This file is indexed.

/usr/share/xcrysden/Tcl/modAtomAtrib.tcl is in xcrysden-data 1.5.53-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
#############################################################################
# Author:                                                                   #
# ------                                                                    #
#  Anton Kokalj                                  Email: Tone.Kokalj@ijs.si  #
#  Department of Physical and Organic Chemistry  Phone: x 386 1 477 3523    #
#  Jozef Stefan Institute                          Fax: x 386 1 477 3811    #
#  Jamova 39, SI-1000 Ljubljana                                             #
#  SLOVENIA                                                                 #
#                                                                           #
# Source: $XCRYSDEN_TOPDIR/Tcl/modAtomAtrib.tcl                                       
# ------                                                                    #
# Copyright (c) 1996-2003 by Anton Kokalj                                   #
#############################################################################

#=============================================================================#
#             ATOMIC COLORS --- ATOMIC COLORS --- ATOMIC COLORS               #
#=============================================================================#
proc ModAtomCol {} {
    global atcol Alist mody
    # Alist - AtomNameLists

    set top .atomcol
    # just in case in window already exists
    if { [winfo exists $top] } { return } 
    toplevel .atomcol
    wm title $top "Atomic Colors"
    wm iconname $top "Atomic Colors"
    #grab $top

    # place $top according to "."
    xcPlace . $top 100 50

    # there will be three frames left, right and bottom
    set l [frame $top.l -relief raised -bd 2]
    set r [frame $top.r -relief raised -bd 2]
    set b [frame $top.b -relief raised -bd 2]

    pack $b -side bottom -padx 0 -pady 0 -ipadx 0 -ipady 0 \
	    -fill both -expand 1
    pack $l $r -side left -padx 0 -pady 0 -ipadx 0 -ipady 0 \
	    -fill both -expand 1

    # in LEFT-FRAME there will be Entrie & scrolllistbox
    Entries $l "Atom:" atcol(atom) 6
    bind $l.frame.entry1 <Return> { AtomColBind }

    set lbox [ScrolledListbox2 $l.lb -width 12 -height 20 -setgrid true]
    bind $lbox <ButtonRelease-1> [list AtomColSelect %W %y]

    # we must rebuilt Alist so that after each atom we add "\n"
    set n 0
    foreach elem $Alist {
	if { $n < 10 } {
	    lappend Atoms "  $n:         $elem"
	} elseif { $n < 100 } {
	    lappend Atoms  " $n:         $elem"
	} else {
	    lappend Atoms   "$n:         $elem"
	}	
	incr n
    }
    eval {$lbox insert 0} $Atoms
    
    # RIGHT-FRAME --- RIGHT-FRAME
    # before we select any atom from above Listbox, a default will be H
    set color        [xc_getvalue $mody(D_ATCOL_ONE) 0]
    set atcol(red)   [lindex $color 0]
    set atcol(green) [lindex $color 1]
    set atcol(blue)  [lindex $color 2]     
    set atcol(atom)  "X"
    set atcol(nat)   0

    set atcol(hxred)   [ d2h [expr int($atcol(red) * 255)  ] ] 
    set atcol(hxgreen) [ d2h [expr int($atcol(green) * 255)] ] 
    set atcol(hxblue)  [ d2h [expr int($atcol(blue) * 255) ] ] 
    
    set fr  [frame $r.1 -relief sunken -bd 2]
    set col [frame $fr.col  -bd 0 \
	    -bg "#$atcol(hxred)$atcol(hxgreen)$atcol(hxblue)" \
	    -width 150 -height 150]
    
    scale $r.red -from 0 -to 1 -length 150 -variable atcol(red) \
	    -orient horizontal -label "Red:" -tickinterval 1.0 \
	    -digits 3 -resolution 0.01 -showvalue true -width 10 \
	    -command Color
    scale $r.green -from 0 -to 1 -length 150 \
	    -variable atcol(green) \
	    -orient horizontal -label "Green:" -tickinterval 0.5 \
	    -digits 3 -resolution 0.01 -showvalue true -width 10 \
	    -command Color
    scale $r.blue -from 0 -to 1 -length 150 \
	    -variable atcol(blue) \
	    -orient horizontal -label "Blue:" -tickinterval 0.5 \
	    -digits 3 -resolution 0.01 -showvalue true -width 10 \
	    -command Color

    pack $fr -side top -fill both -expand 1 -padx 30 -pady 15 -ipadx 0 -ipady 0
    pack $col -side top -fill both -expand 1 -padx 0 -pady 0 
    pack $r.red $r.green $r.blue -side top -fill both -expand 1

