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source: trunk/gui/scripts/molvisviewer.tcl @ 2395

Last change on this file since 2395 was 2015, checked in by gah, 14 years ago
wrong vector method in parallelepiped
File size: 70.8 KB

Line
1
2	# ----------------------------------------------------------------------
3	# COMPONENT: molvisviewer - view a molecule in 3D
4	#
5	# This widget brings up a 3D representation of a molecule
6	# It connects to the Molvis server running on a rendering farm,
7	# transmits data, and displays the results.
8	# ======================================================================
9	# AUTHOR: Michael McLennan, Purdue University
10	# Copyright (c) 2004-2005 Purdue Research Foundation
11	#
12	# See the file "license.terms" for information on usage and
13	# redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES.
14	# ======================================================================
15	package require Itk
16	package require BLT
17	package require Img
18
19	option add *MolvisViewer.width 4i widgetDefault
20	option add *MolvisViewer.height 4i widgetDefault
21	option add *MolvisViewer.foreground black widgetDefault
22	option add MolvisViewer.font --helvetica-medium-r-normal--12- widgetDefault
23
24	# must use this name -- plugs into Rappture::resources::load
25	proc MolvisViewer_init_resources {} {
26	Rappture::resources::register \
27	molvis_server Rappture::MolvisViewer::SetServerList
28	}
29
30	set debug 0
31	proc debug { args } {
32	global debug
33	if { $debug } {
34	puts stderr "[info level -1]: $args"
35	}
36	}
37
38	itcl::class Rappture::MolvisViewer {
39	inherit Rappture::VisViewer
40
41	itk_option define -device device Device ""
42
43	private variable _icon 0
44
45	private variable _mevent; # info used for mouse event operations
46	private variable _rocker; # info used for rock operations
47	private variable _dlist ""; # list of dataobj objects
48	private variable _dataobjs; # data objects on server
49	private variable _dobj2transparency;# maps dataobj => transparency
50	private variable _dobj2raise; # maps dataobj => raise flag 0/1
51
52	private variable _active; # array of active models.
53	private variable _obj2models; # array containing list of models
54	# for each data object.
55	private variable _view
56	private variable _click
57
58	private variable _model
59	private variable _mlist
60	private variable _mrep "ballnstick"
61
62	private variable _imagecache
63	private variable _state
64	private variable _labels "default"
65	private variable _cacheid ""
66	private variable _cacheimage ""
67
68	private variable _delta1 10
69	private variable _delta2 2
70
71	private common _settings ; # Array of settings for all known
72	# widgets
73	private variable _initialized
74
75	private common _downloadPopup; # Download options from popup
76	private variable _pdbdata; # PDB data from run file sent to pymol
77	private common _hardcopy
78	private variable _nextToken 0
79	private variable _outbuf "";
80	private variable _buffering 0;
81	private variable _resizePending 0;
82	private variable _width
83	private variable _height
84	private variable _restore 1; # Restore camera settings
85	private variable _cell 0; # Restore camera settings
86
87	constructor { hostlist args } {
88	Rappture::VisViewer::constructor $hostlist
89	} {
90	# defined below
91	}
92	destructor {
93	# defined below
94	}
95	public proc SetServerList { namelist } {
96	Rappture::VisViewer::SetServerList "pymol" $namelist
97	}
98	private method BuildSettingsTab {}
99	private method DoResize {}
100	private method EventuallyResize { w h }
101	private method GetImage { widget }
102	private method ReceiveImage { size cacheid frame rock }
103	private method WaitIcon { option widget }
104	private method DownloadPopup { popup command }
105	private method EnableDownload { popup what }
106
107	protected method Map {}
108	protected method Pan {option x y}
109	protected method Rebuild { }
110	protected method Rotate {option x y}
111	protected method SendCmd { string }
112	protected method Unmap {}
113	protected method Update { args }
114	protected method Vmouse {option b m x y}
115	protected method Vmouse2 {option b m x y}
116	protected method Zoom {option {factor 10}}
117
118	public method Connect {}
119	public method Disconnect {}
120	public method ResetView {}
121	public method add {dataobj {options ""}}
122	public method delete {args}
123	public method download {option args}
124	public method get {}
125	public method isconnected {}
126	public method labels {option {model "all"}}
127	public method parameters {title args} {
128	# do nothing
129	}
130	public method snap { w h }
131	private method Opacity {option}
132	private method SphereScale {option {models "all"} }
133	private method StickRadius {option {models "all"} }
134	private method OrthoProjection {option}
135	private method Representation {option {model "all"} }
136	private method CartoonTrace {option {model "all"}}
137	private method ComputeParallelepipedVertices { dataobj }
138	private method Cell {option}
139	private method Rock {option}
140	}
141
142	itk::usual MolvisViewer {
143	keep -background -foreground -cursor -font
144	}
145
146	# ----------------------------------------------------------------------
147	# CONSTRUCTOR
148	# ----------------------------------------------------------------------
149	itcl::body Rappture::MolvisViewer::constructor {hostlist args} {
150	# Register events to the dispatcher. Base class expects !rebuild
151	# event to be registered.
152
153	# Rebuild
154	$_dispatcher register !rebuild
155	$_dispatcher dispatch $this !rebuild "[itcl::code $this Rebuild]; list"
156
157	# Resize event
158	$_dispatcher register !resize
159	$_dispatcher dispatch $this !resize "[itcl::code $this DoResize]; list"
160
161	# Rocker
162	$_dispatcher register !rocker
163	$_dispatcher dispatch $this !rocker "[itcl::code $this Rock step]; list"
164	# Mouse Event
165	$_dispatcher register !mevent
166	$_dispatcher dispatch $this !mevent "[itcl::code $this _mevent]; list"
167	$_dispatcher register !pngtimeout
168	$_dispatcher register !waiticon
169
170	array set _downloadPopup {
171	format draft
172	}
173
174	# Populate the slave interpreter with commands to handle responses from
175	# the visualization server.
176	$_parser alias image [itcl::code $this ReceiveImage]
177
178	set _rocker(dir) 1
179	set _rocker(client) 0
180	set _rocker(server) 0
181	set _rocker(on) 0
182	set _state(server) 1
183	set _state(client) 1
184	set _hostlist $hostlist
185	set _restore 1
186
187	array set _view {
188	theta 45
189	phi 45
190	psi 0
191	vx 0
192	vy 0
193	vz 0
194	zoom 0
195	mx 0
196	my 0
197	mz 0
198	x 0
199	y 0
200	z 0
201	width 0
202	height 0
203	}
204
205	# Setup default settings for widget.
206	array set _settings [subst {
207	$this-spherescale 0.25
208	$this-stickradius 0.14
209	$this-cartoontrace no
210	$this-model ballnstick
211	$this-modelimg [Rappture::icon ballnstick]
212	$this-opacity 1.0
213	$this-ortho no
214	$this-rock no
215	$this-showlabels no
216	$this-showcell yes
217	$this-showlabels-initialized no
218	}]
219
220	itk_component add 3dview {
221	label $itk_component(plotarea).vol -image $_image(plot) \
222	-highlightthickness 0 -borderwidth 0
223	} {
224	usual
225	ignore -highlightthickness -borderwidth -background
226	}
227
228	set f [$itk_component(main) component controls]
229	itk_component add reset {
230	button $f.reset -borderwidth 1 -padx 1 -pady 1 \
231	-highlightthickness 0 \
232	-image [Rappture::icon reset-view] \
233	-command [itcl::code $this ResetView]
234	} {
235	usual
236	ignore -highlightthickness
237	}
238	pack $itk_component(reset) -padx 1 -pady 2
239	Rappture::Tooltip::for $itk_component(reset) \
240	"Reset the view to the default zoom level"
241
242	itk_component add zoomin {
243	button $f.zin -borderwidth 1 -padx 1 -pady 1 \
244	-highlightthickness 0 \
245	-image [Rappture::icon zoom-in] \
246	-command [itcl::code $this Zoom in]
247	} {
248	usual
249	ignore -highlightthickness
250	}
251	pack $itk_component(zoomin) -padx 2 -pady 2
252	Rappture::Tooltip::for $itk_component(zoomin) "Zoom in"
253
254	itk_component add zoomout {
255	button $f.zout -borderwidth 1 -padx 1 -pady 1 \
256	-highlightthickness 0 \
257	-image [Rappture::icon zoom-out] \
258	-command [itcl::code $this Zoom out]
259	} {
260	usual
261	ignore -highlightthickness
262	}
263	pack $itk_component(zoomout) -padx 2 -pady 2
264	Rappture::Tooltip::for $itk_component(zoomout) "Zoom out"
265
266	itk_component add labels {
267	Rappture::PushButton $f.labels \
268	-onimage [Rappture::icon molvis-labels-view] \
269	-offimage [Rappture::icon molvis-labels-view] \
270	-command [itcl::code $this labels update] \
271	-variable [itcl::scope _settings($this-showlabels)]
272	}
273	$itk_component(labels) deselect
274	Rappture::Tooltip::for $itk_component(labels) \
275	"Show/hide the labels on atoms"
276	pack $itk_component(labels) -padx 2 -pady {6 2}
277
278	itk_component add rock {
279	Rappture::PushButton $f.rock \
280	-onimage [Rappture::icon molvis-rock-view] \
281	-offimage [Rappture::icon molvis-rock-view] \
282	-command [itcl::code $this Rock toggle] \
283	-variable [itcl::scope _settings($this-rock)]
284	}
285	pack $itk_component(rock) -padx 2 -pady 2
286	Rappture::Tooltip::for $itk_component(rock) "Rock model back and forth"
287
288	itk_component add ortho {
289	label $f.ortho -borderwidth 1 -padx 1 -pady 1 \
290	-relief "raised" -image [Rappture::icon molvis-3dpers]
291	}
292	pack $itk_component(ortho) -padx 2 -pady 2 -ipadx 1 -ipady 1
293	Rappture::Tooltip::for $itk_component(ortho) \
294	"Use orthoscopic projection"
295
296	bind $itk_component(ortho) <ButtonPress> \
297	[itcl::code $this OrthoProjection toggle]
298
299	BuildSettingsTab
300
301	# HACK ALERT. Initially force a requested width of the 3dview label.
