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source: trunk/GSASIIconstrGUI.py @ 4424

Last change on this file since 4424 was 4421, checked in by toby, 5 years ago
add R.B. extractor; misc doc updates; plt bug after strip Hs; grid bug: uncompleted edits; mac horz. line fix
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1	# -- coding: utf-8 --
2	#GSASIIconstrGUI - constraint GUI routines
3	########### SVN repository information ###################
4	# $Date: 2020-05-16 13:55:12 +0000 (Sat, 16 May 2020) $
5	# $Author: toby $
6	# $Revision: 4421 $
7	# $URL: trunk/GSASIIconstrGUI.py $
8	# $Id: GSASIIconstrGUI.py 4421 2020-05-16 13:55:12Z toby $
9	########### SVN repository information ###################
10	'''
11	GSASIIconstrGUI: Constraint GUI routines
12	------------------------------------------
13
14	Used to define constraints and rigid bodies.
15
16	'''
17	from __future__ import division, print_function
18	import sys
19	import copy
20	import os.path
21	import wx
22	import wx.grid as wg
23	import wx.lib.scrolledpanel as wxscroll
24	import wx.lib.gridmovers as gridmovers
25	import random as ran
26	import numpy as np
27	import numpy.ma as ma
28	import numpy.linalg as nl
29	import GSASIIpath
30	GSASIIpath.SetVersionNumber("$Revision: 4421 $")
31	import GSASIIElem as G2elem
32	import GSASIIElemGUI as G2elemGUI
33	import GSASIIstrIO as G2stIO
34	import GSASIImapvars as G2mv
35	import GSASIImath as G2mth
36	import GSASIIlattice as G2lat
37	import GSASIIdataGUI as G2gd
38	import GSASIIctrlGUI as G2G
39	import GSASIIplot as G2plt
40	import GSASIIobj as G2obj
41	import GSASIIspc as G2spc
42	import GSASIIpy3 as G2py3
43	import GSASIIphsGUI as G2phG
44	import GSASIIscriptable as G2sc
45	VERY_LIGHT_GREY = wx.Colour(235,235,235)
46	WACV = wx.ALIGN_CENTER_VERTICAL
47
48	class DragableRBGrid(wg.Grid):
49	'''Simple grid implentation for display of rigid body positions.
50
51	:param parent: frame or panel where grid will be placed
52	:param dict rb: dict with atom labels, types and positions
53	:param function onChange: a callback used every time a value in
54	rb is changed.
55	'''
56	def __init__(self, parent, rb, onChange=None):
57	#wg.Grid.__init__(self, parent, wx.ID_ANY,size=(-1,200))
58	wg.Grid.__init__(self, parent, wx.ID_ANY)
59	self.SetTable(RBDataTable(rb,onChange), True)
60	# Enable Row moving
61	gridmovers.GridRowMover(self)
62	self.Bind(gridmovers.EVT_GRID_ROW_MOVE, self.OnRowMove, self)
63	self.SetColSize(0, 60)
64	self.SetColSize(1, 35)
65	self.SetColSize(5, 40)
66	for r in range(len(rb['RBlbls'])):
67	self.SetReadOnly(r,0,isReadOnly=True)
68	self.SetCellEditor(r,2, wg.GridCellFloatEditor())
69	self.SetCellEditor(r,3, wg.GridCellFloatEditor())
70	self.SetCellEditor(r,4, wg.GridCellFloatEditor())
71
72	def OnRowMove(self,evt):
73	'called when a row move needs to take place'
74	frm = evt.GetMoveRow() # Row being moved
75	to = evt.GetBeforeRow() # Before which row to insert
76	self.GetTable().MoveRow(frm,to)
77
78	def completeEdits(self):
79	'complete any outstanding edits'
80	if self.IsCellEditControlEnabled(): # complete any grid edits in progress
81	#if GSASIIpath.GetConfigValue('debug'): print ('Completing grid edit')
82	self.SaveEditControlValue()
83	self.HideCellEditControl()
84	self.DisableCellEditControl()
85
86	class RBDataTable(wg.GridTableBase):
87	'''A Table to support :class:`DragableRBGrid`
88	'''
89	def __init__(self,rb,onChange):
90	wg.GridTableBase.__init__(self)
91	self.colLabels = ['Label','Type','x','y','z','Select']
92	self.coords = rb['RBcoords']
93	self.labels = rb['RBlbls']
94	self.types = rb['RBtypes']
95	self.index = rb['RBindex']
96	self.select = rb['RBselection']
97	self.onChange = onChange
98
99	# required methods
100	def GetNumberRows(self):
101	return len(self.labels)
102	def GetNumberCols(self):
103	return len(self.colLabels)
104	def IsEmptyCell(self, row, col):
105	return False
106	def GetValue(self, row, col):
107	row = self.index[row]
108	if col == 0:
109	return self.labels[row]
110	elif col == 1:
111	return self.types[row]
112	elif col < 5:
113	return '{:.5f}'.format(self.coords[row][col-2])
114	elif col == 5:
115	return self.select[row]
116	def SetValue(self, row, col, value):
117	row = self.index[row]
118	if col == 0:
119	self.labels[row] = value
120	elif col == 1:
121	self.types[row] = value
122	elif col < 5:
123	self.coords[row][col-2] = float(value)
124	elif col == 5:
125	self.select[row] = value
126	if self.onChange:
127	self.onChange()
128	# implement boolean for selection
129	def GetTypeName(self, row, col):
130	if col==5:
131	return wg.GRID_VALUE_BOOL
132	else:
133	return wg.GRID_VALUE_STRING
134	def CanGetValueAs(self, row, col, typeName):
135	if col==5 and typeName != wg.GRID_VALUE_BOOL:
136	return False
137	return True
138
139	# Display column & row labels
140	def GetColLabelValue(self, col):
141	return self.colLabels[col]
142	def GetRowLabelValue(self,row):
143	return str(row+1)
144
145	# Implement "row movement" by updating the pointer array
146	def MoveRow(self,frm,to):
147	grid = self.GetView()
148	if grid:
149	move = self.index[frm]
150	del self.index[frm]
151	if frm > to:
152	self.index.insert(to,move)
153	else:
154	self.index.insert(to-1,move)
155
156	# Notify the grid
157	grid.BeginBatch()
158	msg = wg.GridTableMessage(
159	self, wg.GRIDTABLE_NOTIFY_ROWS_DELETED, frm, 1
160	)
161	grid.ProcessTableMessage(msg)
162	msg = wg.GridTableMessage(
163	self, wg.GRIDTABLE_NOTIFY_ROWS_INSERTED, to, 1
164	)
165	grid.ProcessTableMessage(msg)
166	grid.EndBatch()
167	if self.onChange:
168	self.onChange()
169
170	def MakeDrawAtom(data,atom):
171	'Convert atom to format needed to draw it'
172	generalData = data['General']
173	if generalData['Type'] in ['nuclear','faulted',]:
174	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
175	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
176	ct,cs = [1,8] #type & color
177	atNum = generalData['AtomTypes'].index(atom[ct])
178	atomInfo[cs] = list(generalData['Color'][atNum])
179	return atomInfo
180
181	class ConstraintDialog(wx.Dialog):
182	'''Window to edit Constraint values
183	'''
184	def __init__(self,parent,title,text,data,separator='*',varname="",varyflag=False):
185	wx.Dialog.__init__(self,parent,-1,'Edit '+title,
186	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
187	self.data = data[:]
188	self.newvar = [varname,varyflag]
189	panel = wx.Panel(self)
190	mainSizer = wx.BoxSizer(wx.VERTICAL)
191	topLabl = wx.StaticText(panel,-1,text)
192	mainSizer.Add((10,10),1)
193	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
194	mainSizer.Add((10,10),1)
195	dataGridSizer = wx.FlexGridSizer(cols=3,hgap=2,vgap=2)
196	self.OkBtn = wx.Button(panel,wx.ID_OK)
197	for id in range(len(self.data)):
198	lbl1 = lbl = str(self.data[id][1])
199	if lbl[-1] != '=': lbl1 = lbl + ' ' + separator + ' '
200	name = wx.StaticText(panel,wx.ID_ANY,lbl1,
201	style=wx.ALIGN_RIGHT)
202	scale = G2G.ValidatedTxtCtrl(panel,self.data[id],0,
203	typeHint=float,
204	OKcontrol=self.DisableOK)
205	dataGridSizer.Add(name,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,5)
206	dataGridSizer.Add(scale,0,wx.RIGHT,3)
207	if ':' in lbl:
208	dataGridSizer.Add(
209	wx.StaticText(panel,-1,G2obj.fmtVarDescr(lbl)),
210	0,wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,3)
211	else:
212	dataGridSizer.Add((-1,-1))
213	if title == 'New Variable':
214	name = wx.StaticText(panel,wx.ID_ANY,"New variable's\nname (optional)",
215	style=wx.ALIGN_CENTER)
216	scale = G2G.ValidatedTxtCtrl(panel,self.newvar,0,
217	typeHint=str,notBlank=False)
218	dataGridSizer.Add(name,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,5)
219	dataGridSizer.Add(scale,0,wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,3)
220	self.refine = wx.CheckBox(panel,label='Refine?')
221	self.refine.SetValue(self.newvar[1]==True)
222	self.refine.Bind(wx.EVT_CHECKBOX, self.OnCheckBox)
223	dataGridSizer.Add(self.refine,0,wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,3)
224
225	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
226	self.OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
227	self.OkBtn.SetDefault()
228	cancelBtn = wx.Button(panel,wx.ID_CANCEL)
229	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
230	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
231	btnSizer.Add((20,20),1)
232	btnSizer.Add(self.OkBtn)
233	btnSizer.Add((20,20),1)
234	btnSizer.Add(cancelBtn)
235	btnSizer.Add((20,20),1)
236
237	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
238	panel.SetSizer(mainSizer)
239	panel.Fit()
240	self.Fit()
241	self.CenterOnParent()
242
243	def DisableOK(self,setting):
244	if setting:
245	self.OkBtn.Enable()
246	else:
247	self.OkBtn.Disable()
248
249	def OnCheckBox(self,event):
250	self.newvar[1] = self.refine.GetValue()
251
252	def OnOk(self,event):
253	parent = self.GetParent()
254	parent.Raise()
255	self.EndModal(wx.ID_OK)
256
257	def OnCancel(self,event):
258	parent = self.GetParent()
259	parent.Raise()
260	self.EndModal(wx.ID_CANCEL)
261
262	def GetData(self):
263	return self.data
264
265	################################################################################
266	##### Constraints
267	################################################################################
268	def UpdateConstraints(G2frame,data):
269	'''Called when Constraints tree item is selected.
270	Displays the constraints in the data window
271	'''
272
273	def FindEquivVarb(name,nameList):
274	'Creates a list of variables appropriate to constrain with name'
275	outList = []
276	#phlist = []
277	items = name.split(':')
278	namelist = [items[2],]
279	if 'dA' in name:
280	namelist = ['dAx','dAy','dAz']
281	elif 'AU' in name:
282	namelist = ['AUiso','AU11','AU22','AU33','AU12','AU13','AU23']
283	elif 'AM' in name:
284	namelist = ['AMx','AMy','AMz']
285	elif items[-1] in ['A0','A1','A2','A3','A4','A5']:
286	namelist = ['A0','A1','A2','A3','A4','A5']
287	elif items[-1] in ['D11','D22','D33','D12','D13','D23']:
288	namelist = ['D11','D22','D33','D12','D13','D23']
289	elif 'Tm' in name:
290	namelist = ['Tmin','Tmax']
291	elif 'MX' in name or 'MY' in name or 'MZ' in name:
292	namelist = ['MXcos','MYcos','MZcos','MXsin','MYsin','MZsin']
293	elif 'mV' in name:
294	namelist = ['mV0','mV1','mV2']
295	elif 'RB' in name:
296	rbfx = 'RB'+items[2][2]
297	if 'T' in name and 'Tr' not in name:
298	namelist = [rbfx+'T11',rbfx+'T22',rbfx+'T33',rbfx+'T12',rbfx+'T13',rbfx+'T23']
299	if 'L' in name:
300	namelist = [rbfx+'L11',rbfx+'L22',rbfx+'L33',rbfx+'L12',rbfx+'L13',rbfx+'L23']
301	if 'S' in name:
302	namelist = [rbfx+'S12',rbfx+'S13',rbfx+'S21',rbfx+'S23',rbfx+'S31',rbfx+'S32',rbfx+'SAA',rbfx+'SBB']
303	if 'U' in name:
304	namelist = [rbfx+'U',]
305
306	for item in nameList:
307	keys = item.split(':')
308	#if keys[0] not in phlist:
309	# phlist.append(keys[0])
310	if items[1] == '*' and keys[2] in namelist: # wildcard -- select only sequential options
311	keys[1] = '*'
312	mitem = ':'.join(keys)
313	if mitem == name: continue
314	if mitem not in outList: outList.append(mitem)
315	elif keys[2] in namelist and item != name:
316	outList.append(item)
317	return outList
318
319	def SelectVarbs(page,FrstVarb,varList,legend,constType):
320	'''Select variables used in constraints after one variable has
321	been selected. This routine determines the appropriate variables to be
322	used based on the one that has been selected and asks for more to be added.
323
324	It then creates the constraint and adds it to the constraints list.
325
326	Called from OnAddEquivalence, OnAddFunction & OnAddConstraint (all but
327	OnAddHold)
328
329	:param list page: defines calling page -- type of variables to be used
330	:parm GSASIIobj.G2VarObj FrstVarb: reference to first selected variable
331	:param list varList: list of other appropriate variables to select from
332	:param str legend: header for selection dialog
333	:param str constType: type of constraint to be generated
334	:returns: a constraint, as defined in
335	:ref:`GSASIIobj <Constraint_definitions_table>`
336	'''
337	choices = [[i]+list(G2obj.VarDescr(i)) for i in varList]
338	meaning = G2obj.getDescr(FrstVarb.name)
339	if not meaning:
340	meaning = "(no definition found!)"
341	l = str(FrstVarb).split(':')
342	# make lists of phases & histograms to iterate over
343	phaselist = [l[0]]
344	if l[0]:
345	phaselbl = ['phase #'+l[0]]
346	if len(Phases) > 1:
347	phaselist += ['all']
348	phaselbl += ['all phases']
349	else:
350	phaselbl = ['']
351	histlist = [l[1]]
352	if l[1] == '*':
353	pass
354	elif l[1]:
355	histlbl = ['histogram #'+l[1]]
356	if len(Histograms) > 1:
357	histlist += ['all']
358	histlbl += ['all histograms']
359	typ = Histograms[G2obj.LookupHistName(l[1])[0]]['Instrument Parameters'][0]['Type'][1]
360	i = 0
361	for hist in Histograms:
362	if Histograms[hist]['Instrument Parameters'][0]['Type'][1] == typ: i += 1
363	if i > 1:
364	histlist += ['all='+typ]
365	histlbl += ['all '+typ+' histograms']
366	else:
367	histlbl = ['']
368	# make a list of equivalent parameter names
369	nameList = [FrstVarb.name]
370	for var in varList:
371	nam = var.split(":")[2]
372	if nam not in nameList: nameList += [nam]
373	# add "wild-card" names to the list of variables
374	if l[1] == '*':
375	pass
376	elif page[1] == 'phs':
377	if 'RB' in FrstVarb.name:
378	pass
379	elif FrstVarb.atom is None:
380	for nam in nameList:
381	for ph,plbl in zip(phaselist,phaselbl):
382	if plbl: plbl = 'For ' + plbl
383	var = ph+"::"+nam
384	if var == str(FrstVarb) or var in varList: continue
385	varList += [var]
386	choices.append([var,plbl,meaning])
387	else:
388	for nam in nameList:
389	for ph,plbl in zip(phaselist,phaselbl):
390	if plbl: plbl = ' in ' + plbl
391	for atype in ['']+TypeList:
392	if atype:
393	albl = "For "+atype+" atoms"
394	akey = "all="+atype
395	else:
396	albl = "For all atoms"
397	akey = "all"
398	var = ph+"::"+nam+":"+akey
399	if var == str(FrstVarb) or var in varList: continue
400	varList += [var]
401	choices.append([var,albl+plbl,meaning])
402	elif page[1] == 'hap':
403	if FrstVarb.name == "Scale":
404	meaning = "Phase fraction"
405	for nam in nameList:
406	for ph,plbl in zip(phaselist,phaselbl):
407	if plbl: plbl = 'For ' + plbl
408	for hst,hlbl in zip(histlist,histlbl):
409	if hlbl:
410	if plbl:
411	hlbl = ' in ' + hlbl
412	else:
413	hlbl = 'For ' + hlbl
414	var = ph+":"+hst+":"+nam
415	if var == str(FrstVarb) or var in varList: continue
416	varList += [var]
417	choices.append([var,plbl+hlbl,meaning])
418	elif page[1] == 'hst':
419	if FrstVarb.name == "Scale":
420	meaning = "Scale factor"
421	for nam in nameList:
422	for hst,hlbl in zip(histlist,histlbl):
423	if hlbl:
424	hlbl = 'For ' + hlbl
425	var = ":"+hst+":"+nam
426	if var == str(FrstVarb) or var in varList: continue
427	varList += [var]
428	choices.append([var,hlbl,meaning])
429	elif page[1] == 'glb' or page[1] == 'sym':
430	pass
431	else:
432	raise Exception('Unknown constraint page '+ page[1])
433	if len(choices):
434	l1 = l2 = 1
435	for i1,i2,i3 in choices:
436	l1 = max(l1,len(i1))
437	l2 = max(l2,len(i2))
438	fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
439	atchoices = [fmt.format(*i1) for i1 in choices] # reformat list as str with columns
440	dlg = G2G.G2MultiChoiceDialog(
441	G2frame,legend,
442	'Constrain '+str(FrstVarb)+' with...',atchoices,
443	toggle=False,size=(625,400),monoFont=True)
444	dlg.CenterOnParent()
445	res = dlg.ShowModal()
446	Selections = dlg.GetSelections()[:]
447	dlg.Destroy()
448	if res != wx.ID_OK: return []
449	if len(Selections) == 0:
450	dlg = wx.MessageDialog(
451	G2frame,
452	'No variables were selected to include with '+str(FrstVarb),
453	'No variables')
454	dlg.CenterOnParent()
455	dlg.ShowModal()
456	dlg.Destroy()
457	return []
458	else:
459	dlg = wx.MessageDialog(
460	G2frame,
461	'There are no appropriate variables to include with '+str(FrstVarb),
462	'No variables')
463	dlg.CenterOnParent()
464	dlg.ShowModal()
465	dlg.Destroy()
466	return []
467	# now process the variables provided by the user
468	varbs = [str(FrstVarb),] # list of selected variables
469	for sel in Selections:
470	var = varList[sel]
471	# phase(s) included
472	l = var.split(':')
473	if l[0] == "all":
474	phlist = [str(Phases[phase]['pId']) for phase in Phases]
475	else:
476	phlist = [l[0]]
477	# histogram(s) included
478	if l[1] == "all":
479	hstlist = [str(Histograms[hist]['hId']) for hist in Histograms]
480	elif '=' in l[1]:
481	htyp = l[1].split('=')[1]
482	hstlist = [str(Histograms[hist]['hId']) for hist in Histograms if
483	Histograms[hist]['Instrument Parameters'][0]['Type'][1] == htyp]
484	else:
485	hstlist = [l[1]]
486	if len(l) == 3:
487	for ph in phlist:
488	for hst in hstlist:
489	var = ph + ":" + hst + ":" + l[2]
490	if var in varbs: continue
491	varbs.append(var)
492	else: # constraints with atoms or rigid bodies
493	if len(l) == 5: # rigid body parameter
494	var = ':'.join(l)
495	if var in varbs: continue
496	varbs.append(var)
497	elif l[3] == "all":
498	for ph in phlist:
499	key = G2obj.LookupPhaseName(ph)[0]
500	for hst in hstlist: # should be blank
501	for iatm,at in enumerate(Phases[key]['Atoms']):
502	var = ph + ":" + hst + ":" + l[2] + ":" + str(iatm)
503	if var in varbs: continue
504	varbs.append(var)
505	elif '=' in l[3]:
506	for ph in phlist:
507	key = G2obj.LookupPhaseName(ph)[0]
508	cx,ct,cs,cia = Phases[key]['General']['AtomPtrs']
509	for hst in hstlist: # should be blank
510	atyp = l[3].split('=')[1]
511	for iatm,at in enumerate(Phases[key]['Atoms']):
512	if at[ct] != atyp: continue
513	var = ph + ":" + hst + ":" + l[2] + ":" + str(iatm)
514	if var in varbs: continue
515	varbs.append(var)
516	else:
517	for ph in phlist:
518	key = G2obj.LookupPhaseName(ph)[0]
519	for hst in hstlist: # should be blank
520	var = ph + ":" + hst + ":" + l[2] + ":" + l[3]
521	if var in varbs: continue
522	varbs.append(var)
523	if len(varbs) >= 1 or 'constraint' in constType:
524	constr = [[1.0,FrstVarb]]
525	for item in varbs[1:]:
526	constr += [[1.0,G2obj.G2VarObj(item)]]
527	if 'equivalence' in constType:
528	return [constr+[None,None,'e']]
529	elif 'function' in constType:
530	return [constr+[None,False,'f']]
531	elif 'constraint' in constType:
532	return [constr+[1.0,None,'c']]
533	else:
534	raise Exception('Unknown constraint type: '+str(constType))
535	else:
536	dlg = wx.MessageDialog(
537	G2frame,
538	'There are no selected variables to include with '+str(FrstVarb),
539	'No variables')
540	dlg.CenterOnParent()
541	dlg.ShowModal()
542	dlg.Destroy()
543	return []
544
545	def ConstraintsLoad(data,newcons=[]):
546	'''Load all constraints. Constraints based on symmetry (etc.)
