.listbox -selectmode single -activestyle dotbox -width 5 -exportselection 0 -yscroll [namespace code {$w.result.data.level.scroll set}] ]
pack $level_list -side left -fill both
scrollbar $w.result.data.level.scroll -command [namespace code {$level_list yview}]
pack $w.result.data.level.scroll -side left -fill y
bind $level_list <<ListboxSelect>> [namespace code UpdateLevels]
pack $w.result.data.level -side left -fill both -expand 1
# Data / cluster
frame $w.result.data.cluster
pack $w.result.data.cluster -side left -fill both -expand 1
label $w.result.data.cluster.label -text "Clusters:"
pack $w.result.data.cluster.label -side top -anchor nw
set clust_list [listbox $w.result.data.cluster.listbox -selectmode multiple -activestyle dotbox -width 10 -exportselection 0 -yscroll [namespace code {$w.result.data.cluster.scroll set}] ]
pack $clust_list -side left -fill both -expand 1
scrollbar $w.result.data.cluster.scroll -command [namespace code {$clust_list yview}]
pack $w.result.data.cluster.scroll -side left -fill y
bind $clust_list <<ListboxSelect>> [namespace code UpdateClusters]
# Data / buttons
frame $w.result.data.buttons
pack $w.result.data.buttons -side left
button $w.result.data.buttons.all -text "All" -command [namespace code {clus_onoff_all 1}]
button $w.result.data.buttons.none -text "None" -command [namespace code {clus_onoff_all 0}]
pack $w.result.data.buttons.all $w.result.data.buttons.none -side top
# Data / confs
frame $w.result.data.confs
pack $w.result.data.confs -side left -fill both -expand 1
label $w.result.data.confs.label -text "Confs:"
pack $w.result.data.confs.label -side top -anchor nw
set conf_list [listbox $w.result.data.confs.listbox -selectmode multiple -activestyle dotbox -width 5 -exportselection 0 -yscroll [namespace code {$w.result.data.confs.scroll set}] ]
pack $conf_list -side left -fill both -expand 1
scrollbar $w.result.data.confs.scroll -command [namespace code {$conf_list yview}]
pack $w.result.data.confs.scroll -side left -fill y
bind $conf_list <<ListboxSelect>> [namespace code UpdateConfs]
# Set up the molecule list
trace variable vmd_initialize_structure w [namespace current]::UpdateMolecules
[namespace current]::UpdateMolecules
}
#############################################################################
# Update GUI
# Update GUI with selected level
proc clustering::UpdateLevels {} {
variable level_list
variable clust_list
variable conf_list
variable confs
variable clust_mol
variable cluster
variable cluster0
variable join_1members
variable colors
variable color
# Reset
$clust_list delete 0 end
$conf_list delete 0 end
if {[info exists confs]} {
unset confs
}
if {[info exists colors]} {
unset colors
}
set color -1
[namespace current]::del_reps $clust_mol
# Copy cluster/level to cluster0
set level [$level_list get [$level_list curselection]]
if {[array exists cluster0]} {unset cluster0}
foreach key [array names cluster $level:*] {
regsub "$level:" $key {} name
set cluster0($name) $cluster($key)
}
# Join 1 members if requested
if {$join_1members} {
[namespace current]::join_1members
}
set nclusters [array size cluster0]
set names [lsort -dictionary [array names cluster0]]
#puts "DEBUG: nclusters= $nclusters; names $names"
# Find number of conformations
set nconfs 0
foreach key [array names cluster0] {
set nconfs [expr {$nconfs + [llength $cluster0($key)]}]
foreach el $cluster0($key) {
lappend oconfs $el
}
}
set oconfs [lsort -integer $oconfs]
#puts "DEBUG: nconfs $nconfs"
#puts "DEBUG: oconfs $oconfs"
# Populate list of conformations
for {set i 0} {$i < [llength $oconfs]} {incr i} {
set el [lindex $oconfs $i]
$conf_list insert end $el
set confs($el) $i
}
# Populate list of clusters and add representations
for {set num 0} {$num < $nclusters} {incr num} {
regsub "$level:" [lindex $names $num] {} name
[namespace current]::populate $num $name
[namespace current]::add_rep $num $name
}
$clust_list selection set 0 [expr {$nclusters-1}]
$conf_list selection set 0 end
