├── Makefile
├── README.md
├── density_profile.tcl
├── density_profile_gui.tcl
├── density_profile_gui.ui
├── density_profile_gui_ui.tcl
├── doc
    ├── ChangeLog
    ├── NOTE.txt.private
    ├── POPC-e-density-profile.png
    ├── POPC-waters-mass-density-profile.png
    ├── README.md
    └── Screenshot-Density Profile Tool.png
├── examples
    ├── Readme.md
    ├── example.tcl
    └── popc
    │   ├── popc_box.psf
    │   └── popc_box.xtc
├── load.tcl
└── pkgIndex.tcl


/Makefile:
--------------------------------------------------------------------------------
 1 | .SILENT:
 2 | 
 3 | VMFILES = pkgIndex.tcl density_profile_gui.tcl density_profile_gui_ui.tcl density_profile.tcl
 4 | VMVERSION = 1.2
 5 | DIR = $(PLUGINDIR)/noarch/tcl/density_profile(VMVERSION)
 6 | 
 7 | 
 8 | bins:
 9 | win32bins:
10 | dynlibs:
11 | staticlibs:
12 | win32staticlibs:
13 | 
14 | distrib:
15 | 	@echo "Copying density_profile $(VMVERSION) files to $(DIR)"
16 | 	mkdir -p $(DIR) 
17 | 	cp $(VMFILES) $(DIR) 
18 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
  1 | VMD Density Profile Tool
  2 | ========================================
  3 | 
  4 | 
  5 | The Density Profile Tool is a VMD [1] analysis plugin that computes
  6 | 1-D projections of various atomic densities. The computation may be
  7 | performed in a single frame, a trajectory, or averaged over multiple
  8 | frames.
  9 | 
 10 |  *  Number density, i.e. average number of atoms per unit volume
 11 |  *  Mass density
 12 |  *  Charge density
 13 |  *  Electron density, i.e. average number of electrons. 
 14 | 
 15 | [1] Visual Molecular Dynamics (VMD), http://www.ks.uiuc.edu/Research/vmd/
 16 | 
 17 | 
 18 | Author
 19 | ----------------------------------------
 20 | Toni Giorgino <br>
 21 | National Research Council of Italy (CNR)  <br>
 22 | toni.giorgino at cnr.it
 23 | 
 24 | 
 25 | 
 26 | Citation
 27 | ----------------------------------------
 28 | 
 29 | Please cite this paper when publishing results obtained with the
 30 | Density Profile Tool:
 31 | 
 32 |  *  Giorgino T. *Computing 1-D atomic densities in macromolecular
 33 |     simulations: The density profile tool for VMD.* Computer Physics
 34 |     Communications. 2014 Jan;185(1):317–22. Available from
 35 |     [doi:10.1016/j.cpc.2013.08.022](https://www.sciencedirect.com/science/article/pii/S0010465513002956)
 36 |     or preprint at [arXiv:1308.5873](https://arxiv.org/abs/1308.5873)
 37 | 
 38 | 
 39 | 
 40 | Installation
 41 | ----------------------------------------
 42 | 
 43 | See instructions [here](https://gist.github.com/tonigi/a9cfaf7642a7fbc13293).
 44 | 
 45 | 
 46 | 
 47 | 
 48 | 	
 49 | Documentation
 50 | ---------------------
 51 | 
 52 | Further documentation is available in the `doc` subdirectory.
 53 | 
 54 | For an extensive description of the tool, together with the comparison
 55 | with experimental data, see the [Density Profile paper](http://www.sciencedirect.com/science/article/pii/S0010465513002956) 
 56 | 
 57 | 
 58 | 
 59 | 
 60 | 
 61 | 
 62 | Quickstart
 63 | ----------------------------------------
 64 | 
 65 | Once correctly installed, a menu item should appear in VMD's
 66 | Extensions menu, under "Extensions>Analysis>Density Profile Tool".
 67 | 
 68 | The plugin can be used interactively or via a scripting interface. See
 69 | the included test script (example.tcl) for an example of in-script
 70 | usage. The script 
 71 | 
 72 | 1. loads Klauda's equilibrated membranes
 73 |    (http://terpconnect.umd.edu/~jbklauda/research/download.html), POPC
 74 |    Bilayer (303.00K, NPT, 35ns, 72 lipids);
 75 | 2. computes the mass density profile for water molecules, showing
 76 |    it as a table and a plot;
 77 | 3. computes the electron density profile for the whole system, showing
 78 |    it as a plot.
 79 | 
 80 | Sample output for point 2.:
 81 | 
 82 | ~~~~~~
 83 | | Bin breaks coordinates: (z, Angstroms)
 84 | 	| Density of water in each bin: (g/mol/A^3)
 85 |  -35.00	  0.00
 86 |  -34.00	  0.28
 87 |  -33.00	  0.65
 88 |  -32.00	  0.61
 89 |  -31.00	  0.62
 90 |  -30.00	  0.60
 91 |  -29.00	  0.62
 92 |  -28.00	  0.56
 93 |  -27.00	  0.56
 94 |  -26.00	  0.61
 95 |  -25.00	  0.55
 96 | [...]
 97 |   28.00	  0.58
 98 |   29.00	  0.64
 99 |   30.00	  0.56
100 |   31.00	  0.57
101 |   32.00	  0.60
102 |   33.00	  0.25
103 |   34.00	  0.00
104 | ~~~~~~
105 | 
106 | 
107 | 
108 | License
109 | ---------------
110 | 
111 | Density Profile Plugin
112 | Copyright (C) 2012 
113 | 
114 | This program is free software: you can redistribute it and/or modify
115 | it under the terms of the GNU General Public License as published by
116 | the Free Software Foundation, either version 3 of the License, or
117 | (at your option) any later version.
118 | 
119 | This program is distributed in the hope that it will be useful,
120 | but WITHOUT ANY WARRANTY; without even the implied warranty of
121 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
122 | GNU General Public License for more details.
123 | 
124 | You should have received a copy of the GNU General Public License
125 | along with this program.  If not, see <http://www.gnu.org/licenses/>.
126 | 


--------------------------------------------------------------------------------
/density_profile.tcl:
--------------------------------------------------------------------------------
  1 | # Core functions for computing density profiles. The Density Profile
  2 | # Tool is a VMD analysis plugin that computes 1-D projections of
  3 | # various atomic densities. The computation is performed in a single
  4 | # frame, a trajectory, or averaged over multiple frames.
  5 | 
  6 | # Toni Giorgino, ISIB-Consiglio Nazionale delle Ricerche, 2012
  7 | # http://doi.org/10.1016/j.cpc.2013.08.022
  8 | # https://github.com/giorginolab/vmd_density_profile
  9 | 
 10 | 
 11 | package provide density_profile 1.1
 12 | package require topotools
 13 | package require pbctools
 14 | 
 15 | # Declare the namespace for this dialog
 16 | namespace eval ::density_profile:: {
 17 |     # Variables matching command line options
 18 |     variable dp_args
 19 |     variable dp_args_defaults {
 20 | 	rho             number
 21 | 	selection       all
 22 | 	axis            z
 23 | 	resolution      1
 24 | 	Zsource         mass
 25 | 	partial_charges 1
 26 | 	frame_from      now
 27 | 	frame_to        now
 28 | 	frame_step      1
 29 | 	average		0
 30 |     }
 31 |     array set dp_args $dp_args_defaults
 32 | 
 33 |     # List of args in "preferred" order
 34 |     variable dp_args_list {rho selection axis resolution Zsource partial_charges \
 35 | 			       frame_from frame_to frame_step average}
 36 | 
 37 | }
 38 | 
 39 | 
 40 | # User-accessible proc
 41 | proc density_profile { args } { return [eval ::density_profile::density_profile $args] }
 42 | 
 43 | 
 44 | # Help
 45 | proc ::density_profile::density_profile_usage { } {
 46 |     variable dp_args
 47 |     variable dp_args_list
 48 |     puts "VMD Density Profile tool.  Computes 1-D projections of various atomic densities."
 49 |     puts "The computation is performed in a single frame, a trajectory, or averaged"
 50 |     puts "over multiple frames. You probably want to wrap your trajectory."
 51 |     puts " "
 52 |     puts "Usage: density_profile <args>"
 53 |     puts "Args (with defaults):"
 54 |     foreach k $dp_args_list {
 55 | 	puts "   -$k $dp_args($k)"
 56 |     }
 57 |     puts " "
 58 |     puts "Density  -rho  is one of  {number|mass|charge|electrons}"
 59 |     puts "See documentation at https://github.com/giorginolab/vmd_density_profile"
 60 | }
 61 | 
 62 | 
 63 | # Command line parsing (sets namespace variables). TODO: allow short
 64 | # substrings, e.g. -sel
 65 | proc ::density_profile::parse_args {args} {
 66 |     variable dp_args
 67 |     foreach {a v} $args {
 68 | 	if {![regexp {^-} $a]} {
 69 | 	    error "Argument should start with -: $a"
 70 | 	} 
 71 | 	set a [string trimleft $a -]
 72 | 	if {![info exists dp_args($a)]} {
 73 | 	    error "Unknown argument: $a"
 74 | 	} 
 75 | 	set dp_args($a) $v
 76 |     }
 77 | }
 78 | 
 79 | 
 80 | # Main entry point. 
 81 | proc ::density_profile::density_profile {args} {
 82 |     variable dp_args
 83 |     variable dp_args_defaults
 84 |     array set dp_args $dp_args_defaults
 85 |     if {[llength $args]==0} {
 86 | 	density_profile_usage
 87 | 	return
 88 |     } 
 89 |     eval parse_args $args
 90 | 
 91 |     # parray dp_args
 92 | 
 93 |     # Compute the bare histogram
 94 |     set lhist [compute]
 95 | 
 96 |     # Reformat the histogram and return it
 97 |     set xbreaks [hist_to_xbreaks $lhist]
 98 |     set framelist [get_framelist]
 99 |     set values [hist_to_values $lhist]
100 | 
101 |     # If averaging or single-frame, flatten inner list
102 |     if { $dp_args(average)==1 || [llength $framelist]==1 } {
103 | 	set values [average_sublists $values]
104 |     }
105 | 
106 |     return [list $values $xbreaks]
107 | 
108 | }
109 | 
110 | 
111 | # Convert histogram into lists of values.  If resolution=2 and
112 | #  hist(2,-3)=0.23   ; hist(2,-1)=0.21;
113 | #  hist(4,-2)=0.42   ; hist(4,0)=0.40 =>
114 | 
115 | # Convert histogram into list of breaks => {-6, -4, -2, 0}
116 | proc ::density_profile::hist_to_xbreaks {lhist} {
117 |     variable dp_args
118 |     array set hist $lhist
119 |     lassign [get_x_range [array names hist]]  binmin binmax
120 | 
121 |     set xbreaks {}
122 |     for {set bin $binmin} {$bin<=$binmax} {incr bin} {
123 | 	lappend xbreaks [expr $bin*$dp_args(resolution)]
124 |     }
125 |     return $xbreaks
126 | }
127 | 
128 | 
129 | # Values, return { {0.23 0} {0 0.42} {0.21 0} {0 0.40} }
130 | proc ::density_profile::hist_to_values {lhist} {
131 |     variable dp_args
132 |     array set hist $lhist
133 |     lassign [get_x_range [array names hist]]  binmin binmax
134 |     set framelist [get_framelist]
135 | 
136 |     # Outer cycle is on bins
137 |     set v {}
138 |     set nbins [expr $binmax-$binmin+1]
139 | 
140 |     for {set idx 0} {$idx<$nbins} {incr idx} {
141 | 	set bin [expr $idx+$binmin]
142 | 	set tmp {}
143 | 	# Inner cycle on frames
144 | 	foreach f $framelist {
145 | 	    lappend tmp $hist($f,$bin)
146 | 	}
147 | 	lappend v $tmp
148 |     }
149 |     return $v
150 | }
151 | 
152 | 
153 | # Average sublists: { {0.23 0} {0 0.42} {0.21 0} {0 0.40} } -> { 0.125
154 | # 0.21 0.105 0.20 }. Also useful for flattening in case of one frame
155 | proc ::density_profile::average_sublists {vl} {
156 |     set res {}
157 |     foreach l $vl {
158 | 	lappend res [vecmean $l]
159 |     }
160 |     return $res
161 | }
162 | 
163 | 
164 | 
165 | # Similar to average_sublists, but returns standard deviation of each bin.
166 | proc ::density_profile::stddev_sublists {vl} {
167 |     set res {}
168 |     foreach l $vl {
169 | 	lappend res [vecstddev $l]
170 |     }
171 |     return $res
172 | }
173 | 
174 | 
175 | 
176 | 
177 | # Compute and return the bare histogram. Relation between bins and
178 | # coordinate is implicit; note that [0..$resolution) goes in bin 0,
179 | # and so on. 
180 | #
181 | # This is the workhorse function, assumes namespace variables are
182 | # properly set.
183 | #
184 | #  bin = [expr int(floor($x/$resolution))] 
185 | #  xmin = $bin * $resolution
186 | #
187 | #  hist(frame,bin)
188 | #
189 | # The hist structure is contrieved because we don't know the bins
190 | # until all of the frames have been scanned
191 | 
192 | proc ::density_profile::compute { } {
193 |     variable dp_args
194 | 
195 |     set resolution $dp_args(resolution)
196 |     set axis $dp_args(axis)
197 | 
198 |     # Check if PBC box is set
199 |     set area [transverse_area]
200 |     set area_len [llength $area]
201 |     if { $area_len == 1 } {
202 | 	if { $area == -1 } { 	
203 | 	    puts "Warning: No periodic cell information. Computing linear densities instead of volume densities."
204 | 	    set area [lrepeat [molinfo top get numframes] 1.0]
205 | 	} elseif { $area <= -2 } {
206 | 	    error "Cannot compute density, check arguments."
207 | 	}
208 |     }
209 |     
210 |     # Values
211 |     set rho [get_rho]
212 | 
213 |     # Build atomselection
214 |     set as [atomselect top $dp_args(selection)]
215 | 
216 |     # Start loop over frames
217 |     array unset hist
218 |     set framelist [get_framelist]
219 |     foreach f $framelist {
220 | 	$as frame $f
221 | 	set xval [$as get $axis]
222 | 
223 | 	# get area now and normalize density 
224 | 	# TODO profile
225 | 	set area_now [lindex $area $f]
226 | 	set rho_norm [vecscale [expr 1./$area_now/$resolution] $rho]
227 | 
228 | 	# make histogram: hist(frame,bin)
229 | 	foreach x $xval vn $rho_norm {
230 | 	    # bin
231 | 	    set bin [expr int(floor($x/$resolution))]
232 | 	    if {! [info exists hist($f,$bin)] } { set hist($f,$bin) 0.0 }
233 | 	    set hist($f,$bin) [expr $hist($f,$bin)+$vn]
234 | 	}
235 |     }
236 |     $as delete
237 | 	
238 |     # make bins for never-seen values
239 |     fill_keys hist
240 | 
241 |     # Return histogram 
242 |     return [array get hist]
243 | 
244 | }
245 | 
246 | 
247 | 
248 | # Sanity check on PBC. Return values
249 | #   -1 if LINEAR densities can be still computed,
250 | #   -2 if non-orthorhombic
251 | #   -3 if wrong axis
252 | #  else return a list of the transversal PBC area per frame
253 | proc ::density_profile::transverse_area { } {
254 |     variable dp_args
255 |     set axis $dp_args(axis)
256 |     set pb_list [pbc get -all]
257 |     set area_list {};		# to hold results
258 | 
259 |     foreach pb $pb_list {
260 | 	lassign $pb a b c alpha beta gamma
261 | 	# heuristic for unset box
262 | 	if {$a<2 || $b<2 || $c<2} {	
263 | 	    return -1;		# immediately
264 | 	} elseif {$alpha!= 90 || $beta!=90 || $gamma!=90} {
265 | 	    puts "Only orthorombic cells are supported"
266 | 	    return -2;		# immediately
267 | 	} else {
268 | 	    switch -- $axis {
269 | 		x { set area [expr $b*$c] }
270 | 		y { set area [expr $a*$c] }
271 | 		z { set area [expr $a*$b] }
272 | 		default {
273 | 		    puts "Wrong axis $axis, must be one of x,y or z"
274 | 		    set area -3
275 | 		}
276 | 	    }
277 | 	    lappend area_list $area
278 | 	}
279 |     }
280 |     return $area_list
281 | }
282 | 
283 | 
284 | 
285 | 
286 | # return the range over the 1st and 2nd dimension of a pseudo-2d array
287 | # e.g. {2,3 5,4 2,4} -> {3 4}
288 | proc ::density_profile::get_x_range {kk} {    
289 |     foreach k $kk {
290 | 	lappend xlist [lindex [split $k ,] 1]
291 |     }
292 |     set xlist [lsort -uniq -integer $xlist]
293 |     set xmin [lindex $xlist 0]
294 |     set xmax [lindex $xlist end]
295 |     return [list $xmin $xmax]
296 | }
297 | 
298 | 
299 | # fill histogram keys so that there is one integer bin per each value
300 | # between mi and max
301 | # 
302 | proc ::density_profile::fill_keys arr {
303 |     upvar $arr inp
304 |     set keys [array names inp]
305 |     lassign [get_x_range $keys]  xmin xmax
306 |     set framelist [get_framelist]
307 |     # puts "Filling frames $framelist, bins $xmin..$xmax"
308 | 
309 |     foreach f $framelist {
310 | 	for {set x $xmin} {$x<=$xmax} {incr x} {
311 | 	    if { ![info exists inp($f,$x)] } {
312 | 		set inp($f,$x) 0
313 | 	    }
314 | 	}
315 |     }
316 | }
317 | 
318 | 
319 | # Auxiliary function, returns {from to step}, after possibly fixing
320 | # "now". TODO first, last
321 | proc ::density_profile::get_framelist {} {
322 |     variable dp_args
323 |     set f $dp_args(frame_from)
324 |     set t $dp_args(frame_to)
325 |     set s $dp_args(frame_step)
326 | 
327 |     # Should be the atom selection frame?
328 |     if { $f=="now" } { set f [molinfo top get frame] }
329 |     if { $t=="now" } { set t [molinfo top get frame] }
330 | 
331 |     for {set i $f} {$i<=$t} {incr i $s} {
332 | 	lappend fl $i
333 |     }
334 |     return $fl
335 | }
336 | 
337 | 
338 | # Return the values of the selected property, as a list of one value
339 | # per selected atom. These will not change per-frame.
340 | # 
341 | proc ::density_profile::get_rho {} {
342 |     variable dp_args
343 |     set as [atomselect top $dp_args(selection)]
344 |     if { [$as num]==0 } {
345 | 	$as delete
346 | 	error "Atom selection did not match any atom."
347 |     }
348 |     switch $dp_args(rho) {
349 | 	number { 
350 | 	    set tval [lrepeat [$as num] 1] 
351 | 	}
352 | 	mass { 
353 | 	    set tval [$as get mass] 
354 | 	}
355 | 	charge { 
356 | 	    set tval [$as get charge] 
357 | 	}
358 | 	electrons { 
359 | 	    set tval [getZ $as]
360 | 	    if {$dp_args(partial_charges)==1} {
361 | 		set pch [$as get charge]
362 | 		set tval [vecsub $tval $pch]
363 | 	    }
364 | 	}
365 | 	default {
366 | 	    $as delete
367 | 	    error "Unknown rho, must be one of {number|mass|charge|electrons}"
368 | 	}
369 |     }
370 |     $as delete
371 |     return $tval
372 | }
373 | 
374 | 
375 | # Similar to [atomselect get ...] , but get Z number, based on the
376 | # $Zsource option  . Requires an atomselection
377 | proc ::density_profile::getZ {as} {
378 |     variable dp_args
379 |     set attr $dp_args(Zsource)
380 | 
381 |     # If anything different than element was required, use
382 |     # topotools. This will modify the "element" attribute, so make a
383 |     # backup and restore when done.
384 |     if { $attr == "element" } {
385 | 	set res [$as get atomicnumber]
386 |     } else {
387 | 	set o_Z [$as get atomicnumber]
388 | 	topo guessatom element $attr
389 | 	set res [$as get atomicnumber]
390 | 	$as set atomicnumber $o_Z
391 |     }
392 | 
393 |     # Z=0 or Z=-1 means unidentified
394 |     if { [lsearch $res 0 ] != -1 || 
395 | 	 [lsearch $res -1] != -1} {
396 | 	error "Could not guess element for some atoms." 
397 |     }
398 | 
399 |     return $res
400 | }
401 | 
402 | 
403 | 