547	are generated by running :func:`GSASIIstrIO.GetPhaseData`.
548	'''
549	G2mv.InitVars()
550	#Find all constraints
551	constraintSet = []
552	for key in data:
553	if key.startswith('_'): continue
554	constraintSet += data[key]
555	if newcons:
556	constraintSet = constraintSet + newcons
557	constDictList,fixedList,ignored = G2stIO.ProcessConstraints(constraintSet)
558	# generate symmetry constraints to check for conflicts
559	rigidbodyDict = G2frame.GPXtree.GetItemPyData(
560	G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies'))
561	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
562	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
563	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
564	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
565	return constDictList,phaseDict,fixedList
566
567	def ConstraintsCheck(data,newcons=[]):
568	'''Load constraints & check them for errors. Since error checking
569	can cause changes in constraints in case of repairable conflicts
570	between equivalences, reload the constraints again after the check.
571	This could probably be done more effectively, but only reloading when
572	needed, but the reload should be quick.
573	'''
574	constDictList,phaseDict,fixedList = ConstraintsLoad(data,newcons)
575	msg = G2mv.EvaluateMultipliers(constDictList,phaseDict)
576	if msg:
577	return 'Unable to interpret multiplier(s): '+msg,''
578	res = G2mv.CheckConstraints('',constDictList,fixedList)
579	# reload constraints in case any were merged in MoveConfEquiv
580	ConstraintsLoad(data,newcons)
581	return res
582
583	def CheckAddedConstraint(newcons):
584	'''Check a new constraint that has just been input.
585	If there is an error display a message and discard the last entry
586
587	Since the varylist is not available, no warning messages
588	should be generated here
589
590	:returns: True if constraint should be added
591	'''
592
593	errmsg,warnmsg = ConstraintsCheck(data,newcons)
594	if errmsg:
595	G2frame.ErrorDialog('Constraint Error',
596	'Error with newly added constraint:\n'+errmsg+
597	'\nIgnoring newly added constraint',parent=G2frame)
598	# reset error status
599	errmsg,warnmsg = ConstraintsCheck(data)
600	if errmsg:
601	print (errmsg)
602	print (G2mv.VarRemapShow([],True))
603	return False
604	elif warnmsg:
605	print ('Unexpected contraint warning:\n'+warnmsg)
606	return True
607
608	def CheckChangedConstraint():
609	'''Check all constraints after an edit has been made.
610	If there is an error display a message and reject the change.
611
612	Since the varylist is not available, no warning messages
613	should be generated.
614
615	:returns: True if the edit should be retained
616	'''
617	errmsg,warnmsg = ConstraintsCheck(data)
618	if errmsg:
619	G2frame.ErrorDialog('Constraint Error',
620	'Error after editing constraint:\n'+errmsg+
621	'\nDiscarding last constraint edit',parent=G2frame)
622	# reset error status
623	errmsg,warnmsg = ConstraintsCheck(data)
624	if errmsg:
625	print (errmsg)
626	print (G2mv.VarRemapShow([],True))
627	return False
628	elif warnmsg:
629	print ('Unexpected contraint warning:\n'+warnmsg)
630	return True
631
632	def PageSelection(page):
633	'Decode page reference'
634	if page[1] == "phs":
635	vartype = "phase"
636	varList = G2obj.removeNonRefined(phaseList) # remove any non-refinable prms from list
637	constrDictEnt = 'Phase'
638	elif page[1] == "hap":
639	vartype = "Histogram*Phase"
640	varList = G2obj.removeNonRefined(hapList) # remove any non-refinable prms from list
641	constrDictEnt = 'HAP'
642	elif page[1] == "hst":
643	vartype = "Histogram"
644	varList = G2obj.removeNonRefined(histList) # remove any non-refinable prms from list
645	constrDictEnt = 'Hist'
646	elif page[1] == "glb":
647	vartype = "Global"
648	varList = G2obj.removeNonRefined(globalList) # remove any non-refinable prms from list
649
650	constrDictEnt = 'Global'
651	elif page[1] == "sym":
652	return None,None,None
653	else:
654	raise Exception('Should not happen!')
655	return vartype,varList,constrDictEnt
656
657	def OnAddHold(event):
658	'''Create a new Hold constraint
659
660	Hold constraints allows the user to select one variable (the list of available
661	variables depends on which tab is currently active).
662	'''
663	page = G2frame.Page
664	vartype,varList,constrDictEnt = PageSelection(page)
665	if vartype is None: return
666	varList = G2obj.SortVariables(varList)
667	title1 = "Hold "+vartype+" variable"
668	if not varList:
669	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
670	parent=G2frame)
671	return
672	l2 = l1 = 1
673	for i in varList:
674	l1 = max(l1,len(i))
675	loc,desc = G2obj.VarDescr(i)
676	l2 = max(l2,len(loc))
677	fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
678	varListlbl = [fmt.format(i,*G2obj.VarDescr(i)) for i in varList]
679	#varListlbl = ["("+i+") "+G2obj.fmtVarDescr(i) for i in varList]
680	legend = "Select variables to hold (Will not be varied, even if vary flag is set)"
681	dlg = G2G.G2MultiChoiceDialog(G2frame,
682	legend,title1,varListlbl,toggle=False,size=(625,400),monoFont=True)
683	dlg.CenterOnParent()
684	if dlg.ShowModal() == wx.ID_OK:
685	for sel in dlg.GetSelections():
686	Varb = varList[sel]
687	VarObj = G2obj.G2VarObj(Varb)
688	newcons = [[[0.0,VarObj],None,None,'h']]
689	if CheckAddedConstraint(newcons):
690	data[constrDictEnt] += newcons
691	dlg.Destroy()
692	wx.CallAfter(OnPageChanged,None)
693
694	def OnAddEquivalence(event):
695	'''add an Equivalence constraint'''
696	page = G2frame.Page
697	vartype,varList,constrDictEnt = PageSelection(page)
698	if vartype is None: return
699	title1 = "Create equivalence constraint between "+vartype+" variables"
700	title2 = "Select additional "+vartype+" variable(s) to be equivalent with "
701	if not varList:
702	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
703	parent=G2frame)
704	return
705	# legend = "Select variables to make equivalent (only one of the variables will be varied when all are set to be varied)"
706	GetAddVars(page,title1,title2,varList,constrDictEnt,'equivalence')
707
708	def OnAddAtomEquiv(event):
709	''' Add equivalences between all parameters on atoms '''
710	page = G2frame.Page
711	vartype,varList,constrDictEnt = PageSelection(page)
712	if vartype is None: return
713	title1 = "Setup equivalent atom variables"
714	title2 = "Select additional atoms(s) to be equivalent with "
715	if not varList:
716	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
717	parent=G2frame)
718	return
719	# legend = "Select atoms to make equivalent (only one of the atom variables will be varied when all are set to be varied)"
720	GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'equivalence')
721
722	def OnAddRiding(event):
723	''' Add riding equivalences between all parameters on atoms '''
724	page = G2frame.Page
725	vartype,varList,constrDictEnt = PageSelection(page)
726	if vartype is None: return
727	title1 = "Setup riding atoms "
728	title2 = "Select additional atoms(s) to ride on "
729	if not varList:
730	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
731	parent=G2frame)
732	return
733	# legend = "Select atoms to ride (only one of the atom variables will be varied when all are set to be varied)"
734	GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'riding')
735
736	def OnAddFunction(event):
737	'''add a Function (new variable) constraint'''
738	page = G2frame.Page
739	vartype,varList,constrDictEnt = PageSelection(page)
740	if vartype is None: return
741	title1 = "Setup new variable based on "+vartype+" variables"
742	title2 = "Include additional "+vartype+" variable(s) to be included with "
743	if not varList:
744	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
745	parent=G2frame)
746	return
747	# legend = "Select variables to include in a new variable (the new variable will be varied when all included variables are varied)"
748	GetAddVars(page,title1,title2,varList,constrDictEnt,'function')
749
750	def OnAddConstraint(event):
751	'''add a constraint equation to the constraints list'''
752	page = G2frame.Page
753	vartype,varList,constrDictEnt = PageSelection(page)
754	if vartype is None: return
755	title1 = "Creating constraint on "+vartype+" variables"
756	title2 = "Select additional "+vartype+" variable(s) to include in constraint with "
757	if not varList:
758	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
759	parent=G2frame)
760	return
761	# legend = "Select variables to include in a constraint equation (the values will be constrainted to equal a specified constant)"
762	GetAddVars(page,title1,title2,varList,constrDictEnt,'constraint')
763
764	def GetAddVars(page,title1,title2,varList,constrDictEnt,constType):
765	'''Get the variables to be added for OnAddEquivalence, OnAddFunction,
766	and OnAddConstraint. Then create and check the constraint.
767	'''
768	#varListlbl = ["("+i+") "+G2obj.fmtVarDescr(i) for i in varList]
769	if constType == 'equivalence':
770	omitVars = G2mv.GetDependentVars()
771	else:
772	omitVars = []
773	varList = G2obj.SortVariables([i for i in varList if i not in omitVars])
774	l2 = l1 = 1
775	for i in varList:
776	l1 = max(l1,len(i))
777	loc,desc = G2obj.VarDescr(i)
778	l2 = max(l2,len(loc))
779	fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
780	varListlbl = [fmt.format(i,*G2obj.VarDescr(i)) for i in varList]
781	dlg = G2G.G2SingleChoiceDialog(G2frame,'Select 1st variable:',
782	title1,varListlbl,monoFont=True,size=(625,400))
783	dlg.CenterOnParent()
784	if dlg.ShowModal() == wx.ID_OK:
785	if constType == 'equivalence':
786	omitVars = G2mv.GetDependentVars() + G2mv.GetIndependentVars()
787	sel = dlg.GetSelection()
788	FrstVarb = varList[sel]
789	VarObj = G2obj.G2VarObj(FrstVarb)
790	moreVarb = G2obj.SortVariables(FindEquivVarb(FrstVarb,[i for i in varList if i not in omitVars]))
791	newcons = SelectVarbs(page,VarObj,moreVarb,title2+FrstVarb,constType)
792	if len(newcons) > 0:
793	if CheckAddedConstraint(newcons):
794	data[constrDictEnt] += newcons
795	dlg.Destroy()
796	wx.CallAfter(OnPageChanged,None)
797
798	def FindNeighbors(phase,FrstName,AtNames):
799	General = phase['General']
800	cx,ct,cs,cia = General['AtomPtrs']
801	Atoms = phase['Atoms']
802	atNames = [atom[ct-1] for atom in Atoms]
803	Cell = General['Cell'][1:7]
804	Amat,Bmat = G2lat.cell2AB(Cell)
805	atTypes = General['AtomTypes']
806	Radii = np.array(General['BondRadii'])
807	AtInfo = dict(zip(atTypes,Radii)) #or General['BondRadii']
808	Orig = atNames.index(FrstName.split()[1])
809	OType = Atoms[Orig][ct]
810	XYZ = G2mth.getAtomXYZ(Atoms,cx)
811	Neigh = []
812	Dx = np.inner(Amat,XYZ-XYZ[Orig]).T
813	dist = np.sqrt(np.sum(Dx**2,axis=1))
814	sumR = AtInfo[OType]+0.5 #H-atoms only!
815	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
816	for j in IndB[0]:
817	if j != Orig:
818	Neigh.append(AtNames[j])
819	return Neigh
820
821	def GetAddAtomVars(page,title1,title2,varList,constrDictEnt,constType):
822	'''Get the atom variables to be added for OnAddAtomEquiv. Then create and
823	check the constraints. Riding for H atoms only.
824	'''
825	Atoms = {G2obj.VarDescr(i)[0]:[] for i in varList if 'Atom' in G2obj.VarDescr(i)[0]}
826	for item in varList:
827	atName = G2obj.VarDescr(item)[0]
828	if atName in Atoms:
829	Atoms[atName].append(item)
830	AtNames = list(Atoms.keys())
831	AtNames.sort()
832	dlg = G2G.G2SingleChoiceDialog(G2frame,'Select 1st atom:',
833	title1,AtNames,monoFont=True,size=(625,400))
834	dlg.CenterOnParent()
835	FrstAtom = ''
836	if dlg.ShowModal() == wx.ID_OK:
837	sel = dlg.GetSelection()
838	FrstAtom = AtNames[sel]
839	if 'riding' in constType:
840	phaseName = (FrstAtom.split(' in ')[1]).strip()
841	phase = Phases[phaseName]
842	AtNames = FindNeighbors(phase,FrstAtom,AtNames)
843	else:
844	AtNames.remove(FrstAtom)
845	dlg.Destroy()
846	if FrstAtom == '':
847	print ('no atom selected')
848	return
849	dlg = G2G.G2MultiChoiceDialog(
850	G2frame,title2+FrstAtom,
851	'Constrain '+str(FrstAtom)+' with...',AtNames,
852	toggle=False,size=(625,400),monoFont=True)
853	if dlg.ShowModal() == wx.ID_OK:
854	Selections = dlg.GetSelections()[:]
855	else:
856	print ('no target atom selected')
857	dlg.Destroy()
858	return
859	dlg.Destroy()
860	for name in Atoms[FrstAtom]:
861	newcons = []
862	constr = []
863	if 'riding' in constType:
864	if 'AUiso' in name:
865	constr = [[1.0,G2obj.G2VarObj(name)]]
866	elif 'AU11' in name:
867	pass
868	elif 'AU' not in name:
869	constr = [[1.0,G2obj.G2VarObj(name)]]
870	else:
871	constr = [[1.0,G2obj.G2VarObj(name)]]
872	pref = ':'+name.rsplit(':',1)[0].split(':',1)[1] #get stuff between phase id & atom id
873	for sel in Selections:
874	name2 = Atoms[AtNames[sel]][0]
875	pid = name2.split(':',1)[0] #get phase id for 2nd atom
876	id = name2.rsplit(':',1)[-1] #get atom no. for 2nd atom
877	if 'riding' in constType:
878	pref = pid+pref
879	if 'AUiso' in pref:
880	parts = pref.split('AUiso')
881	constr += [[1.2,G2obj.G2VarObj('%s:%s'%(parts[0]+'AUiso',id))]]
882	elif 'AU' not in pref:
883	constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pref,id))]]
884	else:
885	constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pid+pref,id))]]
886	if not constr:
887	continue
888	if 'frac' in pref and 'riding' not in constType:
889	newcons = [constr+[1.0,None,'c']]
890	else:
891	newcons = [constr+[None,None,'e']]
892	if len(newcons) > 0:
893	if CheckAddedConstraint(newcons):
894	data[constrDictEnt] += newcons
895	wx.CallAfter(OnPageChanged,None)
896
897	def MakeConstraintsSizer(name,pageDisplay):
898	'''Creates a sizer displaying all of the constraints entered of
899	the specified type.