302
303	# It's a chicken-and-the-egg problem. The size of the 3dview label is set
304	# from the size of the image retrieved from the server. But the size of
305	# the image is specified by the viewport which is the size of the label.
306	# The fly-in-the-ointment is that it takes a non-trival amount of time to
307	# get the first image back from the server. In the meantime the idletasks
308	# have already kicked in. We end up with a 1x1 viewport and image.
309
310	# So the idea is to force a ridiculously big requested width on the label
311	# (that's why we're using the blt::table to manage the geometry). It has
312	# to be big, because we don't know how big the user may want to stretch
313	# the window. This at least forces the sidebarframe to give the 3dview
314	# the maximum size available, which is perfect for an initially closed
315	# sidebar.
316
317	blt::table $itk_component(plotarea) \
318	0,0 $itk_component(3dview) -fill both -reqwidth 10000
319	#
320	# RENDERING AREA
321	#
322
323	set _image(id) ""
324
325	# set up bindings for rotation
326	if 0 {
327	bind $itk_component(3dview) <ButtonPress-1> \
328	[itcl::code $this Rotate click %x %y]
329	bind $itk_component(3dview) <B1-Motion> \
330	[itcl::code $this Rotate drag %x %y]
331	bind $itk_component(3dview) <ButtonRelease-1> \
332	[itcl::code $this Rotate release %x %y]
333	} else {
334	bind $itk_component(3dview) <ButtonPress-1> \
335	[itcl::code $this Vmouse click %b %s %x %y]
336	bind $itk_component(3dview) <B1-Motion> \
337	[itcl::code $this Vmouse drag 1 %s %x %y]
338	bind $itk_component(3dview) <ButtonRelease-1> \
339	[itcl::code $this Vmouse release %b %s %x %y]
340	}
341
342	bind $itk_component(3dview) <ButtonPress-2> \
343	[itcl::code $this Pan click %x %y]
344	bind $itk_component(3dview) <B2-Motion> \
345	[itcl::code $this Pan drag %x %y]
346	bind $itk_component(3dview) <ButtonRelease-2> \
347	[itcl::code $this Pan release %x %y]
348
349	bind $itk_component(3dview) <KeyPress-Left> \
350	[itcl::code $this Pan set -10 0]
351	bind $itk_component(3dview) <KeyPress-Right> \
352	[itcl::code $this Pan set 10 0]
353	bind $itk_component(3dview) <KeyPress-Up> \
354	[itcl::code $this Pan set 0 -10]
355	bind $itk_component(3dview) <KeyPress-Down> \
356	[itcl::code $this Pan set 0 10]
357	bind $itk_component(3dview) <Shift-KeyPress-Left> \
358	[itcl::code $this Pan set -50 0]
359	bind $itk_component(3dview) <Shift-KeyPress-Right> \
360	[itcl::code $this Pan set 50 0]
361	bind $itk_component(3dview) <Shift-KeyPress-Up> \
362	[itcl::code $this Pan set 0 -50]
363	bind $itk_component(3dview) <Shift-KeyPress-Down> \
364	[itcl::code $this Pan set 0 50]
365	bind $itk_component(3dview) <KeyPress-Prior> \
366	[itcl::code $this Zoom out 2]
367	bind $itk_component(3dview) <KeyPress-Next> \
368	[itcl::code $this Zoom in 2]
369
370	bind $itk_component(3dview) <Enter> "focus $itk_component(3dview)"
371
372
373	if {[string equal "x11" [tk windowingsystem]]} {
374	bind $itk_component(3dview) <4> [itcl::code $this Zoom out 2]
375	bind $itk_component(3dview) <5> [itcl::code $this Zoom in 2]
376	}
377
378	# set up bindings to bridge mouse events to server
379	#bind $itk_component(3dview) <ButtonPress> \
380	# [itcl::code $this Vmouse2 click %b %s %x %y]
381	#bind $itk_component(3dview) <ButtonRelease> \
382	# [itcl::code $this Vmouse2 release %b %s %x %y]
383	#bind $itk_component(3dview) <B1-Motion> \
384	# [itcl::code $this Vmouse2 drag 1 %s %x %y]
385	#bind $itk_component(3dview) <B2-Motion> \
386	# [itcl::code $this Vmouse2 drag 2 %s %x %y]
387	#bind $itk_component(3dview) <B3-Motion> \
388	# [itcl::code $this Vmouse2 drag 3 %s %x %y]
389	#bind $itk_component(3dview) <Motion> \
390	# [itcl::code $this Vmouse2 move 0 %s %x %y]
391
392	bind $itk_component(3dview) <Configure> \
393	[itcl::code $this EventuallyResize %w %h]
394	bind $itk_component(3dview) <Unmap> \
395	[itcl::code $this Unmap]
396	bind $itk_component(3dview) <Map> \
397	[itcl::code $this Map]
398
399	eval itk_initialize $args
400	Connect
401	}
402
403	itcl::body Rappture::MolvisViewer::BuildSettingsTab {} {
404	set fg [option get $itk_component(hull) font Font]
405
406	set inner [$itk_component(main) insert end \
407	-title "Settings" \
408	-icon [Rappture::icon wrench]]
409	$inner configure -borderwidth 4
410
411	label $inner.drawinglabel -text "Molecule Representation" \
412	-font "Arial 9 bold"
413
414	label $inner.pict -image $_settings($this-modelimg)
415
416	radiobutton $inner.bstick -text "balls and sticks" \
417	-command [itcl::code $this Representation ballnstick all] \
418	-variable Rappture::MolvisViewer::_settings($this-model) \
419	-value ballnstick -font "Arial 9" -pady 0
420	Rappture::Tooltip::for $inner.bstick \
421	"Display atoms (balls) and connections (sticks) "
422
423	radiobutton $inner.spheres -text "spheres" \
424	-command [itcl::code $this Representation spheres all] \
425	-variable Rappture::MolvisViewer::_settings($this-model) \
426	-value spheres -font "Arial 9" -pady 0
427	Rappture::Tooltip::for $inner.spheres \
428	"Display atoms as spheres. Do not display bonds."
429
430	radiobutton $inner.sticks -text "sticks" \
431	-command [itcl::code $this Representation sticks all] \
432	-variable Rappture::MolvisViewer::_settings($this-model) \
433	-value sticks -font "Arial 9" -pady 0
434	Rappture::Tooltip::for $inner.sticks \
435	"Display bonds as sticks. Do not display atoms."
436
437	radiobutton $inner.lines -text "lines" \
438	-command [itcl::code $this Representation lines all] \
439	-variable [itcl::scope _settings($this-model)] \
440	-value lines -font "Arial 9" -pady 0
441	Rappture::Tooltip::for $inner.lines \
442	"Display bonds as lines. Do not display atoms."
443
444	radiobutton $inner.cartoon -text "cartoon" \
445	-command [itcl::code $this Representation cartoon all] \
446	-variable [itcl::scope _settings($this-model)] \
447	-value cartoon -font "Arial 9" -pady 0
448	Rappture::Tooltip::for $inner.cartoon \
449	"Display cartoon representation of bonds (sticks)."
450
451	scale $inner.spherescale -width 10 -font "Arial 9 bold" \
452	-from 0.1 -to 2.0 -resolution 0.05 -label "Sphere Scale" \
453	-showvalue true -orient horizontal \
454	-command [itcl::code $this SphereScale] \
455	-variable Rappture::MolvisViewer::_settings($this-spherescale)
456	$inner.spherescale set $_settings($this-spherescale)
457	Rappture::Tooltip::for $inner.spherescale \
458	"Adjust scale of atoms (spheres or balls). 1.0 is the full VDW radius."
459
460	scale $inner.stickradius -width 10 -font "Arial 9 bold" \
461	-from 0.1 -to 1.0 -resolution 0.025 -label "Stick Radius" \
462	-showvalue true -orient horizontal \
463	-command [itcl::code $this StickRadius] \
464	-variable Rappture::MolvisViewer::_settings($this-stickradius)
465	Rappture::Tooltip::for $inner.stickradius \
466	"Adjust scale of bonds (sticks)."
467	$inner.stickradius set $_settings($this-stickradius)
468
469	checkbutton $inner.labels -text "Show labels on atoms" \
470	-command [itcl::code $this labels update] \
471	-variable [itcl::scope _settings($this-showlabels)] \
472	-font "Arial 9 bold"
473	Rappture::Tooltip::for $inner.labels \
474	"Display atom symbol and serial number."
475
476	checkbutton $inner.rock -text "Rock model back and forth" \
477	-command [itcl::code $this Rock toggle] \
478	-variable Rappture::MolvisViewer::_settings($this-rock) \
479	-font "Arial 9 bold"
480	Rappture::Tooltip::for $inner.rock \
481	"Rotate the object back and forth around the y-axis."
482
483	checkbutton $inner.ortho -text "Orthoscopic projection" \
484	-command [itcl::code $this OrthoProjection update] \
485	-variable Rappture::MolvisViewer::_settings($this-ortho) \
486	-font "Arial 9 bold"
487	Rappture::Tooltip::for $inner.ortho \
488	"Toggle between orthoscopic/perspective projection modes."