--------------------------------------------------------------------------------
/density_profile_gui.tcl:
--------------------------------------------------------------------------------
  1 | #!/usr/bin/env wish# density_profile_gui.tcl --
  2 | #
  3 | # UI generated by GUI Builder Build 146 on 2012-12-18 18:22:59 from:
  4 | #    /home/toni/compile/vmd-utils/vmd_density_profile/density_profile_gui.ui
  5 | # This file is auto-generated.  Only the code within
  6 | #    '# BEGIN USER CODE'
  7 | #    '# END USER CODE'
  8 | # and code inside the callback subroutines will be round-tripped.
  9 | # The proc names 'ui' and 'init' are reserved.
 10 | #
 11 | 
 12 | package require Tk 8.4
 13 | 
 14 | # Declare the namespace for this dialog
 15 | namespace eval density_profile_gui {}
 16 | 
 17 | # Source the ui file, which must exist
 18 | set density_profile_gui::SCRIPTDIR [file dirname [info script]]
 19 | source [file join $density_profile_gui::SCRIPTDIR density_profile_gui_ui.tcl]
 20 | 
 21 | # BEGIN USER CODE
 22 | # ----------------------------------------
 23 | # GUI functions for computing density profiles.
 24 | # ----------------------------------------
 25 | 
 26 | # This code is a mess because it can be loaded back in guibuilder.
 27 | package provide density_profile_gui 1.1
 28 | 
 29 | namespace eval density_profile_gui {
 30 |     variable already_registered 0
 31 | }
 32 | 
 33 | # VMD-specific stuff. If invoked from VMD, load the backed functions
 34 | # (in package density_profile) and setup some defaults.
 35 | set density_profile_gui::in_vmd [string length [info proc vmd_install_extension]]
 36 | if { $density_profile_gui::in_vmd } {
 37 |     package require density_profile
 38 | } else {
 39 |     #  Kludge to run outside VMD
 40 |     namespace eval ::density_profile:: {}
 41 |     array set ::density_profile::dp_args {}
 42 | }
 43 | 
 44 | # Called right upon menu action
 45 | proc density_profile_gui::density_profile_tk {} {
 46 |     variable density_profile_window
 47 | 
 48 |     if { [winfo exists .density_profile] } {
 49 | 	wm deiconify $density_profile_window
 50 |     } else {
 51 | 	set density_profile_window [ toplevel ".density_profile" ]
 52 | 	wm title $density_profile_window "Density Profile Tool"
 53 | 	density_profile_gui::ui $density_profile_window;
 54 |     }
 55 |     return $density_profile_window
 56 | }
 57 | 
 58 | # Register menu if possible
 59 | proc density_profile_gui::register_menu {} {
 60 |     variable already_registered
 61 |     if {$already_registered==0} {
 62 | 	incr already_registered
 63 | 	vmd_install_extension density_profile_gui density_profile_gui::density_profile_tk "Analysis/Density Profile Tool"
 64 |     }
 65 | }
 66 | 					
 67 | 
 68 | 
 69 | # Only enable Z-related controls for electron densities
 70 | proc density_profile_gui::update_Zsource_state {} {
 71 |     variable ::density_profile::dp_args
 72 |     variable density_profile_window
 73 |     set rho  $dp_args(rho)
 74 |     set state disabled
 75 |     if {$rho=="electrons"} {
 76 | 	set state normal
 77 |     }
 78 |     $density_profile_window.radiobutton_Zsource_element configure -state $state
 79 |     $density_profile_window.radiobutton_Zsource_mass configure -state $state
 80 |     $density_profile_window.radiobutton_Zsource_name configure -state $state
 81 |     $density_profile_window.radiobutton_Zsource_type configure -state $state
 82 |     $density_profile_window.checkbox_Zsource_partial configure -state $state
 83 | }
 84 | 
 85 | 
 86 | 
 87 | # Return the title to show on the vertical axis. For now simply
 88 | # returns rho
 89 | proc density_profile_gui::get_title {} {
 90 |     set rho $::density_profile::dp_args(rho)
 91 |     return $rho
 92 | }
 93 | 
 94 | # Return the unit to show on the vertical axis
 95 | proc density_profile_gui::get_units {} {
 96 |     set rho $::density_profile::dp_args(rho)
 97 |     array set ylabel {number atoms   mass amu  charge e  electrons el}
 98 |     return $ylabel($rho)
 99 | }
100 | 
101 | # Nested list transpose http://wiki.tcl.tk/2748
102 | proc density_profile_gui::transpose {matrix} {
103 |    for {set index 0} {$index < [llength [lindex $matrix 0]]} {incr index} {
104 |        lappend res [lsearch -all -inline -subindices  -index $index $matrix *]
105 |    }
106 |    return $res
107 | }
108 | 
109 | proc density_profile_gui::help_docs {} {
110 |     vmd_open_url https://doi.org/10.1016/j.cpc.2013.08.022
111 | }
112 | 
113 | proc density_profile_gui::help_about {} {
114 |     variable density_profile_window
115 |     tk_messageBox -title "About" -parent $density_profile_window -message \
116 | "
117 | VMD Density Profile Tool
118 | 
119 | Version [package versions density_profile]
120 | 
121 | Toni Giorgino <toni.giorgino cnr.it>
122 | National Research Council of Italy (CNR)
123 | 
124 | Until 2011: 
125 | Computational Biophysics Group
126 | Research Programme on Biomedical Informatics (GRIB-IMIM)
127 | Universitat Pompeu Fabra (UPF)
128 | 
129 | "
130 |     
131 | }
132 | 
133 | 
134 | # Uses density_profile::compute to do the backend computation
135 | proc density_profile_gui::do_plot {} {
136 |     variable ::density_profile::dp_args
137 |     variable density_profile_window
138 | 
139 |     set selection  $dp_args(selection)
140 |     set axis       $dp_args(axis)
141 |     set resolution $dp_args(resolution)
142 |     set average    $dp_args(average)
143 | 
144 |     # Make sure pbcs are set or warn
145 |     set area [density_profile::transverse_area]
146 |     if { [llength $area] == 1 && $area == -1 } { 	
147 | 	set answer [ tk_messageBox -icon question -message "No periodic cell information. Will compute linear densities instead of volume densities. Continue?" \
148 | 			 -type okcancel  -parent $density_profile_window]
149 | 	switch -- $answer {
150 | 	    ok { set area 1 }
151 | 	    cancel { error "Cancelled" }
152 | 	}
153 |     } elseif { [llength $area] == 1 && $area == -2 } {
154 | 	tk_messageBox -icon error -message "Only orthorombic cells are supported" -title Error  -parent $density_profile_window
155 | 	error "Only orthorombic cells are supported"
156 |     }
157 | 
158 |     
159 |     # Compute
160 |     set lhist [density_profile::compute]
161 | 
162 |     set framelist [density_profile::get_framelist]
163 |     set values [density_profile::hist_to_values $lhist]
164 | 
165 |     # breaks -> bin centers
166 |     set xbreaks [density_profile::hist_to_xbreaks $lhist]
167 |     foreach b $xbreaks {
168 | 	lappend xcenters [expr $b+0.5*$resolution]
169 |     }
170 | 
171 |     # Title and Y axis label
172 |     if {$average==1} {
173 | 	set title "Average [get_title] density profile (\u00B1 s.d.)"
174 |     } else {
175 | 	set title "[string totitle [get_title]] density profile"
176 |     }
177 |     set ylabel [get_units]
178 |     if {$area == 1} { 
179 | 	set ylabel "$ylabel/\uc5" 
180 |     } else {
181 | 	set ylabel "$ylabel/\uc5\ub3" 
182 |     }
183 |     set xlabel  "Bin center (\u212B)" 
184 | 
185 |     
186 |     # do plot, average case
187 |     if {$average} {
188 | 	set avg [density_profile::average_sublists $values]
189 | 	set std [density_profile::stddev_sublists $values]
190 | 
191 | 	set avgpstd [vecadd $avg $std]
192 | 	set avgmstd [vecsub $avg $std]
193 | 	
194 | 	set ph [multiplot -x $xcenters -y $avg \
195 | 		    -ylabel $ylabel \
196 | 		    -xlabel $xlabel \
197 | 		    -title $title \
198 | 		    -marker point -radius 2  -fillcolor "#ff0000" -color "#ff0000"  ]
199 | 	$ph add $xcenters $avgpstd -dash "," -linecolor  "#000000"
200 | 	$ph add $xcenters $avgmstd -dash "," -linecolor  "#000000"
201 | 	$ph replot
202 |     } else {
203 | 	# Iterate over frames, build a vector, plot it
204 | 	set ph [multiplot -title $title \
205 | 		          -ylabel $ylabel \
206 | 		          -xlabel $xlabel ]
207 | 	set values_t [transpose $values]
208 | 	foreach tmp $values_t {
209 | 	    $ph add $xcenters $tmp  -linecolor  "#000000"
210 | 	}
211 | 	$ph replot
212 |     }
213 | 
214 | }
215 | # END USER CODE
216 | 
217 | # BEGIN CALLBACK CODE
218 | # ONLY EDIT CODE INSIDE THE PROCS.
219 | 
220 | # density_profile_gui::_checkbutton_2_command --
221 | #
222 | # Callback to handle _checkbutton_2 widget option -command
223 | #
224 | # ARGS:
225 | #    <NONE>
226 | #
227 | proc density_profile_gui::_checkbutton_2_command args {}
228 | 
229 | # density_profile_gui::_entry_1_invalidcommand --
230 | #
231 | # Callback to handle _entry_1 widget option -invalidcommand
232 | #
233 | # ARGS:
234 | #    <NONE>
235 | #
236 | proc density_profile_gui::_entry_1_invalidcommand args {}
237 | 
238 | # density_profile_gui::_entry_1_validatecommand --
239 | #
240 | # Callback to handle _entry_1 widget option -validatecommand
241 | #
242 | # ARGS:
243 | #    <NONE>
244 | #
245 | proc density_profile_gui::_entry_1_validatecommand args {}
246 | 
247 | # density_profile_gui::_entry_1_xscrollcommand --
248 | #
249 | # Callback to handle _entry_1 widget option -xscrollcommand
250 | #
251 | # ARGS:
252 | #    <NONE>
253 | #
254 | proc density_profile_gui::_entry_1_xscrollcommand args {}
255 | 
256 | # density_profile_gui::_entry_2_invalidcommand --
257 | #
258 | # Callback to handle _entry_2 widget option -invalidcommand
259 | #
260 | # ARGS:
261 | #    <NONE>
262 | #
263 | proc density_profile_gui::_entry_2_invalidcommand args {}
264 | 
265 | # density_profile_gui::_entry_2_validatecommand --
266 | #
267 | # Callback to handle _entry_2 widget option -validatecommand
268 | #
269 | # ARGS:
270 | #    <NONE>
271 | #
272 | proc density_profile_gui::_entry_2_validatecommand args {}
273 | 
274 | # density_profile_gui::_entry_2_xscrollcommand --
275 | #
276 | # Callback to handle _entry_2 widget option -xscrollcommand
277 | #
278 | # ARGS:
279 | #    <NONE>
280 | #
281 | proc density_profile_gui::_entry_2_xscrollcommand args {}
282 | 
283 | # density_profile_gui::_entry_3_invalidcommand --
284 | #
285 | # Callback to handle _entry_3 widget option -invalidcommand
286 | #
287 | # ARGS:
288 | #    <NONE>
289 | #
290 | proc density_profile_gui::_entry_3_invalidcommand args {}
291 | 
292 | # density_profile_gui::_entry_3_validatecommand --
293 | #
294 | # Callback to handle _entry_3 widget option -validatecommand
295 | #
296 | # ARGS:
297 | #    <NONE>
298 | #
299 | proc density_profile_gui::_entry_3_validatecommand args {}
300 | 
301 | # density_profile_gui::_entry_3_xscrollcommand --
302 | #
303 | # Callback to handle _entry_3 widget option -xscrollcommand
304 | #
305 | # ARGS:
306 | #    <NONE>
307 | #
308 | proc density_profile_gui::_entry_3_xscrollcommand args {}
309 | 
310 | # density_profile_gui::_entry_4_invalidcommand --
311 | #
312 | # Callback to handle _entry_4 widget option -invalidcommand
313 | #
314 | # ARGS:
315 | #    <NONE>
316 | #
317 | proc density_profile_gui::_entry_4_invalidcommand args {}
318 | 
319 | # density_profile_gui::_entry_4_validatecommand --
320 | #
321 | # Callback to handle _entry_4 widget option -validatecommand
322 | #
323 | # ARGS:
324 | #    <NONE>
325 | #
326 | proc density_profile_gui::_entry_4_validatecommand args {}
327 | 
328 | # density_profile_gui::_entry_4_xscrollcommand --
329 | #
330 | # Callback to handle _entry_4 widget option -xscrollcommand
331 | #
332 | # ARGS:
333 | #    <NONE>
334 | #
335 | proc density_profile_gui::_entry_4_xscrollcommand args {}
336 | 
337 | # density_profile_gui::_entry_5_invalidcommand --
338 | #
339 | # Callback to handle _entry_5 widget option -invalidcommand
340 | #
341 | # ARGS:
342 | #    <NONE>
343 | #
344 | proc density_profile_gui::_entry_5_invalidcommand args {}
345 | 
346 | # density_profile_gui::_entry_5_validatecommand --
347 | #
348 | # Callback to handle _entry_5 widget option -validatecommand
349 | #
350 | # ARGS:
351 | #    <NONE>
352 | #
353 | proc density_profile_gui::_entry_5_validatecommand args {}
354 | 
355 | # density_profile_gui::_entry_5_xscrollcommand --
356 | #
357 | # Callback to handle _entry_5 widget option -xscrollcommand
358 | #
359 | # ARGS:
360 | #    <NONE>
361 | #
362 | proc density_profile_gui::_entry_5_xscrollcommand args {}
363 | 
364 | # density_profile_gui::_radiobutton_2_command --
365 | #
366 | # Callback to handle _radiobutton_2 widget option -command
367 | #
368 | # ARGS:
369 | #    <NONE>
370 | #
371 | proc density_profile_gui::_radiobutton_2_command args {}
372 | 
373 | # density_profile_gui::_radiobutton_3_command --
374 | #
375 | # Callback to handle _radiobutton_3 widget option -command
376 | #
377 | # ARGS:
378 | #    <NONE>
379 | #
380 | proc density_profile_gui::_radiobutton_3_command args {}
381 | 
382 | # density_profile_gui::_radiobutton_4_command --
383 | #
384 | # Callback to handle _radiobutton_4 widget option -command
385 | #
386 | # ARGS:
387 | #    <NONE>
388 | #
389 | proc density_profile_gui::_radiobutton_4_command args {}
390 | 
391 | # density_profile_gui::checkbox_Zsource_partial_command --
392 | #
393 | # Callback to handle checkbox_Zsource_partial widget option -command
394 | #
395 | # ARGS:
396 | #    <NONE>
397 | #
398 | proc density_profile_gui::checkbox_Zsource_partial_command args {}
399 | 
400 | # density_profile_gui::close_command --
401 | #
402 | # Callback to handle close widget option -command
403 | #
404 | # ARGS:
405 | #    <NONE>
406 | #
407 | proc density_profile_gui::close_command args {
408 |     wm withdraw .density_profile
409 | }
410 | 
411 | # density_profile_gui::help_command --
412 | #
413 | # Callback to handle help widget option -command
414 | #
415 | # ARGS:
416 | #    <NONE>
417 | #
418 | proc density_profile_gui::help_command args {
419 |     help_docs
420 | }
421 | 
422 | # density_profile_gui::plot_command --
423 | #
424 | # Callback to handle plot widget option -command
425 | #
426 | # ARGS:
427 | #    <NONE>
428 | #
429 | proc density_profile_gui::plot_command args {
430 |     do_plot
431 | }
432 | 
433 | # density_profile_gui::radiobutton_atoms_command --
434 | #
435 | # Callback to handle radiobutton_atoms widget option -command
436 | #
437 | # ARGS:
438 | #    <NONE>
439 | #
440 | proc density_profile_gui::radiobutton_atoms_command args {update_Zsource_state}
441 | 
442 | # density_profile_gui::radiobutton_charge_command --
443 | #
444 | # Callback to handle radiobutton_charge widget option -command
445 | #
446 | # ARGS:
447 | #    <NONE>
448 | #
449 | proc density_profile_gui::radiobutton_charge_command args {update_Zsource_state}
450 | 
451 | # density_profile_gui::radiobutton_electrons_command --
452 | #
453 | # Callback to handle radiobutton_electrons widget option -command
454 | #
455 | # ARGS:
456 | #    <NONE>
457 | #
458 | proc density_profile_gui::radiobutton_electrons_command args {update_Zsource_state}
459 | 
460 | # density_profile_gui::radiobutton_mass_command --
461 | #
462 | # Callback to handle radiobutton_mass widget option -command
463 | #
464 | # ARGS:
465 | #    <NONE>
466 | #
467 | proc density_profile_gui::radiobutton_mass_command args {update_Zsource_state}
468 | 
469 | # density_profile_gui::radiobutton_Zsource_element_command --
470 | #
471 | # Callback to handle radiobutton_Zsource_element widget option -command
472 | #
473 | # ARGS:
474 | #    <NONE>
475 | #
476 | proc density_profile_gui::radiobutton_Zsource_element_command args {}
477 | 
478 | # density_profile_gui::radiobutton_Zsource_mass_command --
479 | #
480 | # Callback to handle radiobutton_Zsource_mass widget option -command
481 | #
482 | # ARGS:
483 | #    <NONE>
484 | #
485 | proc density_profile_gui::radiobutton_Zsource_mass_command args {}
486 | 
487 | # density_profile_gui::radiobutton_Zsource_name_command --
488 | #
489 | # Callback to handle radiobutton_Zsource_name widget option -command
490 | #
491 | # ARGS:
492 | #    <NONE>
493 | #
494 | proc density_profile_gui::radiobutton_Zsource_name_command args {}
495 | 
496 | # density_profile_gui::radiobutton_Zsource_type_command --
497 | #
498 | # Callback to handle radiobutton_Zsource_type widget option -command
499 | #
500 | # ARGS:
501 | #    <NONE>
502 | #
503 | proc density_profile_gui::radiobutton_Zsource_type_command args {}
504 | 
505 | # END CALLBACK CODE
506 | 
507 | # density_profile_gui::init --
508 | #
509 | #   Call the optional userinit and initialize the dialog.
510 | #   DO NOT EDIT THIS PROCEDURE.
511 | #
512 | # Arguments:
513 | #   root   the root window to load this dialog into
514 | #
515 | # Results:
516 | #   dialog will be created, or a background error will be thrown
517 | #
518 | proc density_profile_gui::init {root args} {
519 |     # Catch this in case the user didn't define it
520 |     catch {density_profile_gui::userinit}
521 |     if {[info exists embed_args]} {
522 | 	# we are running in the plugin
523 | 	density_profile_gui::ui $root
524 |     } elseif {$::argv0 == [info script]} {
525 | 	# we are running in stand-alone mode
526 | 	wm title $root density_profile_gui
527 | 	if {[catch {
528 | 	    # Create the UI
529 | 	    density_profile_gui::ui  $root
530 | 	} err]} {
531 | 	    bgerror $err ; exit 1
532 | 	}
533 |     }
534 |     catch {density_profile_gui::run $root}
535 | }
536 | density_profile_gui::init .
537 | 
538 | 