if {[regexp {^none} [$clust_list get [expr {$nclusters-1}]]]} {
[namespace current]::clus_onoff 0 [expr {$nclusters-1}]
}
}
# Populate cluster listbox
proc clustering::populate {num name} {
variable clust_list
variable conf_list
variable confs
variable cluster0
#puts "DEBUG: populate cluster $num ($name): $cluster0($name)"
# Choose color
set col [[namespace current]::next_color]
set rgb [[namespace current]::index2rgb $col]
set bw [[namespace current]::bw $rgb]
# Add clusters to list and change conformation color
$clust_list insert end [[namespace current]::name_add_count $name]
$clust_list itemconfigure $num -selectbackground $rgb -selectforeground $bw
foreach conf $cluster0($name) {
$conf_list itemconfigure $confs($conf) -selectbackground $rgb -selectforeground $bw
}
}
# Update clusters
proc clustering::UpdateClusters {} {
variable clust_list
variable cluster0
for {set i 0} {$i < [array size cluster0]} {incr i} {
if {[$clust_list selection includes $i]} {
[namespace current]::clus_onoff 1 $i
} else {
[namespace current]::clus_onoff 0 $i
}
}
}
# Update conformations
proc clustering::UpdateConfs {} {
variable clust_mol
variable conf_list
variable confs
variable cluster0
variable clust_list
# Create reverse list of clusters belonging to confs
for {set c 0} {$c < [array size cluster0]} {incr c 1} {
set name [[namespace current]::name_del_count $c]
foreach f $cluster0($name) {
set rconfs($f) $c
}
}
# Create list of selected confs
for {set i 0} {$i < [$conf_list size]} {incr i} {
if {[$conf_list selection includes $i]} {
lappend on [$conf_list get $i]
}
}
# create new cluster
if {![info exists on]} {
for {set c 0} {$c < [array size cluster0]} {incr c} {
$clust_list selection clear $c
mol showrep $clust_mol $c off
}
return
}
foreach f $on {
lappend frames($rconfs($f)) $f
}
# apply changes
set names [array names frames]
for {set c 0} {$c < [array size cluster0]} {incr c} {
if {[lsearch -exact $names $c] == -1} {
$clust_list selection clear $c
mol showrep $clust_mol $c off
} else {
if {[$clust_list selection includes $c] == 0} {
$clust_list selection set $c
mol showrep $clust_mol $c on
}
mol drawframes $clust_mol $c $frames($c)
}
}
}
# Update list of molecules
proc clustering::UpdateMolecules {args} {
# Code adapted from the ramaplot plugin
variable w
variable clust_mol
set mollist [molinfo list]
# Update the molecule browser
$w.calc.options.1.mol.value.menu delete 0 end
$w.calc.options.1.mol.value configure -state disabled
if { [llength $mollist] != 0 } {
foreach id $mollist {
if {[molinfo $id get filetype] != "graphics"} {
$w.calc.options.1.mol.value configure -state normal
$w.calc.options.1.mol.value.menu add radiobutton -value $id \
-label "$id [molinfo $id get name]" -variable [namespace current]::clust_mol
}
}
}
}
# Update representations with atomselection
proc clustering::UpdateSel {} {
variable cluster0
variable clust_mol
for {set i 0} {$i < [array size cluster0]} {incr i} {
mol modselect $i $clust_mol [[namespace current]::set_sel]
}
}
#############################################################################
# Clusters/Conformations and representations
# Add rep for a cluster
proc clustering::add_rep {num name} {
variable cluster0
variable clust_mol
variable clust_list
variable colors
# puts "LGV: [llength $cluster0($name)]"
# if {[llength $cluster0($name)] == 0} {
# return
# }
foreach f $cluster0($name) {
lappend frames $f
}
mol rep lines
mol selection [[namespace current]::set_sel]
mol addrep $clust_mol
mol drawframes $clust_mol $num $frames
set col [lindex $colors $num]
mol modcolor $num $clust_mol ColorID $col
}
# Delete all reps
proc clustering::del_reps {clust_mol} {
set numreps [molinfo $clust_mol get numreps]
for {set f 0} {$f <= $numreps} {incr f 1} {
mol delrep 0 $clust_mol
}
}
# Set on/off one or more clusters
proc clustering::clus_onoff_all {state} {
variable cluster0
for {set c 0} {$c < [array size cluster0]} {incr c 1} {
[namespace current]::clus_onoff $state $c
}
}
# Set on/off a cluster
proc clustering::clus_onoff {state clus} {