489
490	checkbutton $inner.cartoontrace -text "Cartoon Trace" \
491	-command [itcl::code $this CartoonTrace update] \
492	-variable [itcl::scope _settings($this-cartoontrace)] \
493	-font "Arial 9 bold"
494	Rappture::Tooltip::for $inner.cartoontrace \
495	"Set cartoon representation of bonds (sticks)."
496
497	checkbutton $inner.cell -text "Parallelepiped" \
498	-command [itcl::code $this Cell toggle] \
499	-font "Arial 9 bold"
500	$inner.cell select
501
502	label $inner.spacer
503	blt::table $inner \
504	0,0 $inner.drawinglabel -anchor w -columnspan 4 \
505	1,1 $inner.pict -anchor w -rowspan 5 \
506	1,2 $inner.bstick -anchor w -columnspan 2 \
507	2,2 $inner.spheres -anchor w -columnspan 2 \
508	3,2 $inner.sticks -anchor w -columnspan 2 \
509	4,2 $inner.lines -anchor w -columnspan 2 \
510	5,2 $inner.cartoon -anchor w -columnspan 2 \
511	6,0 $inner.labels -anchor w -columnspan 4 -pady {1 0} \
512	7,0 $inner.rock -anchor w -columnspan 4 -pady {1 0} \
513	8,0 $inner.ortho -anchor w -columnspan 4 -pady {1 0} \
514	9,0 $inner.cartoontrace -anchor w -columnspan 4 -pady {1 0} \
515	10,0 $inner.cell -anchor w -columnspan 4 -pady {1 0} \
516	11,1 $inner.spherescale -fill x -columnspan 4 -pady {1 0} \
517	12,1 $inner.stickradius -fill x -columnspan 4 -pady {1 0} \
518
519	blt::table configure $inner c0 -resize expand -width 2
520	blt::table configure $inner c1 c2 -resize none
521	blt::table configure $inner c3 -resize expand
522	blt::table configure $inner r* -resize none
523	blt::table configure $inner r13 -resize expand
524	}
525
526	# ----------------------------------------------------------------------
527	# DESTRUCTOR
528	# ----------------------------------------------------------------------
529	itcl::body Rappture::MolvisViewer::destructor {} {
530	VisViewer::Disconnect
531
532	image delete $_image(plot)
533	array unset _settings $this-*
534	}
535
536	# ----------------------------------------------------------------------
537	# USAGE: download coming
538	# USAGE: download controls <downloadCommand>
539	# USAGE: download now
540	#
541	# Clients use this method to create a downloadable representation
542	# of the plot. Returns a list of the form {ext string}, where
543	# "ext" is the file extension (indicating the type of data) and
544	# "string" is the data itself.
545	# ----------------------------------------------------------------------
546	itcl::body Rappture::MolvisViewer::download {option args} {
547	switch $option {
548	coming {}
549	controls {
550	set popup .molvisviewerdownload
551	if { ![winfo exists .molvisviewerdownload] } {
552	set inner [DownloadPopup $popup [lindex $args 0]]
553	} else {
554	set inner [$popup component inner]
555	}
556	set _downloadPopup(image_controls) $inner.image_frame
557	set num [llength [get]]
558	set num [expr {($num == 1) ? "1 result" : "$num results"}]
559	set word [Rappture::filexfer::label downloadWord]
560	$inner.summary configure -text "$word $num in the following format:"
561	update idletasks ; # Fix initial sizes
562	return $popup
563	}
564	now {
565
566	set popup .molvisviewerdownload
567	if {[winfo exists .molvisviewerdownload]} {
568	$popup deactivate
569	}
570	switch -- $_downloadPopup(format) {
571	"image" {
572	return [$this GetImage [lindex $args 0]]
573	}
574	"pdb" {
575	return [list .pdb $_pdbdata]
576	}
577	}
578	}
579	default {
580	error "bad option \"$option\": should be coming, controls, now"
581	}
582	}
583	}
584
585	#
586	# isconnected --
587	#
588	# Indicates if we are currently connected to the visualization server.
589	#
590	itcl::body Rappture::MolvisViewer::isconnected {} {
591	return [VisViewer::IsConnected]
592	}
593
594
595	#
596	# Connect --
597	#
598	# Establishes a connection to a new visualization server.
599	#
600	itcl::body Rappture::MolvisViewer::Connect {} {
601	global readyForNextFrame
602	set readyForNextFrame 1
603	if { [isconnected] } {
604	return 1
605	}
606	set hosts [GetServerList "pymol"]
607	if { "" == $hosts } {
608	return 0
609	}
610	set _restore 1
611	set result [VisViewer::Connect $hosts]
612	if { $result } {
613	$_dispatcher event -idle !rebuild
614	}
615	return $result
616	}
617
618	#
619	# Disconnect --
620	#
621	# Clients use this method to disconnect from the current rendering
622	# server.
623	#
624	itcl::body Rappture::MolvisViewer::Disconnect {} {
625	VisViewer::Disconnect
626
627	# disconnected -- no more data sitting on server
628	catch { after cancel $_rocker(afterid) }
629	catch { after cancel $_mevent(afterid) }
630	array unset _dataobjs
631	array unset _model
632	array unset _mlist
633	array unset _imagecache
634
635	set _state(server) 1
636	set _state(client) 1
637	set _outbuf ""
638	global readyForNextFrame
639	set readyForNextFrame 1
640	}
641
642	itcl::body Rappture::MolvisViewer::SendCmd { cmd } {
643	debug "in SendCmd ($cmd)\n"
644
645	if { $_buffering } {
646	# Just buffer the commands. Don't send them yet.
647	if { $_state(server) != $_state(client) } {
648	append _outbuf "frame -defer $_state(client)\n"
649	set _state(server) $_state(client)
650	}
651	if { $_rocker(server) != $_rocker(client) } {
652	append _outbuf "rock -defer $_rocker(client)\n"
653	set _rocker(server) $_rocker(client)
654	}
655	append _outbuf "$cmd\n"
656	} else {
657	if { $_state(server) != $_state(client) } {
658	if { ![SendBytes "frame -defer $_state(client)\n"] } {
659	set _state(server) $_state(client)
660	}
661	}
662	if { $_rocker(server) != $_rocker(client) } {
663	if { ![SendBytes "rock -defer $_rocker(client)\n"] } {
664	set _rocker(server) $_rocker(client)
665	}
666	}
667	SendBytes "$cmd\n"
668	}
669	}
670
671	#
672	# ReceiveImage -bytes <size>
673	#
674	# Invoked automatically whenever the "image" command comes in from
675	# the rendering server. Indicates that binary image data with the
676	# specified <size> will follow.
677	#
678	set count 0
679	itcl::body Rappture::MolvisViewer::ReceiveImage { size cacheid frame rock } {
680	global readyForNextFrame
681	set readyForNextFrame 1
682	set tag "$frame,$rock"
683	global count
684	incr count
685	if { $cacheid != $_cacheid } {
686	array unset _imagecache
687	set _cacheid $cacheid
688	}
689	#debug "reading $size bytes from proxy\n"
690	set data [ReceiveBytes $size]
691	#debug "success: reading $size bytes from proxy\n"
692	if { $cacheid == "print" } {
693	# $frame is the token that we sent to the proxy.
694	set _hardcopy($this-$frame) $data
695	} else {
696	set _imagecache($tag) $data
697	#debug "CACHED: $tag,$cacheid"
698	$_image(plot) configure -data $data
699	set _image(id) $tag
700	}
701	}
702
703
704	# ----------------------------------------------------------------------
705	# USAGE: Rebuild
706	#
707	# Called automatically whenever something changes that affects the
708	# data in the widget. Clears any existing data and rebuilds the
709	# widget to display new data.
710	# ----------------------------------------------------------------------
711	itcl::body Rappture::MolvisViewer::Rebuild {} {
712	debug "in rebuild"
713	set changed 0
714
715	# Turn on buffering of commands to the server. We don't want to
716	# be preempted by a server disconnect/reconnect (that automatically
717	# generates a new call to Rebuild).
718	#blt::bltdebug 100
719	set _buffering 1
720	set _cell 0
721
722	if { $_restore } {
723	set _rocker(server) 0
724	set _cacheid 0
725	SendCmd "raw -defer {set auto_color,0}"
726	SendCmd "raw -defer {set auto_show_lines,0}"
727	}
728	set dlist [get]
729	foreach dataobj $dlist {
730	set model [$dataobj get components.molecule.model]
731	if {"" == $model } {
732	set model "molecule"
733	scan $dataobj "::libraryObj%d" suffix
734	set model $model$suffix
735	}
736	lappend _obj2models($dataobj) $model
737	set state [$dataobj get components.molecule.state]
738	if {"" == $state} {
739	set state $_state(server)
740	}
741	if { ![info exists _mlist($model)] } { # new, turn on
742	set _mlist($model) 2
743	} elseif { $_mlist($model) == 1 } { # on, leave on
744	set _mlist($model) 3
745	} elseif { $_mlist($model) == 0 } { # off, turn on
746	set _mlist($model) 2
747	}
748	if { ![info exists _dataobjs($model-$state)] } {
749	set data1 ""
750	set serial 1
751
752	foreach _atom [$dataobj children -type atom components.molecule] {
753	set symbol [$dataobj get components.molecule.$_atom.symbol]
754	set xyz [$dataobj get components.molecule.$_atom.xyz]
755	regsub {,} $xyz {} xyz
756	scan $xyz "%f %f %f" x y z
757	set recname "ATOM "
758	set altLoc ""
759	set resName ""
760	set chainID ""
761	set Seqno ""
762	set occupancy 1
763	set tempFactor 0
764	set recID ""
765	set segID ""
766	set element ""
767	set charge ""
768	set atom $symbol
769	set line [format "%6s%5d %4s%1s%3s %1s%5s %8.3f%8.3f%8.3f%6.2f%6.2f%8s\n" $recname $serial $atom $altLoc $resName $chainID $Seqno $x $y $z $occupancy $tempFactor $recID]
770	append data1 $line
771	incr serial
772	}
773	if {"" != $data1} {
774	# Save the PDB data in case the user wants to later save it.