--------------------------------------------------------------------------------
/density_profile_gui.ui:
--------------------------------------------------------------------------------
  1 | # GUIBUILDER FILE Build 146
  2 | # Created: 2012-12-18 18:22:52 by GUI Builder Build 146
  3 | language tcl 8.4
  4 | widget {Tk frame} f {
  5 | 	geometry min_column {40 119}
  6 | 	geometry min_row {17 44 40 38 48 40 45 2 27}
  7 | 	geometry pad_column {0 0}
  8 | 	geometry pad_row {0 0 0 0 0 0 0 0 0}
  9 | 	geometry resize_column {0 3}
 10 | 	geometry resize_row {1 3 0 1 0 0 0 1 1}
 11 | 	geometry weight_column {0 1}
 12 | 	geometry weight_row {0 1 0 0 0 0 0 0 0}
 13 | 	data GROUP Tk
 14 | 	data ID {}
 15 | 	data MASTER {}
 16 | 	data TYPE {Tk frame}
 17 | 	data level 0
 18 | }
 19 | widget {Tk frame} _frame_1 {
 20 | 	geometry -column 2
 21 | 	geometry -columnspan 1
 22 | 	geometry -row 5
 23 | 	geometry -rowspan 1
 24 | 	geometry -sticky w
 25 | 	geometry min_column {40 40 40 40 40}
 26 | 	geometry min_row 7
 27 | 	geometry pad_column {0 0 0 0 0}
 28 | 	geometry pad_row 0
 29 | 	geometry resize_column {1 1 1 1 1}
 30 | 	geometry resize_row 0
 31 | 	geometry weight_column {0 0 0 0 0}
 32 | 	geometry weight_row 0
 33 | 	data GROUP Tk
 34 | 	data ID _frame_1
 35 | 	data MASTER {}
 36 | 	data TYPE {Tk frame}
 37 | 	data level 1
 38 | }
 39 | widget {Tk frame} _frame_2 {
 40 | 	geometry -column 2
 41 | 	geometry -columnspan 1
 42 | 	geometry -row 6
 43 | 	geometry -rowspan 1
 44 | 	geometry -sticky w
 45 | 	geometry min_column {40 40 40 40 40}
 46 | 	geometry min_row 16
 47 | 	geometry pad_column {0 0 0 0 0}
 48 | 	geometry pad_row 0
 49 | 	geometry resize_column {0 0 1 1 0}
 50 | 	geometry resize_row 0
 51 | 	geometry weight_column {0 0 0 0 0}
 52 | 	geometry weight_row 0
 53 | 	data GROUP Tk
 54 | 	data ID frame_Zsource
 55 | 	data MASTER {}
 56 | 	data TYPE {Tk frame}
 57 | 	data level 1
 58 | }
 59 | widget {Tk frame} _frame_3 {
 60 | 	geometry -column 2
 61 | 	geometry -columnspan 1
 62 | 	geometry -row 3
 63 | 	geometry -rowspan 1
 64 | 	geometry -sticky w
 65 | 	geometry min_column {40 40 40 40}
 66 | 	geometry min_row 15
 67 | 	geometry pad_column {0 0 0 0}
 68 | 	geometry pad_row 0
 69 | 	geometry resize_column {0 0 0 0}
 70 | 	geometry resize_row 0
 71 | 	geometry weight_column {0 0 0 0}
 72 | 	geometry weight_row 0
 73 | 	data GROUP Tk
 74 | 	data ID _frame_3
 75 | 	data MASTER {}
 76 | 	data TYPE {Tk frame}
 77 | 	data level 1
 78 | }
 79 | widget {Tk frame} _frame_4 {
 80 | 	geometry -column 1
 81 | 	geometry -columnspan 2
 82 | 	geometry -row 9
 83 | 	geometry -rowspan 1
 84 | 	geometry -sticky news
 85 | 	geometry min_column {40 40 40}
 86 | 	geometry min_row 10
 87 | 	geometry pad_column {0 0 0}
 88 | 	geometry pad_row 0
 89 | 	geometry resize_column {0 3 3}
 90 | 	geometry resize_row 1
 91 | 	geometry weight_column {0 1 1}
 92 | 	geometry weight_row 0
 93 | 	data GROUP Tk
 94 | 	data ID _frame_4
 95 | 	data MASTER {}
 96 | 	data TYPE {Tk frame}
 97 | 	data level 1
 98 | }
 99 | widget {Tk frame} _frame_5 {
100 | 	geometry -column 2
101 | 	geometry -columnspan 1
102 | 	geometry -row 7
103 | 	geometry -rowspan 1
104 | 	geometry -sticky ew
105 | 	geometry min_column {40 24 40 27 40 78}
106 | 	geometry min_row 2
107 | 	geometry pad_column {0 0 0 0 0 0}
108 | 	geometry pad_row 0
109 | 	geometry resize_column {3 0 3 0 3 1}
110 | 	geometry resize_row 0
111 | 	geometry weight_column {1 0 1 0 1 0}
112 | 	geometry weight_row 0
113 | 	data GROUP Tk
114 | 	data ID _frame_5
115 | 	data MASTER {}
116 | 	data TYPE {Tk frame}
117 | 	data level 1
118 | }
119 | widget {Tk label} _label_1 {
120 | 	configure -font {helvetica 10}
121 | 	configure -text {Atom selection}
122 | 	geometry -column 1
123 | 	geometry -columnspan 1
124 | 	geometry -row 4
125 | 	geometry -rowspan 1
126 | 	geometry -sticky e
127 | 	geometry min_column {40 40 40 40 40}
128 | 	geometry min_row 40
129 | 	geometry pad_column {0 0 0 0 0}
130 | 	geometry pad_row 0
131 | 	geometry resize_column {0 0 0 0 0}
132 | 	geometry resize_row 0
133 | 	geometry weight_column {0 0 0 0 0}
134 | 	geometry weight_row 0
135 | 	data GROUP Tk
136 | 	data ID _label_1
137 | 	data MASTER {}
138 | 	data TYPE {Tk label}
139 | }
140 | widget {Tk label} _label_2 {
141 | 	configure -font {helvetica 10}
142 | 	configure -text {Projection axis}
143 | 	geometry -column 1
144 | 	geometry -columnspan 1
145 | 	geometry -row 5
146 | 	geometry -rowspan 1
147 | 	geometry -sticky e
148 | 	geometry min_column {40 40 40 40 40}
149 | 	geometry min_row 40
150 | 	geometry pad_column {0 0 0 0 0}
151 | 	geometry pad_row 0
152 | 	geometry resize_column {0 0 0 0 0}
153 | 	geometry resize_row 0
154 | 	geometry weight_column {0 0 0 0 0}
155 | 	geometry weight_row 0
156 | 	data GROUP Tk
157 | 	data ID _label_2
158 | 	data MASTER {}
159 | 	data TYPE {Tk label}
160 | }
161 | widget {Tk label} _label_3 {
162 | 	configure -font {helvetica 10}
163 | 	configure -text {Resolution (Å)}
164 | 	geometry -column 4
165 | 	geometry -columnspan 1
166 | 	geometry -row 1
167 | 	geometry -rowspan 1
168 | 	geometry -sticky e
169 | 	geometry min_column {40 40 40 40 40}
170 | 	geometry min_row 40
171 | 	geometry pad_column {0 0 0 0 0}
172 | 	geometry pad_row 0
173 | 	geometry resize_column {0 0 0 0 0}
174 | 	geometry resize_row 0
175 | 	geometry weight_column {0 0 0 0 0}
176 | 	geometry weight_row 0
177 | 	data GROUP Tk
178 | 	data ID _label_3
179 | 	data MASTER _frame_1
180 | 	data TYPE {Tk label}
181 | }
182 | widget {Tk label} _label_5 {
183 | 	configure -font {helvetica 10}
184 | 	configure -justify right
185 | 	configure -text {Guess atomic number Z\nfrom attribute}
186 | 	geometry -column 1
187 | 	geometry -columnspan 1
188 | 	geometry -row 6
189 | 	geometry -rowspan 1
190 | 	geometry -sticky e
191 | 	geometry min_column {40 40 40 40 40}
192 | 	geometry min_row 40
193 | 	geometry pad_column {0 0 0 0 0}
194 | 	geometry pad_row 0
195 | 	geometry resize_column {0 0 0 0 0}
196 | 	geometry resize_row 0
197 | 	geometry weight_column {0 0 0 0 0}
198 | 	geometry weight_row 0
199 | 	data GROUP Tk
200 | 	data ID _label_5
201 | 	data MASTER {}
202 | 	data TYPE {Tk label}
203 | }
204 | widget {Tk entry} _entry_1 {
205 | 	configure -font {helvetica 10}
206 | 	configure -justify center
207 | 	configure -textvariable density_profile::dp_args(selection)
208 | 	geometry -column 2
209 | 	geometry -columnspan 1
210 | 	geometry -row 4
211 | 	geometry -rowspan 1
212 | 	geometry -sticky ew
213 | 	geometry min_column {40 40 40 40 40}
214 | 	geometry min_row 40
215 | 	geometry pad_column {0 0 0 0 0}
216 | 	geometry pad_row 0
217 | 	geometry resize_column {0 0 0 0 0}
218 | 	geometry resize_row 0
219 | 	geometry weight_column {0 0 0 0 0}
220 | 	geometry weight_row 0
221 | 	data GROUP Tk
222 | 	data ID _entry_1
223 | 	data MASTER {}
224 | 	data TYPE {Tk entry}
225 | }
226 | widget {Tk label} _label_6 {
227 | 	configure -font {helvetica 10 bold}
228 | 	configure -text {VMD Density Profile Tool}
229 | 	geometry -column 1
230 | 	geometry -columnspan 2
231 | 	geometry -row 1
232 | 	geometry -rowspan 1
233 | 	geometry -sticky s
234 | 	geometry min_column {40 40 40 40 40}
235 | 	geometry min_row 40
236 | 	geometry pad_column {0 0 0 0 0}
237 | 	geometry pad_row 0
238 | 	geometry resize_column {0 0 0 0 0}
239 | 	geometry resize_row 0
240 | 	geometry weight_column {0 0 0 0 0}
241 | 	geometry weight_row 0
242 | 	data GROUP Tk
243 | 	data ID _label_6
244 | 	data MASTER {}
245 | 	data TYPE {Tk label}
246 | }
247 | widget {Tk radiobutton} _radiobutton_2 {
248 | 	configure -font {helvetica 10}
249 | 	configure -text x
250 | 	configure -value x
251 | 	configure -variable density_profile::dp_args(axis)
252 | 	geometry -column 1
253 | 	geometry -columnspan 1
254 | 	geometry -row 1
255 | 	geometry -rowspan 1
256 | 	geometry -sticky ew
257 | 	geometry min_column {40 40 40 40 40}
258 | 	geometry min_row 40
259 | 	geometry pad_column {0 0 0 0 0}
260 | 	geometry pad_row 0
261 | 	geometry resize_column {0 0 0 0 0}
262 | 	geometry resize_row 0
263 | 	geometry weight_column {0 0 0 0 0}
264 | 	geometry weight_row 0
265 | 	data GROUP Tk
266 | 	data ID _radiobutton_2
267 | 	data MASTER _frame_1
268 | 	data TYPE {Tk radiobutton}
269 | }
270 | widget {Tk radiobutton} _radiobutton_3 {
271 | 	configure -font {helvetica 10}
272 | 	configure -text y
273 | 	configure -value y
274 | 	configure -variable density_profile::dp_args(axis)
275 | 	geometry -column 2
276 | 	geometry -columnspan 1
277 | 	geometry -row 1
278 | 	geometry -rowspan 1
279 | 	geometry -sticky ew
280 | 	geometry min_column {40 40 40 40 40}
281 | 	geometry min_row 40
282 | 	geometry pad_column {0 0 0 0 0}
283 | 	geometry pad_row 0
284 | 	geometry resize_column {0 0 0 0 0}
285 | 	geometry resize_row 0
286 | 	geometry weight_column {0 0 0 0 0}
287 | 	geometry weight_row 0
288 | 	data GROUP Tk
289 | 	data ID _radiobutton_3
290 | 	data MASTER _frame_1
291 | 	data TYPE {Tk radiobutton}
292 | }
293 | widget {Tk radiobutton} _radiobutton_4 {
294 | 	configure -font {helvetica 10}
295 | 	configure -text z
296 | 	configure -value z
297 | 	configure -variable density_profile::dp_args(axis)
298 | 	geometry -column 3
299 | 	geometry -columnspan 1
300 | 	geometry -row 1
301 | 	geometry -rowspan 1
302 | 	geometry -sticky ew
303 | 	geometry min_column {40 40 40 40 40}
304 | 	geometry min_row 40
305 | 	geometry pad_column {0 0 0 0 0}
306 | 	geometry pad_row 0
307 | 	geometry resize_column {0 0 0 0 0}
308 | 	geometry resize_row 0
309 | 	geometry weight_column {0 0 0 0 0}
310 | 	geometry weight_row 0
311 | 	data GROUP Tk
312 | 	data ID _radiobutton_4
313 | 	data MASTER _frame_1
314 | 	data TYPE {Tk radiobutton}
315 | }
316 | widget {Tk entry} _entry_2 {
317 | 	configure -justify center
318 | 	configure -textvariable density_profile::dp_args(resolution)
319 | 	configure -width 8
320 | 	geometry -column 5
321 | 	geometry -columnspan 1
322 | 	geometry -row 1
323 | 	geometry -rowspan 1
324 | 	geometry -sticky ew
325 | 	geometry min_column {40 40 40 40 40}
326 | 	geometry min_row 40
327 | 	geometry pad_column {0 0 0 0 0}
328 | 	geometry pad_row 0
329 | 	geometry resize_column {0 0 0 0 0}
330 | 	geometry resize_row 0
331 | 	geometry weight_column {0 0 0 0 0}
332 | 	geometry weight_row 0
333 | 	data GROUP Tk
334 | 	data ID _entry_2
335 | 	data MASTER _frame_1
336 | 	data TYPE {Tk entry}
337 | }
338 | widget {Tk radiobutton} _radiobutton_5 {
339 | 	configure -font {helvetica 10}
340 | 	configure -state disabled
341 | 	configure -text name
342 | 	configure -value name
343 | 	configure -variable density_profile::dp_args(Zsource)
344 | 	geometry -column 3
345 | 	geometry -columnspan 1
346 | 	geometry -row 1
347 | 	geometry -rowspan 1
348 | 	geometry -sticky {}
349 | 	geometry min_column {40 40 40 40 40}
350 | 	geometry min_row 40
351 | 	geometry pad_column {0 0 0 0 0}
352 | 	geometry pad_row 0
353 | 	geometry resize_column {0 0 0 0 0}
354 | 	geometry resize_row 0
355 | 	geometry weight_column {0 0 0 0 0}
356 | 	geometry weight_row 0
357 | 	data GROUP Tk
358 | 	data ID radiobutton_Zsource_name
359 | 	data MASTER _frame_2
360 | 	data TYPE {Tk radiobutton}
361 | }
362 | widget {Tk radiobutton} _radiobutton_6 {
363 | 	configure -font {helvetica 10}
364 | 	configure -state disabled
365 | 	configure -text type
366 | 	configure -value type
367 | 	configure -variable density_profile::dp_args(Zsource)
368 | 	geometry -column 4
369 | 	geometry -columnspan 1
370 | 	geometry -row 1
371 | 	geometry -rowspan 1
372 | 	geometry -sticky {}
373 | 	geometry min_column {40 40 40 40 40}
374 | 	geometry min_row 40
375 | 	geometry pad_column {0 0 0 0 0}
376 | 	geometry pad_row 0
377 | 	geometry resize_column {0 0 0 0 0}
378 | 	geometry resize_row 0
379 | 	geometry weight_column {0 0 0 0 0}
380 | 	geometry weight_row 0
381 | 	data GROUP Tk
382 | 	data ID radiobutton_Zsource_type
383 | 	data MASTER _frame_2
384 | 	data TYPE {Tk radiobutton}
385 | }
386 | widget {Tk radiobutton} _radiobutton_7 {
387 | 	configure -font {helvetica 10}
388 | 	configure -state disabled
389 | 	configure -text element
390 | 	configure -value element
391 | 	configure -variable density_profile::dp_args(Zsource)
392 | 	geometry -column 2
393 | 	geometry -columnspan 1
394 | 	geometry -row 1
395 | 	geometry -rowspan 1
396 | 	geometry -sticky {}
397 | 	geometry min_column {40 40 40 40 40}
398 | 	geometry min_row 40
399 | 	geometry pad_column {0 0 0 0 0}
400 | 	geometry pad_row 0
401 | 	geometry resize_column {0 0 0 0 0}
402 | 	geometry resize_row 0
403 | 	geometry weight_column {0 0 0 0 0}
404 | 	geometry weight_row 0
405 | 	data GROUP Tk
406 | 	data ID radiobutton_Zsource_element
407 | 	data MASTER _frame_2
408 | 	data TYPE {Tk radiobutton}
409 | }
410 | widget {Tk label} _label_7 {
411 | 	configure -font {helvetica 10}
412 | 	configure -text {Density profile of}
413 | 	geometry -column 1
414 | 	geometry -columnspan 1
415 | 	geometry -row 3
416 | 	geometry -rowspan 1
417 | 	geometry -sticky e
418 | 	geometry min_column {40 40 40 40 40}
419 | 	geometry min_row 40
420 | 	geometry pad_column {0 0 0 0 0}
421 | 	geometry pad_row 0
422 | 	geometry resize_column {0 0 0 0 0}
423 | 	geometry resize_row 0
424 | 	geometry weight_column {0 0 0 0 0}
425 | 	geometry weight_row 0
426 | 	data GROUP Tk
427 | 	data ID _label_7
428 | 	data MASTER {}
429 | 	data TYPE {Tk label}
430 | }
431 | widget {Tk radiobutton} _radiobutton_9 {
432 | 	configure -font {helvetica 10}
433 | 	configure -text mass
434 | 	configure -value mass
435 | 	configure -variable density_profile::dp_args(rho)