    # BOTTOM FRAME --- BOTTOM FRAME
    # OK, Default & Cancel Button
    set col [button $b.upd -text "Update Color" \
	    -command AtomColUpD]
    set def [button $b.def -text "Default Color" \
	    -command [list AtomColLoad default]]
    set can [button $b.can -text "Reset All" \
	    -command AtomColReset]
    set clo [button $b.clo -text "Close" -command [list AtomColOK $top]]
    
    pack $col $def $can $clo -side left -expand 1 -pady 10 -padx 5
            
    return
}


proc AtomColBind {} {
    global atcol

    set atcol(nat) [Aname2Nat $atcol(atom)]
    if ![regexp {[0-9]+} $atcol(nat)] {
	tk_dialog .atradup "ERROR" $atcol(nat) error 0 OK
	return
    }
    
    AtomColLoad
    return
}


proc Color { {trash {}} } {
    global atcol

    set atcol(hxred) [ d2h [expr int($atcol(red) * 255)] ]
    set atcol(hxgreen) [ d2h [expr int($atcol(green) * 255)] ]
    set atcol(hxblue) [ d2h [expr int($atcol(blue) * 255)] ] 
    
    .atomcol.r.1.col configure \
	    -bg "#$atcol(hxred)$atcol(hxgreen)$atcol(hxblue)"

} 


proc AtomColSelect { w y } {
    global atcol mody

    # $w is the name of listbox widget who contains groups
    # $y is the vertical position of "selection"
    puts stdout "$w select anchor [$w nearest $y]"
    $w select anchor [$w nearest $y]
    set nline [$w curselection]
    set atom [$w get $nline]

    # now we must purify atom variable, because it's sometning like "  8:  O"
    # we will take a number instead of name (communication with xcrys)
    regexp {[0-9]+} $atom atcol(nat)
    
    # to update entry we also need atom name
    regexp {[A-Za-z]+} $atom atcol(atom)

    AtomColLoad

    return
}


proc AtomColLoad { {type {}} } {
    global mody atcol
    
    if { $type == "default"} {
	set color [xc_getdefault $mody(D_ATCOL_ONE) $atcol(nat)]	
    } else {
	puts stdout "GETVALUE::"
	set color [xc_getvalue $mody(D_ATCOL_ONE) $atcol(nat)]
    }

    set atcol(red) [lindex $color 0]
    set atcol(green) [lindex $color 1]
    set atcol(blue) [lindex $color 2] 

    Color
    puts stdout "ATOM=\"$atcol(nat)\"; NAME=$atcol(atom)"
    flush stdout
}


proc AtomColOK {top} {
    global atcol

    if { [winfo exists $top] } { 
	#grab release $top
	destroy $top
    }
    return
}


proc AtomColUpD {} {
    global mody atcol

    puts stdout "xc_newvalue .mesa $mody(L_ATCOL_ONE) $atcol(nat) $atcol(red) $atcol(green) $atcol(blue)"
    flush stdout
    xc_newvalue .mesa $mody(L_ATCOL_ONE) $atcol(nat) \
	    $atcol(red) $atcol(green) $atcol(blue)

    return
}


proc AtomColReset {} {
    global mody atcol
    
    # reset atomic colors
    xc_resetvar .mesa $mody(R_ATCOL)
    # update display
    AtomColLoad

    return
}


#=============================================================================#
#               ATOMIC RADII --- ATOMIC RADII --- ATOMIC RADII                #
#=============================================================================#
proc ModAtomRad {} {
    global atrad Alist mody
    # Alist - AtomNameLists

    set top .atomrad
    # just in case in window already exists
    if { [winfo exists $top] } { return } 
    toplevel $top
    wm title $top "Atomic Radii"
    wm iconname $top "Atomic Radii"
    #grab $top

    # place $top according to "."
    xcPlace . $top 100 50

    # there will be three frames left, right and bottom
    set l [frame $top.l -relief raised -bd 2]
    set r [frame $top.r -relief raised -bd 2]
    set b [frame $top.b -relief raised -bd 2]

    pack $b -side bottom -padx 0 -pady 0 -ipadx 0 -ipady 0 \
	    -fill both -expand 1
    pack $l $r -side left -padx 0 -pady 0 -ipadx 0 -ipady 0 \
	    -fill both -expand 1
    