variable clust_mol
variable cluster0
variable clust_list
variable conf_list
variable confs
variable w
set name [[namespace current]::name_del_count $clus]
#puts "DEBUG: cluster $clus name $name"
if { $state == 0 } {
$clust_list selection clear $clus
} else {
$clust_list selection set $clus
}
set this $cluster0($name)
if { $state == 0 } {
foreach f $this {
$conf_list selection clear $confs($f)
}
mol showrep $clust_mol $clus off
} else {
foreach f $this {
$conf_list selection set $confs($f)
lappend frames $f
}
mol drawframes $clust_mol $clus $frames
mol showrep $clust_mol $clus on
}
}
# Set on one or more clusters
proc clustering::clus_on {clus} {
[namespace current]::clus_onoff 1 $clus
}
# Set off one or more clusters
proc clustering::clus_off {clus} {
[namespace current]::clus_onoff 0 $clus
}
#############################################################################
# Other
# Select next available color
proc clustering::next_color {} {
variable colors
variable color
incr color
#puts "Color $color [lindex [colorinfo colors] $color]"
# Avoid same color as VMD background
if {[colorinfo index [colorinfo category Display Background]] == $color} {
incr color
#puts " ...same as bg ... switch to $color"
}
# Recycle colors
if {$color > [colorinfo num]} {
set color 0
#puts " ...over max ... switch to $color"
}
#puts "DEBUG: color $color"
lappend colors $color
return $color
}
# Convert a VMD color index to rgb
proc clustering::index2rgb {i} {
set len 2
lassign [colorinfo rgb $i] r g b
set r [expr {int($r*255)}]
set g [expr {int($g*255)}]
set b [expr {int($b*255)}]
#puts "$i $r $g $b"
return [format "#%.${len}X%.${len}X%.${len}X" $r $g $b]
}
# Select black or white color depending on the brightness of the rgb passed
proc clustering::bw {rgb} {
set r [scan [string range $rgb 1 2] "%2x"]
set g [scan [string range $rgb 3 4] "%2x"]
set b [scan [string range $rgb 5 6] "%2x"]
set brightness [expr {$r * 0.299 + $g * 0.587 + $b * 0.114}]
if {$brightness < 186} {
return "#FFFFFF"
} else {
return "#000000"
}
}
# Parse selection
proc clustering::set_sel {} {
variable w
variable bb_only
variable trace_only
variable noh
variable bb_def
regsub -all "\#.*?\n" [$w.sel.left.sel get 1.0 end] "" temp1
regsub -all "\n" $temp1 " " temp2
regsub -all " $" $temp2 "" temp3
if { $trace_only } {
append sel "($temp3) and name CA"
} elseif { $bb_only } {
append sel "($temp3) and name $bb_def"
} elseif { $noh} {
append sel "($temp3) and noh"
} else {
append sel $temp3
}
return $sel
}
# Join single member clusters in a separate cluster
proc clustering::join_1members {} {
variable cluster0
foreach name [array names cluster0] {
#puts "$name - $cluster0($name)"
if {[llength $cluster0($name)] == 1} {
if [info exists cluster0(none)] {
set cluster0(none) [concat $cluster0(none) $cluster0($name)]
} else {
set cluster0(none) $cluster0($name)
}
unset cluster0($name)
}
}
}
# Decrease all members of a list by 1
proc clustering::decrease_list {data} {
for {set i 0} {$i < [llength $data]} {incr i} {
lset data $i [expr {[lindex $data $i] - 1}]
}
return $data
}
# Control selection modifiers
proc clustering::ctrlbb { obj } {
variable w
variable bb_only
variable trace_only
variable noh
if {$obj == "bb"} {
set trace_only 0
set noh 0
} elseif {$obj == "trace"} {
set bb_only 0
set noh 0
} elseif {$obj == "noh"} {
set trace_only 0
set bb_only 0
}
}
# Add number of conformations to cluster name
proc clustering::name_add_count {name} {
variable cluster0
return "$name ([llength $cluster0($name)])"
}
# Remove number of conformations from cluster name
proc clustering::name_del_count {index} {
variable clust_list
if { [ regexp {^([0-9]+|none) \(} [$clust_list get $index] dummy name ] } {
return $name
}
}
# About
proc clustering::about { {parent .clustering} } {
variable webpage
set vn [package present clustering]
tk_messageBox -title "About Clustering v$vn" -parent $parent -message \
"Clustering v$vn
Cluster is a VMD plugin to visualize clusters of conformations of a structure.