436 | 	geometry -column 2
437 | 	geometry -columnspan 1
438 | 	geometry -row 1
439 | 	geometry -rowspan 1
440 | 	geometry -sticky {}
441 | 	geometry min_column {40 40 40 40 40}
442 | 	geometry min_row 40
443 | 	geometry pad_column {0 0 0 0 0}
444 | 	geometry pad_row 0
445 | 	geometry resize_column {0 0 0 0 0}
446 | 	geometry resize_row 0
447 | 	geometry weight_column {0 0 0 0 0}
448 | 	geometry weight_row 0
449 | 	data GROUP Tk
450 | 	data ID radiobutton_mass
451 | 	data MASTER _frame_3
452 | 	data TYPE {Tk radiobutton}
453 | }
454 | widget {Tk radiobutton} _radiobutton_10 {
455 | 	configure -font {helvetica 10}
456 | 	configure -text charge
457 | 	configure -value charge
458 | 	configure -variable density_profile::dp_args(rho)
459 | 	geometry -column 3
460 | 	geometry -columnspan 1
461 | 	geometry -row 1
462 | 	geometry -rowspan 1
463 | 	geometry -sticky {}
464 | 	geometry min_column {40 40 40 40 40}
465 | 	geometry min_row 40
466 | 	geometry pad_column {0 0 0 0 0}
467 | 	geometry pad_row 0
468 | 	geometry resize_column {0 0 0 0 0}
469 | 	geometry resize_row 0
470 | 	geometry weight_column {0 0 0 0 0}
471 | 	geometry weight_row 0
472 | 	data GROUP Tk
473 | 	data ID radiobutton_charge
474 | 	data MASTER _frame_3
475 | 	data TYPE {Tk radiobutton}
476 | }
477 | widget {Tk radiobutton} _radiobutton_11 {
478 | 	configure -font {helvetica 10}
479 | 	configure -text electrons
480 | 	configure -value electrons
481 | 	configure -variable density_profile::dp_args(rho)
482 | 	geometry -column 4
483 | 	geometry -columnspan 1
484 | 	geometry -row 1
485 | 	geometry -rowspan 1
486 | 	geometry -sticky {}
487 | 	geometry min_column {40 40 40 40 40}
488 | 	geometry min_row 40
489 | 	geometry pad_column {0 0 0 0 0}
490 | 	geometry pad_row 0
491 | 	geometry resize_column {0 0 0 0 0}
492 | 	geometry resize_row 0
493 | 	geometry weight_column {0 0 0 0 0}
494 | 	geometry weight_row 0
495 | 	data GROUP Tk
496 | 	data ID radiobutton_electrons
497 | 	data MASTER _frame_3
498 | 	data TYPE {Tk radiobutton}
499 | }
500 | widget {Tk button} _button_1 {
501 | 	configure -font {helvetica 10 bold}
502 | 	configure -text Plot
503 | 	geometry -column 2
504 | 	geometry -columnspan 1
505 | 	geometry -row 1
506 | 	geometry -rowspan 1
507 | 	geometry -sticky nsew
508 | 	geometry min_column {40 40 40 40 40}
509 | 	geometry min_row 40
510 | 	geometry pad_column {0 0 0 0 0}
511 | 	geometry pad_row 0
512 | 	geometry resize_column {0 0 0 0 0}
513 | 	geometry resize_row 0
514 | 	geometry weight_column {0 0 0 0 0}
515 | 	geometry weight_row 0
516 | 	data GROUP Tk
517 | 	data ID plot
518 | 	data MASTER _frame_4
519 | 	data TYPE {Tk button}
520 | }
521 | widget {Tk button} _button_2 {
522 | 	configure -font {helvetica 10 bold}
523 | 	configure -text Close
524 | 	geometry -column 3
525 | 	geometry -columnspan 1
526 | 	geometry -row 1
527 | 	geometry -rowspan 1
528 | 	geometry -sticky nsew
529 | 	geometry min_column {40 40 40 40 40}
530 | 	geometry min_row 40
531 | 	geometry pad_column {0 0 0 0 0}
532 | 	geometry pad_row 0
533 | 	geometry resize_column {0 0 0 0 0}
534 | 	geometry resize_row 0
535 | 	geometry weight_column {0 0 0 0 0}
536 | 	geometry weight_row 0
537 | 	data GROUP Tk
538 | 	data ID close
539 | 	data MASTER _frame_4
540 | 	data TYPE {Tk button}
541 | }
542 | widget {Tk radiobutton} _radiobutton_1 {
543 | 	configure -font {helvetica 10}
544 | 	configure -text number
545 | 	configure -value number
546 | 	configure -variable density_profile::dp_args(rho)
547 | 	geometry -column 1
548 | 	geometry -columnspan 1
549 | 	geometry -row 1
550 | 	geometry -rowspan 1
551 | 	geometry -sticky {}
552 | 	geometry min_column {40 40 40 40 40}
553 | 	geometry min_row 40
554 | 	geometry pad_column {0 0 0 0 0}
555 | 	geometry pad_row 0
556 | 	geometry resize_column {0 0 0 0 0}
557 | 	geometry resize_row 0
558 | 	geometry weight_column {0 0 0 0 0}
559 | 	geometry weight_row 0
560 | 	data GROUP Tk
561 | 	data ID radiobutton_atoms
562 | 	data MASTER _frame_3
563 | 	data TYPE {Tk radiobutton}
564 | }
565 | widget {Tk checkbutton} _checkbutton_1 {
566 | 	configure -font {helvetica 10}
567 | 	configure -state disabled
568 | 	configure -text {Consider partial charges}
569 | 	configure -variable density_profile::dp_args(partial_charges)
570 | 	geometry -column 5
571 | 	geometry -columnspan 1
572 | 	geometry -row 1
573 | 	geometry -rowspan 1
574 | 	geometry -sticky w
575 | 	geometry min_column {40 40 40 40 40}
576 | 	geometry min_row 40
577 | 	geometry pad_column {0 0 0 0 0}
578 | 	geometry pad_row 0
579 | 	geometry resize_column {0 0 0 0 0}
580 | 	geometry resize_row 0
581 | 	geometry weight_column {0 0 0 0 0}
582 | 	geometry weight_row 0
583 | 	data GROUP Tk
584 | 	data ID checkbox_Zsource_partial
585 | 	data MASTER _frame_2
586 | 	data TYPE {Tk checkbutton}
587 | }
588 | widget {Tk label} _label_4 {
589 | 	configure -font {helvetica 10}
590 | 	configure -pady 6
591 | 	configure -text {Computes 1-D projections of various atomic densities. The computation is performed in a single frame, a trajectory, or averaged over multiple frames.}
592 | 	configure -wraplength 400
593 | 	geometry -column 1
594 | 	geometry -columnspan 2
595 | 	geometry -row 2
596 | 	geometry -rowspan 1
597 | 	geometry -sticky nsew
598 | 	geometry min_column {40 40 40 40 40}
599 | 	geometry min_row 40
600 | 	geometry pad_column {0 0 0 0 0}
601 | 	geometry pad_row 0
602 | 	geometry resize_column {0 0 0 0 0}
603 | 	geometry resize_row 0
604 | 	geometry weight_column {0 0 0 0 0}
605 | 	geometry weight_row 0
606 | 	data GROUP Tk
607 | 	data ID _label_4
608 | 	data MASTER {}
609 | 	data TYPE {Tk label}
610 | }
611 | widget {Tk label} _label_8 {
612 | 	configure -font {helvetica 10}
613 | 	configure -text {Frames from}
614 | 	geometry -column 1
615 | 	geometry -columnspan 1
616 | 	geometry -row 7
617 | 	geometry -rowspan 1
618 | 	geometry -sticky e
619 | 	geometry min_column {40 40 40 40 40}
620 | 	geometry min_row 40
621 | 	geometry pad_column {0 0 0 0 0}
622 | 	geometry pad_row 0
623 | 	geometry resize_column {0 0 0 0 0}
624 | 	geometry resize_row 0
625 | 	geometry weight_column {0 0 0 0 0}
626 | 	geometry weight_row 0
627 | 	data GROUP Tk
628 | 	data ID _label_8
629 | 	data MASTER {}
630 | 	data TYPE {Tk label}
631 | }
632 | widget {Tk label} _label_9 {
633 | 	configure -font {helvetica 10}
634 | 	configure -text First
635 | 	geometry -column 1
636 | 	geometry -columnspan 1
637 | 	geometry -row 1
638 | 	geometry -rowspan 1
639 | 	geometry -sticky {}
640 | 	geometry min_column {40 40 40 40 40}
641 | 	geometry min_row 40
642 | 	geometry pad_column {0 0 0 0 0}
643 | 	geometry pad_row 0
644 | 	geometry resize_column {0 0 0 0 0}
645 | 	geometry resize_row 0
646 | 	geometry weight_column {0 0 0 0 0}
647 | 	geometry weight_row 0
648 | 	data GROUP Tk
649 | 	data ID _label_9
650 | 	data MASTER _frame_5
651 | 	data TYPE {Tk label}
652 | }
653 | widget {Tk entry} _entry_3 {
654 | 	configure -justify center
655 | 	configure -textvariable density_profile::dp_args(frame_from)
656 | 	configure -width 8
657 | 	geometry -column 1
658 | 	geometry -columnspan 1
659 | 	geometry -row 1
660 | 	geometry -rowspan 1
661 | 	geometry -sticky ew
662 | 	geometry min_column {40 40 40 40 40}
663 | 	geometry min_row 40
664 | 	geometry pad_column {0 0 0 0 0}
665 | 	geometry pad_row 0
666 | 	geometry resize_column {0 0 0 0 0}
667 | 	geometry resize_row 0
668 | 	geometry weight_column {0 0 0 0 0}
669 | 	geometry weight_row 0
670 | 	data GROUP Tk
671 | 	data ID _entry_3
672 | 	data MASTER _frame_5
673 | 	data TYPE {Tk entry}
674 | }
675 | widget {Tk label} _label_10 {
676 | 	configure -font {helvetica 10}
677 | 	configure -text { to}
678 | 	geometry -column 2
679 | 	geometry -columnspan 1
680 | 	geometry -row 1
681 | 	geometry -rowspan 1
682 | 	geometry -sticky e
683 | 	geometry min_column {40 40 40 40 40}
684 | 	geometry min_row 40
685 | 	geometry pad_column {0 0 0 0 0}
686 | 	geometry pad_row 0
687 | 	geometry resize_column {0 0 0 0 0}
688 | 	geometry resize_row 0
689 | 	geometry weight_column {0 0 0 0 0}
690 | 	geometry weight_row 0
691 | 	data GROUP Tk
692 | 	data ID _label_10
693 | 	data MASTER _frame_5
694 | 	data TYPE {Tk label}
695 | }
696 | widget {Tk checkbutton} _checkbutton_2 {
697 | 	configure -font {helvetica 10}
698 | 	configure -text Average
699 | 	configure -variable density_profile::dp_args(average)
700 | 	geometry -column 6
701 | 	geometry -columnspan 1
702 | 	geometry -row 1
703 | 	geometry -rowspan 1
704 | 	geometry -sticky e
705 | 	geometry min_column {40 40 40 40 40}
706 | 	geometry min_row 40
707 | 	geometry pad_column {0 0 0 0 0}
708 | 	geometry pad_row 0
709 | 	geometry resize_column {0 0 0 0 0}
710 | 	geometry resize_row 0
711 | 	geometry weight_column {0 0 0 0 0}
712 | 	geometry weight_row 0
713 | 	data GROUP Tk
714 | 	data ID _checkbutton_2
715 | 	data MASTER _frame_5
716 | 	data TYPE {Tk checkbutton}
717 | }
718 | widget {Tk entry} _entry_4 {
719 | 	configure -justify center
720 | 	configure -textvariable density_profile::dp_args(frame_to)
721 | 	configure -width 8
722 | 	geometry -column 3
723 | 	geometry -columnspan 1
724 | 	geometry -row 1
725 | 	geometry -rowspan 1
726 | 	geometry -sticky ew
727 | 	geometry min_column {40 40 40 40 40}
728 | 	geometry min_row 40
729 | 	geometry pad_column {0 0 0 0 0}
730 | 	geometry pad_row 0
731 | 	geometry resize_column {0 0 0 0 0}
732 | 	geometry resize_row 0
733 | 	geometry weight_column {0 0 0 0 0}
734 | 	geometry weight_row 0
735 | 	data GROUP Tk
736 | 	data ID _entry_4
737 | 	data MASTER _frame_5
738 | 	data TYPE {Tk entry}
739 | }
740 | widget {Tk label} _label_11 {
741 | 	configure -font {helvetica 10}
742 | 	configure -text { step}
743 | 	geometry -column 4
744 | 	geometry -columnspan 1
745 | 	geometry -row 1
746 | 	geometry -rowspan 1
747 | 	geometry -sticky e
748 | 	geometry min_column {40 40 40 40 40}
749 | 	geometry min_row 40
750 | 	geometry pad_column {0 0 0 0 0}
751 | 	geometry pad_row 0
752 | 	geometry resize_column {0 0 0 0 0}
753 | 	geometry resize_row 0
754 | 	geometry weight_column {0 0 0 0 0}
755 | 	geometry weight_row 0
756 | 	data GROUP Tk
757 | 	data ID _label_11
758 | 	data MASTER _frame_5
759 | 	data TYPE {Tk label}
760 | }
761 | widget {Tk entry} _entry_5 {
762 | 	configure -justify center
763 | 	configure -textvariable density_profile::dp_args(frame_step)
764 | 	configure -width 8
765 | 	geometry -column 5
766 | 	geometry -columnspan 1
767 | 	geometry -row 1
768 | 	geometry -rowspan 1
769 | 	geometry -sticky ew
770 | 	geometry min_column {40 40 40 40 40}
771 | 	geometry min_row 40
772 | 	geometry pad_column {0 0 0 0 0}
773 | 	geometry pad_row 0
774 | 	geometry resize_column {0 0 0 0 0}
775 | 	geometry resize_row 0
776 | 	geometry weight_column {0 0 0 0 0}
777 | 	geometry weight_row 0
778 | 	data GROUP Tk
779 | 	data ID _entry_5
780 | 	data MASTER _frame_5
781 | 	data TYPE {Tk entry}
782 | }
783 | widget {Tk label} _label_12 {
784 | 	configure -font {helvetica 10}
785 | 	configure -pady 6
786 | 	configure -text {See console for information and data files}
787 | 	geometry -column 1
788 | 	geometry -columnspan 2
789 | 	geometry -row 8
790 | 	geometry -rowspan 1
791 | 	geometry -sticky {}
792 | 	geometry min_column {40 40 40 40 40}
793 | 	geometry min_row 40
794 | 	geometry pad_column {0 0 0 0 0}
795 | 	geometry pad_row 0
796 | 	geometry resize_column {0 0 0 0 0}
797 | 	geometry resize_row 0
798 | 	geometry weight_column {0 0 0 0 0}
799 | 	geometry weight_row 0
800 | 	data GROUP Tk
801 | 	data ID _label_12
802 | 	data MASTER {}
803 | 	data TYPE {Tk label}
804 | }
805 | widget {Tk button} _button_3 {
806 | 	configure -bitmap questhead
807 | 	configure -font {helvetica 10 bold}
808 | 	configure -text ?
809 | 	geometry -column 1
810 | 	geometry -columnspan 1
811 | 	geometry -row 1
812 | 	geometry -rowspan 1
813 | 	geometry -sticky nsew
814 | 	geometry min_column {40 40 40 40 40}
815 | 	geometry min_row 40
816 | 	geometry pad_column {0 0 0 0 0}
817 | 	geometry pad_row 0
818 | 	geometry resize_column {0 0 0 0 0}
819 | 	geometry resize_row 0
820 | 	geometry weight_column {0 0 0 0 0}
821 | 	geometry weight_row 0
822 | 	data GROUP Tk
823 | 	data ID help
824 | 	data MASTER _frame_4
825 | 	data TYPE {Tk button}
826 | }
827 | widget {Tk radiobutton} _radiobutton_8 {
828 | 	configure -font {helvetica 10}
829 | 	configure -state disabled
830 | 	configure -text mass
831 | 	configure -value mass
832 | 	configure -variable density_profile::dp_args(Zsource)
833 | 	geometry -column 1
834 | 	geometry -columnspan 1
835 | 	geometry -row 1
836 | 	geometry -rowspan 1
837 | 	geometry -sticky {}
838 | 	geometry min_column {40 40 40 40 40}
839 | 	geometry min_row 40
840 | 	geometry pad_column {0 0 0 0 0}
841 | 	geometry pad_row 0
842 | 	geometry resize_column {0 0 0 0 0}
843 | 	geometry resize_row 0
844 | 	geometry weight_column {0 0 0 0 0}
845 | 	geometry weight_row 0
846 | 	data GROUP Tk
847 | 	data ID radiobutton_Zsource_mass
848 | 	data MASTER _frame_2
849 | 	data TYPE {Tk radiobutton}
850 | }
851 | menu {Menu menu} MENU {
852 | 	data MASTER {}
853 | 	data level 0
854 | }
855 | menu {Menu cascade} menuitem1 {
856 | 	configure -label Help
857 | 	data MASTER MENU
858 | }
859 | menu {Menu command} menuitem2 {
860 | 	configure -command density_profile_gui::help_docs
861 | 	configure -label Documentation...
862 | 	data MASTER menuitem1
863 | }
864 | menu {Menu command} menuitem3 {
865 | 	configure -command density_profile_gui::help_about
866 | 	configure -label About...
867 | 	data MASTER menuitem1
868 | }
869 | 
870 | 