775	set _pdbdata $data1
776	set nBytes [string length $data1]
777
778	# We know we're buffered here, so append the "loadpdb" command
779	# with the data payload immediately afterwards.
780	SendCmd "loadpdb -defer follows $model $state $nBytes"
781	append _outbuf $data1
782	set _dataobjs($model-$state) 1
783	}
784	# note that pdb files always overwrite xyz files
785	set data2 [$dataobj get components.molecule.pdb]
786	if {"" != $data2} {
787	# Save the PDB data in case the user wants to later save it.
788	set _pdbdata $data2
789	set nBytes [string length $data2]
790
791	# We know we're buffered here, so append the "loadpdb" command
792	# with the data payload immediately afterwards.
793	SendCmd "loadpdb -defer follows $model $state $nBytes"
794	append _outbuf $data2
795	set _dataobjs($model-$state) 1
796	}
797	# lammps dump file overwrites pdb file (change this?)
798	set lammpstypemap [$dataobj get components.molecule.lammpstypemap]
799	set lammpsdata [$dataobj get components.molecule.lammps]
800	if {"" != $lammpsdata} {
801	set data3 ""
802	set modelcount 0
803	foreach lammpsline [split $lammpsdata "\n"] {
804	if {[scan $lammpsline "%d %d %f %f %f" id type x y z] == 5} {
805	set recname "ATOM "
806	set altLoc ""
807	set resName ""
808	set chainID ""
809	set Seqno ""
810	set occupancy 1
811	set tempFactor 0
812	set recID ""
813	set segID ""
814	set element ""
815	set charge ""
816	if { "" == $lammpstypemap} {
817	set atom $type
818	} else {
819	set atom [lindex $lammpstypemap [expr {$type - 1}]]
820	if { "" == $atom} {
821	set atom $type
822	}
823	}
824	set pdbline [format "%6s%5d %4s%1s%3s %1s%5s %8.3f%8.3f%8.3f%6.2f%6.2f%8s\n" $recname $id $atom $altLoc $resName $chainID $Seqno $x $y $z $occupancy $tempFactor $recID]
825	append data3 $pdbline
826	}
827	# only read first model
828	if {[regexp "^ITEM: ATOMS" $lammpsline]} {
829	incr modelcount
830	if {$modelcount > 1} {
831	break
832	}
833	}
834	}
835	if {"" != $data3} {
836	# Save the PDB data in case the user wants to later save it.
837	set _pdbdata $data3
838	set nBytes [string length $data3]
839
840	# We know we're buffered here, so append the "loadpdb"
841	# command with the data payload immediately afterwards.
842	SendCmd "loadpdb -defer follows $model $state $nBytes"
843	append _outbuf $data3
844	}
845	set _dataobjs($model-$state) 1
846	}
847	}
848	if { ![info exists _model($model-transparency)] } {
849	set _model($model-transparency) ""
850	}
851	if { ![info exists _model($model-rep)] } {
852	set _model($model-rep) ""
853	set _model($model-newrep) $_mrep
854	}
855	if { $_model($model-transparency) != $_dobj2transparency($dataobj) } {
856	set _model($model-newtransparency) $_dobj2transparency($dataobj)
857	}
858	if { $_dobj2transparency($dataobj) == "ghost"} {
859	array unset _active $model
860	} else {
861	set _active($model) $dataobj
862	}
863	set vector [$dataobj get components.parallelepiped.vector]
864	if { $vector != "" } {
865	set vertices [ComputeParallelepipedVertices $dataobj]
866	SendCmd "raw -defer {verts = \[$vertices\]\n}"
867	SendCmd "raw -defer {run \$PYMOL_PATH/rappture/box.py\n}"
868	SendCmd "raw -defer {draw_box(verts)\n}"
869	set _cell 1
870	}
871	}
872
873	# enable/disable models as required (0=off->off, 1=on->off, 2=off->on,
874	# 3=on->on)
875
876	foreach model [array names _mlist] {
877	if { $_mlist($model) == 1 } {
878	SendCmd "disable -defer $model"
879	set _mlist($model) 0
880	set changed 1
881	} elseif { $_mlist($model) == 2 } {
882	set _mlist($model) 1
883	SendCmd "enable -defer $model"
884	set changed 1
885	} elseif { $_mlist($model) == 3 } {
886	set _mlist($model) 1
887	}
888	if { $_mlist($model) == 1 } {
889	if { [info exists _model($model-newtransparency)] \|\|
890	[info exists _model($model-newrep)] } {
891	if { ![info exists _model($model-newrep)] } {
892	set _model($model-newrep) $_model($model-rep)
893	}
894	if { ![info exists _model($model-newtransparency)] } {
895	set _model($model-newtransparency) $_model($model-transparency)
896	}
897	set rep $_model($model-newrep)
898	set transp $_model($model-newtransparency)
899	SendCmd "representation -defer -model $model $rep"
900	set changed 1
901	set _model($model-transparency) $_model($model-newtransparency)
902	set _model($model-rep) $_model($model-newrep)
903	catch {
904	unset _model($model-newtransparency)
905	unset _model($model-newrep)
906	}
907	}
908	}
909
910	}
911
912	if { $changed } {
913	array unset _imagecache
914	}
915	if { $dlist == "" } {
916	set _state(server) 1
917	set _state(client) 1
918	SendCmd "frame 1"
919	set flush 1
920	} elseif { ![info exists _imagecache($state,$_rocker(client))] } {
921	set _state(server) $state
922	set _state(client) $state
923	SendCmd "frame $state"
924	set flush 1
925	} else {
926	set _state(client) $state
927	Update
928	set flush 0
929	}
930	if { $_restore } {
931	# Set or restore viewing parameters. We do this for the first
932	# model and assume this works for everything else.
933	set w [winfo width $itk_component(3dview)]
934	set h [winfo height $itk_component(3dview)]
935	SendCmd [subst {
936	reset
937	screen $w $h
938	rotate $_view(mx) $_view(my) $_view(mz)
939	pan $_view(x) $_view(y)
940	zoom $_view(zoom)
941	}]
942	debug "rebuild: rotate $_view(mx) $_view(my) $_view(mz)"
943
944	SendCmd "raw -defer {zoom complete=1}"
945	set _restore 0
946	}
947	if { $changed } {
948	# Default settings for all models.
949	SphereScale update
950	StickRadius update
951	labels update
952	Opacity update
953	CartoonTrace update
954	Cell update
955	OrthoProjection update
956	Representation update
957	}
958	set inner [$itk_component(main) panel "Settings"]
959	if { $_cell } {
960	$inner.cell configure -state normal
961	} else {
962	$inner.cell configure -state disabled
963	}
964	if { $flush } {
965	global readyForNextFrame
966	set readyForNextFrame 0; # Don't advance to the next frame
967	# until we get an image.
968	SendCmd "bmp"; # Flush the results.
969	}
970	set _buffering 0; # Turn off buffering.
971
972	blt::busy hold $itk_component(hull)
973
974	# Actually write the commands to the server socket.
975	# If it fails, we don't care. We're finished here.
976	SendBytes $_outbuf;
977	set _outbuf ""; # Clear the buffer.
978	blt::busy release $itk_component(hull)
979
980	debug "exiting rebuild"
981	}
982
983	itcl::body Rappture::MolvisViewer::Unmap { } {
984	# Pause rocking loop while unmapped (saves CPU time)
985	Rock pause
986
987	# Blank image, mark current image dirty
988	# This will force reload from cache, or remain blank if cache is cleared
989	# This prevents old image from briefly appearing when a new result is added
990	# by result viewer
991
992	#$_image(plot) blank
993	set _image(id) ""
994	}
995
996	itcl::body Rappture::MolvisViewer::Map { } {
997	if { [isconnected] } {
998	# Resume rocking loop if it was on
999	Rock unpause
1000	# Rebuild image if modified, or redisplay cached image if not
1001	$_dispatcher event -idle !rebuild
1002	}
1003	}
1004
1005	itcl::body Rappture::MolvisViewer::DoResize { } {
1006	SendCmd "screen $_width $_height"
1007	$_image(plot) configure -width $_width -height $_height
1008	# Immediately invalidate cache, defer update until mapped
1009	array unset _imagecache
1010	set _resizePending 0
1011	}
1012
1013	itcl::body Rappture::MolvisViewer::EventuallyResize { w h } {
1014	set _width $w
1015	set _height $h
1016	if { !$_resizePending } {
1017	$_dispatcher event -idle !resize
1018	set _resizePending 1
1019	}
1020	}
1021
1022	# ----------------------------------------------------------------------
1023	# USAGE: $this Pan click x y
1024	# $this Pan drag x y
1025	# $this Pan release x y
1026	#
1027	# Called automatically when the user clicks on one of the zoom
1028	# controls for this widget. Changes the zoom for the current view.