900
901	:param str name: the type of constraints to be displayed ('HAP',
902	'Hist', 'Phase', 'Global', 'Sym-Generated')
903	:param wx.Panel pageDisplay: parent panel for sizer
904	:returns: wx.Sizer created by method
905	'''
906	if name == 'Sym-Generated': #show symmetry generated constraints
907	Sizer1 = wx.BoxSizer(wx.VERTICAL)
908	Sizer1.Add(wx.StaticText(pageDisplay,wx.ID_ANY,
909	'Equivalences generated based on cell/space group input'))
910	Sizer1.Add((-1,5))
911	Sizer = wx.FlexGridSizer(0,2,0,0)
912	Sizer1.Add(Sizer)
913	for sym in G2mv.GetSymEquiv():
914	Sizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,'EQUIV'),
915	0,wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER\|wx.RIGHT\|wx.LEFT,3)
916	Sizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,sym))
917	Sizer.Add((-1,-1))
918	Sizer.Add((-1,2))
919	return Sizer1
920	constSizer = wx.FlexGridSizer(0,6,0,0)
921	maxlen = 50 # characters before wrapping a constraint
922	for Id,item in enumerate(data[name]):
923	refineflag = False
924	helptext = ""
925	eqString = ['',]
926	problemItem = False
927	for term in item[:-3]:
928	if str(term[1]) in G2mv.problemVars:
929	problemItem = True
930	if item[-1] == 'h': # Hold on variable
931	constSizer.Add((-1,-1),0) # blank space for edit button
932	typeString = 'FIXED'
933	var = str(item[0][1])
934	varMean = G2obj.fmtVarDescr(var)
935	eqString[-1] = var +' '
936	helptext = "Prevents variable:\n"+ var + " ("+ varMean + ")\nfrom being changed"
937	elif item[-1] == 'f' or item[-1] == 'e' or item[-1] == 'c': # not true on original-style (2011?) constraints
938	constEdit = wx.Button(pageDisplay,wx.ID_ANY,'Edit',style=wx.BU_EXACTFIT)
939	constEdit.Bind(wx.EVT_BUTTON,OnConstEdit)
940	constSizer.Add(constEdit,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1) # edit button
941	Indx[constEdit.GetId()] = [Id,name]
942	if item[-1] == 'f':
943	helptext = "A new variable"
944	if item[-3]:
945	helptext += " named "+str(item[-3])
946	helptext += " is created from a linear combination of the following variables:\n"
947	for term in item[:-3]:
948	var = str(term[1])
949	if len(eqString[-1]) > maxlen:
950	eqString.append(' ')
951	m = term[0]
952	if eqString[-1] != '':
953	if m >= 0:
954	eqString[-1] += ' + '
955	else:
956	eqString[-1] += ' - '
957	m = abs(m)
958	if m == 1:
959	eqString[-1] += '{:} '.format(var)
960	else:
961	eqString[-1] += '{:g}*{:} '.format(m,var)
962	varMean = G2obj.fmtVarDescr(var)
963	helptext += "\n" + var + " ("+ varMean + ")"
964	# Add ISODISTORT help items
965	if '_Explain' in data:
966	# this ignores the phase number. TODO: refactor that in
967	hlptxt = None
968	try:
969	hlptxt = data['_Explain'].get(item[-3])
970	except TypeError:
971	# note that phase RanId is item[-3].phase
972	hlptxt = data['_Explain'].get(str(item[-3].phase)+item[-3].name)
973	if hlptxt:
974	helptext += '\n\n'
975	helptext += hlptxt
976	# typeString = 'NEWVAR'
977	# if item[-3]:
978	# eqString[-1] += ' = '+item[-3]
979	# else:
980	# eqString[-1] += ' = New Variable'
981	if item[-3]:
982	typeString = str(item[-3]) + ' = '
983	else:
984	typeString = 'New Variable = '
985	#print 'refine',item[-2]
986	refineflag = True
987	elif item[-1] == 'c':
988	helptext = "The following variables constrained to equal a constant:"
989	for term in item[:-3]:
990	var = str(term[1])
991	if len(eqString[-1]) > maxlen:
992	eqString.append(' ')
993	m = term[0]
994	if eqString[-1] != '':
995	if term[0] > 0:
996	eqString[-1] += ' + '
997	else:
998	eqString[-1] += ' - '
999	m = -term[0]
1000	if m == 1:
1001	eqString[-1] += '{:} '.format(var)
1002	else:
1003	eqString[-1] += '{:g}*{:} '.format(m,var)
1004	varMean = G2obj.fmtVarDescr(var)
1005	helptext += "\n" + var + " ("+ varMean + ")"
1006	typeString = 'CONST'
1007	eqString[-1] += ' = '+str(item[-3])
1008	elif item[-1] == 'e':
1009	helptext = "The following variables are set to be equivalent, noting multipliers:"
1010	normval = item[:-3][1][0]
1011	for i,term in enumerate(item[:-3]):
1012	var = str(term[1])
1013	if term[0] == 0: term[0] = 1.0
1014	if len(eqString[-1]) > maxlen:
1015	eqString.append(' ')
1016	if i == 0: # move independent variable to end
1017	indepterm = term
1018	continue
1019	elif eqString[-1] != '':
1020	eqString[-1] += ' = '
1021	if normval/term[0] == 1:
1022	eqString[-1] += '{:}'.format(var)
1023	else:
1024	eqString[-1] += '{:g}*{:} '.format(normval/term[0],var)
1025	varMean = G2obj.fmtVarDescr(var)
1026	helptext += "\n" + var + " ("+ varMean + ")"
1027	if normval/indepterm[0] == 1:
1028	eqString[-1] += ' = {:} '.format(indepterm[1])
1029	else:
1030	eqString[-1] += ' = {:g}*{:} '.format(normval/indepterm[0],str(indepterm[1]))
1031	typeString = 'EQUIV'
1032	else:
1033	print ('Unexpected constraint'+item)
1034
1035	else:
1036	print ('Removing old-style constraints')
1037	data[name] = []
1038	return constSizer
1039	constDel = wx.Button(pageDisplay,wx.ID_ANY,'Delete',style=wx.BU_EXACTFIT)
1040	constDel.Bind(wx.EVT_BUTTON,OnConstDel)
1041	Indx[constDel.GetId()] = [Id,name]
1042	constSizer.Add(constDel,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1) # delete button
1043	if helptext:
1044	ch = G2G.HelpButton(pageDisplay,helptext)
1045	constSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1)
1046	else:
1047	constSizer.Add((-1,-1))
1048	if refineflag:
1049	ch = G2G.G2CheckBox(pageDisplay,'',item,-2)
1050	constSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1)
1051	else:
1052	constSizer.Add((-1,-1))
1053	constSizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,typeString),
1054	0,wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER\|wx.RIGHT\|wx.LEFT,3)
1055	if problemItem: eqString[-1] += ' -- Conflict: see console'
1056	if len(eqString) > 1:
1057	Eq = wx.BoxSizer(wx.VERTICAL)
1058	for s in eqString:
1059	line = wx.StaticText(pageDisplay,wx.ID_ANY,s)
1060	if problemItem: line.SetBackgroundColour(wx.YELLOW)
1061	Eq.Add(line,0,wx.ALIGN_CENTER_VERTICAL)
1062	Eq.Add((-1,4))
1063	else:
1064	Eq = wx.StaticText(pageDisplay,wx.ID_ANY,eqString[0])
1065	if problemItem: Eq.SetBackgroundColour(wx.YELLOW)
1066	constSizer.Add(Eq,1,wx.ALIGN_CENTER_VERTICAL)
1067	return constSizer
1068
1069	def OnConstDel(event):
1070	'Delete a constraint'
1071	Obj = event.GetEventObject()
1072	Id,name = Indx[Obj.GetId()]
1073	del data[name][Id]
1074	ConstraintsLoad(data)
1075	wx.CallAfter(OnPageChanged,None)
1076
1077	def OnConstEdit(event):
1078	'''Called to edit an individual contraint in response to a
1079	click on its Edit button
1080	'''
1081	Obj = event.GetEventObject()
1082	Id,name = Indx[Obj.GetId()]
1083	if data[name][Id][-1] == 'f':
1084	items = data[name][Id][:-3]
1085	constType = 'New Variable'
1086	if data[name][Id][-3]:
1087	varname = str(data[name][Id][-3])
1088	else:
1089	varname = ""
1090	lbl = 'Enter value for each term in constraint; sum = new variable'
1091	dlg = ConstraintDialog(G2frame,constType,lbl,items,
1092	varname=varname,varyflag=data[name][Id][-2])
1093	elif data[name][Id][-1] == 'c':
1094	items = data[name][Id][:-3]+[
1095	[str(data[name][Id][-3]),'fixed value =']]
1096	constType = 'Constraint'
1097	lbl = 'Edit value for each term in constant constraint sum'
1098	dlg = ConstraintDialog(G2frame,constType,lbl,items)
1099	elif data[name][Id][-1] == 'e':
1100	items = data[name][Id][:-3]
1101	constType = 'Equivalence'
1102	lbl = 'The following terms are set to be equal:'
1103	dlg = ConstraintDialog(G2frame,constType,lbl,items,'/')
1104	else:
1105	return
1106	try:
1107	prev = copy.deepcopy(data[name][Id])
1108	if dlg.ShowModal() == wx.ID_OK:
1109	result = dlg.GetData()
1110	for i in range(len(data[name][Id][:-3])):
1111	if type(data[name][Id][i]) is tuple: # fix non-mutable construct
1112	data[name][Id][i] = list(data[name][Id][i])
1113	data[name][Id][i][0] = result[i][0]
1114	if data[name][Id][-1] == 'c':
1115	data[name][Id][-3] = str(result[-1][0])
1116	elif data[name][Id][-1] == 'f':
1117	data[name][Id][-2] = dlg.newvar[1]
1118	if type(data[name][Id][-3]) is str:
1119	# process the variable name to put in global form (::var)
1120	varname = str(dlg.newvar[0]).strip().replace(' ','_')
1121	if varname.startswith('::'):
1122	varname = varname[2:]
1123	varname = varname.replace(':',';')
1124	if varname:
1125	data[name][Id][-3] = varname
1126	else:
1127	data[name][Id][-3] = ''
1128	if not CheckChangedConstraint():
1129	data[name][Id] = prev
1130	else:
1131	data[name][Id] = prev
1132	except:
1133	import traceback
1134	print (traceback.format_exc())
1135	finally:
1136	dlg.Destroy()
1137	wx.CallAfter(OnPageChanged,None)
1138
1139	def UpdateConstraintPanel(panel,typ):
1140	'''Update the contents of the selected Constraint
1141	notebook tab. Called in :func:`OnPageChanged`
1142	'''
1143	if panel.GetSizer(): panel.GetSizer().Clear(True)
1144	Siz = wx.BoxSizer(wx.VERTICAL)
1145	Siz.Add((5,5),0)
1146	Siz.Add(MakeConstraintsSizer(typ,panel),1,wx.EXPAND)
1147	panel.SetSizer(Siz,True)
1148	Size = Siz.GetMinSize()
1149	Size[0] += 40
1150	Size[1] = max(Size[1],450) + 20
1151	panel.SetSize(Size)
1152	panel.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
1153	panel.Show()
1154
1155	def OnPageChanged(event):
1156	'''Called when a tab is pressed or when a "select tab" menu button is
1157	used (see RaisePage), or to refresh the current tab contents (event=None)
1158	'''
1159	if event: #page change event!
1160	page = event.GetSelection()
1161	else: # called directly, get current page
1162	page = G2frame.constr.GetSelection()
1163	G2frame.constr.ChangeSelection(page)
1164	text = G2frame.constr.GetPageText(page)
1165	G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_EQUIVALANCEATOMS,False)
1166	# G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_ADDRIDING,False)
1167	if text == 'Histogram/Phase':
1168	enableEditCons = [False]+4*[True]
1169	G2frame.Page = [page,'hap']
1170	UpdateConstraintPanel(HAPConstr,'HAP')
1171	elif text == 'Histogram':
1172	enableEditCons = [False]+4*[True]
1173	G2frame.Page = [page,'hst']
1174	UpdateConstraintPanel(HistConstr,'Hist')
1175	elif text == 'Phase':
1176	enableEditCons = 5*[True]
1177	G2frame.Page = [page,'phs']
1178	G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_EQUIVALANCEATOMS,True)
1179	# G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_ADDRIDING,True)
1180	if 'DELETED' in str(PhaseConstr): #seems to be no other way to do this (wx bug)
1181	if GSASIIpath.GetConfigValue('debug'):
1182	print ('DBG_wx error: PhaseConstr not cleanly deleted after Refine')
1183	return
1184	UpdateConstraintPanel(PhaseConstr,'Phase')
1185	elif text == 'Global':
1186	enableEditCons = [False]+4*[True]
1187	G2frame.Page = [page,'glb']
1188	UpdateConstraintPanel(GlobalConstr,'Global')
1189	else:
1190	enableEditCons = 5*[False]
1191	G2frame.Page = [page,'sym']
1192	UpdateConstraintPanel(SymConstr,'Sym-Generated')
1193	# remove menu items when not allowed
1194	for obj,flag in zip(G2frame.dataWindow.ConstraintEdit.GetMenuItems(),enableEditCons):
1195	obj.Enable(flag)
1196	G2frame.dataWindow.SetDataSize()
1197
1198	def RaisePage(event):
1199	'Respond to a "select tab" menu button'
1200	try:
1201	i = (G2G.wxID_CONSPHASE,
1202	G2G.wxID_CONSHAP,
1203	G2G.wxID_CONSHIST,
1204	G2G.wxID_CONSGLOBAL,
1205	G2G.wxID_CONSSYM,
1206	).index(event.GetId())
1207	G2frame.constr.SetSelection(i)
1208	wx.CallAfter(OnPageChanged,None)
1209	except ValueError:
1210	print('Unexpected event in RaisePage')
1211
1212	def SetStatusLine(text):
1213	G2frame.GetStatusBar().SetStatusText(text,1)
1214
1215	# UpdateConstraints execution starts here
1216	if not data:
1217	data.update({'Hist':[],'HAP':[],'Phase':[],'Global':[]}) #empty dict - fill it
1218	if 'Global' not in data: #patch
1219	data['Global'] = []
1220	# DEBUG code ########################################
1221	#import GSASIIconstrGUI
1222	#reload(GSASIIconstrGUI)
1223	#reload(G2obj)
1224	#reload(G2stIO)
1225	#import GSASIIstrMain
1226	#reload(GSASIIstrMain)
1227	#reload(G2mv)
1228	#reload(G2gd)
1229	###################################################
1230	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
1231	if not len(Phases) or not len(Histograms):
1232	dlg = wx.MessageDialog(G2frame,'You need both phases and histograms to see Constraints',
1233	'No phases or histograms')
1234	dlg.CenterOnParent()
1235	dlg.ShowModal()
1236	dlg.Destroy()
1237	return
1238	G2obj.IndexAllIds(Histograms,Phases)
1239	for p in Phases:
1240	if 'ISODISTORT' in Phases[p]:
1241	G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_SHOWISO,True)
1242	break
1243	##################################################################################
1244	# patch: convert old-style (str) variables in constraints to G2VarObj objects
1245	for key,value in data.items():
1246	if key.startswith('_'): continue
1247	j = 0
1248	for cons in value:
1249	#print cons # DEBUG
1250	for i in range(len(cons[:-3])):
1251	if type(cons[i][1]) is str:
1252	cons[i][1] = G2obj.G2VarObj(cons[i][1])
1253	j += 1
1254	if j:
1255	print (str(key) + ': '+str(j)+' variable(s) as strings converted to objects')
1256	##################################################################################
1257	rigidbodyDict = G2frame.GPXtree.GetItemPyData(
1258	G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1259	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1260	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1261	badPhaseParms = ['Ax','Ay','Az','Amul','AI/A','Atype','SHorder','AwaveType','FwaveType','PwaveType','MwaveType','Vol','isMag',]
1262	globalList = list(rbDict.keys())
1263	globalList.sort()
1264	try:
1265	AtomDict = dict([Phases[phase]['pId'],Phases[phase]['Atoms']] for phase in Phases)
1266	except KeyError:
1267	G2frame.ErrorDialog('Constraint Error','Constraints cannot be set until a cycle of least squares'+
1268	' has been run.\nWe suggest you refine a scale factor.')
1269	return
1270
1271	# create a list of the phase variables
1272	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable,MFtable,maxSSwave = G2stIO.GetPhaseData(Phases,rbIds=rbIds,Print=False)
1273	phaseList = []
1274	for item in phaseDict:
1275	if item.split(':')[2] not in badPhaseParms:
1276	phaseList.append(item)
1277	phaseList.sort()
1278	phaseAtNames = {}
1279	phaseAtTypes = {}
1280	TypeList = []
1281	for item in phaseList:
1282	Split = item.split(':')
1283	if Split[2][:2] in ['AU','Af','dA','AM']:
1284	Id = int(Split[0])
1285	phaseAtNames[item] = AtomDict[Id][int(Split[3])][0]
1286	phaseAtTypes[item] = AtomDict[Id][int(Split[3])][1]
1287	if phaseAtTypes[item] not in TypeList:
1288	TypeList.append(phaseAtTypes[item])
1289	else:
1290	phaseAtNames[item] = ''
1291	phaseAtTypes[item] = ''
1292
1293	# create a list of the hist*phase variables
1294	seqList = G2frame.testSeqRefineMode()
1295	if seqList: # for sequential refinement, only process 1st histgram in list
1296	histDict = {seqList[0]:Histograms[seqList[0]]}
1297	else:
1298	histDict = Histograms
1299	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,histDict,Print=False,resetRefList=False)
1300	hapList = sorted([i for i in hapDict.keys() if i.split(':')[2] not in ('Type',)])
1301	if seqList: # convert histogram # to wildcard
1302	wildList = [] # list of variables with "*" for histogram number
1303	for i in hapList:
1304	s = i.split(':')
1305	if s[1] == "": continue
1306	s[1] = '*'
1307	sj = ':'.join(s)
1308	if sj not in wildList: wildList.append(sj)
1309	hapList = wildList
1310	histVary,histDict,controlDict = G2stIO.GetHistogramData(histDict,Print=False)
1311	histList = list(histDict.keys())
1312	histList.sort()
1313	if seqList: # convert histogram # to wildcard
1314	wildList = [] # list of variables with "*" for histogram number
1315	for i in histList:
1316	s = i.split(':')
1317	if s[1] == "": continue
1318	s[1] = '*'
1319	sj = ':'.join(s)
1320	if sj not in wildList: wildList.append(sj)
1321	histList = wildList
1322	Indx = {}
1323	G2frame.Page = [0,'phs']
1324
1325	G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.ConstraintMenu)
1326	SetStatusLine('')
1327
1328	G2frame.Bind(wx.EVT_MENU, OnAddConstraint, id=G2G.wxID_CONSTRAINTADD)
1329	G2frame.Bind(wx.EVT_MENU, OnAddFunction, id=G2G.wxID_FUNCTADD)
1330	G2frame.Bind(wx.EVT_MENU, OnAddEquivalence, id=G2G.wxID_EQUIVADD)
1331	G2frame.Bind(wx.EVT_MENU, OnAddHold, id=G2G.wxID_HOLDADD)
1332	G2frame.Bind(wx.EVT_MENU, OnAddAtomEquiv, id=G2G.wxID_EQUIVALANCEATOMS)
1333	# G2frame.Bind(wx.EVT_MENU, OnAddRiding, id=G2G.wxID_ADDRIDING)
1334	def OnShowISODISTORT(event):
1335	ShowIsoDistortCalc(G2frame)
1336	G2frame.Bind(wx.EVT_MENU, OnShowISODISTORT, id=G2G.wxID_SHOWISO)
1337	# tab commands
1338	for id in (G2G.wxID_CONSPHASE,
1339	G2G.wxID_CONSHAP,
1340	G2G.wxID_CONSHIST,
1341	G2G.wxID_CONSGLOBAL,
1342	G2G.wxID_CONSSYM,
1343	):
1344	G2frame.Bind(wx.EVT_MENU, RaisePage,id=id)
1345
1346	#G2frame.constr = G2G.GSNoteBook(parent=G2frame.dataWindow,size=G2frame.dataWindow.GetClientSize())
1347	G2frame.constr = G2G.GSNoteBook(parent=G2frame.dataWindow)
1348	G2frame.dataWindow.GetSizer().Add(G2frame.constr,1,wx.ALL\|wx.EXPAND)
1349	# note that order of pages is hard-coded in RaisePage
1350	PhaseConstr = wx.ScrolledWindow(G2frame.constr)
1351	G2frame.constr.AddPage(PhaseConstr,'Phase')
1352	HAPConstr = wx.ScrolledWindow(G2frame.constr)
1353	G2frame.constr.AddPage(HAPConstr,'Histogram/Phase')
1354	HistConstr = wx.ScrolledWindow(G2frame.constr)
1355	G2frame.constr.AddPage(HistConstr,'Histogram')
1356	GlobalConstr = wx.ScrolledWindow(G2frame.constr)
1357	G2frame.constr.AddPage(GlobalConstr,'Global')
1358	SymConstr = wx.ScrolledWindow(G2frame.constr)
1359	G2frame.constr.AddPage(SymConstr,'Sym-Generated')
1360	wx.CallAfter(OnPageChanged,None)
1361	G2frame.constr.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
1362	# validate all the constrants -- should not see any errors here normally
1363	errmsg,warnmsg = ConstraintsCheck(data)
1364	if errmsg:
1365	G2frame.ErrorDialog('Constraint Error',
1366	'Error in constraints:\n'+errmsg+'\nCheck console output for more information',
1367	parent=G2frame)
1368	print (errmsg)
1369	print (G2mv.VarRemapShow([],True))
1370	elif warnmsg:
1371	print ('Unexpected contraint warning:\n'+warnmsg)
1372
1373	################################################################################
1374	# check scale & phase fractions, create constraint if needed
1375	################################################################################
1376	def CheckAllScalePhaseFractions(G2frame):
1377	'''Check if scale factor and all phase fractions are refined without a constraint
1378	for all used histograms, if so, offer the user a chance to create a constraint
1379	on the sum of phase fractions
1380	'''
1381	histograms, phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
1382	for i,hist in enumerate(histograms):
1383	CheckScalePhaseFractions(G2frame,hist,histograms,phases)
1384
1385	def CheckScalePhaseFractions(G2frame,hist,histograms,phases):
1386	'''Check if scale factor and all phase fractions are refined without a constraint
1387	for histogram hist, if so, offer the user a chance to create a constraint
1388	on the sum of phase fractions
1389	'''
1390	if G2frame.testSeqRefineMode():
1391	histStr = '*'
1392	else:
1393	histStr = str(histograms[hist]['hId'])
1394	# Is this powder?
1395	if not hist.startswith('PWDR '): return
1396	# do this only if the scale factor is varied
1397	if not histograms[hist]['Sample Parameters']['Scale'][1]: return
1398	# are all phase fractions varied in all used histograms?
1399	phaseCount = 0
1400	for p in phases:
1401	if hist not in phases[p]['Histograms']: continue
1402	if phases[p]['Histograms'][hist]['Use'] and not phases[p]['Histograms'][hist]['Scale'][1]:
1403	return
1404	else:
1405	phaseCount += 1
1406
1407	# all phase fractions and scale factor varied, now scan through constraints
1408	sub = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
1409	Constraints = G2frame.GPXtree.GetItemPyData(sub)
1410	for c in Constraints.get('HAP',[]):
1411	if c[-1] != 'c': continue
1412	if not c[-3]: continue
1413	if len(c[:-3]) != phaseCount: continue
1414	# got a constraint equation with right number of terms, is it on phase fractions for
1415	# the correct histogram?