More information at:
$webpage
Copyright (C) Luis Gracia <[email protected]>
"
}
#############################################################################
# Import
proc clustering::import {type} {
variable clust_file
variable cluster
variable level_list
set clust_file [tk_getOpenFile -title "Cluster filename" -filetypes [list {"Cluster files" {.out .log .dat .clg}} {"All Files" *}] ]
if {[file readable $clust_file]} {
set fileid [open $clust_file "r"]
if {[array exists cluster]} {unset cluster}
$level_list delete 0 end
[namespace current]::import_$type $fileid
close $fileid
}
}
# NMRCLUSTER (http://neon.chem.le.ac.uk/nmrclust, not working)
proc clustering::import_nmrcluster {fileid} {
variable level_list
variable cluster
# Read data
set i 0
while {![eof $fileid]} {
gets $fileid line
if { [ regexp {^Members:([ 0-9]+)} $line dummy data ] } {
incr i 1
set cluster(0:$i) [[namespace current]::decrease_list $data]
} elseif { [ regexp {^Outliers:([ 0-9]+)} $line dummy data ] } {
foreach d $data {
incr i 1
set cluster(0:$i) [expr {$d - 1}]
}
}
}
$level_list insert end 0
$level_list selection set 0
[namespace current]::UpdateLevels
}
# XCLUSTER (http://www.schrodinger.com)
proc clustering::import_xcluster {fileid} {
variable level_list
variable cluster
# Read data
while {![eof $fileid]} {
gets $fileid line
if { [ regexp {^Starting} $line ] } {
} elseif { [ regexp {^Clustering ([0-9]+); threshold distance ([0-9.]+); ([0-9]+) cluster} $line dummy level threshold ncluster ] } {
#puts "DEBUG: clustering $level $threshold $ncluster"
$level_list insert end $level
} elseif { [ regexp {^Cluster +([0-9]+); Leading member= +([0-9]+); +([0-9]+) members, sep_rat +([0-9.]+)} $line dummy num clust_leader clust_size clust_sep ] } {
#puts "DEBUG: cluster $num $clust_leader $clust_size $clust_sep"
} elseif { [ regexp {^([ 0-9]+)$} $line dummy data ] } {
append cluster($level:$num) [[namespace current]::decrease_list $data]
#puts "DEBUG: adding level $level cluster $num data $data"
}
}
$level_list selection set 0
[namespace current]::UpdateLevels
}
# Output from cutree from R package stats (http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cutree.html)
proc clustering::import_cutree {fileid} {
variable level_list
variable cluster
# Read data
set sep { }
# - levels
gets $fileid line
set levels [split $line $sep]
#puts "DEBUG: levels [join $levels {, }]"
foreach level $levels {
$level_list insert end $level
}
# - membership
while {![eof $fileid]} {
gets $fileid line
if { [regexp {^$} $line dummy] } {
} elseif { [regexp {^#} $line dummy] } {
} else {
set temp [split $line $sep]
set obj [lindex $temp 0]
set membership [lrange $temp 1 end]
#puts "DEBUG: obj $obj; membership [join $membership {, }]"
for {set i 0} {$i < [llength $membership]} {incr i} {
set level [lindex $levels $i]
set num [lindex $membership $i]
#puts "DEBUG: assign $i - $level - $num"
lappend cluster($level:$num) [expr {$obj - 1}]
}
}
}
$level_list selection set 0
[namespace current]::UpdateLevels
}
# GROMACS, output from g_cluster (http://www.gromacs.org/documentation/reference/online/g_cluster.html)
proc clustering::import_gcluster {fileid} {
variable level_list
variable cluster
set start_reading 0
# Read data
while {![eof $fileid]} {
gets $fileid line
if { [regexp {^cl\. \|} $line dummy] } {
#puts "DEBUG: start to read"