1029	# ----------------------------------------------------------------------
1030	itcl::body Rappture::MolvisViewer::Pan {option x y} {
1031	if { $option == "set" } {
1032	set dx $x
1033	set dy $y
1034	set _view(x) [expr $_view(x) + $dx]
1035	set _view(y) [expr $_view(y) + $dy]
1036	SendCmd "pan $dx $dy"
1037	return
1038	}
1039	if { ![info exists _mevent(x)] } {
1040	set option "click"
1041	}
1042	if { $option == "click" } {
1043	$itk_component(3dview) configure -cursor hand1
1044	}
1045	if { $option == "drag" \|\| $option == "release" } {
1046	set dx [expr $x - $_mevent(x)]
1047	set dy [expr $y - $_mevent(y)]
1048	set _view(x) [expr $_view(x) + $dx]
1049	set _view(y) [expr $_view(y) + $dy]
1050	SendCmd "pan $dx $dy"
1051	}
1052	set _mevent(x) $x
1053	set _mevent(y) $y
1054	if { $option == "release" } {
1055	$itk_component(3dview) configure -cursor ""
1056	}
1057	}
1058
1059	# ----------------------------------------------------------------------
1060	# USAGE: Zoom in
1061	# USAGE: Zoom out
1062	# USAGE: Zoom reset
1063	#
1064	# Called automatically when the user clicks on one of the zoom
1065	# controls for this widget. Changes the zoom for the current view.
1066	# ----------------------------------------------------------------------
1067	itcl::body Rappture::MolvisViewer::Zoom {option {factor 10}} {
1068	switch -- $option {
1069	"in" {
1070	set _view(zoom) [expr $_view(zoom) + $factor]
1071	SendCmd "zoom $factor"
1072	}
1073	"out" {
1074	set _view(zoom) [expr $_view(zoom) - $factor]
1075	SendCmd "zoom -$factor"
1076	}
1077	"reset" {
1078	set _view(zoom) 0
1079	SendCmd "reset"
1080	}
1081	}
1082	}
1083
1084	itcl::body Rappture::MolvisViewer::Update { args } {
1085	set tag "$_state(client),$_rocker(client)"
1086	if { $_image(id) != "$tag" } {
1087	if { [info exists _imagecache($tag)] } {
1088	$_image(plot) configure -data $_imagecache($tag)
1089	set _image(id) "$tag"
1090	}
1091	}
1092	}
1093
1094	# ----------------------------------------------------------------------
1095	# USAGE: Rock on\|off\|toggle
1096	# USAGE: Rock pause\|unpause\|step
1097	#
1098	# Used to control the "rocking" model for the molecule being displayed.
1099	# Clients should use only the on/off/toggle options; the rest are for
1100	# internal control of the rocking motion.
1101	# ----------------------------------------------------------------------
1102	itcl::body Rappture::MolvisViewer::Rock { option } {
1103	# cancel any pending rocks
1104	if { [info exists _rocker(afterid)] } {
1105	after cancel $_rocker(afterid)
1106	unset _rocker(afterid)
1107	}
1108	if { ![winfo viewable $itk_component(3dview)] } {
1109	return
1110	}
1111	set _rocker(on) $_settings($this-rock)
1112	if { $option == "step"} {
1113	if { $_rocker(client) >= 10 } {
1114	set _rocker(dir) -1
1115	} elseif { $_rocker(client) <= -10 } {
1116	set _rocker(dir) 1
1117	}
1118	set _rocker(client) [expr {$_rocker(client) + $_rocker(dir)}]
1119	if { ![info exists _imagecache($_state(server),$_rocker(client))] } {
1120	set _rocker(server) $_rocker(client)
1121	SendCmd "rock $_rocker(client)"
1122	}
1123	Update
1124	}
1125	if { $_rocker(on) && $option != "pause" } {
1126	set _rocker(afterid) [after 200 [itcl::code $this Rock step]]
1127	}
1128	}
1129
1130
1131	itcl::body Rappture::MolvisViewer::Vmouse2 {option b m x y} {
1132	set now [clock clicks -milliseconds]
1133	set vButton [expr $b - 1]
1134	set vModifier 0
1135	set vState 1
1136
1137	if { $m & 1 } { set vModifier [expr $vModifier \| 1 ] }
1138	if { $m & 4 } { set vModifier [expr $vModifier \| 2 ] }
1139	if { $m & 131072 } { set vModifier [expr $vModifier \| 4 ] }
1140
1141	if { $option == "click" } { set vState 0 }
1142	if { $option == "release" } { set vState 1 }
1143	if { $option == "drag" } { set vState 2 }
1144	if { $option == "move" } { set vState 3 }
1145
1146	if { $vState == 2 \|\| $vState == 3} {
1147	set diff 0
1148
1149	catch { set diff [expr $now - $_mevent(time)] }
1150	if {$diff < 75} { # 75ms between motion updates
1151	return
1152	}
1153	}
1154	SendCmd "vmouse $vButton $vModifier $vState $x $y"
1155	set _mevent(time) $now
1156	}
1157
1158	itcl::body Rappture::MolvisViewer::Vmouse {option b m x y} {
1159	set now [clock clicks -milliseconds]
1160	# cancel any pending delayed dragging events
1161	if { [info exists _mevent(afterid)] } {
1162	after cancel $_mevent(afterid)
1163	unset _mevent(afterid)
1164	}
1165
1166	if { ![info exists _mevent(x)] } {
1167	set option "click"
1168	}
1169	if { $option == "click" } {
1170	$itk_component(3dview) configure -cursor fleur
1171	}
1172	if { $option == "drag" \|\| $option == "release" } {
1173	set diff 0
1174	catch { set diff [expr $now - $_mevent(time) ] }
1175	if {$diff < 25 && $option == "drag" } { # 75ms between motion updates
1176	set _mevent(afterid) [after [expr 25 - $diff] [itcl::code $this Vmouse drag $b $m $x $y]]
1177	return
1178	}
1179	set w [winfo width $itk_component(3dview)]
1180	set h [winfo height $itk_component(3dview)]
1181	if {$w <= 0 \|\| $h <= 0} {
1182	return
1183	}
1184	set x1 [expr double($w) / 3]
1185	set x2 [expr $x1 * 2]
1186	set y1 [expr double($h) / 3]
1187	set y2 [expr $y1 * 2]
1188	set dx [expr $x - $_mevent(x)]
1189	set dy [expr $y - $_mevent(y)]
1190	set mx 0
1191	set my 0
1192	set mz 0
1193
1194	if { $_mevent(x) < $x1 } {
1195	set mz $dy
1196	} elseif { $_mevent(x) < $x2 } {
1197	set mx $dy
1198	} else {
1199	set mz [expr -$dy]
1200	}
1201
1202	if { $_mevent(y) < $y1 } {
1203	set mz [expr -$dx]
1204	} elseif { $_mevent(y) < $y2 } {
1205	set my $dx
1206	} else {
1207	set mz $dx
1208	}
1209	# Accumlate movements
1210	set _view(mx) [expr {$_view(mx) + $mx}]
1211	set _view(my) [expr {$_view(my) + $my}]
1212	set _view(mz) [expr {$_view(mz) + $mz}]
1213	SendCmd "rotate $mx $my $mz"
1214	debug "_vmmouse: rotate $_view(mx) $_view(my) $_view(mz)"
1215	}
1216	set _mevent(x) $x
1217	set _mevent(y) $y
1218	set _mevent(time) $now
1219	if { $option == "release" } {
1220	$itk_component(3dview) configure -cursor ""
1221	}
1222	}
1223
1224	# ----------------------------------------------------------------------
1225	# USAGE: Rotate click <x> <y>
1226	# USAGE: Rotate drag <x> <y>
1227	# USAGE: Rotate release <x> <y>
1228	#
1229	# Called automatically when the user clicks/drags/releases in the
1230	# plot area. Moves the plot according to the user's actions.
1231	# ----------------------------------------------------------------------
1232	itcl::body Rappture::MolvisViewer::Rotate {option x y} {
1233	set now [clock clicks -milliseconds]
1234	#update idletasks
1235	# cancel any pending delayed dragging events
1236	if { [info exists _mevent(afterid)] } {
1237	after cancel $_mevent(afterid)
1238	unset _mevent(afterid)
1239	}
1240	switch -- $option {
1241	click {
1242	$itk_component(3dview) configure -cursor fleur
1243	set _click(x) $x
1244	set _click(y) $y
1245	set _click(theta) $_view(theta)
1246	set _click(phi) $_view(phi)
1247	}
1248	drag {
1249	if {[array size _click] == 0} {
1250	Rotate click $x $y
1251	} else {
1252	set w [winfo width $itk_component(3dview)]
1253	set h [winfo height $itk_component(3dview)]
1254	if {$w <= 0 \|\| $h <= 0} {
1255	return
1256	}
1257	# set diff 0
1258	# catch { set diff [expr $now - $_mevent(time) ] }
1259	# if {$diff < 175 && $option == "drag" } { # 75ms between motion updates
1260	# set _mevent(afterid) [after [expr 175 - $diff] [itcl::code $this Rotate drag $x $y]]
1261	# return
1262	# }
1263
1264	if {[catch {
1265	# this fails sometimes for no apparent reason
1266	set dx [expr {double($x-$_click(x))/$w}]
1267	set dy [expr {double($y-$_click(y))/$h}]
1268	}]} {
1269	return
1270	}
1271
1272	#
1273	# Rotate the camera in 3D
1274	#
1275	if {$_view(psi) > 90 \|\| $_view(psi) < -90} {
1276	# when psi is flipped around, theta moves backwards
1277	set dy [expr {-$dy}]
1278	}
1279	set theta [expr {$_view(theta) - $dy*180}]
1280	while {$theta < 0} { set theta [expr {$theta+180}] }
1281	while {$theta > 180} { set theta [expr {$theta-180}] }
1282
1283	if {abs($theta) >= 30 && abs($theta) <= 160} {
1284	set phi [expr {$_view(phi) - $dx*360}]
1285	while {$phi < 0} { set phi [expr {$phi+360}] }
1286	while {$phi > 360} { set phi [expr {$phi-360}] }
1287	set psi $_view(psi)
1288	} else {
1289	set phi $_view(phi)
1290	set psi [expr {$_view(psi) - $dx*360}]
1291	while {$psi < -180} { set psi [expr {$psi+360}] }
1292	while {$psi > 180} { set psi [expr {$psi-360}] }
1293	}
1294	array set _view [subst {
1295	theta $theta
1296	phi $phi
1297	psi $psi
1298	}]
1299	foreach { vx vy vz } [Euler2XYZ $theta $phi $psi] break
1300	set a [expr $vx - $_view(vx)]
1301	set a [expr -$a]
1302	set b [expr $vy - $_view(vy)]
1303	set c [expr $vz - $_view(vz)]
1304	array set _view [subst {
1305	vx $vx
1306	vy $vy
1307	vz $vz
1308	}]
1309	SendCmd "rotate $a $b $c"
1310	debug "Rotate $x $y: rotate $_view(vx) $_view(vy) $_view(vz)"
1311	set _click(x) $x
1312	set _click(y) $y
1313	}
1314	}
1315	release {
1316	Rotate drag $x $y
1317	$itk_component(3dview) configure -cursor ""
1318	catch {unset _click}
1319	}
1320	default {
1321	error "bad option \"$option\": should be click, drag, release"
1322	}
1323	}
1324	set _mevent(time) $now
1325	}
1326
1327	# ----------------------------------------------------------------------
1328	# USAGE: Representation spheres\|ballnstick\|lines\|sticks
1329	#
1330	# Used internally to change the molecular representation used to render
1331	# our scene.