    # in LEFT-FRAME there will be a scrolllistbox
    set lbox [ScrolledListbox2 $l.lb -width 12 -height 15 -setgrid true]
    bind $lbox <ButtonRelease-1> [list AtomRadSelect %W %y]

    # we must rebuilt Alist so that after each atom we add "\n"
    set n 0
    foreach elem $Alist {
	if { $n < 10 } {
	    lappend Atoms "  $n:         $elem"
	} elseif { $n < 100 } {
	    lappend Atoms  " $n:         $elem"
	} else {
	    lappend Atoms   "$n:         $elem"
	}	
	incr n
    }
    eval {$lbox insert 0} $Atoms
    
    # RIGHT-FRAME --- RIGHT-FRAME
    # before we select any atom from above Listbox, a default will be X
    set atrad(covf)   [xc_getvalue $mody(D_COVF)]
    set atrad(scale)  [xc_getvalue $mody(D_ATRAD_SCALE)]
    set atrad(atom)   "X"
    set atrad(rad)    [xc_getvalue $mody(D_ATRAD_ONE) 0]
    set atrad(covrad) [xc_getvalue $mody(D_RCOV_ONE)  0]
    set atrad(nat)    0

    set atrad(covf_old)  $atrad(covf)
    set atrad(scale_old) $atrad(scale)

    set f11 [frame $r.1 -relief groove -bd 2]
    Entries $f11 {"Chemical connectivity factor:"} atrad(covf) 8 0
    set b12 [button $f11.frame.b12 -text "Clear" \
	    -command [list AtRadClr atrad(covf) $f11.frame.entry1]]
    set b11 [button $f11.frame.b11 -text "Default" \
	    -command [list AtRadDef atrad(covf) D_COVF]]
    set b13 [button $f11.frame.b13 -text "Update" \
		 -command AtRadUpdateConF]
    pack $f11 -side top -padx 5 -pady 5 -fill x -ipady 10
    pack $b12 $b11 $b13 -side left -side left -padx 5 -pady 5 
    focus $f11.frame.entry1

    set f21 [frame $r.2 -relief groove -bd 2]
    Entries $f21 {"SpaceFill/Ball scale factor:"} atrad(scale) 8 0
    set b22 [button $f21.frame.b22 -text "Clear" \
	    -command [list AtRadClr atrad(scale) $f21.frame.entry1]]
    set b21 [button $f21.frame.b21 -text "Default" \
	    -command [list AtRadDef atrad(scale) D_ATRAD_SCALE]]
    set b23 [button $f21.frame.b23 -text "Update" \
	    -command AtRadUpdateScale]
    pack $f21 -side top -padx 5 -pady 5 -expand 1 -fill x -ipady 10
    pack $b22 $b21 $b23 -side left -side left -padx 5 -pady 5
    
    # t.k.: start here ...
    set f31 [frame $r.3 -relief groove -bd 2]
    set lbl [label $f31.lbl -text "Change radius:" -relief flat]
    pack $lbl -side top
    #set f311 [frame $f31.1]
    #set f312 [frame $f31.2]
    #pack $f311 $f312 -side top -fill x
    Entries $f31 {"Atom:" "Display radius:" "Covalent radius:"} {
	{atrad(atom)} {atrad(rad)} {atrad(covrad)}
    } 8 0

    set b3 [button $f31.frame.b3 -text "Clear" -command [list AtRadClr atrad(rad) $f31.frame.entry2]]
    pack $b3 -side left -side left -padx 5 -pady 5

    set b31 [button $f31.b31 -text "Update Radius"  -command AtRadUpD]
    set res [button $f31.res -text "Reset All"      -command AtRadReset]
    set b32 [button $f31.b32 -text "Default Radius" -command [list AtRadLoad default]]
    pack $f31 -side top -padx 5 -pady 5 -fill x -ipady 10
    pack $b31 $res $b32  -side left -side left -padx 5 -pady 5 -expand 1
    # /t.k.
    