1416	if all([(i[1].name == 'Scale' and i[1].varname().split(':')[1] == histStr) for i in c[:-3]]):
1417	# got a constraint, this is OK
1418	return
1419	dlg = wx.MessageDialog(G2frame,'You are refining the scale factor and all phase fractions for histogram #'+
1420	histStr+'. This will produce an unstable refinement. '+
1421	'Do you want to constrain the sum of phase fractions?','Create constraint?',wx.OK\|wx.CANCEL)
1422	if dlg.ShowModal() != wx.ID_OK:
1423	dlg.Destroy()
1424	return
1425	dlg.Destroy()
1426
1427	constr = []
1428	for p in phases:
1429	if hist not in phases[p]['Histograms']: continue
1430	if not phases[p]['Histograms'][hist]['Use']: continue
1431	constr += [[1.0,G2obj.G2VarObj(':'.join((str(phases[p]['pId']),histStr,'Scale')))]]
1432	constr += [1.0,None,'c']
1433	Constraints['HAP'] += [constr]
1434
1435	################################################################################
1436	#### Make nuclear/magnetic phase transition constraints - called by OnTransform in G2phsGUI
1437	################################################################################
1438
1439	def TransConstraints(G2frame,oldPhase,newPhase,Trans,Vec,atCodes):
1440	'''Add constraints for new magnetic phase created via transformation of old
1441	nuclear one
1442	NB: A = [G11,G22,G33,2G12,2G13,2*G23]
1443	'''
1444
1445	def SetUniqAj(pId,iA,SGData):
1446	SGLaue = SGData['SGLaue']
1447	SGUniq = SGData['SGUniq']
1448	if SGLaue in ['m3','m3m']:
1449	if iA in [0,1,2]:
1450	parm = '%d::%s'%(pId,'A0')
1451	else:
1452	parm = None
1453	elif SGLaue in ['4/m','4/mmm']:
1454	if iA in [0,1]:
1455	parm = '%d::%s'%(pId,'A0')
1456	elif iA == 2:
1457	parm = '%d::%s'%(pId,'A2')
1458	else:
1459	parm = None
1460	elif SGLaue in ['6/m','6/mmm','3m1', '31m', '3']:
1461	if iA in [0,1,3]:
1462	parm = '%d::%s'%(pId,'A0')
1463	elif iA == 2:
1464	parm = '%d::%s'%(pId,'A2')
1465	else:
1466	parm = None
1467	elif SGLaue in ['3R', '3mR']:
1468	if ia in [0,1,2]:
1469	parm = '%d::%s'%(pId,'A0')
1470	else:
1471	parm = '%d::%s'%(pId,'A3')
1472	elif SGLaue in ['mmm',]:
1473	if iA in [0,1,2]:
1474	parm = '%d::A%s'%(pId,iA)
1475	else:
1476	parm = None
1477	elif SGLaue == '2/m':
1478	if iA in [0,1,2]:
1479	parm = '%d::A%s'%(pId,iA)
1480	elif iA == 3 and SGUniq == 'c':
1481	parm = '%d::A%s'%(pId,iA)
1482	elif iA == 4 and SGUniq == 'b':
1483	parm = '%d::A%s'%(pId,iA)
1484	elif iA == 5 and SGUniq == 'a':
1485	parm = '%d::A%s'%(pId,iA)
1486	else:
1487	parm = None
1488	else:
1489	parm = '%d::A%s'%(pId,iA)
1490	return parm
1491
1492	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
1493	UseList = newPhase['Histograms']
1494	detTrans = np.abs(nl.det(Trans))
1495	invTrans = nl.inv(Trans)
1496	opId = oldPhase['pId']
1497	npId = newPhase['pId']
1498	cx,ct,cs,cia = newPhase['General']['AtomPtrs']
1499	nAtoms = newPhase['Atoms']
1500	oSGData = oldPhase['General']['SGData']
1501	nSGData = newPhase['General']['SGData']
1502	#oAcof = G2lat.cell2A(oldPhase['General']['Cell'][1:7])
1503	#nAcof = G2lat.cell2A(newPhase['General']['Cell'][1:7])
1504	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
1505	if not item:
1506	print('Error: no constraints in Data Tree')
1507	return
1508	constraints = G2frame.GPXtree.GetItemPyData(item)
1509	xnames = ['dAx','dAy','dAz']
1510	# constraints on matching atom params between phases
1511	for ia,code in enumerate(atCodes):
1512	atom = nAtoms[ia]
1513	if not ia and atom[cia] == 'A':
1514	wx.MessageDialog(G2frame,
1515	'Anisotropic thermal motion constraints are not developed at the present time',
1516	'Anisotropic thermal constraint?',style=wx.ICON_INFORMATION).ShowModal()
1517	siteSym = G2spc.SytSym(atom[cx:cx+3],nSGData)[0]
1518	CSX = G2spc.GetCSxinel(siteSym)
1519	# CSU = G2spc.GetCSuinel(siteSym)
1520	item = code.split('+')[0]
1521	iat,opr = item.split(':')
1522	Nop = abs(int(opr))%100-1
1523	if '-' in opr:
1524	Nop *= -1
1525	Opr = oldPhase['General']['SGData']['SGOps'][abs(Nop)][0]
1526	if Nop < 0: #inversion
1527	Opr *= -1
1528	XOpr = np.inner(Opr,Trans)
1529	for i,ix in enumerate(list(CSX[0])):
1530	if not ix:
1531	continue
1532	name = xnames[i]
1533	IndpCon = [1.0,G2obj.G2VarObj('%d::%s:%d'%(npId,name,ia))]
1534	DepCons = []
1535	for iop,opval in enumerate(XOpr[i]):
1536	if opval:
1537	DepCons.append([opval,G2obj.G2VarObj('%d::%s:%s'%(opId,xnames[iop],iat))])
1538	if len(DepCons) == 1:
1539	constraints['Phase'].append([DepCons[0],IndpCon,None,None,'e'])
1540	elif len(DepCons) > 1:
1541	for Dep in DepCons:
1542	Dep[0] *= -1
1543	constraints['Phase'].append([IndpCon]+DepCons+[0.0,None,'c'])
1544	for name in ['Afrac','AUiso']:
1545	IndpCon = [1.0,G2obj.G2VarObj('%d::%s:%d'%(npId,name,ia))]
1546	DepCons = [1.0,G2obj.G2VarObj('%d::%s:%s'%(opId,name,iat))]
1547	constraints['Phase'].append([DepCons,IndpCon,None,None,'e'])
1548
1549	# unfinished Anisotropic constraint generation
1550	# Uids = [[0,0,'AU11'],[1,1,'AU22'],[2,2,'AU33'],[0,1,'AU12'],[0,2,'AU13'],[1,2,'AU23']]
1551	# DepConsDict = dict(zip(Us,[[],[],[],[],[],[]]))
1552	# for iu,Uid in enumerate(Uids):
1553	# UMT = np.zeros((3,3))
1554	# UMT[Uid[0],Uid[1]] = 1
1555	# nUMT = G2lat.prodMGMT(UMT,invTrans)
1556	# nUT = G2lat.UijtoU6(nUMT)
1557	# for iu,nU in enumerate(nUT):
1558	# if abs(nU) > 1.e-8:
1559	# parm = '%d::%s;%s'%(opId,Us[iu],iat)
1560	# DepConsDict[Uid[2]].append([abs(nU%1.),G2obj.G2VarObj(parm)])
1561	# nUcof = atom[iu:iu+6]
1562	# conStrings = []
1563	# for iU,Usi in enumerate(Us):
1564	# parm = '%d::%s;%d'%(npId,Usi,ia)
1565	# parmDict[parm] = nUcof[iU]
1566	# varyList.append(parm)
1567	# IndpCon = [1.0,G2obj.G2VarObj(parm)]
1568	# conStr = str([IndpCon,DepConsDict[Usi]])
1569	# if conStr in conStrings:
1570	# continue
1571	# conStrings.append(conStr)
1572	# if len(DepConsDict[Usi]) == 1:
1573	# if DepConsDict[Usi][0]:
1574	# constraints['Phase'].append([IndpCon,DepConsDict[Usi][0],None,None,'e'])
1575	# elif len(DepConsDict[Usi]) > 1:
1576	# for Dep in DepConsDict[Usi]:
1577	# Dep[0] *= -1
1578	# constraints['Phase'].append([IndpCon]+DepConsDict[Usi]+[0.0,None,'c'])
1579
1580	#how do I do Uij's for most Trans?
1581
1582	# constraints on lattice parameters between phases
1583	# T = nl.inv(Trans).T
1584	T = Trans.T
1585	conMat = [
1586	[T[0,0]2,T[0,1]2,T[0,2]*2,T[0,0]T[0,1],T[0,0]T[0,2],T[0,1]T[0,2]],
1587	[T[1,0]2,T[1,1]2,T[1,2]*2,T[1,0]T[1,1],T[1,0]T[1,2],T[1,1]T[1,2]],
1588	[T[2,0]2,T[2,1]2,T[2,2]*2,T[2,0]T[2,1],T[2,0]T[2,2],T[2,1]T[2,2]],
1589	[2.T[0,0]T[1,0],2.T[0,1]T[1,1],2.T[0,2]T[1,2],T[0,0]T[1,1]+T[0,1]T[1,0],T[0,0]T[1,2]+T[0,2]T[1,0],T[0,1]T[1,2]+T[0,2]T[1,1]],
1590	[2.T[0,0]T[2,0],2.T[0,1]T[2,1],2.T[0,2]T[2,2],T[0,0]T[2,1]+T[0,1]T[2,0],T[0,0]T[2,2]+T[0,2]T[2,0],T[0,1]T[2,2]+T[0,2]T[2,1]],
1591	[2.T[1,0]T[2,0],2.T[1,1]T[2,1],2.T[1,2]T[2,2],T[1,0]T[2,1]+T[1,1]T[2,0],T[1,0]T[2,2]+T[1,2]T[2,0],T[1,1]T[2,2]+T[1,2]T[2,1]]
1592	]
1593	# Gnew = conMat * A:
1594	# T00*2a0 T01*2a1 T02*2a2 T00T01a3 T00T02a4 T01T02a5
1595	# T10*2a0 T11*2a1 T12*2a2 T10T11a3 T10T12a4 T11T12a5
1596	# T20*2a0 T21*2a1 T22*2a2 T20T21a3 T20T22a4 T21T22a5
1597	# 2T00T10a0 2T01T11a1 2T02T12a2 (T00T11 + T01T10)a3 (T00T12 + T02T10)a4 (T01T12 + T02T11)a5
1598	# 2T00T20a0 2T01T21a1 2T02T22a2 (T00T21 + T01T20)a3 (T00T22 + T02T20)a4 (T01T22 + T02T21)a5
1599	# 2T10T20a0 2T11T21a1 2T12T22a2 (T10T21 + T11T20)a3 (T10T22 + T12T20)a4 (T11T22 + T12T21)a5
1600	# Generated as symbolic code using:
1601	# import sym
1602	# A0, A1, A2, A3, A4, A5 = sym.symbols('A0, A1, A2, A3, A4, A5')
1603	# G = sym.Matrix([ [A0, A3/2., A4/2.], [A3/2., A1, A5/2.], [A4/2., A5/2., A2]])
1604	# transformation matrix
1605	# T00, T10, T20, T01, T11, T21, T02, T12, T22 = sym.symbols('T00, T10, T20, T01, T11, T21, T02, T12, T22')
1606	# Tr = sym.Matrix([ [T00, T10, T20], [T01, T11, T21], [T02, T12, T22],])
1607	# Gnew = (Tr.TG)Tr
1608
1609	#print('old A',G2lat.cell2A(oldPhase['General']['Cell'][1:7]))
1610	#print('new A',G2lat.cell2A(newPhase['General']['Cell'][1:7]))
1611
1612	#this is still incorrect for hex/trig/ortho/tetragonal --> monoclinic
1613
1614	# for iAnew,Asi in enumerate(['A0','A1','A2','A3','A4','A5']): # loop through A[i] for new cell
1615	# Nparm = str(npId) + '::' + Asi
1616	# if Nparm != SetUniqAj(npId,iAnew,nSGData):
1617	# continue # skip: Ai constrained from Aj or must be zero
1618	# multDict = {}
1619	# for iAorg in range(6):
1620	# cA = conMat[iAnew][iAorg] # coeff for A[i] in constraint matrix
1621	# if abs(cA) < 1.e-8: continue
1622	# parm = SetUniqAj(opId,iAorg,oSGData) # translate to unique A[i] in original cell
1623	# if not parm: continue # must be zero
1624	# # sum coeff
1625	# if parm in multDict:
1626	# multDict[parm] += cA
1627	# else:
1628	# multDict[parm] = cA
1629	# # any non-zero multipliers?
1630	# maxMult = 0
1631	# for i in multDict:
1632	# maxMult = max(maxMult,abs(multDict[i]))
1633	# if maxMult <= 0: # Nparm computes as zero; Fix this parameter
1634	# constraints['Phase'] += [[
1635	# [0.0,G2obj.G2VarObj(Nparm)],
1636	# None,None,'h']]
1637	# elif len(multDict) == 1: # create equivalence
1638	# key = list(multDict.keys())[0]
1639	# constraints['Phase'] += [[
1640	# [1.0,G2obj.G2VarObj(key)],
1641	# [multDict[key],G2obj.G2VarObj(Nparm)],
1642	# None,None,'e']]
1643	# else: # create constraint
1644	# constr = [[-1.0,G2obj.G2VarObj(Nparm)]]
1645	# for key in multDict:
1646	# constr += [[multDict[key],G2obj.G2VarObj(key)]]
1647	# constr += [0.0,None,'c']
1648	# constraints['Phase'] += [constr]
1649
1650	# constraints on HAP Scale, etc.
1651	for hId,hist in enumerate(UseList): #HAP - seems OK
1652	ohapkey = '%d:%d:'%(opId,hId)
1653	nhapkey = '%d:%d:'%(npId,hId)
1654	IndpCon = [1.0,G2obj.G2VarObj(ohapkey+'Scale')]
1655	DepCons = [detTrans,G2obj.G2VarObj(nhapkey+'Scale')]
1656	constraints['HAP'].append([DepCons,IndpCon,None,None,'e'])
1657	for name in ['Size;i','Mustrain;i']:
1658	IndpCon = [1.0,G2obj.G2VarObj(ohapkey+name)]
1659	DepCons = [1.0,G2obj.G2VarObj(nhapkey+name)]
1660	constraints['HAP'].append([IndpCon,DepCons,None,None,'e'])
1661
1662	################################################################################
1663	#### Rigid bodies
1664	################################################################################
1665	resRBsel = None
1666	def UpdateRigidBodies(G2frame,data):
1667	'''Called when Rigid bodies tree item is selected.
1668	Displays the rigid bodies in the data window
1669	'''
1670	if not data.get('RBIds') or not data:
1671	data.update({'Vector':{'AtInfo':{}},'Residue':{'AtInfo':{}},
1672	'RBIds':{'Vector':[],'Residue':[]}}) #empty/bad dict - fill it
1673
1674	global resList,resRBsel
1675	Indx = {}
1676	resList = []
1677	plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':30.,'viewDir':[0,0,1],}
1678
1679	G2frame.rbBook = G2G.GSNoteBook(parent=G2frame.dataWindow)
1680	G2frame.dataWindow.GetSizer().Add(G2frame.rbBook,1,wx.ALL\|wx.EXPAND)
1681	VectorRB = wx.ScrolledWindow(G2frame.rbBook)
1682	VectorRBDisplay = wx.Panel(VectorRB)
1683	G2frame.rbBook.AddPage(VectorRB,'Vector rigid bodies')
1684	ResidueRB = wx.ScrolledWindow(G2frame.rbBook)
1685	ResidueRBDisplay = wx.Panel(ResidueRB)
1686	G2frame.rbBook.AddPage(ResidueRB,'Residue rigid bodies')
1687
1688	def OnPageChanged(event):
1689	global resList
1690	resList = []
1691	if event: #page change event!
1692	page = event.GetSelection()
1693	else:
1694	page = G2frame.rbBook.GetSelection()
1695	G2frame.rbBook.ChangeSelection(page)
1696	text = G2frame.rbBook.GetPageText(page)
1697	if text == 'Vector rigid bodies':
1698	G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.VectorBodyMenu)
1699	G2frame.Bind(wx.EVT_MENU, AddVectorRB, id=G2G.wxID_VECTORBODYADD)
1700	G2frame.Bind(wx.EVT_MENU, ExtractPhaseRB, id=G2G.wxID_VECTORBODYIMP)
1701	G2frame.Bind(wx.EVT_MENU, AddVectTrans, id=G2G.wxID_VECTORBODYEXTD)
1702	G2frame.Bind(wx.EVT_MENU, SaveVectorRB, id=G2G.wxID_VECTORBODYSAV)
1703	G2frame.Bind(wx.EVT_MENU, ReadVectorRB, id=G2G.wxID_VECTORBODYRD)
1704	G2frame.Page = [page,'vrb']
1705	UpdateVectorRB()
1706	elif text == 'Residue rigid bodies':