set start_reading 1
}
if {$start_reading == 1} {
if { [regexp {^\s*(\d+)\s+\|\s+([\d.e-]+)\s+([\d.]+)\s+\|\s+([\d.e-]+)\s+([\d.]+)\s+\|([\s\d.e-]+)} $line dummy num size st_rmsd middle mid_rmsd members ] } {
# start a new cluster
#puts "DEBUG: cluster $num size $size middle $middle"
#puts "DEBUG: -> $members"
set cluster(0:$num) $members
append times $members
} elseif { [regexp {^\s*(\d+)\s+\|\s+([\d.e-]+)\s+\|\s+([\d.e-]+)\s+\|([\s\d.e-]+)} $line dummy num size middle members ] } {
# start a new cluster with only one conf
#puts "DEBUG: cluster $num size $size middle $middle"
#puts "DEBUG: -> $members"
set cluster(0:$num) $members
append times $members
} elseif { [regexp {^\s+\|\s+\|\s+\|([\s\d.e-]+)} $line dummy members] } {
# add conformations to a cluster
#puts "DEBUG: -> $members"
append cluster(0:$num) $members
append times $members
}
}
}
# Convert time into steps
set sorted [lsort -real $times]
for {set i 0} {$i < [llength $sorted]} {incr i} {
set corr([lindex $sorted $i]) $i
}
foreach key [array names cluster] {
if {[info exists temp2]} {
unset temp2
}
foreach el $cluster($key) {
lappend temp2 $corr($el)
}
set cluster($key) $temp2
}
$level_list insert end 0
$level_list selection set 0
[namespace current]::UpdateLevels
}
# CHARMM
proc clustering::import_charmm {fileid} {
variable level_list
variable cluster
# Read data
while {![eof $fileid]} {
gets $fileid line
#puts "DEBUG: $line"
if { [ regexp {^\s+(\d+)\s+(\d+)\s+(\d+)\s+([\d.eE+-]+)} $line dummy num member series distance ] } {
#puts "DEBUG: $num -> $member -> $series -> $distance"
lappend cluster(0:$num) [expr {$member - 1}]
}
}
$level_list insert end 0
$level_list selection set 0
[namespace current]::UpdateLevels
}
# Raw (list of cluster ids)
proc clustering::import_raw {fileid} {
variable level_list
variable cluster
set member 0
while {![eof $fileid]} {
gets $fileid line
if { [llength $line] == 1 } {
set ID [expr {int($line)}]
lappend cluster(0:$ID) $member
incr member
}
}
$level_list insert end 0
$level_list selection set 0
[namespace current]::UpdateLevels
}
#############################################################################
# Calculate
proc clustering::calculate {} {
variable cluster
variable level_list
variable clust_mol
variable calc_num
variable calc_cutoff
variable calc_first
variable calc_last
variable calc_step
variable calc_distfunc
variable calc_selupdate
variable calc_weight
# Get selection
set seltext [[namespace current]::set_sel]
if {$seltext == ""} {
showMessage "Selection is empty selection!"
return -code return
}
set sel [atomselect $clust_mol $seltext]
# Cluster
set result [measure cluster $sel num $calc_num cutoff $calc_cutoff \
first $calc_first last $calc_last step $calc_step \
distfunc $calc_distfunc selupdate $calc_selupdate weight $calc_weight]
set nclusters [llength $result]
if {$nclusters > 0} {
if {[array exists cluster]} {unset cluster}
$level_list delete 0 end
# Add cluster
for {set num 0} {$num < [expr {$nclusters - 1}]} {incr num} {
if {[llength [lindex $result $num]] > 0} {
set cluster(0:$num) [lindex $result $num]
}
}
# Add unclustered frames
set num [expr {$nclusters - 1}]
set nocluster [lindex $result $num]
for {set i 0} {$i < [llength $nocluster]} {incr i} {
set cluster(0:$num) [lindex $nocluster $i]
incr num
}
$level_list insert end 0