1332	# ----------------------------------------------------------------------
1333	itcl::body Rappture::MolvisViewer::Representation {option {model "all"} } {
1334	if { $option == $_mrep } {
1335	return
1336	}
1337	if { $option == "update" } {
1338	set option $_settings($this-model)
1339	}
1340	if { $option == "sticks" } {
1341	set _settings($this-modelimg) [Rappture::icon lines]
1342	} else {
1343	set _settings($this-modelimg) [Rappture::icon $option]
1344	}
1345	set inner [$itk_component(main) panel "Settings"]
1346	$inner.pict configure -image $_settings($this-modelimg)
1347
1348	# Save the current option to set all radiobuttons -- just in case.
1349	# This method gets called without the user clicking on a radiobutton.
1350	set _settings($this-model) $option
1351	set _mrep $option
1352
1353	if { $model == "all" } {
1354	set models [array names _mlist]
1355	} else {
1356	set models $model
1357	}
1358
1359	foreach model $models {
1360	if { [info exists _model($model-rep)] } {
1361	if { $_model($model-rep) != $option } {
1362	set _model($model-newrep) $option
1363	} else {
1364	catch { unset _model($model-newrep) }
1365	}
1366	}
1367	}
1368	if { [isconnected] } {
1369	SendCmd "representation -model $model $option"
1370	#$_dispatcher event -idle !rebuild
1371	}
1372	}
1373
1374
1375	# ----------------------------------------------------------------------
1376	# USAGE: OrthoProjection on\|off\|toggle
1377	# USAGE: OrthoProjection update
1378	#
1379	# Used internally to turn labels associated with atoms on/off, and to
1380	# update the positions of the labels so they sit on top of each atom.
1381	# ----------------------------------------------------------------------
1382	itcl::body Rappture::MolvisViewer::OrthoProjection {option} {
1383	switch -- $option {
1384	"orthoscopic" {
1385	set ortho 1
1386	}
1387	"perspective" {
1388	set ortho 0
1389	}
1390	"toggle" {
1391	set ortho [expr {$_settings($this-ortho) == 0}]
1392	}
1393	"update" {
1394	set ortho $_settings($this-ortho)
1395	}
1396	default {
1397	error "bad option \"$option\": should be on, off, toggle, or update"
1398	}
1399	}
1400	if { $ortho == $_settings($this-ortho) && $option != "update"} {
1401	# nothing to do
1402	return
1403	}
1404	if { $ortho } {
1405	$itk_component(ortho) configure -image [Rappture::icon molvis-3dorth]
1406	Rappture::Tooltip::for $itk_component(ortho) \
1407	"Use perspective projection"
1408	set _settings($this-ortho) 1
1409	SendCmd "orthoscopic on"
1410	} else {
1411	$itk_component(ortho) configure -image [Rappture::icon molvis-3dpers]
1412	Rappture::Tooltip::for $itk_component(ortho) \
1413	"Use orthoscopic projection"
1414	set _settings($this-ortho) 0
1415	SendCmd "orthoscopic off"
1416	}
1417	}
1418
1419	# ----------------------------------------------------------------------
1420	# USAGE: Cell on\|off\|toggle
1421	#
1422	# Used internally to turn labels associated with atoms on/off, and to
1423	# update the positions of the labels so they sit on top of each atom.
1424	# ----------------------------------------------------------------------
1425	itcl::body Rappture::MolvisViewer::Cell {option} {
1426	switch -- $option {
1427	"on" - "off" {
1428	set cell $option
1429	}
1430	"toggle" {
1431	set cell [expr {$_settings($this-showcell) == 0}]
1432	}
1433	"update" {
1434	set cell $_settings($this-showcell)
1435	}
1436	default {
1437	error "bad option \"$option\": should be on, off, toggle, or update"
1438	}
1439	}
1440	if { $cell == $_settings($this-showcell) && $option != "update"} {
1441	# nothing to do
1442	return
1443	}
1444	if { $cell } {
1445	Rappture::Tooltip::for $itk_component(ortho) \
1446	"Hide the cell."
1447	set _settings($this-showcell) 1
1448	SendCmd "raw {show everything,unitcell}"
1449	} else {
1450	Rappture::Tooltip::for $itk_component(ortho) \
1451	"Show the cell."
1452	set _settings($this-showcell) 0
1453	SendCmd "raw {hide everything,unitcell}"
1454	}
1455	}
1456
1457
1458	# ----------------------------------------------------------------------
1459	# USAGE: add <dataobj> ?<settings>?
1460	#
1461	# Clients use this to add a data object to the plot. The optional
1462	# <settings> are used to configure the plot. Allowed settings are
1463	# -color, -brightness, -width, -linestyle, and -raise. Only
1464	# -brightness and -raise do anything.
1465	# ----------------------------------------------------------------------
1466	itcl::body Rappture::MolvisViewer::add { dataobj {options ""}} {
1467	array set params {
1468	-color auto
1469	-brightness 0
1470	-width 1
1471	-raise 0
1472	-linestyle solid
1473	-description ""
1474	-param ""
1475	}
1476
1477	foreach {opt val} $options {
1478	if {![info exists params($opt)]} {
1479	error "bad settings \"$opt\": should be [join [lsort [array names params]] {, }]"
1480	}
1481	set params($opt) $val
1482	}
1483
1484	set pos [lsearch -exact $dataobj $_dlist]
1485
1486	if {$pos < 0} {
1487	if {![Rappture::library isvalid $dataobj]} {
1488	error "bad value \"$dataobj\": should be Rappture::library object"
1489	}
1490
1491	if { !$_settings($this-showlabels-initialized) } {
1492	set showlabels [$dataobj get components.molecule.about.emblems]
1493	if { $showlabels != "" && [string is boolean $showlabels] } {
1494	set _settings($this-showlabels) $showlabels
1495	}
1496	}
1497
1498	lappend _dlist $dataobj
1499	if { $params(-brightness) >= 0.5 } {
1500	set _dobj2transparency($dataobj) "ghost"
1501	} else {
1502	set _dobj2transparency($dataobj) "normal"
1503	}
1504	set _dobj2raise($dataobj) $params(-raise)
1505	debug "setting parameters for $dataobj\n"
1506
1507	if { [isconnected] } {
1508	$_dispatcher event -idle !rebuild
1509	}
1510	}
1511	}
1512
1513	#
1514	# ResetView
1515	#
1516	itcl::body Rappture::MolvisViewer::ResetView {} {
1517	array set _view {
1518	theta 45
1519	phi 45
1520	psi 0
1521	mx 0
1522	my 0
1523	mz 0
1524	x 0
1525	y 0
1526	z 0
1527	zoom 0
1528	width 0
1529	height 0
1530	}
1531	SendCmd "reset"
1532	SendCmd "rotate $_view(mx) $_view(my) $_view(mz)"
1533	debug "ResetView: rotate $_view(mx) $_view(my) $_view(mz)"
1534	SendCmd "pan $_view(x) $_view(y)"
1535	SendCmd "zoom $_view(zoom)"
1536	}
1537
1538	# ----------------------------------------------------------------------
1539	# USAGE: get
1540	#
1541	# Clients use this to query the list of objects being plotted, in
1542	# order from bottom to top of this result.
1543	# ----------------------------------------------------------------------
1544	itcl::body Rappture::MolvisViewer::get {} {
1545	# put the dataobj list in order according to -raise options
1546	set dlist $_dlist
1547	foreach obj $dlist {
1548	if {[info exists _dobj2raise($obj)] && $_dobj2raise($obj)} {
1549	set i [lsearch -exact $dlist $obj]
1550	if {$i >= 0} {
1551	set dlist [lreplace $dlist $i $i]
1552	lappend dlist $obj
1553	}
1554	}
1555	}
1556	return $dlist
1557	}
1558
1559	# ----------------------------------------------------------------------
1560	# USAGE: delete ?<dataobj> <dataobj> ...?
1561	#
1562	# Clients use this to delete a dataobj from the plot. If no dataobjs
1563	# are specified, then all dataobjs are deleted.