--------------------------------------------------------------------------------
/density_profile_gui_ui.tcl:
--------------------------------------------------------------------------------
  1 | # density_profile_gui_ui.tcl --
  2 | #
  3 | # UI generated by GUI Builder Build 146 on 2012-12-18 18:22:52 from:
  4 | #    /home/toni/compile/vmd-utils/vmd_density_profile/density_profile_gui.ui
  5 | # THIS IS AN AUTOGENERATED FILE AND SHOULD NOT BE EDITED.
  6 | # The associated callback file should be modified instead.
  7 | #
  8 | 
  9 | # Declare the namespace for this dialog
 10 | namespace eval density_profile_gui {}
 11 | 
 12 | package require Tk
 13 | # density_profile_gui::ui --
 14 | #
 15 | #   Create the UI for this dialog.
 16 | #
 17 | # ARGS:
 18 | #   root     the parent window for this form
 19 | #   args     a catch-all for other args, but none are expected
 20 | #
 21 | proc density_profile_gui::ui {root args} {
 22 |     # this handles '.' as a special case
 23 |     set base [expr {($root == ".") ? "" : $root}]
 24 |     variable ROOT $root
 25 |     variable BASE $base
 26 |     variable SCRIPTDIR ; # defined in main script
 27 | 
 28 | 
 29 |     # Widget Initialization
 30 |     variable _frame_1 [frame $BASE._frame_1]
 31 |     variable frame_Zsource [frame $BASE.frame_Zsource]
 32 |     variable _frame_3 [frame $BASE._frame_3]
 33 |     variable _frame_4 [frame $BASE._frame_4]
 34 |     variable _frame_5 [frame $BASE._frame_5]
 35 |     variable _label_1 [label $BASE._label_1 \
 36 | 	    -font {helvetica 10} \
 37 | 	    -text "Atom selection"]
 38 |     variable _label_2 [label $BASE._label_2 \
 39 | 	    -font {helvetica 10} \
 40 | 	    -text "Projection axis"]
 41 |     variable _label_3 [label $BASE._label_3 \
 42 | 	    -font {helvetica 10} \
 43 | 	    -text "Resolution (\u00C5)"]
 44 |     variable _label_5 [label $BASE._label_5 \
 45 | 	    -font {helvetica 10} \
 46 | 	    -justify "right" \
 47 | 	    -text "Guess atomic number Z\nfrom attribute"]
 48 |     variable _entry_1 [entry $BASE._entry_1 \
 49 | 	    -font {helvetica 10} \
 50 | 	    -invalidcommand [namespace code [list _entry_1_invalidcommand]] \
 51 | 	    -justify "center" \
 52 | 	    -textvariable "density_profile::dp_args(selection)" \
 53 | 	    -validatecommand [namespace code [list _entry_1_validatecommand]] \
 54 | 	    -xscrollcommand [namespace code [list _entry_1_xscrollcommand]]]
 55 |     variable _label_6 [label $BASE._label_6 \
 56 | 	    -font {helvetica 10 bold} \
 57 | 	    -text "VMD Density Profile Tool"]
 58 |     variable _radiobutton_2 [radiobutton $BASE._radiobutton_2 \
 59 | 	    -command [namespace code [list _radiobutton_2_command]] \
 60 | 	    -font {helvetica 10} \
 61 | 	    -text "x" \
 62 | 	    -value "x" \
 63 | 	    -variable "density_profile::dp_args(axis)"]
 64 |     variable _radiobutton_3 [radiobutton $BASE._radiobutton_3 \
 65 | 	    -command [namespace code [list _radiobutton_3_command]] \
 66 | 	    -font {helvetica 10} \
 67 | 	    -text "y" \
 68 | 	    -value "y" \
 69 | 	    -variable "density_profile::dp_args(axis)"]
 70 |     variable _radiobutton_4 [radiobutton $BASE._radiobutton_4 \
 71 | 	    -command [namespace code [list _radiobutton_4_command]] \
 72 | 	    -font {helvetica 10} \
 73 | 	    -text "z" \
 74 | 	    -value "z" \
 75 | 	    -variable "density_profile::dp_args(axis)"]
 76 |     variable _entry_2 [entry $BASE._entry_2 \
 77 | 	    -invalidcommand [namespace code [list _entry_2_invalidcommand]] \
 78 | 	    -justify "center" \
 79 | 	    -textvariable "density_profile::dp_args(resolution)" \
 80 | 	    -validatecommand [namespace code [list _entry_2_validatecommand]] \
 81 | 	    -width 8 \
 82 | 	    -xscrollcommand [namespace code [list _entry_2_xscrollcommand]]]
 83 |     variable radiobutton_Zsource_name [radiobutton $BASE.radiobutton_Zsource_name \
 84 | 	    -command [namespace code [list radiobutton_Zsource_name_command]] \
 85 | 	    -font {helvetica 10} \
 86 | 	    -state "disabled" \
 87 | 	    -text "name" \
 88 | 	    -value "name" \
 89 | 	    -variable "density_profile::dp_args(Zsource)"]
 90 |     variable radiobutton_Zsource_type [radiobutton $BASE.radiobutton_Zsource_type \
 91 | 	    -command [namespace code [list radiobutton_Zsource_type_command]] \
 92 | 	    -font {helvetica 10} \
 93 | 	    -state "disabled" \
 94 | 	    -text "type" \
 95 | 	    -value "type" \
 96 | 	    -variable "density_profile::dp_args(Zsource)"]
 97 |     variable radiobutton_Zsource_element [radiobutton $BASE.radiobutton_Zsource_element \
 98 | 	    -command [namespace code [list radiobutton_Zsource_element_command]] \
 99 | 	    -font {helvetica 10} \
100 | 	    -state "disabled" \
101 | 	    -text "element" \
102 | 	    -value "element" \
103 | 	    -variable "density_profile::dp_args(Zsource)"]
104 |     variable _label_7 [label $BASE._label_7 \
105 | 	    -font {helvetica 10} \
106 | 	    -text "Density profile of"]
107 |     variable radiobutton_mass [radiobutton $BASE.radiobutton_mass \
108 | 	    -command [namespace code [list radiobutton_mass_command]] \
109 | 	    -font {helvetica 10} \
110 | 	    -text "mass" \
111 | 	    -value "mass" \
112 | 	    -variable "density_profile::dp_args(rho)"]
113 |     variable radiobutton_charge [radiobutton $BASE.radiobutton_charge \
114 | 	    -command [namespace code [list radiobutton_charge_command]] \
115 | 	    -font {helvetica 10} \
116 | 	    -text "charge" \
117 | 	    -value "charge" \
118 | 	    -variable "density_profile::dp_args(rho)"]
119 |     variable radiobutton_electrons [radiobutton $BASE.radiobutton_electrons \
120 | 	    -command [namespace code [list radiobutton_electrons_command]] \
121 | 	    -font {helvetica 10} \
122 | 	    -text "electrons" \
123 | 	    -value "electrons" \
124 | 	    -variable "density_profile::dp_args(rho)"]
125 |     variable plot [button $BASE.plot \
126 | 	    -command [namespace code [list plot_command]] \
127 | 	    -font {helvetica 10 bold} \
128 | 	    -text "Plot"]
129 |     variable close [button $BASE.close \
130 | 	    -command [namespace code [list close_command]] \
131 | 	    -font {helvetica 10 bold} \
132 | 	    -text "Close"]
133 |     variable radiobutton_atoms [radiobutton $BASE.radiobutton_atoms \
134 | 	    -command [namespace code [list radiobutton_atoms_command]] \
135 | 	    -font {helvetica 10} \
136 | 	    -text "number" \
137 | 	    -value "number" \
138 | 	    -variable "density_profile::dp_args(rho)"]
139 |     variable checkbox_Zsource_partial [checkbutton $BASE.checkbox_Zsource_partial \
140 | 	    -command [namespace code [list checkbox_Zsource_partial_command]] \
141 | 	    -font {helvetica 10} \
142 | 	    -state "disabled" \
143 | 	    -text "Consider partial charges" \
144 | 	    -variable "density_profile::dp_args(partial_charges)"]
145 |     variable _label_4 [label $BASE._label_4 \
146 | 	    -font {helvetica 10} \
147 | 	    -pady 6 \
148 | 	    -text "Computes 1-D projections of various atomic densities. The computation is performed in a single frame, a trajectory, or averaged over multiple frames." \
149 | 	    -wraplength 400]
150 |     variable _label_8 [label $BASE._label_8 \
151 | 	    -font {helvetica 10} \
152 | 	    -text "Frames from"]
153 |     variable _label_9 [label $BASE._label_9 \
154 | 	    -font {helvetica 10} \
155 | 	    -text "First"]
156 |     variable _entry_3 [entry $BASE._entry_3 \
157 | 	    -invalidcommand [namespace code [list _entry_3_invalidcommand]] \
158 | 	    -justify "center" \
159 | 	    -textvariable "density_profile::dp_args(frame_from)" \
160 | 	    -validatecommand [namespace code [list _entry_3_validatecommand]] \
161 | 	    -width 8 \
162 | 	    -xscrollcommand [namespace code [list _entry_3_xscrollcommand]]]
163 |     variable _label_10 [label $BASE._label_10 \
164 | 	    -font {helvetica 10} \
165 | 	    -text " to"]
166 |     variable _checkbutton_2 [checkbutton $BASE._checkbutton_2 \
167 | 	    -command [namespace code [list _checkbutton_2_command]] \
168 | 	    -font {helvetica 10} \
169 | 	    -text "Average" \
170 | 	    -variable "density_profile::dp_args(average)"]
171 |     variable _entry_4 [entry $BASE._entry_4 \
172 | 	    -invalidcommand [namespace code [list _entry_4_invalidcommand]] \
173 | 	    -justify "center" \
174 | 	    -textvariable "density_profile::dp_args(frame_to)" \
175 | 	    -validatecommand [namespace code [list _entry_4_validatecommand]] \
176 | 	    -width 8 \
177 | 	    -xscrollcommand [namespace code [list _entry_4_xscrollcommand]]]
178 |     variable _label_11 [label $BASE._label_11 \
179 | 	    -font {helvetica 10} \
180 | 	    -text " step"]
181 |     variable _entry_5 [entry $BASE._entry_5 \
182 | 	    -invalidcommand [namespace code [list _entry_5_invalidcommand]] \
183 | 	    -justify "center" \
184 | 	    -textvariable "density_profile::dp_args(frame_step)" \
185 | 	    -validatecommand [namespace code [list _entry_5_validatecommand]] \
186 | 	    -width 8 \
187 | 	    -xscrollcommand [namespace code [list _entry_5_xscrollcommand]]]
188 |     variable _label_12 [label $BASE._label_12 \
189 | 	    -font {helvetica 10} \
190 | 	    -pady 6 \
191 | 	    -text "See console for information and data files"]
192 |     variable help [button $BASE.help \
193 | 	    -bitmap "questhead" \
194 | 	    -command [namespace code [list help_command]] \
195 | 	    -font {helvetica 10 bold} \
196 | 	    -text "?"]
197 |     variable radiobutton_Zsource_mass [radiobutton $BASE.radiobutton_Zsource_mass \
198 | 	    -command [namespace code [list radiobutton_Zsource_mass_command]] \
199 | 	    -font {helvetica 10} \
200 | 	    -state "disabled" \
201 | 	    -text "mass" \
202 | 	    -value "mass" \
203 | 	    -variable "density_profile::dp_args(Zsource)"]
204 |     variable menu [menu $BASE.menu]
205 |     variable menuitem1 [menu $BASE.menuitem1 \
206 | 	    -tearoff 0]
207 |     $BASE.menu add cascade \
208 | 	    -label "Help" \
209 | 	    -menu $BASE.menuitem1
210 |     $BASE.menuitem1 add command \
211 | 	    -command "density_profile_gui::help_docs" \
212 | 	    -label "Documentation..."
213 |     $BASE.menuitem1 add command \
214 | 	    -command "density_profile_gui::help_about" \
215 | 	    -label "About..."
216 | 
217 | 
218 |     # Geometry Management
219 | 
220 |     grid $BASE._frame_1 -in $root -row 5 -column 2 \
221 | 	    -columnspan 1 \
222 | 	    -ipadx 0 \
223 | 	    -ipady 0 \
224 | 	    -padx 0 \
225 | 	    -pady 0 \
226 | 	    -rowspan 1 \
227 | 	    -sticky "w"
228 |     grid $BASE.frame_Zsource -in $root -row 6 -column 2 \
229 | 	    -columnspan 1 \
230 | 	    -ipadx 0 \
231 | 	    -ipady 0 \
232 | 	    -padx 0 \
233 | 	    -pady 0 \
234 | 	    -rowspan 1 \
235 | 	    -sticky "w"
236 |     grid $BASE._frame_3 -in $root -row 3 -column 2 \
237 | 	    -columnspan 1 \
238 | 	    -ipadx 0 \
239 | 	    -ipady 0 \
240 | 	    -padx 0 \
241 | 	    -pady 0 \
242 | 	    -rowspan 1 \
243 | 	    -sticky "w"
244 |     grid $BASE._frame_4 -in $root -row 9 -column 1 \