1707	G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RigidBodyMenu)
1708	G2frame.Bind(wx.EVT_MENU, AddResidueRB, id=G2G.wxID_RIGIDBODYADD)
1709	G2frame.Bind(wx.EVT_MENU, ExtractPhaseRB, id=G2G.wxID_RIGIDBODYIMP)
1710	G2frame.Bind(wx.EVT_MENU, OnImportRigidBody, id=G2G.wxID_RIGIDBODYIMPORT)
1711	G2frame.Bind(wx.EVT_MENU, OnSaveRigidBody, id=G2G.wxID_RIGIDBODYSAVE)
1712	G2frame.Bind(wx.EVT_MENU, OnDefineTorsSeq, id=G2G.wxID_RESIDUETORSSEQ) #enable only if residue RBs exist?
1713	G2frame.Bind(wx.EVT_MENU, DumpVectorRB, id=G2G.wxID_RESBODYSAV)
1714	G2frame.Bind(wx.EVT_MENU, LoadVectorRB, id=G2G.wxID_RESBODYRD)
1715	G2frame.Page = [page,'rrb']
1716	UpdateResidueRB()
1717	else:
1718	G2gd.SetDataMenuBar(G2frame)
1719	#G2frame.Page = [page,'rrb']
1720
1721	def getMacroFile(macName):
1722	defDir = os.path.join(os.path.split(__file__)[0],'GSASIImacros')
1723	dlg = wx.FileDialog(G2frame,message='Choose '+macName+' rigid body macro file',
1724	defaultDir=defDir,defaultFile="",wildcard="GSAS-II macro file (.mac)\|.mac",
1725	style=wx.FD_OPEN \| wx.FD_CHANGE_DIR)
1726	try:
1727	if dlg.ShowModal() == wx.ID_OK:
1728	macfile = dlg.GetPath()
1729	macro = open(macfile,'Ur')
1730	head = macro.readline()
1731	if macName not in head:
1732	print (head)
1733	print ('** ERROR - wrong restraint macro file selected, try again **')
1734	macro = []
1735	else: # cancel was pressed
1736	macro = []
1737	finally:
1738	dlg.Destroy()
1739	return macro #advanced past 1st line
1740
1741	def getTextFile():
1742	dlg = wx.FileDialog(G2frame,'Choose rigid body text file', G2frame.LastGPXdir, '',
1743	"GSAS-II text file (.txt)\|.txt\|XYZ file (.xyz)\|.xyz\|"
1744	"Sybyl mol2 file (.mol2)\|.mol2\|PDB file (.pdb;.ent)\|.pdb;.ent",
1745	wx.FD_OPEN \| wx.FD_CHANGE_DIR)
1746	try:
1747	if dlg.ShowModal() == wx.ID_OK:
1748	txtfile = dlg.GetPath()
1749	ext = os.path.splitext(txtfile)[1]
1750	text = open(txtfile,'Ur')
1751	else: # cancel was pressed
1752	ext = ''
1753	text = []
1754	finally:
1755	dlg.Destroy()
1756	if 'ent' in ext:
1757	ext = '.pdb'
1758	return text,ext.lower()
1759
1760	def OnImportRigidBody(event):
1761	page = G2frame.rbBook.GetSelection()
1762	if 'Vector' in G2frame.rbBook.GetPageText(page):
1763	pass
1764	elif 'Residue' in G2frame.rbBook.GetPageText(page):
1765	ImportResidueRB()
1766
1767	def OnSaveRigidBody(event):
1768	page = G2frame.rbBook.GetSelection()
1769	if 'Vector' in G2frame.rbBook.GetPageText(page):
1770	pass
1771	elif 'Residue' in G2frame.rbBook.GetPageText(page):
1772	SaveResidueRB()
1773
1774	def DumpVectorRB(event):
1775	global resRBsel
1776	if resRBsel not in data['Residue']:
1777	return
1778	rbData = data['Residue'][resRBsel]
1779	pth = G2G.GetExportPath(G2frame)
1780	dlg = wx.FileDialog(G2frame, 'Choose file to save residue rigid body',
1781	pth, '', 'RRB files (.resbody)\|.resbody',
1782	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1783	try:
1784	if dlg.ShowModal() == wx.ID_OK:
1785	filename = dlg.GetPath()
1786	filename = os.path.splitext(filename)[0]+'.resbody' # set extension
1787	fp = open(filename,'w')
1788	fp.write('Name: '+rbData['RBname']+'\n')
1789	fp.write('atNames: ')
1790	for i in rbData['atNames']:
1791	fp.write(str(i)+" ")
1792	fp.write('\n')
1793	for item in rbData['rbSeq']:
1794	fp.write('rbSeq: ')
1795	fp.write('{:d} {:d} {:.1f}: '.format(*item[:3]))
1796	for num in item[3]:
1797	fp.write('{:d} '.format(num))
1798	fp.write('\n')
1799	for i,sym in enumerate(rbData['rbTypes']):
1800	fp.write("{:3s}".format(sym))
1801	fp.write('{:8.5f}{:9.5f}{:9.5f} '
1802	.format(*rbData['rbXYZ'][i]))
1803	fp.write('\n')
1804	fp.close()
1805	print ('Vector rigid body saved to: '+filename)
1806
1807	finally:
1808	dlg.Destroy()
1809
1810	def LoadVectorRB(event):
1811	AtInfo = data['Residue']['AtInfo']
1812	pth = G2G.GetExportPath(G2frame)
1813	dlg = wx.FileDialog(G2frame, 'Choose file to read vector rigid body',
1814	pth, '', 'RRB files (.resbody)\|.resbody',
1815	wx.FD_OPEN)
1816	try:
1817	if dlg.ShowModal() == wx.ID_OK:
1818	filename = dlg.GetPath()
1819	filename = os.path.splitext(filename)[0]+'.resbody' # set extension
1820	fp = open(filename,'r')
1821	l = fp.readline().strip()
1822	if 'Name' not in l:
1823	fp.close()
1824	G2frame.ErrorDialog('Read Error',
1825	'File '+filename+' does not start with Name\nFirst line ='
1826	+l+'\ninvalid file',parent=G2frame)
1827	return
1828	name = l.split(':')[1].strip()
1829	line = fp.readline().strip().split(':')[1].split()
1830	atNames = [i for i in line]
1831	types = []
1832	coords = []
1833	l = fp.readline().strip()
1834	rbSeq = []
1835	while 'rbSeq' in l:
1836	tag,vals,lst = l.split(':')
1837	seq = []
1838	for t,v in zip((int,int,float),vals.split()):
1839	seq.append(t(v))
1840	seq.append([])
1841	for num in lst.split():
1842	seq[-1].append(int(num))
1843	rbSeq.append(seq)
1844	l = fp.readline().strip()
1845	while l:
1846	nums = l.strip().split()
1847	types.append(nums.pop(0))
1848	t = types[-1]
1849	if t not in AtInfo:
1850	Info = G2elem.GetAtomInfo(t)
1851	AtInfo[t] = [Info['Drad'],Info['Color']]
1852	coords.append([float(nums.pop(0)) for j in range(3)])
1853	l = fp.readline().strip()
1854	fp.close()
1855	else:
1856	return
1857	finally:
1858	dlg.Destroy()
1859	coords = np.array(coords)
1860	rbid = ran.randint(0,sys.maxsize)
1861	data['Residue'][rbid] = {'RBname':name,
1862	'rbXYZ': coords,
1863	'rbRef':[0,1,2,False],
1864	'rbTypes':types, 'atNames':atNames,
1865	'useCount':0,
1866	'rbSeq':rbSeq, 'SelSeq':[0,0],}
1867	data['RBIds']['Residue'].append(rbid)
1868	UpdateResidueRB()
1869
1870	def AddVectorRB(event):
1871	'Create a new vector rigid body'
1872	AtInfo = data['Vector']['AtInfo']
1873	dlg = G2G.MultiIntegerDialog(G2frame,'New Rigid Body',['No. atoms','No. translations'],[1,1])
1874	if dlg.ShowModal() == wx.ID_OK:
1875	nAtoms,nTrans = dlg.GetValues()
1876	rbid = ran.randint(0,sys.maxsize)
1877	vecMag = [1.0 for i in range(nTrans)]
1878	vecRef = [False for i in range(nTrans)]
1879	vecVal = [np.zeros((nAtoms,3)) for j in range(nTrans)]
1880	rbTypes = ['C' for i in range(nAtoms)]
1881	Info = G2elem.GetAtomInfo('C')
1882	AtInfo['C'] = [Info['Drad'],Info['Color']]
1883	data['Vector'][rbid] = {'RBname':'UNKRB','VectMag':vecMag,'rbXYZ':np.zeros((nAtoms,3)),
1884	'rbRef':[0,1,2,False],'VectRef':vecRef,'rbTypes':rbTypes,'rbVect':vecVal,'useCount':0}
1885	data['RBIds']['Vector'].append(rbid)
1886	dlg.Destroy()
1887	UpdateVectorRB()
1888
1889	def ExtractPhaseRB(event):
1890	'Extract a rigid body from a file with a phase'
1891	def SetupDrawing(atmData):
1892	'''Add the dicts needed for G2plt.PlotStructure to work to the
1893	reader .Phase object
1894	'''
1895	generalData = atmData['General']
1896	generalData['BondRadii'] = []
1897
1898	G2phG.SetDrawingDefaults(atmData['Drawing'])
1899	atmData['Drawing'].update(
1900	{'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':150.,
1901	'viewDir':[0,0,1],'atomPtrs': [2, 1, 6, 17],
1902	})
1903	atmData['Drawing']['showRigidBodies'] = False
1904	generalData['Map'] = {'MapType':False, 'rho':[]}
1905	generalData['AtomTypes'] = []
1906	generalData['BondRadii'] = []
1907	generalData['AngleRadii'] = []
1908	generalData['vdWRadii'] = []
1909	generalData['Color'] = []
1910	generalData['Isotopes'] = {}
1911	generalData['Isotope'] = {}
1912	cx,ct,cs,cia = generalData['AtomPtrs']
1913	generalData['Mydir'] = G2frame.dirname
1914	for iat,atom in enumerate(atmData['Atoms']):
1915	atom[ct] = atom[ct].lower().capitalize() #force elem symbol to standard form
1916	if atom[ct] not in generalData['AtomTypes'] and atom[ct] != 'UNK':
1917	Info = G2elem.GetAtomInfo(atom[ct])
1918	if not Info:
1919	atom[ct] = 'UNK'
1920	continue
1921	atom[ct] = Info['Symbol'] # N.B. symbol might be changed by GetAtomInfo
1922	generalData['AtomTypes'].append(atom[ct])
1923	generalData['Z'] = Info['Z']
1924	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
1925	generalData['BondRadii'].append(Info['Drad'])
1926	generalData['AngleRadii'].append(Info['Arad'])
1927	generalData['vdWRadii'].append(Info['Vdrad'])
1928	if atom[ct] in generalData['Isotope']:
1929	if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]:
1930	isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
1931	generalData['Isotope'][atom[ct]] = isotope
1932	else:
1933	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
1934	if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]:
1935	isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
1936	generalData['Isotope'][atom[ct]] = isotope
1937	generalData['Color'].append(Info['Color'])
1938	if generalData['Type'] == 'magnetic':
1939	if len(landeg) < len(generalData['AtomTypes']):
1940	landeg.append(2.0)
1941	atmData['Drawing']['Atoms'] = []
1942	for atom in atmData['Atoms']:
1943	atmData['Drawing']['Atoms'].append(MakeDrawAtom(atmData,atom))
1944
1945	def onCancel(event,page=0):
1946	'complete or bail out from RB define, cleaning up'
1947	G2frame.rbBook.DeletePage(G2frame.rbBook.FindPage(pagename))
1948	G2frame.rbBook.SetSelection(page)
1949
1950	def Page1():
1951	'''Show the GUI for first stage of the rigid body with all atoms in
1952	phase in crystal coordinates. Select the atoms to go onto the
1953	next stage
1954	'''
1955	def ShowSelection(selections):
1956	'respond to change in atom selections'
1957	ct,cs = [1,8]
1958	generalData = rd.Phase['General']
1959	for i,atom in enumerate(rd.Phase['Drawing']['Atoms']):
1960	if i in selections:
1961	factor = 1
1962	else:
1963	factor = 2.5
1964	atNum = generalData['AtomTypes'].index(atom[ct])
1965	atom[cs] = list(np.array(generalData['Color'][atNum])//factor)
1966	draw(*drawArgs)
1967	def onPage1OK(event):
1968	'1st section has been completed, move onto next'
1969	G2frame.G2plotNB.Delete(rd.Phase['General']['Name'])
1970	GetCoords(atmsel)
1971	Page2()
1972
1973	SetupDrawing(rd.Phase) # add information to reader object to allow plotting
1974	atomlist = [atom[0] for atom in rd.Phase['Atoms']]
1975	atmsel = list(range(len(rd.Phase['Atoms'])))
1976	# broken -- # why no bonds?
1977	#for atm in rd.Phase['Drawing']['Atoms']:
1978	# atm[6] = 'balls & sticks'
1979
1980	draw,drawArgs = G2plt.PlotStructure(G2frame,rd.Phase,True)
1981	ShowSelection(atmsel)
1982
1983	if G2frame.rbBook.FindPage(pagename) is not None:
1984	G2frame.rbBook.DeletePage(G2frame.rbBook.FindPage(pagename))
1985
1986	RBImp = wx.ScrolledWindow(G2frame.rbBook)
1987	RBImpPnl = wx.Panel(RBImp)
1988	G2frame.rbBook.AddPage(RBImp,pagename)
1989	G2frame.rbBook.SetSelection(G2frame.rbBook.FindPage(pagename))
1990
1991	mainSizer = G2G.G2MultiChoiceWindow(RBImpPnl,
1992	'Select atoms to import',
1993	atomlist,atmsel,OnChange=ShowSelection)
1994
1995	# OK/Cancel buttons
1996	btnsizer = wx.StdDialogButtonSizer()
1997	OKbtn = wx.Button(RBImpPnl, wx.ID_OK, 'Continue')
1998	OKbtn.SetDefault()
1999	btnsizer.AddButton(OKbtn)
2000	OKbtn.Bind(wx.EVT_BUTTON,onPage1OK)
2001	btn = wx.Button(RBImpPnl, wx.ID_CANCEL)
2002	btn.Bind(wx.EVT_BUTTON,onCancel)
2003	btnsizer.AddButton(btn)
2004	btnsizer.Realize()
2005	mainSizer.Add(btnsizer,0,wx.ALIGN_CENTER,50)
2006
2007	RBImpPnl.SetSizer(mainSizer,True)
2008
2009	mainSizer.Layout()
2010	Size = mainSizer.GetMinSize()
2011	Size[0] += 40
2012	Size[1] = max(Size[1],G2frame.GetSize()[1]-200) + 20
2013	RBImpPnl.SetSize(Size)
2014	RBImp.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
2015	RBImp.Scroll(0,0)
2016
2017	def Page2():
2018	'''Show the GUI for the second stage, where selected atoms are
2019	now in Cartesian space, manipulate the axes and export selected
2020	atoms to a vector or residue rigid body.
2021	'''
2022	def UpdateDraw(event=None):
2023	'Called when info changes in grid, replots'
2024	UpdateVectorBody(rbData)
2025	DrawCallback()
2026
2027	def onSetAll(event):
2028	'Set all atoms as selected'
2029	for i in range(len(rd.Phase['RBselection'])):
2030	rd.Phase['RBselection'][i] = True
2031	grid.ForceRefresh()
2032	UpdateDraw()
2033
2034	def onToggle(event):
2035	'Toggles selection state for all atoms'
2036	grid.completeEdits()
2037	for i in range(len(rd.Phase['RBselection'])):
2038	rd.Phase['RBselection'][i] = not rd.Phase['RBselection'][i]
2039	grid.ForceRefresh()
2040	UpdateDraw()
2041
2042	def onSetOrigin(event):
2043	'Resets origin to midpoint between all selected atoms'
2044	grid.completeEdits()
2045	center = np.array([0.,0.,0.])
2046	count = 0
2047	for i in range(len(rd.Phase['RBselection'])):
2048	if rd.Phase['RBselection'][i]:
2049	count += 1
2050	center += rd.Phase['RBcoords'][i]
2051	if count:
2052	rd.Phase['RBcoords'] -= center/count
2053	grid.ForceRefresh()
2054	UpdateDraw()
2055
2056	def onSetX(event):
2057	grid.completeEdits()
2058	center = np.array([0.,0.,0.])
2059	count = 0
2060	for i in range(len(rd.Phase['RBselection'])):
2061	if rd.Phase['RBselection'][i]:
2062	count += 1
2063	center += rd.Phase['RBcoords'][i]
2064	if not count:
2065	return
2066	XP = center/count
2067	if np.sqrt(sum(XP**2)) < 0.1:
2068	G2G.G2MessageBox(G2frame,
2069	'The selected atom(s) are too close to the origin',
2070	'near origin')
2071	return
2072	XP /= np.sqrt(np.sum(XP**2))
2073	Z = np.array((0,0,1.))
2074	YP = np.cross(Z,XP)
2075	ZP = np.cross(XP,YP)
2076	trans = np.array((XP,YP,ZP))
2077	# update atoms in place
2078	rd.Phase['RBcoords'][:] = np.inner(trans,rd.Phase['RBcoords']).T
2079	grid.ForceRefresh()
2080	UpdateDraw()
2081
2082	def onSetPlane(event):
2083	'''Compute least-squares plane for selected atoms;
2084	move atoms so that LS plane aligned with x-y plane,
2085	with minimum required change to x
2086	'''
2087	grid.completeEdits()
2088	#X,Y,Z = rd.Phase['RBcoords'][rd.Phase['RBselection']].T
2089	XYZ = rd.Phase['RBcoords'][rd.Phase['RBselection']]
2090	Z = copy.copy(XYZ[:,2])
2091	if len(Z) < 3:
2092	G2G.G2MessageBox(G2frame,'A plane requires three or more atoms',
2093	'Need more atoms')
2094	return
2095	XY0 = copy.copy(XYZ)
2096	XY0[:,2] = 1
2097	# solve for ax + bx + z + c = 0 or equivalently ax + bx + c = -z
2098	try:
2099	(a,b,c), resd, rank, sing = nl.lstsq(XY0, -Z)
2100	except:
2101	G2G.G2MessageBox(G2frame,
2102	'Error computing plane; are atoms in a line?',
2103	'Computation error')
2104	return
2105	# new coordinate system is z' (zp, normal to plane = [a,b,1]),
2106	# y' = z' cross x (YP, = [0,1,-b])
2107	# x' = (z' cross x) cross z'
2108	# this puts XP as close as possible to X with XP & YP in plane
2109	ZP = np.array([a,b,1])
2110	ZP /= np.sqrt(np.sum(ZP**2))
2111	YP = np.array([0,1,-b])
2112	YP /= np.sqrt(np.sum(YP**2))
2113	XP = np.cross(YP,ZP)
2114	trans = np.array((XP,YP,ZP))
2115	# update atoms in place
2116	rd.Phase['RBcoords'][:] = np.inner(trans,rd.Phase['RBcoords']).T
2117	grid.ForceRefresh()
2118	UpdateDraw()
2119
2120	def onAddVector(event):
2121	'''Adds selected atoms as a new vector rigid body.
2122	Closes out the importer tab when done.
2123	'''
2124	grid.completeEdits()
2125	rb = MakeVectorBody(os.path.split(filename)[1])
2126	UpdateVectorBody(rb,True)
2127	if len(rb['rbTypes']) < 3: return # must have at least 3 atoms
2128	rbid = ran.randint(0,sys.maxsize)
2129	data['Vector'][rbid] = rb
2130	data['RBIds']['Vector'].append(rbid)
2131	AtInfo = data['Vector']['AtInfo']
2132	for t in rb['rbTypes']:
2133	if t in data['Vector']['AtInfo']: continue
2134	Info = G2elem.GetAtomInfo(t)
2135	data['Vector']['AtInfo'][t] = [Info['Drad'],Info['Color']]
2136	G2frame.G2plotNB.Delete('Rigid body')
2137	onCancel(event,0)
2138
2139	def onAddResidue(event):
2140	'''Adds selected atoms as a new residue rigid body.