    # BOTTOM FRAME --- BOTTOM FRAME
    # OK button
    set clo [button $b.clo -text "OK" -command [list AtRadOK $top]]
    
    pack $clo -side left -expand 1 -pady 10 -padx 5
            
    return
}


proc AtRadUpdateConF {} {
    global atrad mody
    if { $atrad(covf_old) != $atrad(covf) } {
	xc_newvalue .mesa $mody(L_COV_SCALE) $atrad(covf)
    }
    set atrad(covf_old)  $atrad(covf)
}


proc AtRadUpdateScale {} {    
    global atrad mody
    if { $atrad(scale_old) != $atrad(scale) } {
	xc_newvalue .mesa $mody(L_ATRAD_SCALE) $atrad(scale)
    }   
    set atrad(scale_old) $atrad(scale)
}


proc AtRadUpD {} {
    global mody atrad

    # from atrad(atom) --> atrad(nat)
    set atrad(nat) [Aname2Nat $atrad(atom)]
    if ![regexp {[0-9]+} $atrad(nat)] {
	tk_dialog .atradup "ERROR" $atrad(nat) error 0 OK
	return
    }
    
    xc_newvalue .mesa $mody(L_ATRAD_ONE) $atrad(nat) $atrad(rad)
    xc_newvalue .mesa $mody(L_RCOV_ONE)  $atrad(nat) $atrad(covrad)
    
    return
}


proc AtRadLoad { {type {}} } {
    global mody atrad
    
    # from atrad(atom) -> atrad(nat)
    puts stdout "AtRadLoad:: $atrad(nat)"
    flush stdout
    if { $type == "default"} {
	set atrad(rad)    [xc_getdefault $mody(D_ATRAD_ONE) $atrad(nat)]
	set atrad(covrad) [xc_getdefault $mody(D_RCOV_ONE) $atrad(nat)]
    } else {
	set atrad(rad)    [xc_getvalue $mody(D_ATRAD_ONE) $atrad(nat)]
	set atrad(covrad) [xc_getvalue $mody(D_RCOV_ONE) $atrad(nat)]
    }
    return
}


proc AtRadReset {} {
    global mody

    # reset atomic radius
    xc_resetvar .mesa $mody(R_ATRAD)
    # t.k.: insert the RCOV code here ...
    xc_resetvar .mesa $mody(R_RCOV)
    # update a display
    AtRadLoad

    return
}    


proc AtRadOK {top} {
    global atrad mody
    
    puts stdout "AtRadOK:: mody(L_COV_SCALE) = $atrad(covf)"
    puts stdout "AtRadOK:: mody(L_ATRAD_SCALE) $atrad(scale)"
    flush stdout
    # update all parameters
    # first Chemical connectivity factor
    if { $atrad(covf_old) != $atrad(covf) } {
	xc_newvalue .mesa $mody(L_COV_SCALE) $atrad(covf)
    }
    # spacefill/ball scale factor
    if { $atrad(scale_old) != $atrad(scale) } {
	xc_newvalue .mesa $mody(L_ATRAD_SCALE) $atrad(scale)
    }

    # is atomname ok
    #set atrad(nat) [Aname2Nat $atrad(atom)]
    #if ![regexp {[0-9]+} $atrad(nat)] {
    #	 tk_dialog .atradup "ERROR" $atrad(nat) error 0 OK
    #	 return
    #}
    #xc_newvalue .mesa $mody(L_ATRAD_ONE) $atrad(nat) $atrad(rad)
    
    # now we can exit
    if { [winfo exists $top] } { 
	#grab release $top
	destroy $top
    }
}


proc AtomRadSelect { w y } {
    global atrad mody

    # $w is the name of listbox widget who contains groups
    # $y is the vertical position of "selection"
    puts stdout "$w select anchor [$w nearest $y]"
    $w select anchor [$w nearest $y]
    set nline [$w curselection]
    set atom [$w get $nline]

    # now we must purify atom variable, because it's sometning like "  8:  O"
    # we will take a number instead of name (communication with xcrys)
    regexp {[0-9]+} $atom atrad(nat)
    
    # to update entry we also need atom name
    regexp {[A-Za-z]+} $atom atrad(atom)

    AtRadLoad

    return
}


proc AtRadDef {var const} {
    upvar #0 $var varn
    global mody 

    set varn [xc_getdefault $mody($const)]

    return
}

proc AtRadClr {var w} {
    upvar #0 $var varn
    
    set varn ""
    focus $w
    return
}