245 | 	    -columnspan 2 \
246 | 	    -ipadx 0 \
247 | 	    -ipady 0 \
248 | 	    -padx 0 \
249 | 	    -pady 0 \
250 | 	    -rowspan 1 \
251 | 	    -sticky "news"
252 |     grid $BASE._frame_5 -in $root -row 7 -column 2 \
253 | 	    -columnspan 1 \
254 | 	    -ipadx 0 \
255 | 	    -ipady 0 \
256 | 	    -padx 0 \
257 | 	    -pady 0 \
258 | 	    -rowspan 1 \
259 | 	    -sticky "ew"
260 |     grid $BASE._label_1 -in $root -row 4 -column 1 \
261 | 	    -columnspan 1 \
262 | 	    -ipadx 0 \
263 | 	    -ipady 0 \
264 | 	    -padx 0 \
265 | 	    -pady 0 \
266 | 	    -rowspan 1 \
267 | 	    -sticky "e"
268 |     grid $BASE._label_2 -in $root -row 5 -column 1 \
269 | 	    -columnspan 1 \
270 | 	    -ipadx 0 \
271 | 	    -ipady 0 \
272 | 	    -padx 0 \
273 | 	    -pady 0 \
274 | 	    -rowspan 1 \
275 | 	    -sticky "e"
276 |     grid $BASE._label_3 -in $base._frame_1 -row 1 -column 4 \
277 | 	    -columnspan 1 \
278 | 	    -ipadx 0 \
279 | 	    -ipady 0 \
280 | 	    -padx 0 \
281 | 	    -pady 0 \
282 | 	    -rowspan 1 \
283 | 	    -sticky "e"
284 |     grid $BASE._label_5 -in $root -row 6 -column 1 \
285 | 	    -columnspan 1 \
286 | 	    -ipadx 0 \
287 | 	    -ipady 0 \
288 | 	    -padx 0 \
289 | 	    -pady 0 \
290 | 	    -rowspan 1 \
291 | 	    -sticky "e"
292 |     grid $BASE._entry_1 -in $root -row 4 -column 2 \
293 | 	    -columnspan 1 \
294 | 	    -ipadx 0 \
295 | 	    -ipady 0 \
296 | 	    -padx 0 \
297 | 	    -pady 0 \
298 | 	    -rowspan 1 \
299 | 	    -sticky "ew"
300 |     grid $BASE._label_6 -in $root -row 1 -column 1 \
301 | 	    -columnspan 2 \
302 | 	    -ipadx 0 \
303 | 	    -ipady 0 \
304 | 	    -padx 0 \
305 | 	    -pady 0 \
306 | 	    -rowspan 1 \
307 | 	    -sticky "s"
308 |     grid $BASE._radiobutton_2 -in $base._frame_1 -row 1 -column 1 \
309 | 	    -columnspan 1 \
310 | 	    -ipadx 0 \
311 | 	    -ipady 0 \
312 | 	    -padx 0 \
313 | 	    -pady 0 \
314 | 	    -rowspan 1 \
315 | 	    -sticky "ew"
316 |     grid $BASE._radiobutton_3 -in $base._frame_1 -row 1 -column 2 \
317 | 	    -columnspan 1 \
318 | 	    -ipadx 0 \
319 | 	    -ipady 0 \
320 | 	    -padx 0 \
321 | 	    -pady 0 \
322 | 	    -rowspan 1 \
323 | 	    -sticky "ew"
324 |     grid $BASE._radiobutton_4 -in $base._frame_1 -row 1 -column 3 \
325 | 	    -columnspan 1 \
326 | 	    -ipadx 0 \
327 | 	    -ipady 0 \
328 | 	    -padx 0 \
329 | 	    -pady 0 \
330 | 	    -rowspan 1 \
331 | 	    -sticky "ew"
332 |     grid $BASE._entry_2 -in $base._frame_1 -row 1 -column 5 \
333 | 	    -columnspan 1 \
334 | 	    -ipadx 0 \
335 | 	    -ipady 0 \
336 | 	    -padx 0 \
337 | 	    -pady 0 \
338 | 	    -rowspan 1 \
339 | 	    -sticky "ew"
340 |     grid $BASE.radiobutton_Zsource_name -in $base.frame_Zsource -row 1 -column 3 \
341 | 	    -columnspan 1 \
342 | 	    -ipadx 0 \
343 | 	    -ipady 0 \
344 | 	    -padx 0 \
345 | 	    -pady 0 \
346 | 	    -rowspan 1 \
347 | 	    -sticky ""
348 |     grid $BASE.radiobutton_Zsource_type -in $base.frame_Zsource -row 1 -column 4 \
349 | 	    -columnspan 1 \
350 | 	    -ipadx 0 \
351 | 	    -ipady 0 \
352 | 	    -padx 0 \
353 | 	    -pady 0 \
354 | 	    -rowspan 1 \
355 | 	    -sticky ""
356 |     grid $BASE.radiobutton_Zsource_element -in $base.frame_Zsource -row 1 -column 2 \
357 | 	    -columnspan 1 \
358 | 	    -ipadx 0 \
359 | 	    -ipady 0 \
360 | 	    -padx 0 \
361 | 	    -pady 0 \
362 | 	    -rowspan 1 \
363 | 	    -sticky ""
364 |     grid $BASE._label_7 -in $root -row 3 -column 1 \
365 | 	    -columnspan 1 \
366 | 	    -ipadx 0 \
367 | 	    -ipady 0 \
368 | 	    -padx 0 \
369 | 	    -pady 0 \
370 | 	    -rowspan 1 \
371 | 	    -sticky "e"
372 |     grid $BASE.radiobutton_mass -in $base._frame_3 -row 1 -column 2 \
373 | 	    -columnspan 1 \
374 | 	    -ipadx 0 \
375 | 	    -ipady 0 \
376 | 	    -padx 0 \
377 | 	    -pady 0 \
378 | 	    -rowspan 1 \
379 | 	    -sticky ""
380 |     grid $BASE.radiobutton_charge -in $base._frame_3 -row 1 -column 3 \
381 | 	    -columnspan 1 \
382 | 	    -ipadx 0 \
383 | 	    -ipady 0 \
384 | 	    -padx 0 \
385 | 	    -pady 0 \
386 | 	    -rowspan 1 \
387 | 	    -sticky ""
388 |     grid $BASE.radiobutton_electrons -in $base._frame_3 -row 1 -column 4 \
389 | 	    -columnspan 1 \
390 | 	    -ipadx 0 \
391 | 	    -ipady 0 \
392 | 	    -padx 0 \
393 | 	    -pady 0 \
394 | 	    -rowspan 1 \
395 | 	    -sticky ""
396 |     grid $BASE.plot -in $base._frame_4 -row 1 -column 2 \
397 | 	    -columnspan 1 \
398 | 	    -ipadx 0 \
399 | 	    -ipady 0 \
400 | 	    -padx 0 \
401 | 	    -pady 0 \
402 | 	    -rowspan 1 \
403 | 	    -sticky "nsew"
404 |     grid $BASE.close -in $base._frame_4 -row 1 -column 3 \
405 | 	    -columnspan 1 \
406 | 	    -ipadx 0 \
407 | 	    -ipady 0 \
408 | 	    -padx 0 \
409 | 	    -pady 0 \
410 | 	    -rowspan 1 \
411 | 	    -sticky "nsew"
412 |     grid $BASE.radiobutton_atoms -in $base._frame_3 -row 1 -column 1 \
413 | 	    -columnspan 1 \
414 | 	    -ipadx 0 \
415 | 	    -ipady 0 \
416 | 	    -padx 0 \
417 | 	    -pady 0 \
418 | 	    -rowspan 1 \
419 | 	    -sticky ""
420 |     grid $BASE.checkbox_Zsource_partial -in $base.frame_Zsource -row 1 -column 5 \
421 | 	    -columnspan 1 \
422 | 	    -ipadx 0 \
423 | 	    -ipady 0 \
424 | 	    -padx 0 \
425 | 	    -pady 0 \
426 | 	    -rowspan 1 \
427 | 	    -sticky "w"
428 |     grid $BASE._label_4 -in $root -row 2 -column 1 \
429 | 	    -columnspan 2 \
430 | 	    -ipadx 0 \
431 | 	    -ipady 0 \
432 | 	    -padx 0 \
433 | 	    -pady 0 \
434 | 	    -rowspan 1 \
435 | 	    -sticky "nsew"
436 |     grid $BASE._label_8 -in $root -row 7 -column 1 \
437 | 	    -columnspan 1 \
438 | 	    -ipadx 0 \
439 | 	    -ipady 0 \
440 | 	    -padx 0 \
441 | 	    -pady 0 \
442 | 	    -rowspan 1 \
443 | 	    -sticky "e"
444 |     grid $BASE._label_9 -in $base._frame_5 -row 1 -column 1 \
445 | 	    -columnspan 1 \
446 | 	    -ipadx 0 \
447 | 	    -ipady 0 \
448 | 	    -padx 0 \
449 | 	    -pady 0 \
450 | 	    -rowspan 1 \
451 | 	    -sticky ""
452 |     grid $BASE._entry_3 -in $base._frame_5 -row 1 -column 1 \
453 | 	    -columnspan 1 \
454 | 	    -ipadx 0 \
455 | 	    -ipady 0 \
456 | 	    -padx 0 \
457 | 	    -pady 0 \
458 | 	    -rowspan 1 \
459 | 	    -sticky "ew"
460 |     grid $BASE._label_10 -in $base._frame_5 -row 1 -column 2 \
461 | 	    -columnspan 1 \
462 | 	    -ipadx 0 \
463 | 	    -ipady 0 \
464 | 	    -padx 0 \
465 | 	    -pady 0 \
466 | 	    -rowspan 1 \
467 | 	    -sticky "e"
468 |     grid $BASE._checkbutton_2 -in $base._frame_5 -row 1 -column 6 \
469 | 	    -columnspan 1 \
470 | 	    -ipadx 0 \
471 | 	    -ipady 0 \
472 | 	    -padx 0 \
473 | 	    -pady 0 \
474 | 	    -rowspan 1 \
475 | 	    -sticky "e"
476 |     grid $BASE._entry_4 -in $base._frame_5 -row 1 -column 3 \
477 | 	    -columnspan 1 \
478 | 	    -ipadx 0 \
479 | 	    -ipady 0 \
480 | 	    -padx 0 \
481 | 	    -pady 0 \
482 | 	    -rowspan 1 \
483 | 	    -sticky "ew"
484 |     grid $BASE._label_11 -in $base._frame_5 -row 1 -column 4 \
485 | 	    -columnspan 1 \
486 | 	    -ipadx 0 \
487 | 	    -ipady 0 \
488 | 	    -padx 0 \
489 | 	    -pady 0 \
490 | 	    -rowspan 1 \
491 | 	    -sticky "e"
492 |     grid $BASE._entry_5 -in $base._frame_5 -row 1 -column 5 \
493 | 	    -columnspan 1 \
494 | 	    -ipadx 0 \
495 | 	    -ipady 0 \
496 | 	    -padx 0 \
497 | 	    -pady 0 \
498 | 	    -rowspan 1 \
499 | 	    -sticky "ew"
500 |     grid $BASE._label_12 -in $root -row 8 -column 1 \
501 | 	    -columnspan 2 \
502 | 	    -ipadx 0 \
503 | 	    -ipady 0 \
504 | 	    -padx 0 \
505 | 	    -pady 0 \
506 | 	    -rowspan 1 \
507 | 	    -sticky ""
508 |     grid $BASE.help -in $base._frame_4 -row 1 -column 1 \
509 | 	    -columnspan 1 \
510 | 	    -ipadx 0 \
511 | 	    -ipady 0 \
512 | 	    -padx 0 \
513 | 	    -pady 0 \
514 | 	    -rowspan 1 \
515 | 	    -sticky "nsew"
516 |     grid $BASE.radiobutton_Zsource_mass -in $base.frame_Zsource -row 1 -column 1 \
517 | 	    -columnspan 1 \
518 | 	    -ipadx 0 \
519 | 	    -ipady 0 \
520 | 	    -padx 0 \
521 | 	    -pady 0 \
522 | 	    -rowspan 1 \
523 | 	    -sticky ""
524 | 
525 |     # Resize Behavior
526 |     grid rowconfigure $root 1 -weight 0 -minsize 17 -pad 0
527 |     grid rowconfigure $root 2 -weight 1 -minsize 44 -pad 0
528 |     grid rowconfigure $root 3 -weight 0 -minsize 40 -pad 0
529 |     grid rowconfigure $root 4 -weight 0 -minsize 38 -pad 0
530 |     grid rowconfigure $root 5 -weight 0 -minsize 48 -pad 0
531 |     grid rowconfigure $root 6 -weight 0 -minsize 40 -pad 0
532 |     grid rowconfigure $root 7 -weight 0 -minsize 45 -pad 0
533 |     grid rowconfigure $root 8 -weight 0 -minsize 2 -pad 0
534 |     grid rowconfigure $root 9 -weight 0 -minsize 27 -pad 0
535 |     grid columnconfigure $root 1 -weight 0 -minsize 40 -pad 0
536 |     grid columnconfigure $root 2 -weight 1 -minsize 119 -pad 0
537 |     grid rowconfigure $base._frame_1 1 -weight 0 -minsize 7 -pad 0
538 |     grid columnconfigure $base._frame_1 1 -weight 0 -minsize 40 -pad 0
539 |     grid columnconfigure $base._frame_1 2 -weight 0 -minsize 40 -pad 0
540 |     grid columnconfigure $base._frame_1 3 -weight 0 -minsize 40 -pad 0
541 |     grid columnconfigure $base._frame_1 4 -weight 0 -minsize 40 -pad 0
542 |     grid columnconfigure $base._frame_1 5 -weight 0 -minsize 40 -pad 0
543 |     grid rowconfigure $base.frame_Zsource 1 -weight 0 -minsize 16 -pad 0
544 |     grid columnconfigure $base.frame_Zsource 1 -weight 0 -minsize 40 -pad 0
545 |     grid columnconfigure $base.frame_Zsource 2 -weight 0 -minsize 40 -pad 0
546 |     grid columnconfigure $base.frame_Zsource 3 -weight 0 -minsize 40 -pad 0
547 |     grid columnconfigure $base.frame_Zsource 4 -weight 0 -minsize 40 -pad 0
548 |     grid columnconfigure $base.frame_Zsource 5 -weight 0 -minsize 40 -pad 0
549 |     grid rowconfigure $base._frame_3 1 -weight 0 -minsize 15 -pad 0
550 |     grid columnconfigure $base._frame_3 1 -weight 0 -minsize 40 -pad 0
551 |     grid columnconfigure $base._frame_3 2 -weight 0 -minsize 40 -pad 0
552 |     grid columnconfigure $base._frame_3 3 -weight 0 -minsize 40 -pad 0
553 |     grid columnconfigure $base._frame_3 4 -weight 0 -minsize 40 -pad 0
554 |     grid rowconfigure $base._frame_4 1 -weight 0 -minsize 10 -pad 0
555 |     grid columnconfigure $base._frame_4 1 -weight 0 -minsize 40 -pad 0
556 |     grid columnconfigure $base._frame_4 2 -weight 1 -minsize 40 -pad 0
557 |     grid columnconfigure $base._frame_4 3 -weight 1 -minsize 40 -pad 0
558 |     grid rowconfigure $base._frame_5 1 -weight 0 -minsize 2 -pad 0
559 |     grid columnconfigure $base._frame_5 1 -weight 1 -minsize 40 -pad 0
560 |     grid columnconfigure $base._frame_5 2 -weight 0 -minsize 24 -pad 0
561 |     grid columnconfigure $base._frame_5 3 -weight 1 -minsize 40 -pad 0
562 |     grid columnconfigure $base._frame_5 4 -weight 0 -minsize 27 -pad 0
563 |     grid columnconfigure $base._frame_5 5 -weight 1 -minsize 40 -pad 0
564 |     grid columnconfigure $base._frame_5 6 -weight 0 -minsize 78 -pad 0
565 |     $ROOT configure -menu $BASE.menu
566 | }
567 | 