2141	Closes out the importer tab when done.
2142	'''
2143	grid.completeEdits()
2144	name = os.path.split(filename)[1]
2145	rbXYZ = []
2146	rbTypes = []
2147	atNames = []
2148	for i in rd.Phase['RBindex']:
2149	if rd.Phase['RBselection'][i]:
2150	rbXYZ.append(rd.Phase['RBcoords'][i])
2151	rbTypes.append(rd.Phase['RBtypes'][i])
2152	atNames.append(rd.Phase['RBlbls'][i])
2153	if len(rbTypes) < 3: return # must have at least 3 atoms
2154	rbXYZ = np.array(rbXYZ)
2155	rbid = ran.randint(0,sys.maxsize)
2156	data['Residue'][rbid] = {'RBname':name,'rbXYZ':rbXYZ,
2157	'rbTypes':rbTypes,'atNames':atNames,'rbRef':[0,1,2,False],
2158	'rbSeq':[],'SelSeq':[0,0],'useCount':0}
2159	data['RBIds']['Residue'].append(rbid)
2160	AtInfo = data['Residue']['AtInfo']
2161	for t in rbTypes:
2162	if t in data['Residue']['AtInfo']: continue
2163	Info = G2elem.GetAtomInfo(t)
2164	data['Residue']['AtInfo'][t] = [Info['Drad'],Info['Color']]
2165
2166	print ('Rigid body added')
2167	G2frame.G2plotNB.Delete('Rigid body')
2168	onCancel(event,1)
2169
2170	if G2frame.rbBook.FindPage(pagename) is not None:
2171	G2frame.rbBook.DeletePage(G2frame.rbBook.FindPage(pagename))
2172	RBImp = wx.ScrolledWindow(G2frame.rbBook)
2173	RBImpPnl = wx.Panel(RBImp)
2174	G2frame.rbBook.AddPage(RBImp,pagename)
2175	G2frame.rbBook.SetSelection(G2frame.rbBook.FindPage(pagename))
2176	generalData = rd.Phase['General']
2177	AtInfo = {}
2178	ct = 1
2179	for t in rd.Phase['RBtypes']:
2180	if t in AtInfo: continue
2181	Info = G2elem.GetAtomInfo(t)
2182	AtInfo[t] = [Info['Drad'],Info['Color']]
2183	plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':30.,'viewDir':[0,0,1],}
2184
2185	rd.Phase['RBindex'] = list(range(len(rd.Phase['RBtypes'])))
2186	rd.Phase['RBselection'] = len(rd.Phase['RBtypes']) * [True]
2187	rbData = MakeVectorBody()
2188	DrawCallback = G2plt.PlotRigidBody(G2frame,'Vector',
2189	AtInfo,rbData,plotDefaults)
2190
2191	mainSizer = wx.BoxSizer(wx.HORIZONTAL)
2192	gridSizer = wx.BoxSizer(wx.VERTICAL)
2193	grid = DragableRBGrid(RBImpPnl,rd.Phase,UpdateDraw)
2194	gridSizer.Add(grid)
2195	gridSizer.Add(
2196	wx.StaticText(RBImpPnl,wx.ID_ANY,'Reorder atoms by dragging'),
2197	0,wx.ALL)
2198	mainSizer.Add(gridSizer)
2199	mainSizer.Add((5,5))
2200	btnSizer = wx.BoxSizer(wx.VERTICAL)
2201	btn = wx.Button(RBImpPnl, wx.ID_OK, 'Set All')
2202	btn.Bind(wx.EVT_BUTTON,onSetAll)
2203	btnSizer.Add(btn,0,wx.ALIGN_CENTER)
2204	btn = wx.Button(RBImpPnl, wx.ID_OK, 'Toggle')
2205	btn.Bind(wx.EVT_BUTTON,onToggle)
2206	btnSizer.Add(btn,0,wx.ALIGN_CENTER)
2207	btnSizer.Add((-1,15))
2208	btnSizer.Add(
2209	wx.StaticText(RBImpPnl,wx.ID_ANY,'Reorient using selected\natoms...'),
2210	0,wx.ALL)
2211	btnSizer.Add((-1,5))
2212	btn = wx.Button(RBImpPnl, wx.ID_OK, 'Set origin')
2213	btn.Bind(wx.EVT_BUTTON,onSetOrigin)
2214	btnSizer.Add(btn,0,wx.ALIGN_CENTER)
2215	btn = wx.Button(RBImpPnl, wx.ID_OK, 'Place in xy plane')
2216	btn.Bind(wx.EVT_BUTTON,onSetPlane)
2217	btnSizer.Add(btn,0,wx.ALIGN_CENTER)
2218	btn = wx.Button(RBImpPnl, wx.ID_OK, 'Define selection as X')
2219	btn.Bind(wx.EVT_BUTTON,onSetX)
2220	btnSizer.Add(btn,0,wx.ALIGN_CENTER)
2221	btnSizer.Add((-1,15))
2222	btnSizer.Add(
2223	wx.StaticText(RBImpPnl,wx.ID_ANY,'Use selected atoms to\ncreate...'),
2224	0,wx.ALL)
2225	btnSizer.Add((-1,5))
2226	btn = wx.Button(RBImpPnl, wx.ID_OK, 'a Vector Body')
2227	btn.Bind(wx.EVT_BUTTON,onAddVector)
2228	btnSizer.Add(btn,0,wx.ALIGN_CENTER)
2229	btn = wx.Button(RBImpPnl, wx.ID_OK, 'a Residue Body')
2230	btn.Bind(wx.EVT_BUTTON,onAddResidue)
2231	btnSizer.Add(btn,0,wx.ALIGN_CENTER)
2232	btn = wx.Button(RBImpPnl, wx.ID_CANCEL)
2233	btn.Bind(wx.EVT_BUTTON,onCancel)
2234	btnSizer.Add((-1,10))
2235	btnSizer.Add(btn,0,wx.ALIGN_CENTER)
2236
2237	mainSizer.Add(btnSizer)
2238	RBImpPnl.SetSizer(mainSizer,True)
2239	mainSizer.Layout()
2240	Size = mainSizer.GetMinSize()
2241	Size[0] += 40
2242	Size[1] = max(Size[1],G2frame.GetSize()[1]-200) + 20
2243	RBImpPnl.SetSize(Size)
2244	RBImp.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
2245	RBImp.Scroll(0,0)
2246
2247	def GetCoords(atmsel):
2248	'''Create orthogonal coordinates for selected atoms.
2249	Place the origin at the center of the body
2250	'''
2251	atms = rd.Phase['Atoms']
2252	cell = rd.Phase['General']['Cell'][1:7]
2253	Amat,Bmat = G2lat.cell2AB(cell)
2254	rd.Phase['RBcoords'] = np.array([np.inner(Amat,atms[i][3:6]) for i in atmsel])
2255	rd.Phase['RBcoords'] -= rd.Phase['RBcoords'].mean(axis=0) # origin to middle
2256	rd.Phase['RBtypes'] = [atms[i][1] for i in atmsel]
2257	rd.Phase['RBlbls'] = [atms[i][0] for i in atmsel]
2258
2259	def UpdateVectorBody(rb,useSelection=False):
2260	'''Put the atoms in order to pass for plotting or for storage as
2261	a vector rigid body.
2262
2263	:param dict rb: rigid body contents created in :func:`MakeVectorBody`
2264	:param bool useSelection: True if the rd.Phase['RBselection']
2265	values will be used to select which atoms are included in the
2266	rigid body. If False (default) they are included in rb
2267	and are used for plotting.
2268	'''
2269	coordlist = []
2270	typeslist = []
2271	sellist = []
2272	for i in rd.Phase['RBindex']:
2273	use = True
2274	if useSelection and not rd.Phase['RBselection'][i]: use = False
2275	if use:
2276	coordlist.append(rd.Phase['RBcoords'][i])
2277	typeslist.append(rd.Phase['RBtypes'][i])
2278	sellist.append(rd.Phase['RBselection'][i])
2279	coordlist = np.array(coordlist)
2280	rb['rbXYZ'] = coordlist
2281	rb['rbVect'] = [coordlist]
2282	rb['rbTypes'] = typeslist
2283	if not useSelection:
2284	rb['Selection'] = sellist
2285	elif 'Selection' in rb:
2286	del rb['Selection']
2287
2288	def MakeVectorBody(name=''):
2289	'''Make the basic vector rigid body dict (w/o coordinates) used for
2290	export and for plotting
2291	'''
2292	nTrans = 1
2293	vecMag = [1.0]
2294	vecRef = [False]
2295	rb = {'RBname':name,'VectMag':vecMag,
2296	'rbRef':[0,1,2,False],'VectRef':vecRef,
2297	'useCount':0}
2298	UpdateVectorBody(rb)
2299	return rb
2300
2301	# get importer type and a phase file of that type
2302	G2sc.LoadG2fil()
2303	choices = [rd.formatName for rd in G2sc.Readers['Phase']]
2304	dlg = G2G.G2SingleChoiceDialog(G2frame,'Select the format of the file',
2305	'select format',choices)
2306	try:
2307	if dlg.ShowModal() == wx.ID_OK:
2308	col = dlg.GetSelection()
2309	else:
2310	col = None
2311	finally:
2312	dlg.Destroy()
2313	reader = G2sc.Readers['Phase'][col]
2314
2315	choices = reader.formatName + " file ("
2316	w = ""
2317	for extn in reader.extensionlist:
2318	if w != "": w += ";"
2319	w += "*" + extn
2320	choices += w + ")\|" + w
2321	#choices += "\|zip archive (.zip)\|*.zip"
2322	if not reader.strictExtension:
2323	choices += "\|any file (.)\|."
2324	typ = '( type '+reader.formatName+')'
2325	filelist = G2G.GetImportFile(G2frame,
2326	message="Choose phase input file"+typ,
2327	defaultFile="",wildcard=choices,style=wx.FD_OPEN)
2328	if len(filelist) != 1: return
2329
2330	# read in the phase file
2331	filename = filelist[0]
2332	rd = reader
2333	with open(filename, 'Ur') as fp:
2334	rd.ReInitialize()
2335	rd.errors = ""
2336	if not rd.ContentsValidator(filename): # Report error
2337	G2fil.G2Print("Warning: File {} has a validation error".format(filename))
2338	return
2339	if len(rd.selections) > 1:
2340	print("File {} has {} phases. This is unexpected."
2341	.format(filename,len(rd.selections)))
2342	return
2343
2344	rd.objname = os.path.basename(filename)
2345	try:
2346	flag = rd.Reader(filename)
2347	except:
2348	G2fil.G2Print("Warning: read of file {} failed".format(filename))
2349	return
2350
2351	pagename = 'Rigid body importer'
2352	Page1()
2353	return
2354
2355	def AddVectTrans(event):
2356	'Add a translation to an existing vector rigid body'
2357	choices = []
2358	rbIdlist = []
2359	for rbid in data['RBIds']['Vector']:
2360	if rbid != 'AtInfo':
2361	rbIdlist.append(rbid)
2362	choices.append(data['Vector'][rbid]['RBname'])
2363	if len(choices) == 0:
2364	G2G.G2MessageBox(G2frame,'No Vector Rigid Bodies found',
2365	'No VR Bodies')
2366	return
2367	elif len(choices) == 1:
2368	rbid = rbIdlist[0]
2369	else:
2370	dlg = G2G.G2SingleChoiceDialog(G2frame,'Select the rigid body to save',
2371	'select format',choices)
2372	try:
2373	if dlg.ShowModal() == wx.ID_OK:
2374	rbid = rbIdlist[dlg.GetSelection()]
2375	else:
2376	return
2377	finally:
2378	dlg.Destroy()
2379	data['Vector'][rbid]['VectMag'] += [1.0]
2380	data['Vector'][rbid]['VectRef'] += [False]
2381	nAtoms = len(data['Vector'][rbid]['rbXYZ'])
2382	data['Vector'][rbid]['rbVect'] += [np.zeros((nAtoms,3))]
2383	UpdateVectorRB()
2384
2385	def SaveVectorRB(event):
2386	choices = []
2387	rbIdlist = []
2388	for rbid in data['RBIds']['Vector']:
2389	if rbid != 'AtInfo':
2390	rbIdlist.append(rbid)
2391	choices.append(data['Vector'][rbid]['RBname'])
2392	if len(choices) == 0:
2393	G2G.G2MessageBox(G2frame,'No Vector Rigid Bodies found',
2394	'No VR Bodies')
2395	return
2396	elif len(choices) == 1:
2397	rbid = rbIdlist[0]
2398	else:
2399	dlg = G2G.G2SingleChoiceDialog(G2frame,'Select the rigid body to save',
2400	'select format',choices)
2401	try:
2402	if dlg.ShowModal() == wx.ID_OK:
2403	rbid = rbIdlist[dlg.GetSelection()]
2404	else:
2405	return
2406	finally:
2407	dlg.Destroy()
2408
2409	pth = G2G.GetExportPath(G2frame)
2410	dlg = wx.FileDialog(G2frame, 'Choose file to save vector rigid body',
2411	pth, '', 'VRB files (.vecbody)\|.vecbody',
2412	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2413	try:
2414	if dlg.ShowModal() == wx.ID_OK:
2415	filename = dlg.GetPath()
2416	filename = os.path.splitext(filename)[0]+'.vecbody' # set extension
2417	fp = open(filename,'w')
2418	fp.write('Name: '+data['Vector'][rbid]['RBname']+'\n')
2419	fp.write('Trans: ')
2420	for i in data['Vector'][rbid]['VectMag']:
2421	fp.write(str(i)+" ")
2422	fp.write('\n')
2423	ntrans = len(data['Vector'][rbid]['VectMag'])
2424	for i,sym in enumerate(data['Vector'][rbid]['rbTypes']):
2425	fp.write("{:3s}".format(sym))
2426	for j in range(ntrans):
2427	fp.write('{:8.5f}{:9.5f}{:9.5f} '
2428	.format(*data['Vector'][rbid]['rbVect'][j][i]))
2429	fp.write('\n')
2430	fp.close()
2431	print ('Vector rigid body saved to: '+filename)
2432	finally:
2433	dlg.Destroy()
2434
2435	def ReadVectorRB(event):
2436	AtInfo = data['Vector']['AtInfo']
2437	pth = G2G.GetExportPath(G2frame)
2438	dlg = wx.FileDialog(G2frame, 'Choose file to read vector rigid body',
2439	pth, '', 'VRB files (.vecbody)\|.vecbody',
2440	wx.FD_OPEN)
2441	try:
2442	if dlg.ShowModal() == wx.ID_OK:
2443	filename = dlg.GetPath()
2444	filename = os.path.splitext(filename)[0]+'.vecbody' # set extension
2445	fp = open(filename,'r')
2446	l = fp.readline().strip()
2447	if 'Name' not in l:
2448	fp.close()
2449	G2frame.ErrorDialog('Read Error',
2450	'File '+filename+' does not start with Name\nFirst line ='
2451	+l+'\ninvalid file',parent=G2frame)
2452	return
2453	name = l.split(':')[1].strip()
2454	trans = fp.readline().strip().split(':')[1].split()
2455	vecMag = [float(i) for i in trans]
2456	ntrans = len(trans)
2457	vecs = [[] for i in range(ntrans)]
2458	types = []
2459	l = fp.readline().strip()
2460	while l:
2461	nums = l.strip().split()
2462	types.append(nums.pop(0))
2463	t = types[-1]
2464	if t not in AtInfo:
2465	Info = G2elem.GetAtomInfo(t)
2466	AtInfo[t] = [Info['Drad'],Info['Color']]
2467	for i in range(ntrans):
2468	vecs[i].append([float(nums.pop(0)) for j in range(3)])
2469	l = fp.readline().strip()
2470	fp.close()
2471	else:
2472	return
2473	finally:
2474	dlg.Destroy()
2475	natoms = len(types)
2476	vecs = [np.array(vecs[i]) for i in range(ntrans)]
2477	rbid = ran.randint(0,sys.maxsize)
2478	data['Vector'][rbid] = {'RBname':name,'VectMag':vecMag,
2479	'rbXYZ':np.zeros((natoms,3)),
2480	'rbRef':[0,1,2,False],'VectRef':ntrans*[False],
2481	'rbTypes':types,
2482	'rbVect':vecs,'useCount':0}
2483	data['RBIds']['Vector'].append(rbid)
2484	UpdateVectorRB()
2485
2486	def AddResidueRB(event):
2487	global resRBsel
2488	AtInfo = data['Residue']['AtInfo']
2489	macro = getMacroFile('rigid body')
2490	if not macro:
2491	return
2492	macStr = macro.readline()
2493	while macStr:
2494	items = macStr.split()
2495	if 'I' == items[0]:
2496	resRBsel = ran.randint(0,sys.maxsize)
2497	rbName = items[1]
2498	rbTypes = []
2499	rbXYZ = []
2500	rbSeq = []
2501	atNames = []
2502	nAtms,nSeq,nOrig,mRef,nRef = [int(items[i]) for i in [2,3,4,5,6]]
2503	for iAtm in range(nAtms):
2504	macStr = macro.readline().split()
2505	atName = macStr[0]
2506	atType = macStr[1]
2507	atNames.append(atName)
2508	rbXYZ.append([float(macStr[i]) for i in [2,3,4]])
2509	rbTypes.append(atType)
2510	if atType not in AtInfo:
2511	Info = G2elem.GetAtomInfo(atType)
2512	AtInfo[atType] = [Info['Drad'],Info['Color']]
2513	rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[nOrig-1])
2514	for iSeq in range(nSeq):
2515	macStr = macro.readline().split()
2516	mSeq = int(macStr[0])
2517	for jSeq in range(mSeq):
2518	macStr = macro.readline().split()
2519	iBeg = int(macStr[0])-1
2520	iFin = int(macStr[1])-1
2521	angle = 0.0
2522	nMove = int(macStr[2])
2523	iMove = [int(macStr[i])-1 for i in range(3,nMove+3)]
2524	rbSeq.append([iBeg,iFin,angle,iMove])
2525	data['Residue'][resRBsel] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbTypes,
2526	'atNames':atNames,'rbRef':[nOrig-1,mRef-1,nRef-1,True],'rbSeq':rbSeq,
2527	'SelSeq':[0,0],'useCount':0}
2528	data['RBIds']['Residue'].append(resRBsel)
2529	print ('Rigid body '+rbName+' added')
2530	macStr = macro.readline()
2531	macro.close()
2532	UpdateResidueRB()
2533
2534	def ImportResidueRB():
2535	global resRBsel
2536	AtInfo = data['Residue']['AtInfo']
2537	text,ext = getTextFile()
2538	if not text:
2539	return
2540	resRBsel = ran.randint(0,sys.maxsize)
2541	rbTypes = []
2542	rbXYZ = []
2543	atNames = []
2544	txtStr = text.readline()
2545	if 'xyz' in ext:
2546	txtStr = text.readline()
2547	txtStr = text.readline()
2548	elif 'mol2' in ext:
2549	while 'ATOM' not in txtStr:
2550	txtStr = text.readline()
2551	txtStr = text.readline()
2552	elif 'pdb' in ext:
2553	while 'ATOM' not in txtStr[:6] and 'HETATM' not in txtStr[:6]:
2554	txtStr = text.readline()
2555	items = txtStr.split()
2556	nat = 1
2557	while len(items):
2558	if 'txt' in ext:
2559	atName = items[0]
2560	atType = items[1]
2561	rbXYZ.append([float(items[i]) for i in [2,3,4]])
2562	elif 'xyz' in ext:
2563	atType = items[0]
2564	rbXYZ.append([float(items[i]) for i in [1,2,3]])
2565	atName = '%s%d'%(atType,nat)
2566	elif 'mol2' in ext:
2567	atType = items[1]
2568	atName = items[1]+items[0]
2569	rbXYZ.append([float(items[i]) for i in [2,3,4]])
2570	elif 'pdb' in ext:
2571	atType = items[-1]
2572	if not items[2][-1].isnumeric():
2573	atName = '%s%d'%(items[2],nat)
2574	else:
2575	atName = '5s'%items[2]
2576	xyz = txtStr[30:55].split()
2577	rbXYZ.append([float(x) for x in xyz])
2578	atNames.append(atName)
2579	rbTypes.append(atType)
2580	if atType not in AtInfo:
2581	Info = G2elem.GetAtomInfo(atType)
2582	AtInfo[atType] = [Info['Drad'],Info['Color']]
2583	txtStr = text.readline()
2584	if 'mol2' in ext and 'BOND' in txtStr:
2585	break
2586	if 'pdb' in ext and ('ATOM' not in txtStr[:6] and 'HETATM' not in txtStr[:6]):
2587	break
2588	items = txtStr.split()
2589	nat += 1
2590	if len(atNames) < 3:
2591	G2G.G2MessageBox(G2frame,'Not enough atoms in rigid body; must be 3 or more')
2592	else:
2593	rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[0])
2594	Xxyz = rbXYZ[1]
2595	X = Xxyz/np.sqrt(np.sum(Xxyz**2))
2596	Yxyz = rbXYZ[2]
2597	Y = Yxyz/np.sqrt(np.sum(Yxyz**2))
2598	Mat = G2mth.getRBTransMat(X,Y)
2599	rbXYZ = np.inner(Mat,rbXYZ).T
2600	data['Residue'][resRBsel] = {'RBname':'UNKRB','rbXYZ':rbXYZ,'rbTypes':rbTypes,
2601	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
2602	data['RBIds']['Residue'].append(resRBsel)
2603	print ('Rigid body UNKRB added')
2604	text.close()
2605	UpdateResidueRB()
2606
2607	def SaveResidueRB():
2608	global resRBsel
2609	pth = G2G.GetExportPath(G2frame)
2610	dlg = wx.FileDialog(G2frame, 'Choose PDB file for Atom XYZ', pth, '',
2611	'PDB files (.pdb)\|.pdb',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2612	try:
2613	if dlg.ShowModal() == wx.ID_OK:
2614	filename = dlg.GetPath()
2615	filename = os.path.splitext(filename)[0]+'.pdb' # make extension .pdb
2616	File = open(filename,'w')
2617	rbData = data['Residue'][resRBsel]
2618	for iat,xyz in enumerate(rbData['rbXYZ']):
2619	File.write('ATOM %6d %-4s%3s 1 %8.3f%8.3f%8.3f 1.00 0.00 %2s\n'%(
2620	iat,rbData['atNames'][iat],rbData['RBname'][:3],xyz[0],xyz[1],xyz[2],rbData['rbTypes'][iat]))
2621	File.close()
2622	print ('Atom XYZ saved to: '+filename)
2623	finally:
2624	dlg.Destroy()
2625
2626
2627	def FindNeighbors(Orig,XYZ,atTypes,atNames,AtInfo):
2628	Radii = []
2629	for Atype in atTypes:
2630	Radii.append(AtInfo[Atype][0])
2631	Radii = np.array(Radii)
2632	Neigh = []
2633	Dx = XYZ-XYZ[Orig]
2634	dist = np.sqrt(np.sum(Dx**2,axis=1))
2635	sumR = Radii[Orig]+Radii
2636	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
2637	for j in IndB[0]:
2638	if j != Orig and atTypes[j] != 'H':
2639	Neigh.append(atNames[j])
2640	return Neigh
2641
2642	def FindAllNeighbors(XYZ,atTypes,atNames,AtInfo):
2643	NeighDict = {}
2644	for iat,xyz in enumerate(atNames):
2645	NeighDict[atNames[iat]] = FindNeighbors(iat,XYZ,atTypes,atNames,AtInfo)
2646	return NeighDict
2647
2648	def FindRiding(Orig,Pivot,NeighDict):
2649	riding = [Orig,Pivot]
2650	iAdd = 1
2651	new = True
2652	while new:
2653	newAtms = NeighDict[riding[iAdd]]
2654	for At in newAtms:
2655	new = False
2656	if At not in riding:
2657	riding.append(At)
2658	new = True
2659	iAdd += 1
2660	if iAdd < len(riding):
2661	new = True
2662	return riding[2:]
2663
2664	def OnDefineTorsSeq(event):
2665	global resRBsel
2666	rbData = data['Residue'][resRBsel]
2667	if not len(rbData):
2668	return
2669	atNames = rbData['atNames']
2670	AtInfo = data['Residue']['AtInfo']
2671	atTypes = rbData['rbTypes']
2672	XYZ = rbData['rbXYZ']
2673	neighDict = FindAllNeighbors(XYZ,atTypes,atNames,AtInfo)
2674	TargList = []
2675	dlg = wx.SingleChoiceDialog(G2frame,'Select origin atom for torsion sequence','Origin atom',rbData['atNames'])