1564	# ----------------------------------------------------------------------
1565	itcl::body Rappture::MolvisViewer::delete { args } {
1566	if {[llength $args] == 0} {
1567	set args $_dlist
1568	}
1569
1570	# delete all specified dataobjs
1571	set changed 0
1572	foreach dataobj $args {
1573	set pos [lsearch -exact $_dlist $dataobj]
1574	if {$pos >= 0} {
1575	set _dlist [lreplace $_dlist $pos $pos]
1576	if { [info exists _obj2models($dataobj)] } {
1577	foreach model $_obj2models($dataobj) {
1578	array unset _active $model
1579	}
1580	}
1581	array unset _obj2models $dataobj
1582	array unset _dobj2transparency $dataobj
1583	array unset _dobj2color $dataobj
1584	array unset _dobj2width $dataobj
1585	array unset _dobj2dashes $dataobj
1586	array unset _dobj2raise $dataobj
1587	set changed 1
1588	}
1589	}
1590
1591	# if anything changed, then rebuild the plot
1592	if {$changed} {
1593	if { [isconnected] } {
1594	$_dispatcher event -idle !rebuild
1595	}
1596	}
1597	}
1598
1599	# ----------------------------------------------------------------------
1600	# OPTION: -device
1601	# ----------------------------------------------------------------------
1602	itcl::configbody Rappture::MolvisViewer::device {
1603	if {$itk_option(-device) != "" } {
1604
1605	if {![Rappture::library isvalid $itk_option(-device)]} {
1606	error "bad value \"$itk_option(-device)\": should be Rappture::library object"
1607	}
1608	$this delete
1609	$this add $itk_option(-device)
1610	} else {
1611	$this delete
1612	}
1613
1614	if { [isconnected] } {
1615	$_dispatcher event -idle !rebuild
1616	}
1617	}
1618
1619
1620
1621	itcl::body Rappture::MolvisViewer::WaitIcon { option widget } {
1622	switch -- $option {
1623	"start" {
1624	$_dispatcher dispatch $this !waiticon \
1625	"[itcl::code $this WaitIcon "next" $widget] ; list"
1626	set _icon 0
1627	$widget configure -image [Rappture::icon bigroller${_icon}]
1628	$_dispatcher event -after 100 !waiticon
1629	}
1630	"next" {
1631	incr _icon
1632	if { $_icon >= 8 } {
1633	set _icon 0
1634	}
1635	$widget configure -image [Rappture::icon bigroller${_icon}]
1636	$_dispatcher event -after 100 !waiticon
1637	}
1638	"stop" {
1639	$_dispatcher cancel !waiticon
1640	}
1641	}
1642	}
1643
1644	itcl::body Rappture::MolvisViewer::GetImage { widget } {
1645	set token "print[incr _nextToken]"
1646	set var ::Rappture::MolvisViewer::_hardcopy($this-$token)
1647	set $var ""
1648
1649	set controls $_downloadPopup(image_controls)
1650	set combo $controls.size_combo
1651	set size [$combo translate [$combo value]]
1652	switch -- $size {
1653	"standard" {
1654	set width 1200
1655	set height 1200
1656	}
1657	"highquality" {
1658	set width 2400
1659	set height 2400
1660	}
1661	"draft" {
1662	set width 400
1663	set height 400
1664	}
1665	default {
1666	error "unknown image size [$inner.image_size_combo value]"
1667	}
1668	}
1669	# Setup an automatic timeout procedure.
1670	$_dispatcher dispatch $this !pngtimeout "set $var {} ; list"
1671
1672	set popup .molvisviewerprint
1673	if { ![winfo exists $popup] } {
1674	Rappture::Balloon $popup -title "Generating file..."
1675	set inner [$popup component inner]
1676	label $inner.title -text "Generating hardcopy." -font "Arial 10 bold"
1677	label $inner.please -text "This may take a minute." -font "Arial 10"
1678	label $inner.icon -image [Rappture::icon bigroller0]
1679	button $inner.cancel -text "Cancel" -font "Arial 10 bold" \
1680	-command [list set $var ""]
1681	blt::table $inner \
1682	0,0 $inner.title -columnspan 2 \
1683	1,0 $inner.please -anchor w \
1684	1,1 $inner.icon -anchor e \
1685	2,0 $inner.cancel -columnspan 2
1686	blt::table configure $inner r0 -pady 4
1687	blt::table configure $inner r2 -pady 4
1688	bind $inner.cancel <KeyPress-Return> [list $inner.cancel invoke]
1689	} else {
1690	set inner [$popup component inner]
1691	}
1692	set combo $controls.bgcolor_combo
1693	set bgcolor [$combo translate [$combo value]]
1694
1695	$_dispatcher event -after 60000 !pngtimeout
1696	WaitIcon start $inner.icon
1697	grab set -local $inner
1698	focus $inner.cancel
1699
1700	SendCmd "print $token $width $height $bgcolor"
1701
1702	$popup activate $widget below
1703	# We wait here for either
1704	# 1) the png to be delivered or
1705	# 2) timeout or
1706	# 3) user cancels the operation.
1707	tkwait variable $var
1708
1709	# Clean up.
1710	$_dispatcher cancel !pngtimeout
1711	WaitIcon stop $inner.icon
1712	grab release $inner
1713	$popup deactivate
1714	update
1715
1716	if { $_hardcopy($this-$token) != "" } {
1717	set combo $controls.type_combo
1718	set type [$combo translate [$combo value]]
1719	switch -- $type {
1720	"jpg" {
1721	set img [image create photo -data $_hardcopy($this-$token)]
1722	set bytes [$img data -format "jpeg -quality 100"]
1723	set bytes [Rappture::encoding::decode -as b64 $bytes]
1724	return [list .jpg $bytes]
1725	}
1726	"gif" {
1727	set img [image create photo -data $_hardcopy($this-$token)]
1728	set bytes [$img data -format "gif"]
1729	set bytes [Rappture::encoding::decode -as b64 $bytes]
1730	return [list .gif $bytes]
1731	}
1732	"png" {
1733	return [list .png $_hardcopy($this-$token)]
1734	}
1735	}
1736	}
1737	return ""
1738	}
1739
1740	# ----------------------------------------------------------------------
1741	# USAGE: SphereScale radius ?model?
1742	# SphereScale update ?model?
1743	#
1744	# Used internally to change the molecular atom scale used to render
1745	# our scene.
1746	#
1747	# Note: Only sets the specified radius for active models. If the model
1748	# is inactive, then it overridden with the value "0.1".
1749	# ----------------------------------------------------------------------
1750
1751	itcl::body Rappture::MolvisViewer::SphereScale { option {models "all"} } {
1752	if { $option == "update" } {
1753	set radius $_settings($this-spherescale)
1754	} elseif { [string is double $option] } {
1755	set radius $option
1756	if { ($radius < 0.1) \|\| ($radius > 2.0) } {
1757	error "bad atom size \"$radius\""
1758	}
1759	} else {
1760	error "bad option \"$option\""
1761	}
1762	set _settings($this-spherescale) $radius
1763	if { $models == "all" } {
1764	SendCmd "spherescale -model all $radius"
1765	return
1766	}
1767	set overrideradius [expr $radius * 0.8]
1768	SendCmd "spherescale -model all $overrideradius"
1769	foreach model $models {
1770	if { [info exists _active($model)] } {
1771	SendCmd "spherescale -model $model $radius"
1772	}
1773	}
1774	}
1775
1776	# ----------------------------------------------------------------------
1777	# USAGE: StickRadius radius ?models?
1778	# StickRadius update ?models?
1779	#
1780	# Used internally to change the stick radius used to render
1781	# our scene.
1782	#
1783	# Note: Only sets the specified radius for active models. If the model
1784	# is inactive, then it overridden with the value "0.25".
1785	# ----------------------------------------------------------------------
1786
1787	itcl::body Rappture::MolvisViewer::StickRadius { option {models "all"} } {
1788	if { $option == "update" } {
1789	set radius $_settings($this-stickradius)
1790	} elseif { [string is double $option] } {
1791	set radius $option
1792	if { ($radius < 0.1) \|\| ($radius > 2.0) } {
1793	error "bad stick radius \"$radius\""
1794	}
1795	} else {
1796	error "bad option \"$option\""
1797	}
1798	set _settings($this-stickradius) $radius
1799	if { $models == "all" } {
1800	SendCmd "stickradius -model all $radius"
1801	return
1802	}
1803	set overrideradius [expr $radius * 0.8]
1804	SendCmd "stickradius -model all $overrideradius"
1805	foreach model $models {
1806	if { [info exists _active($model)] } {
1807	SendCmd "stickradius -model $model $radius"
1808	}
1809	}
1810	}
1811
1812	# ----------------------------------------------------------------------
1813	# USAGE: Opacity value ?models?
1814	# Opacity update ?models?
1815	#
1816	# Used internally to change the opacity (transparency) used to render
1817	# our scene.
1818	#
1819	# Note: Only sets the specified transparency for active models. If the model
1820	# is inactive, then it overridden with the value "0.75".
1821	# ----------------------------------------------------------------------
1822
1823	itcl::body Rappture::MolvisViewer::Opacity { option } {
1824	if { $option == "update" } {
1825	set opacity $_settings($this-opacity)
1826	} elseif { [string is double $option] } {
1827	set opacity $option
1828	if { ($opacity < 0.0) \|\| ($opacity > 1.0) } {
1829	error "bad opacity \"$opacity\""
1830	}
1831	} else {
1832	error "bad option \"$option\""
1833	}
1834	set _settings($this-opacity) $opacity
1835	set transparency [expr 1.0 - $opacity]
1836	set models [array names _active]
1837	if { [llength $models] == 0 } {
1838	SendCmd "transparency -model all $transparency"
1839	return
1840	}
1841	set overridetransparency 0.60
1842	SendCmd "transparency -model all $overridetransparency"
1843	foreach model $models {
1844	SendCmd "transparency -model $model $transparency"
1845	}
1846	}
1847
1848	# ----------------------------------------------------------------------
1849	# USAGE: labels on\|off\|toggle
1850	# USAGE: labels update
1851	#
1852	# Used internally to turn labels associated with atoms on/off, and to
1853	# update the positions of the labels so they sit on top of each atom.