--------------------------------------------------------------------------------
/doc/ChangeLog:
--------------------------------------------------------------------------------
 1 | 2016-02-02  Toni  <toni@pcgiorgino.isib.cnr.it>
 2 | 
 3 | 	* 1.3 Moved docs
 4 | 
 5 | 2014-06-11  Toni  <toni@pcgiorgino.isib.cnr.it>
 6 | 
 7 | 	* 1.2 Moved to GitHub
 8 | 
 9 | 2013-08-09  Toni  <...@...>
10 | 
11 | 	* 1.1 Added support for variable cell sizes
12 | 
13 | 2013-05-13  Toni  <...@...>
14 | 
15 | 	* 1.0 Initial release
16 | 
17 | 


--------------------------------------------------------------------------------
/doc/NOTE.txt.private:
--------------------------------------------------------------------------------
 1 | ::MultiPlot::Plot5::plothandle configure -hline {.333 -dash "." -fill blue} -plot
 2 | 
 3 | 
 4 | export TCLLIBPATH=$PWD
 5 | 
 6 | 
 7 | 
 8 | 
 9 | structure of a split plugin
10 | 
11 | package provide chirality_gui 1.1
12 | namespace eval ::chirality::GUI:: {
13 | proc chirality_gui { } { return [eval ::chirality::GUI::chirality_gui] }
14 | 
15 | 
16 | ...
17 | 
18 | package provide chirality 1.1
19 | namespace eval ::chirality:: {
20 | 
21 | 
22 | CHIRALITY
23 | 	       Core	     Gui
24 | namespace      ::what::	     ::what::GUI::
25 | package	       what	     what_gui
26 | filename       what.tcl	     what_gui.tcl
27 | 
28 | MINE
29 | 	       Core	     Gui
30 | namespace      ::what::	     ::what::
31 | package	       what	     what_gui   (free)
32 | filename       what_core.tcl what.tcl   (= namespace)
33 | 
34 | 
35 | 
36 | Guibuilder uses the namespace (first level) given as file name
37 | 
38 | Saving as nnn::mmm works, but may create problems in windows
39 | 
40 | Solution: do not use sub-namespace, but make a different package
41 | 
42 | 
43 | 