2676	if dlg.ShowModal() == wx.ID_OK:
2677	Orig = dlg.GetSelection()
2678	TargList = neighDict[atNames[Orig]]
2679	dlg.Destroy()
2680	if not len(TargList):
2681	return
2682	dlg = wx.SingleChoiceDialog(G2frame,'Select pivot atom for torsion sequence','Pivot atom',TargList)
2683	if dlg.ShowModal() == wx.ID_OK:
2684	Piv = atNames.index(TargList[dlg.GetSelection()])
2685	riding = FindRiding(atNames[Orig],atNames[Piv],neighDict)
2686	Riding = []
2687	for atm in riding:
2688	Riding.append(atNames.index(atm))
2689	rbData['rbSeq'].append([Orig,Piv,0.0,Riding])
2690	dlg.Destroy()
2691	UpdateResidueRB()
2692
2693	def UpdateVectorRB(Scroll=0):
2694	AtInfo = data['Vector']['AtInfo']
2695	refChoice = {}
2696	if 'DELETED' in str(G2frame.GetStatusBar()): #seems to be no other way to do this (wx bug)
2697	if GSASIIpath.GetConfigValue('debug'):
2698	print ('DBG_wx error: Rigid Body/Status not cleanly deleted after Refine')
2699	return
2700	SetStatusLine(' You may use e.g. "c60" or "s60" for a vector entry')
2701	def rbNameSizer(rbid,rbData):
2702
2703	def OnRBName(event):
2704	event.Skip()
2705	Obj = event.GetEventObject()
2706	rbData['RBname'] = Obj.GetValue()
2707
2708	def OnDelRB(event):
2709	Obj = event.GetEventObject()
2710	rbid = Indx[Obj.GetId()]
2711	if rbid in data['Vector']:
2712	del data['Vector'][rbid]
2713	data['RBIds']['Vector'].remove(rbid)
2714	rbData['useCount'] -= 1
2715	wx.CallAfter(UpdateVectorRB)
2716	def OnPlotRB(event):
2717	Obj = event.GetEventObject()
2718	G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,rbData,plotDefaults)
2719
2720	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
2721	nameSizer.Add(wx.StaticText(VectorRBDisplay,-1,'Rigid body name: '),
2722	0,wx.ALIGN_CENTER_VERTICAL)
2723	RBname = wx.TextCtrl(VectorRBDisplay,-1,rbData['RBname'])
2724	Indx[RBname.GetId()] = rbid
2725	RBname.Bind(wx.EVT_TEXT_ENTER,OnRBName)
2726	RBname.Bind(wx.EVT_KILL_FOCUS,OnRBName)
2727	nameSizer.Add(RBname,0,wx.ALIGN_CENTER_VERTICAL)
2728	nameSizer.Add((5,0),)
2729	plotRB = wx.Button(VectorRBDisplay,wx.ID_ANY,'Plot',
2730	style=wx.BU_EXACTFIT)
2731	plotRB.Bind(wx.EVT_BUTTON, OnPlotRB)
2732	Indx[plotRB.GetId()] = rbid
2733	nameSizer.Add(plotRB,0,wx.ALIGN_CENTER_VERTICAL)
2734	nameSizer.Add((5,0),)
2735	if not rbData['useCount']:
2736	delRB = wx.Button(VectorRBDisplay,wx.ID_ANY,"Delete",
2737	style=wx.BU_EXACTFIT)
2738	delRB.Bind(wx.EVT_BUTTON, OnDelRB)
2739	Indx[delRB.GetId()] = rbid
2740	nameSizer.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
2741	return nameSizer
2742
2743	def rbRefAtmSizer(rbid,rbData):
2744
2745	def OnRefSel(event):
2746	Obj = event.GetEventObject()
2747	iref = Indx[Obj.GetId()]
2748	sel = Obj.GetValue()
2749	rbData['rbRef'][iref] = atNames.index(sel)
2750	FillRefChoice(rbid,rbData)
2751
2752	refAtmSizer = wx.BoxSizer(wx.HORIZONTAL)
2753	atNames = [name+str(i) for i,name in enumerate(rbData['rbTypes'])]
2754	rbRef = rbData.get('rbRef',[0,1,2,False])
2755	rbData['rbRef'] = rbRef
2756	if rbData['useCount']:
2757	refAtmSizer.Add(wx.StaticText(VectorRBDisplay,-1,
2758	'Orientation reference atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \
2759	atNames[rbRef[1]],atNames[rbRef[2]])),0)
2760	else:
2761	refAtmSizer.Add(wx.StaticText(VectorRBDisplay,-1,
2762	'Orientation reference atoms A-B-C: '),0,wx.ALIGN_CENTER_VERTICAL)
2763	for i in range(3):
2764	choices = [atNames[j] for j in refChoice[rbid][i]]
2765	refSel = wx.ComboBox(VectorRBDisplay,-1,value='',
2766	choices=choices,style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2767	refSel.SetValue(atNames[rbRef[i]])
2768	refSel.Bind(wx.EVT_COMBOBOX, OnRefSel)
2769	Indx[refSel.GetId()] = i
2770	refAtmSizer.Add(refSel,0,wx.ALIGN_CENTER_VERTICAL)
2771	return refAtmSizer
2772
2773	def rbVectMag(rbid,imag,rbData):
2774
2775	def OnRBVectorMag(event):
2776	event.Skip()
2777	Obj = event.GetEventObject()
2778	rbid,imag = Indx[Obj.GetId()]
2779	try:
2780	val = float(Obj.GetValue())
2781	if val <= 0.:
2782	raise ValueError
2783	rbData['VectMag'][imag] = val
2784	except ValueError:
2785	pass
2786	Obj.SetValue('%8.4f'%(val))
2787	wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
2788	G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,data['Vector'][rbid],plotDefaults)
2789
2790	def OnRBVectorRef(event):
2791	Obj = event.GetEventObject()
2792	rbid,imag = Indx[Obj.GetId()]
2793	rbData['VectRef'][imag] = Obj.GetValue()
2794
2795	magSizer = wx.BoxSizer(wx.HORIZONTAL)
2796	magSizer.Add(wx.StaticText(VectorRBDisplay,-1,'Translation magnitude: '),
2797	0,wx.ALIGN_CENTER_VERTICAL)
2798	magValue = wx.TextCtrl(VectorRBDisplay,-1,'%8.4f'%(rbData['VectMag'][imag]))
2799	Indx[magValue.GetId()] = [rbid,imag]
2800	magValue.Bind(wx.EVT_TEXT_ENTER,OnRBVectorMag)
2801	magValue.Bind(wx.EVT_KILL_FOCUS,OnRBVectorMag)
2802	magSizer.Add(magValue,0,wx.ALIGN_CENTER_VERTICAL)
2803	magSizer.Add((5,0),)
2804	magref = wx.CheckBox(VectorRBDisplay,-1,label=' Refine?')
2805	magref.SetValue(rbData['VectRef'][imag])
2806	magref.Bind(wx.EVT_CHECKBOX,OnRBVectorRef)
2807	Indx[magref.GetId()] = [rbid,imag]
2808	magSizer.Add(magref,0,wx.ALIGN_CENTER_VERTICAL)
2809	return magSizer
2810
2811	def rbVectors(rbid,imag,mag,XYZ,rbData):
2812
2813	def TypeSelect(event):
2814	AtInfo = data['Vector']['AtInfo']
2815	r,c = event.GetRow(),event.GetCol()
2816	if vecGrid.GetColLabelValue(c) == 'Type':
2817	PE = G2elemGUI.PickElement(G2frame,oneOnly=True)
2818	if PE.ShowModal() == wx.ID_OK:
2819	if PE.Elem != 'None':
2820	El = PE.Elem.strip().lower().capitalize()
2821	if El not in AtInfo:
2822	Info = G2elem.GetAtomInfo(El)
2823	AtInfo[El] = [Info['Drad'],Info['Color']]
2824	rbData['rbTypes'][r] = El
2825	vecGrid.SetCellValue(r,c,El)
2826	PE.Destroy()
2827	wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
2828
2829	def ChangeCell(event):
2830	r,c = event.GetRow(),event.GetCol()
2831	if r >= 0 and (0 <= c < 3):
2832	try:
2833	val = float(vecGrid.GetCellValue(r,c))
2834	rbData['rbVect'][imag][r][c] = val
2835	except ValueError:
2836	pass
2837	G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,data['Vector'][rbid],plotDefaults)
2838	wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
2839
2840	vecSizer = wx.BoxSizer()
2841	Types = 3[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_STRING,]+3[wg.GRID_VALUE_FLOAT+':10,5',]
2842	colLabels = ['Vector x','Vector y','Vector z','Type','Cart x','Cart y','Cart z']
2843	table = []
2844	rowLabels = []
2845	for ivec,xyz in enumerate(rbData['rbVect'][imag]):
2846	table.append(list(xyz)+[rbData['rbTypes'][ivec],]+list(XYZ[ivec]))
2847	rowLabels.append(str(ivec))
2848	vecTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
2849	vecGrid = G2G.GSGrid(VectorRBDisplay)
2850	vecGrid.SetTable(vecTable, True)
2851	if 'phoenix' in wx.version():
2852	vecGrid.Bind(wg.EVT_GRID_CELL_CHANGED, ChangeCell)
2853	else:
2854	vecGrid.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeCell)
2855	if not imag:
2856	vecGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, TypeSelect)
2857	attr = wx.grid.GridCellAttr()
2858	attr.IncRef()
2859	attr.SetEditor(G2G.GridFractionEditor(vecGrid))
2860	for c in range(3):
2861	attr.IncRef()
2862	vecGrid.SetColAttr(c, attr)
2863	for row in range(vecTable.GetNumberRows()):
2864	if imag:
2865	vecGrid.SetCellStyle(row,3,VERY_LIGHT_GREY,True)
2866	for col in [4,5,6]:
2867	vecGrid.SetCellStyle(row,col,VERY_LIGHT_GREY,True)
2868	# vecGrid.SetScrollRate(0,0)
2869	vecGrid.AutoSizeColumns(False)
2870	vecSizer.Add(vecGrid)
2871	return vecSizer
2872
2873	def FillRefChoice(rbid,rbData):
2874	choiceIds = [i for i in range(len(rbData['rbTypes']))]
2875
2876	rbRef = rbData.get('rbRef',[-1,-1,-1,False])
2877	for i in range(3):
2878	choiceIds.remove(rbRef[i])
2879	refChoice[rbid] = [choiceIds[:],choiceIds[:],choiceIds[:]]
2880	for i in range(3):
2881	refChoice[rbid][i].append(rbRef[i])
2882	refChoice[rbid][i].sort()
2883
2884	if VectorRB.GetSizer(): VectorRB.GetSizer().Clear(True)
2885	VectorRBSizer = wx.BoxSizer(wx.VERTICAL)
2886	first = True
2887	for rbid in data['RBIds']['Vector']:
2888	if rbid != 'AtInfo':
2889	rbData = data['Vector'][rbid]
2890	FillRefChoice(rbid,rbData)
2891	if not first:
2892	G2G.HorizontalLine(VectorRBSizer,VectorRBDisplay)
2893	VectorRBSizer.Add(rbNameSizer(rbid,rbData),0)
2894	VectorRBSizer.Add(rbRefAtmSizer(rbid,rbData),0)
2895	XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']])
2896	for imag,mag in enumerate(rbData['VectMag']):
2897	XYZ += mag*rbData['rbVect'][imag]
2898	VectorRBSizer.Add(rbVectMag(rbid,imag,rbData),0)
2899	VectorRBSizer.Add(rbVectors(rbid,imag,mag,XYZ,rbData),0)
2900	VectorRBSizer.Add((5,5),0)
2901	data['Vector'][rbid]['rbXYZ'] = XYZ
2902	first = False
2903	VectorRBSizer.Layout()
2904	VectorRBDisplay.SetSizer(VectorRBSizer,True)
2905	Size = VectorRBSizer.GetMinSize()
2906	Size[0] += 40
2907	Size[1] = max(Size[1],450) + 20
2908	VectorRBDisplay.SetSize(Size)
2909	VectorRB.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
2910	VectorRB.Scroll(0,Scroll)
2911
2912	def UpdateResidueRB():
2913	'''Draw the contents of the Residue Rigid Body tab for Rigid Bodies tree entry
2914	'''
2915	global resRBsel
2916	def rbNameSizer(rbid,rbData):
2917
2918	def OnDelRB(event):
2919	Obj = event.GetEventObject()
2920	rbid = Indx[Obj.GetId()]
2921	if rbid in data['Residue']:
2922	del data['Residue'][rbid]
2923	data['RBIds']['Residue'].remove(rbid)
2924	wx.CallAfter(UpdateResidueRB)
2925
2926	def OnStripH(event):
2927	Obj = event.GetEventObject()
2928	rbid = Indx[Obj.GetId()]
2929	if rbid in data['Residue']:
2930	newNames = []
2931	newTypes = []
2932	newXYZ = []
2933	for i,atype in enumerate(rbData['rbTypes']):
2934	if atype != 'H':
2935	newNames.append(rbData['atNames'][i])
2936	newTypes.append(rbData['rbTypes'][i])
2937	newXYZ.append(rbData['rbXYZ'][i])
2938	rbData['atNames'] = newNames
2939	rbData['rbTypes'] = newTypes
2940	rbData['rbXYZ'] = newXYZ
2941	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
2942	wx.CallAfter(UpdateResidueRB)
2943
2944	def OnPlotRB(event):
2945	Obj = event.GetEventObject()
2946	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
2947
2948	# start of rbNameSizer
2949	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
2950	nameSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'Residue name: '),
2951	0,wx.ALIGN_CENTER_VERTICAL)
2952	nameSizer.Add(G2G.ValidatedTxtCtrl(ResidueRBDisplay,rbData,'RBname'),0,WACV)
2953	nameSizer.Add((5,0),)
2954	plotRB = wx.Button(ResidueRBDisplay,wx.ID_ANY,'Plot',
2955	style=wx.BU_EXACTFIT)
2956	plotRB.Bind(wx.EVT_BUTTON, OnPlotRB)
2957	Indx[plotRB.GetId()] = rbid
2958	nameSizer.Add(plotRB,0,wx.ALIGN_CENTER_VERTICAL)
2959	nameSizer.Add((5,0),)
2960	if not rbData['useCount']:
2961	delRB = wx.Button(ResidueRBDisplay,wx.ID_ANY,"Delete",
2962	style=wx.BU_EXACTFIT)
2963	delRB.Bind(wx.EVT_BUTTON, OnDelRB)
2964	Indx[delRB.GetId()] = rbid
2965	nameSizer.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
2966	if 'H' in rbData['rbTypes']:
2967	stripH = wx.Button(ResidueRBDisplay,wx.ID_ANY,
2968	"Strip H-atoms",
2969	style=wx.BU_EXACTFIT)
2970	stripH.Bind(wx.EVT_BUTTON, OnStripH)
2971	Indx[stripH.GetId()] = rbid
2972	nameSizer.Add(stripH,0,wx.ALIGN_CENTER_VERTICAL)
2973	return nameSizer
2974
2975	def rbResidues(rbid,rbData):
2976
2977	def TypeSelect(event):
2978	AtInfo = data['Residue']['AtInfo']
2979	r,c = event.GetRow(),event.GetCol()
2980	if resGrid.GetColLabelValue(c) == 'Type':
2981	PE = G2elemGUI.PickElement(G2frame,oneOnly=True)
2982	if PE.ShowModal() == wx.ID_OK:
2983	if PE.Elem != 'None':
2984	El = PE.Elem.strip().lower().capitalize()
2985	if El not in AtInfo:
2986	Info = G2elem.GetAtomInfo(El)
2987	AtInfo[El] = [Info['Drad']['Color']]
2988	rbData['rbTypes'][r] = El
2989	resGrid.SetCellValue(r,c,El)
2990	PE.Destroy()
2991
2992	def ChangeCell(event):
2993	r,c = event.GetRow(),event.GetCol()
2994	if r >= 0 and (0 <= c < 3):
2995	try:
2996	val = float(resGrid.GetCellValue(r,c))
2997	rbData['rbXYZ'][r][c] = val
2998	except ValueError:
2999	pass
3000
3001	def RowSelect(event):
3002	r,c = event.GetRow(),event.GetCol()
3003	if c < 0: #only row clicks
3004	for iGrid in resList:
3005	iGrid.ClearSelection()
3006	resGrid.SelectRow(r,True)
3007
3008	def OnRefSel(event):
3009	Obj = event.GetEventObject()
3010	iref,res,jref = Indx[Obj.GetId()]
3011	sel = Obj.GetValue()
3012	ind = atNames.index(sel)
3013	if rbData['rbTypes'][ind] == 'H':
3014	G2G.G2MessageBox(G2frame,'You should not select an H-atom for rigid body orientation')
3015	rbData['rbRef'][iref] = ind
3016	FillRefChoice(rbid,rbData)
3017	for i,ref in enumerate(RefObjs[jref]):
3018	ref.SetItems([atNames[j] for j in refChoice[rbid][i]])
3019	ref.SetValue(atNames[rbData['rbRef'][i]])
3020	rbXYZ = rbData['rbXYZ']
3021	if not iref: #origin change
3022	rbXYZ -= rbXYZ[ind]
3023	#TODO - transform all atom XYZ by axis choices
3024	Xxyz = rbXYZ[rbData['rbRef'][1]]
3025	X = Xxyz/np.sqrt(np.sum(Xxyz**2))
3026	Yxyz = rbXYZ[rbData['rbRef'][2]]
3027	Y = Yxyz/np.sqrt(np.sum(Yxyz**2))
3028	Mat = G2mth.getRBTransMat(X,Y)
3029	rbXYZ = np.inner(Mat,rbXYZ).T
3030	rbData['rbXYZ'] = rbXYZ
3031	res.ClearSelection()
3032	resTable = res.GetTable()
3033	for r in range(res.GetNumberRows()):
3034	row = resTable.GetRowValues(r)
3035	row[2:4] = rbXYZ[r]
3036	resTable.SetRowValues(r,row)
3037	res.ForceRefresh()
3038	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
3039
3040	Types = 2[wg.GRID_VALUE_STRING,]+3[wg.GRID_VALUE_FLOAT+':10,5',]
3041	colLabels = ['Name','Type','Cart x','Cart y','Cart z']
3042	table = []
3043	rowLabels = []
3044	for ivec,xyz in enumerate(rbData['rbXYZ']):
3045	table.append([rbData['atNames'][ivec],]+[rbData['rbTypes'][ivec],]+list(xyz))
3046	rowLabels.append(str(ivec))
3047	vecTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
3048	resGrid = G2G.GSGrid(ResidueRBDisplay)
3049	Indx[resGrid.GetId()] = rbid
3050	resList.append(resGrid)
3051	resGrid.SetTable(vecTable, True)
3052	if 'phoenix' in wx.version():
3053	resGrid.Bind(wg.EVT_GRID_CELL_CHANGED, ChangeCell)
3054	else:
3055	resGrid.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeCell)
3056	resGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, TypeSelect)
3057	resGrid.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
3058	attr = wx.grid.GridCellAttr()
3059	attr.IncRef()
3060	attr.SetEditor(G2G.GridFractionEditor(resGrid))
3061	for c in range(3):
3062	attr.IncRef()
3063	resGrid.SetColAttr(c, attr)
3064	for row in range(vecTable.GetNumberRows()):
3065	for col in range(5):
3066	resGrid.SetCellStyle(row,col,VERY_LIGHT_GREY,True)
3067	resGrid.AutoSizeColumns(False)
3068	vecSizer = wx.BoxSizer()
3069	vecSizer.Add(resGrid)
3070
3071	refAtmSizer = wx.BoxSizer(wx.HORIZONTAL)
3072	atNames = rbData['atNames']
3073	rbRef = rbData['rbRef']
3074	if rbData['rbRef'][3] or rbData['useCount']:
3075	refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
3076	'Orientation reference non-H atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \
3077	atNames[rbRef[1]],atNames[rbRef[2]])),0)
3078	else:
3079	refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
3080	'Orientation reference non-H atoms A-B-C: '),0,wx.ALIGN_CENTER_VERTICAL)
3081	refObj = [0,0,0]
3082	for i in range(3):
3083	choices = [atNames[j] for j in refChoice[rbid][i]]
3084	refSel = wx.ComboBox(ResidueRBDisplay,-1,value='',
3085	choices=choices,style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3086	refSel.SetValue(atNames[rbRef[i]])
3087	refSel.Bind(wx.EVT_COMBOBOX, OnRefSel)
3088	Indx[refSel.GetId()] = [i,resGrid,len(RefObjs)]
3089	refObj[i] = refSel
3090	refAtmSizer.Add(refSel,0,wx.ALIGN_CENTER_VERTICAL)
3091	RefObjs.append(refObj)
3092
3093	mainSizer = wx.BoxSizer(wx.VERTICAL)
3094	mainSizer.Add(refAtmSizer)
3095	mainSizer.Add(vecSizer)
3096	return mainSizer
3097
3098	def Add2SeqSizer(seqSizer,angSlide,rbid,iSeq,Seq,atNames):
3099
3100	def ChangeAngle(event):
3101	event.Skip()
3102	Obj = event.GetEventObject()
3103	rbid,Seq = Indx[Obj.GetId()][:2]
3104	val = Seq[2]
3105	try:
3106	val = float(Obj.GetValue())
3107	Seq[2] = val
3108	except ValueError:
3109	pass
3110	Obj.SetValue('%8.2f'%(val))
3111	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,data['Residue'][rbid],plotDefaults)
3112
3113	def OnRadBtn(event):
3114	Obj = event.GetEventObject()
3115	Seq,iSeq,angId = Indx[Obj.GetId()]
3116	data['Residue'][rbid]['SelSeq'] = [iSeq,angId]
3117	angSlide.SetValue(int(100*Seq[2]))
3118
3119	def OnDelBtn(event):
3120	Obj = event.GetEventObject()
3121	rbid,Seq = Indx[Obj.GetId()]
3122	data['Residue'][rbid]['rbSeq'].remove(Seq)
3123	wx.CallAfter(UpdateResidueRB)
3124
3125	iBeg,iFin,angle,iMove = Seq
3126	ang = wx.TextCtrl(ResidueRBDisplay,wx.ID_ANY,
3127	'%8.2f'%(angle),size=(70,-1),style=wx.TE_PROCESS_ENTER)
3128	if not iSeq:
3129	radBt = wx.RadioButton(ResidueRBDisplay,wx.ID_ANY,
3130	'',style=wx.RB_GROUP)
3131	data['Residue'][rbid]['SelSeq'] = [iSeq,ang.GetId()]
3132	radBt.SetValue(True)
3133	else:
3134	radBt = wx.RadioButton(ResidueRBDisplay,wx.ID_ANY,'')
3135	radBt.Bind(wx.EVT_RADIOBUTTON,OnRadBtn)
3136	seqSizer.Add(radBt)
3137	delBt = wx.Button(ResidueRBDisplay,wx.ID_ANY,'Del',
3138	style=wx.BU_EXACTFIT)
3139	delBt.Bind(wx.EVT_BUTTON,OnDelBtn)
3140	seqSizer.Add(delBt)
3141	bond = wx.StaticText(ResidueRBDisplay,wx.ID_ANY,
3142	'%s %s'%(atNames[iBeg],atNames[iFin]),size=(50,20))
3143	seqSizer.Add(bond,0,wx.ALIGN_CENTER_VERTICAL)
3144	Indx[radBt.GetId()] = [Seq,iSeq,ang.GetId()]
3145	Indx[delBt.GetId()] = [rbid,Seq]
3146	Indx[ang.GetId()] = [rbid,Seq,ang]
3147	ang.Bind(wx.EVT_TEXT_ENTER,ChangeAngle)
3148	ang.Bind(wx.EVT_KILL_FOCUS,ChangeAngle)
3149	seqSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
3150	atms = ''
3151	for i in iMove:
3152	atms += ' %s,'%(atNames[i])
3153	moves = wx.StaticText(ResidueRBDisplay,wx.ID_ANY,
3154	atms[:-1],size=(200,20))
3155	seqSizer.Add(moves,1,wx.ALIGN_CENTER_VERTICAL\|wx.EXPAND\|wx.RIGHT)
3156	return seqSizer
3157
3158	def SlideSizer():
3159
3160	def OnSlider(event):
3161	Obj = event.GetEventObject()
3162	rbData = Indx[Obj.GetId()]
3163	iSeq,angId = rbData['SelSeq']
3164	val = float(Obj.GetValue())/100.