1854	# ----------------------------------------------------------------------
1855	itcl::body Rappture::MolvisViewer::labels {option {models "all"}} {
1856	set showlabels $_settings($this-showlabels)
1857	if { $option == "update" } {
1858	set showlabels $_settings($this-showlabels)
1859	} elseif { [string is boolean $option] } {
1860	set showlabels $option
1861	} else {
1862	error "bad option \"$option\""
1863	}
1864	set _settings($this-showlabels) $showlabels
1865	if { $models == "all" } {
1866	SendCmd "label -model all $showlabels"
1867	return
1868	}
1869	SendCmd "label -model all off"
1870	if { $showlabels } {
1871	foreach model $models {
1872	if { [info exists _active($model)] } {
1873	SendCmd "label -model $model $showlabels"
1874	}
1875	}
1876	}
1877	}
1878
1879	# ----------------------------------------------------------------------
1880	# USAGE: CartoonTrace on\|off\|toggle
1881	# USAGE: CartoonTrace update
1882	#
1883	# Used internally to turn labels associated with atoms on/off, and to
1884	# update the positions of the labels so they sit on top of each atom.
1885	# ----------------------------------------------------------------------
1886	itcl::body Rappture::MolvisViewer::CartoonTrace {option {models "all"}} {
1887	set trace $_settings($this-cartoontrace)
1888	if { $option == "update" } {
1889	set trace $_settings($this-cartoontrace)
1890	} elseif { [string is boolean $option] } {
1891	set trace $option
1892	} else {
1893	error "bad option \"$option\""
1894	}
1895	set _settings($this-cartoontrace) $trace
1896	if { $models == "all" } {
1897	SendCmd "cartoontrace -model all $trace"
1898	return
1899	}
1900	SendCmd "cartoontrace -model all off"
1901	if { $trace } {
1902	foreach model $models {
1903	if { [info exists _active($model)] } {
1904	SendCmd "cartoontrace -model $model $trace"
1905	}
1906	}
1907	}
1908	}
1909
1910	itcl::body Rappture::MolvisViewer::DownloadPopup { popup command } {
1911	Rappture::Balloon $popup \
1912	-title "[Rappture::filexfer::label downloadWord] as..."
1913	set inner [$popup component inner]
1914	label $inner.summary -text "" -anchor w -font "Arial 11 bold"
1915	radiobutton $inner.pdb_button -text "PDB Protein Data Bank Format File" \
1916	-variable [itcl::scope _downloadPopup(format)] \
1917	-command [itcl::code $this EnableDownload $popup pdb] \
1918	-font "Arial 10 " \
1919	-value pdb
1920	Rappture::Tooltip::for $inner.pdb_button \
1921	"Save as PDB Protein Data Bank format file."
1922	radiobutton $inner.image_button -text "Image File" \
1923	-variable [itcl::scope _downloadPopup(format)] \
1924	-command [itcl::code $this EnableDownload $popup image] \
1925	-font "Arial 10 " \
1926	-value image
1927	Rappture::Tooltip::for $inner.image_button \
1928	"Save as digital image."
1929
1930	set controls [frame $inner.image_frame -bd 2 -relief groove]
1931	label $controls.size_label -text "Size:" \
1932	-font "Arial 9"
1933	set img $_image(plot)
1934	set res "[image width $img]x[image height $img]"
1935	Rappture::Combobox $controls.size_combo -width 20 -editable no
1936	$controls.size_combo choices insert end \
1937	"draft" "Draft (400x400)" \
1938	"standard" "Standard (1200x1200)" \
1939	"highquality" "High Quality (2400x2400)"
1940
1941	label $controls.bgcolor_label -text "Background:" \
1942	-font "Arial 9"
1943	Rappture::Combobox $controls.bgcolor_combo -width 20 -editable no
1944	$controls.bgcolor_combo choices insert end \
1945	"black" "Black" \
1946	"white" "White" \
1947	"none" "Transparent (PNG only)"
1948
1949	label $controls.type_label -text "Type:" \
1950	-font "Arial 9"
1951	Rappture::Combobox $controls.type_combo -width 20 -editable no
1952	$controls.type_combo choices insert end \
1953	"jpg" "JPEG Joint Photographic Experts Group Format (*.jpg)" \
1954	"png" "PNG Portable Network Graphics Format (*.png)"
1955
1956	button $inner.go -text [Rappture::filexfer::label download] \
1957	-command $command
1958
1959	blt::table $controls \
1960	1,0 $controls.size_label -anchor e \
1961	1,1 $controls.size_combo -anchor w -fill x \
1962	2,0 $controls.bgcolor_label -anchor e \
1963	2,1 $controls.bgcolor_combo -anchor w -fill x \
1964	3,0 $controls.type_label -anchor e \
1965	3,1 $controls.type_combo -anchor w -fill x
1966	blt::table configure $controls r0 -height 16
1967	blt::table configure $controls -padx 4 -pady {0 6}
1968	blt::table $inner \
1969	0,0 $inner.summary -cspan 2 \
1970	1,0 $inner.pdb_button -cspan 2 -anchor w \
1971	2,0 $inner.image_button -cspan 2 -rspan 2 -anchor nw -ipadx 2 -ipady 2 \
1972	3,1 $controls -fill both \
1973	6,0 $inner.go -cspan 2 -pady 5
1974	blt::table configure $inner c0 -width 11
1975	blt::table configure $inner r2 -height 11
1976	#blt::table configure $inner c1 -width 8
1977	raise $inner.image_button
1978	$inner.pdb_button invoke
1979	$controls.bgcolor_combo value "Black"
1980	$controls.size_combo value "Draft (400x400)"
1981	$controls.type_combo value "PNG Portable Network Graphics Format (*.png)"
1982	return $inner
1983	}
1984
1985	itcl::body Rappture::MolvisViewer::EnableDownload { popup what } {
1986	set inner [$popup component inner]
1987	switch -- $what {
1988	"pdb" {
1989	foreach w [winfo children $inner.image_frame] {
1990	$w configure -state disabled
1991	}
1992	}
1993	"image" {
1994	foreach w [winfo children $inner.image_frame] {
1995	$w configure -state normal
1996	}
1997	}
1998	default {
1999	error "unknown type of download"
2000	}
2001	}
2002	}
2003
2004	itcl::body Rappture::MolvisViewer::snap { w h } {
2005	if { $w <= 0 \|\| $h <= 0 } {
2006	set w [image width $_image(plot)]
2007	set h [image height $_image(plot)]
2008	}
2009	set tag "$_state(client),$_rocker(client)"
2010	if { $_image(id) != "$tag" } {
2011	while { ![info exists _imagecache($tag)] } {
2012	update idletasks
2013	update
2014	after 100
2015	}
2016	if { [info exists _imagecache($tag)] } {
2017	$_image(plot) configure -data $_imagecache($tag)
2018	set _image(id) "$tag"
2019	}
2020	}
2021	set img [image create picture -width $w -height $h]
2022	$img resample $_image(plot)
2023	return $img
2024	}
2025
2026	# FIXME: Handle 2D vectors
2027	itcl::body Rappture::MolvisViewer::ComputeParallelepipedVertices { dataobj } {
2028	# Create a vector for every 3D point
2029	blt::vector point0(3) point1(3) point2(3) point3(3) point4(3) point5(3) \
2030	point6(3) point7(3) origin(3) scale(3)
2031
2032	set count 0
2033	set parent [$dataobj element -as object "components.parallelepiped"]
2034	foreach child [$parent children] {
2035	if { ![string match "vector*" $child] } {
2036	continue
2037	}
2038	incr count
2039	set values [$parent get $child]
2040	regexp -all {,} $values { } values
2041	point$count set $values
2042	}
2043	itcl::delete object $parent
2044	if { $count < 1 \|\| $count > 3 } {
2045	error "bad number of vectors supplied to parallelepiped"
2046	}
2047	point0 set { 0.0 0.0 0.0 }
2048	point4 expr {point2 + point1}
2049	point5 expr {point4 + point3}
2050	point6 expr {point2 + point3}
2051	point7 expr {point1 + point3}
2052
2053	set values [$dataobj get components.parallelepiped.scale]
2054	set n [llength $values]
2055	scale set { 1.0 1.0 1.0 }
2056	if { $n == 1 } {
2057	set scale(0:2) [lindex $values 0]
2058	} elseif { $n == 2 } {
2059	set scale(0:1) [lindex $values 0]
2060	} elseif { $n == 3 } {
2061	scale set $values
2062	}
2063	set values [$dataobj get components.parallelepiped.origin]
2064	set n [llength $values]
2065	origin set { 0.0 0.0 0.0 }
2066	if { $n == 1 } {
2067	set origin(0) [lindex $values 0]
2068	} elseif { $n == 2 } {
2069	set origin(0) [lindex $values 0]
2070	set origin(1) [lindex $values 1]
2071	} elseif { $n == 3 } {
2072	origin set $values
2073	}
2074
2075	# Scale and translate points
2076	for { set i 0 } { $i < 8 } { incr i } {
2077	point${i} expr "(point${i} * scale) + origin"
2078	}
2079
2080	# Generate vertices as a string for PyMOL
2081	set vertices ""
2082	foreach n { 0 1 0 2 0 3 1 4 2 4 2 6 1 7 3 7 5 7 4 5 3 6 5 } {
2083	set values [point${n} range 0 end]
2084	append vertices "\[ [join $values {, }] \], \\\n"
2085	}
2086	set values [point6 range 0 end]
2087	append vertices "\[ [join $values {, }] \] \\\n"
2088	blt::vector destroy point0 point1 point2 point3 point4 point5 point6 \
2089	point7 origin scale
2090	return $vertices
2091	}

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