--------------------------------------------------------------------------------
/doc/POPC-e-density-profile.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/giorginolab/vmd_density_profile/4f3861a66935475add76642d46cbd812438ec502/doc/POPC-e-density-profile.png


--------------------------------------------------------------------------------
/doc/POPC-waters-mass-density-profile.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/giorginolab/vmd_density_profile/4f3861a66935475add76642d46cbd812438ec502/doc/POPC-waters-mass-density-profile.png


--------------------------------------------------------------------------------
/doc/README.md:
--------------------------------------------------------------------------------
  1 | VMD Density Profile Tool (1.3)
  2 | ==============================
  3 | 
  4 | 
  5 | The *Density Profile Tool* is a VMD analysis plugin that computes 1-D projections of various atomic densities. The computation can be performed in a single frame, a trajectory, or averaged over multiple frames.
  6 | 
  7 | -   Atomic (number) density, i.e. average number of atoms
  8 | 
  9 | -   Mass density
 10 | 
 11 | -   Charge density
 12 | 
 13 | -   Electron density, i.e. number density of electrons.
 14 | 
 15 | This tool is fully described in the reference given below. This page serves only as a quick-reference.
 16 | 
 17 | 
 18 | 
 19 | 
 20 | 
 21 | Installation
 22 | ----------------------------------------
 23 | 
 24 | See instructions [here](https://gist.github.com/tonigi/a9cfaf7642a7fbc13293).
 25 | 
 26 | 
 27 | **NOTE: This code comes without any warranty of fitness for any use. It is UNSUPPORTED. After you download it, you are on your own.** By downloading the software you agree to comply with the terms of the
 28 | 3-clause BSD license.
 29 |  
 30 | 
 31 | You may or may not be able to get support by posting to the [External tools](https://sourceforge.net/p/membplugin/discussion/external_tools/) forum hosted at the [MEMBPLUGIN](http://membplugin.sourceforge.net) site.
 32 | 
 33 | 
 34 | 
 35 | Citation
 36 | --------
 37 | 
 38 | Please cite the following publication:
 39 | 
 40 | -   Toni Giorgino, Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD, *Computer Physics Communications* Volume 185, Issue 1, January 2014, Pages 317–322, [doi:10.1016/j.cpc.2013.08.022](http://dx.doi.org/10.1016/j.cpc.2013.08.022) – [arXiv:1308.5873](http://arxiv.org/abs/1308.5873)
 41 | 
 42 | Usage (GUI)
 43 | -----------
 44 | 
 45 | The plugin is accessible from VMD in *Extensions \> Analysis \> Density Profile Tool*. By default, the profile is computed for the current frame in the *top* molecule. For mass and charge computation, a topology file must be loaded.
 46 | 
 47 | When dealing with a trajectory, the behaviour depends on the *average* check box: if selected, density profiles for all of the frames will be plotted; otherwise, the average plus or minus the standard deviation will be displayed.
 48 | 
 49 | If periodic cell information is available in the molecule (e.g. as set in *pbctools*), the density will be properly normalized with respect to the volume. Otherwise, it will be simply projected along a linear axis. **IMPORTANT: you will still need to wrap the trajectory yourself.**
 50 | 
 51 | *Electron density* calculations require the atomic number *Z* (i.e., the element) to be known for each atom. This information may be obtained from either the *mass*, *name*, *type*, or *element* atom properties (see VMD manual). Selecting ***mass* is highly recommended** because *element* is usually unset, and guessing from *type* or *name* requires error-prone heuristics. Atomic number guessing is based on the [topotools guessatom](http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/#TOC-guessatom-property-from-) function and algorithm. Note that the heuristics will likely be inappropriate in the case of united atom/coarse grain forcefields.
 52 | 
 53 | 
 54 | ![Screenshot](Screenshot-Density%20Profile%20Tool.png)
 55 | 
 56 | 
 57 | Usage (command line)
 58 | --------------------
 59 | 
 60 | A command line interface is available to perform the same calculations as the GUI. See help with
 61 | 
 62 |     vmd > package require density_profile
 63 |     vmd > density_profile
 64 | 
 65 |     Usage: density_profile <args>
 66 |     Args (with defaults):
 67 |        -rho electrons
 68 |        -selection name P11
 69 |        -axis z
 70 |        -resolution 1
 71 |        -Zsource type
 72 |        -partial_charges 1
 73 |        -frame_from 0
 74 |        -frame_to 130
 75 |        -frame_step 1
 76 |        -average 1
 77 | 
 78 | Where `-rho` is one of *number, mass, charge* or *electrons*. In the latter case, `-Zsource` must be one of *mass, element, name, type*. The function returns two lists:
 79 | 
 80 | -   The **lower coordinate** of each bin, i.e. a list of bin breaks.
 81 | 
 82 | -   A list of **densities for each bin**. Each element of the list is
 83 | 
 84 |     -   a single value, if only one frame is selected, or *average* is 1
 85 | 
 86 |     -   a list of density values, one for each of the frames computed
 87 | 
 88 | **IMPORTANT: when used on the command line, bin BREAKS are returned. When plotting, dots are placed in bin CENTERS.**
 89 | 
 90 | Units
 91 | -----
 92 | 
 93 | Assuming that periodic box information is available, results are given in the following units:
 94 | 
 95 | -   Atomic density: atoms/Å<sup>3</sup>
 96 | 
 97 | -   Mass density: amu/Å<sup>3</sup>=Da/Å<sup>3</sup>
 98 | 
 99 | -   Charge density: e/Å<sup>3</sup>
100 | 
101 | -   Electron density: electrons/Å<sup>3</sup>
102 | 
103 | **Unit conversions:**
104 | 
105 | -   in moles per liter, multiply by 1661 ų mol/l (or the value appropriate at your temperature)
106 | 
107 | -   1 amu/Å<sup>3</sup> = 1.66 g/cm<sup>3</sup> = 1660 kg/m<sup>3</sup>
108 | 
109 | 
110 | 
111 | Example
112 | -------
113 | 
114 | See attached screenshots. 
115 | 
116 | Solvent density profile around a POPC membrane. Note how the water density in bulk goes to the macroscopic value of 18/30 amu/ų.
117 | 
118 | ![attachment:POPC-waters-mass-density-profile.png](POPC-waters-mass-density-profile.png)
119 | 
120 | 
121 | Electron density profile of a POPC membrane (solvent included).
122 | 
123 | ![attachment:POPC-e-density-profile.png](POPC-e-density-profile.png)
124 | 
125 | 
126 | 
127 | Limitations
128 | -----------
129 | 
130 | -   Atoms are assumed as point-like;
131 | 
132 | -   only orthorhombic cells are supported;
133 | 
134 | -   to compute volumetric densities, cell information must be present for *all* frames.
135 | 
136 | 
137 | 
138 | 
139 | 
140 | Acknowledgments
141 | ---------------
142 | 
143 | Former support from the Agència de Gestió d'Ajuts Universitaris i de Recerca - Generalitat de Catalunya is gratefully acknowledged.
144 | 
145 | 


--------------------------------------------------------------------------------
/doc/Screenshot-Density Profile Tool.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/giorginolab/vmd_density_profile/4f3861a66935475add76642d46cbd812438ec502/doc/Screenshot-Density Profile Tool.png


--------------------------------------------------------------------------------
/examples/Readme.md:
--------------------------------------------------------------------------------
 1 | Examples
 2 | ========
 3 | 
 4 | This directory contains miscellaneous examples for the Density Profile tool.
 5 | 
 6 | File        | Description
 7 | ----------- | ----------------
 8 | example.tcl | Downloads and computes various profiles on Klauda's *popc72-c36npt* simulations.
 9 | popc/       | A few ns of a trivial POPC simulation
10 | 
11 | Data for the paper *Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD* are available on request.
12 | 
13 | 
14 | 


--------------------------------------------------------------------------------
/examples/example.tcl:
--------------------------------------------------------------------------------
 1 | # Test script for the Density Profile Plugin
 2 | 
 3 | # The script can also be used from the GUI (VMD Main
 4 | # window->Extensions->Analysis->Density Profile Tool). This script
 5 | # only illustrates the command-line interface.
 6 | 
 7 | 
 8 | 
 9 | # Initialization: load Klauda's equilibrated membranes,
10 | #  http://terpconnect.umd.edu/~jbklauda/research/download.html POPC
11 | #  Bilayer (303.00K, NPT, 35ns, 72 lipids): PDB, CHARMM PSF, CHARMM36
12 | #  Current directory needs be writable.
13 | 
14 | mol delete all
15 | vmd_mol_urlload  http://terpconnect.umd.edu/~jbklauda/research/download/popc72-c36npt.pdb popc72-c36npt.pdb
16 | vmd_mol_urlload  http://terpconnect.umd.edu/~jbklauda/research/download/popc72-c36npt.psf popc72-c36npt.psf
17 | mol new popc72-c36npt.psf waitfor all
18 | mol addfile popc72-c36npt.pdb waitfor all
19 | pbc set { 48.4331 48.4331 66.913 }; # Set box size
20 | 
21 | 
22 | # Define a convenience function to pretty-print two lists
23 | proc pptable {l1 l2} { foreach i1 $l1 i2 $l2 { puts " [format %6.2f $i1]\t[format %6.2f $i2]" }  }
24 | 
25 | 
26 | 
27 | # Begin analysis
28 | 
29 | # - Load package
30 | package require density_profile
31 | 
32 | # - Compute mass density for water molecules only
33 | set wdens [density_profile -rho mass -selection water]
34 | 
35 | # - In $wdens we now have
36 | # index 0: list of densities [g/mol/A^3]: from 0 (center) to ~0.6 (bulk)
37 | # index 1: list of bin breaks [A]: -35, -34, ... 34
38 | 
39 | # - Show output as a table
40 | puts "**************************************************"
41 | puts "| Bin breaks coordinates: (z, Angstroms)"
42 | puts "\t| Density of water in each bin: (g/mol/A^3)"
43 | pptable [lindex $wdens 1] [lindex $wdens 0]
44 | 
45 | 
46 | # - The same as plots (assume you have a graphics terminal)
47 | multiplot -x [lindex $wdens 1] -y [lindex $wdens 0] -marker point -plot \
48 | 	-title "Water mass density (g/mol/A^3); dots: bulk value" \
49 | 	-xlabel "Distance from membrane center z (A)" \
50 | 	-hline {0.6 -dash .}
51 | 
52 | 
53 | 
54 | # - Compute the electron density of full system (small membrane, only
55 | #   one frame: lower resolution); show graphically.
56 | set edens [density_profile -rho electrons -selection all -resolution 2]
57 | multiplot -x [lindex $edens 1] -y [lindex $edens 0] -marker point -plot \
58 | 	-title "Electron density (1/A^3); dots: value for bulk water" \
59 | 	-xlabel "Distance from membrane center z (A)" \
60 | 	-hline {0.33 -dash .}
61 | 
62 | 


--------------------------------------------------------------------------------
/examples/popc/popc_box.xtc:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/giorginolab/vmd_density_profile/4f3861a66935475add76642d46cbd812438ec502/examples/popc/popc_box.xtc


--------------------------------------------------------------------------------
/load.tcl:
--------------------------------------------------------------------------------
1 | set density_profile_dir [file dirname [file normalize [info script]]]
2 | 
3 | puts "density_profile) Adding directory $density_profile_dir to auto_path and registering the menu"
4 | 
5 | lappend auto_path $density_profile_dir
6 | package require density_profile_gui
7 | ::density_profile_gui::register_menu
8 | 


--------------------------------------------------------------------------------
/pkgIndex.tcl:
--------------------------------------------------------------------------------
 1 | # Tcl package index file, version 1.1
 2 | # This file is generated by the "pkg_mkIndex" command
 3 | # and sourced either when an application starts up or
 4 | # by a "package unknown" script.  It invokes the
 5 | # "package ifneeded" command to set up package-related
 6 | # information so that packages will be loaded automatically
 7 | # in response to "package require" commands.  When this
 8 | # script is sourced, the variable $dir must contain the
 9 | # full path name of this file's directory.
10 | 
11 | 
12 | package ifneeded density_profile 1.1 [list source [file join $dir density_profile.tcl]]
13 | package ifneeded density_profile_gui 1.1 [list source [file join $dir density_profile_gui.tcl]]
14 | 
15 | # Piggy-back the pkgIndex mechanism to register in extension menu (only once)
16 | catch { package require density_profile_gui; density_profile_gui::register_menu; }
17 | 
18 | 


--------------------------------------------------------------------------------