3165	rbData['rbSeq'][iSeq][2] = val
3166	Indx[angId][2].SetValue('%8.2f'%(val))
3167	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
3168
3169	slideSizer = wx.BoxSizer(wx.HORIZONTAL)
3170	slideSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'Selected torsion angle:'),0)
3171	iSeq,angId = rbData['SelSeq']
3172	angSlide = wx.Slider(ResidueRBDisplay,-1,
3173	int(100*rbData['rbSeq'][iSeq][2]),0,36000,size=(200,20),
3174	style=wx.SL_HORIZONTAL)
3175	angSlide.Bind(wx.EVT_SLIDER, OnSlider)
3176	Indx[angSlide.GetId()] = rbData
3177	slideSizer.Add(angSlide,0)
3178	return slideSizer,angSlide
3179
3180	def FillRefChoice(rbid,rbData):
3181	choiceIds = [i for i in range(len(rbData['atNames']))]
3182	for seq in rbData['rbSeq']:
3183	for i in seq[3]:
3184	try:
3185	choiceIds.remove(i)
3186	except ValueError:
3187	pass
3188	rbRef = rbData['rbRef']
3189	for i in range(3):
3190	try:
3191	choiceIds.remove(rbRef[i])
3192	except ValueError:
3193	pass
3194	refChoice[rbid] = [choiceIds[:],choiceIds[:],choiceIds[:]]
3195	for i in range(3):
3196	refChoice[rbid][i].append(rbRef[i])
3197	refChoice[rbid][i].sort()
3198
3199	def OnSelect(event):
3200	global resRBsel
3201	sel = select.GetSelection()
3202	if sel == 0: return # 1st entry is blank
3203	rbname = rbchoice[sel-1]
3204	resRBsel = RBnames[rbname]
3205	wx.CallLater(100,UpdateResidueRB)
3206
3207	#----- beginning of UpdateResidueRB -----------------------------------------------
3208	AtInfo = data['Residue']['AtInfo']
3209	refChoice = {}
3210	RefObjs = []
3211
3212	GS = ResidueRBDisplay.GetSizer()
3213	if GS:
3214	try: #get around a c++ error in wx 4.0; doing is again seems to be OK
3215	GS.Clear(True)
3216	except:
3217	GS.Clear(True)
3218
3219	RBnames = {}
3220	for rbid in data['RBIds']['Residue']:
3221	RBnames.update({data['Residue'][rbid]['RBname']:rbid,})
3222	if not RBnames:
3223	return
3224	rbchoice = list(RBnames.keys())
3225	if GS:
3226	ResidueRBSizer = GS
3227	else:
3228	ResidueRBSizer = wx.BoxSizer(wx.VERTICAL)
3229	if len(RBnames) > 1:
3230	selSizer = wx.BoxSizer(wx.HORIZONTAL)
3231	selSizer.Add(wx.StaticText(ResidueRBDisplay,
3232	label=' Select residue to view:'),0)
3233	rbchoice.sort()
3234	select = wx.ComboBox(ResidueRBDisplay,choices=['']+rbchoice)
3235	select.Bind(wx.EVT_COMBOBOX,OnSelect)
3236	selSizer.Add(select,0)
3237	ResidueRBSizer.Add(selSizer,0)
3238	if resRBsel not in data['RBIds']['Residue']:
3239	resRBsel = RBnames[rbchoice[0]]
3240	rbData = data['Residue'][resRBsel]
3241	FillRefChoice(resRBsel,rbData)
3242	ResidueRBSizer.Add(rbNameSizer(resRBsel,rbData),0)
3243	ResidueRBSizer.Add(rbResidues(resRBsel,rbData),0)
3244	if len(rbData['rbSeq']):
3245	ResidueRBSizer.Add((-1,15),0)
3246	slideSizer,angSlide = SlideSizer()
3247	seqSizer = wx.FlexGridSizer(0,5,4,8)
3248	for lbl in 'Sel','','Bond','Angle','Riding atoms':
3249	seqSizer.Add(wx.StaticText(ResidueRBDisplay,wx.ID_ANY,lbl))
3250	ResidueRBSizer.Add(seqSizer)
3251	# for iSeq,Seq in enumerate(rbData['rbSeq']):
3252	# ResidueRBSizer.Add(SeqSizer(angSlide,resRBsel,iSeq,Seq,rbData['atNames']))
3253	for iSeq,Seq in enumerate(rbData['rbSeq']):
3254	Add2SeqSizer(seqSizer,angSlide,resRBsel,iSeq,Seq,rbData['atNames'])
3255	ResidueRBSizer.Add(slideSizer,)
3256
3257	ResidueRBSizer.Add((5,25),)
3258	ResidueRBSizer.Layout()
3259	ResidueRBDisplay.SetSizer(ResidueRBSizer,True)
3260	ResidueRBDisplay.SetAutoLayout(True)
3261	Size = ResidueRBSizer.GetMinSize()
3262	ResidueRBDisplay.SetSize(Size)
3263
3264	Size[0] += 40
3265	Size[1] = max(Size[1],450) + 20
3266	ResidueRB.SetSize(Size)
3267	ResidueRB.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
3268	G2frame.dataWindow.SendSizeEvent()
3269
3270	ResidueRBDisplay.Show()
3271
3272	def SetStatusLine(text):
3273	G2frame.GetStatusBar().SetStatusText(text,1)
3274
3275	G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RigidBodyMenu)
3276	SetStatusLine('')
3277	UpdateVectorRB()
3278	G2frame.rbBook.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
3279	wx.CallAfter(OnPageChanged,None)
3280
3281	def ShowIsoDistortCalc(G2frame,phase=None):
3282	'''Compute the ISODISTORT mode values from the current coordinates.
3283	Called in response to the (Phase/Atoms tab) AtomCompute or
3284	Constraints/Edit Constr. "Show ISODISTORT modes" menu item, which
3285	should be enabled only when Phase['ISODISTORT'] is defined.
3286	'''
3287	def _onClose(event):
3288	dlg.EndModal(wx.ID_CANCEL)
3289	def fmtHelp(item,fullname):
3290	helptext = "A new variable"
3291	if item[-3]:
3292	helptext += " named "+str(item[-3])
3293	helptext += " is a linear combination of the following parameters:\n"
3294	first = True
3295	for term in item[:-3]:
3296	line = ''
3297	var = str(term[1])
3298	m = term[0]
3299	if first:
3300	first = False
3301	line += ' = '
3302	else:
3303	if m >= 0:
3304	line += ' + '
3305	else:
3306	line += ' - '
3307	m = abs(m)
3308	line += '%.3f*%s '%(m,var)
3309	varMean = G2obj.fmtVarDescr(var)
3310	helptext += "\n" + line + " ("+ varMean + ")"
3311	helptext += '\n\nISODISTORT full name: '+str(fullname)
3312	return helptext
3313
3314	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() # init for constraint
3315	isophases = [p for p in Phases if 'ISODISTORT' in Phases[p]]
3316
3317	if not isophases:
3318	G2frame.ErrorDialog('no ISODISTORT phases',
3319	'Unexpected error: no ISODISTORT phases')
3320	return
3321	if phase and phase not in isophases:
3322	G2frame.ErrorDialog('not ISODISTORT phase',
3323	'Unexpected error: selected phase is not an ISODISTORT phase')
3324	print('Unexpected error: selected phase is not an ISODISTORT phase',
3325	phase,isophases)
3326	elif not phase and len(isophases) == 1:
3327	phase = isophases[0]
3328	elif not phase:
3329	dlg = wx.SingleChoiceDialog(G2frame,'Select phase from ISODISTORT phases',
3330	'Select Phase',isophases)
3331	if dlg.ShowModal() == wx.ID_OK:
3332	sel = dlg.GetSelection()
3333	phase = isophases[sel]
3334	else:
3335	return
3336	# if len(data.get('Histograms',[])) == 0:
3337	# G2frame.ErrorDialog(
3338	# 'No data',
3339	# 'Sorry, this computation requires that a histogram first be added to the phase'
3340	# )
3341	# return
3342
3343	covdata = G2frame.GPXtree.GetItemPyData(
3344	G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Covariance'))
3345	# make a lookup table for named NewVar Phase constraints
3346	sub = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
3347	Constraints = G2frame.GPXtree.GetItemPyData(sub)
3348	constDict = {}
3349	for c in Constraints['Phase']:
3350	if c[-1] != 'f' or not c[-3]: continue
3351	constDict[str(c[-3])] = c
3352
3353	parmDict,varyList = G2frame.MakeLSParmDict()
3354
3355	dlg = wx.Dialog(G2frame,wx.ID_ANY,'ISODISTORT mode values',#size=(630,400),
3356	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
3357	mainSizer = wx.BoxSizer(wx.VERTICAL)
3358	if 'ISODISTORT' not in Phases[phase]:
3359	G2frame.ErrorDialog('not ISODISTORT phase',
3360	'Unexpected error: selected phase is not an ISODISTORT phase')
3361	return
3362	data = Phases[phase]
3363	ISO = data['ISODISTORT']
3364	mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,
3365	'ISODISTORT mode computation for cordinates in phase '+
3366	str(data['General'].get('Name'))))
3367	aSizer = wx.BoxSizer(wx.HORIZONTAL)
3368	panel1 = wxscroll.ScrolledPanel(
3369	dlg, wx.ID_ANY,#size=(100,200),
3370	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
3371	subSizer1 = wx.FlexGridSizer(cols=2,hgap=5,vgap=2)
3372	panel2 = wxscroll.ScrolledPanel(
3373	dlg, wx.ID_ANY,#size=(100,200),
3374	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
3375	subSizer2 = wx.FlexGridSizer(cols=3,hgap=5,vgap=2)
3376	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'Parameter name '))
3377	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
3378	subSizer2.Add((-1,-1))
3379	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'Mode name '))
3380	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
3381	# ISODISTORT displacive modes
3382	if 'G2VarList' in ISO:
3383	deltaList = []
3384	for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']):
3385	dvar = gv.varname()
3386	var = dvar.replace('::dA','::A')
3387	albl = Ilbl[:Ilbl.rfind('_')]
3388	v = Ilbl[Ilbl.rfind('_')+1:]
3389	pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)]
3390	if var in parmDict:
3391	cval = parmDict[var][0]
3392	else:
3393	dlg.EndModal(wx.ID_CANCEL)
3394	G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var))
3395	return
3396	deltaList.append(cval-pval)
3397	modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList)
3398	for lbl,xyz,var,val,norm,G2mode in zip(
3399	ISO['IsoVarList'],deltaList,
3400	ISO['IsoModeList'],modeVals,ISO['NormList'],ISO['G2ModeList'] ):
3401	#GSASIIpath.IPyBreak()
3402	if str(G2mode) in constDict:
3403	ch = G2G.HelpButton(panel2,fmtHelp(constDict[str(G2mode)],var))
3404	subSizer2.Add(ch,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1)
3405	else:
3406	subSizer2.Add((-1,-1))
3407	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
3408	try:
3409	value = G2py3.FormatSigFigs(xyz)
3410	except TypeError:
3411	value = str(xyz)
3412	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
3413	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
3414	try:
3415	value = G2py3.FormatSigFigs(val/norm)
3416	if 'varyList' in covdata:
3417	if str(G2mode) in covdata['varyList']:
3418	sig = covdata['sig'][covdata['varyList'].index(str(G2mode))]
3419	value = G2mth.ValEsd(val/norm,sig/norm)
3420	except TypeError:
3421	value = '?'
3422	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
3423	#GSASIIpath.IPyBreak()
3424	# ISODISTORT occupancy modes
3425	if 'G2OccVarList' in ISO:
3426	deltaList = []
3427	for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']):
3428	var = gv.varname()
3429	albl = Ilbl[:Ilbl.rfind('_')]
3430	pval = ISO['BaseOcc'][albl]
3431	if var in parmDict:
3432	cval = parmDict[var][0]
3433	else:
3434	dlg.EndModal(wx.ID_CANCEL)
3435	G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var))
3436	return
3437	deltaList.append(cval-pval)
3438	modeVals = np.inner(ISO['Var2OccMatrix'],deltaList)
3439	for lbl,delocc,var,val,norm,G2mode in zip(
3440	ISO['OccVarList'],deltaList,
3441	ISO['OccModeList'],modeVals,ISO['OccNormList'],ISO['G2OccModeList']):
3442	if str(G2mode) in constDict:
3443	ch = G2G.HelpButton(panel2,fmtHelp(constDict[str(G2mode)],var))
3444	subSizer2.Add(ch,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1)
3445	else:
3446	subSizer2.Add((-1,-1))
3447	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
3448	try:
3449	value = G2py3.FormatSigFigs(delocc)
3450	except TypeError:
3451	value = str(delocc)
3452	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
3453	#subSizer.Add((10,-1))
3454	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
3455	try:
3456	value = G2py3.FormatSigFigs(val/norm)
3457	if 'varyList' in covdata:
3458	if str(G2mode) in covdata['varyList']:
3459	sig = covdata['sig'][covdata['varyList'].index(str(G2mode))]
3460	value = G2mth.ValEsd(val/norm,sig/norm)
3461	except TypeError:
3462	value = '?'
3463	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
3464
3465	# finish up ScrolledPanel
3466	panel1.SetSizer(subSizer1)
3467	panel2.SetSizer(subSizer2)
3468	panel1.SetAutoLayout(1)
3469	panel1.SetupScrolling()
3470	panel2.SetAutoLayout(1)
3471	panel2.SetupScrolling()
3472	# Allow window to be enlarged but not made smaller
3473	dlg.SetSizer(mainSizer)
3474	w1,l1 = subSizer1.GetSize()
3475	w2,l2 = subSizer2.GetSize()
3476	panel1.SetMinSize((w1+10,200))
3477	panel2.SetMinSize((w2+20,200))
3478	aSizer.Add(panel1,1, wx.ALL\|wx.EXPAND,1)
3479	aSizer.Add(panel2,2, wx.ALL\|wx.EXPAND,1)
3480	mainSizer.Add(aSizer,1, wx.ALL\|wx.EXPAND,1)
3481
3482	# make OK button
3483	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
3484	btn = wx.Button(dlg, wx.ID_CLOSE)
3485	btn.Bind(wx.EVT_BUTTON,_onClose)
3486	btnsizer.Add(btn)
3487	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
3488
3489	mainSizer.Fit(dlg)
3490	dlg.SetMinSize(dlg.GetSize())
3491	dlg.ShowModal()
3492	dlg.Destroy()

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