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source: trunk/GSASIIphsGUI.py @ 1489

Last change on this file since 1489 was 1489, checked in by vondreele, 9 years ago
correct Uij to U6 conversions Uij = Uk/2 for i != j; k > 2 in G2lattice & G2spc This fixes derivative issues for aniso tropic atoms in Al2O3 change names of sytsyms e.g. 2(100) to 2(x) for non-hex/trig space groups. Removes possible ambiguity with ortho, etc. cases. Still checking extinction issues
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1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2014-09-07 18:37:26 +0000 (Sun, 07 Sep 2014) $
5	# $Author: vondreele $
6	# $Revision: 1489 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1489 2014-09-07 18:37:26Z vondreele $
9	########### SVN repository information ###################
10	'''
11	GSASIIphsGUI: Phase GUI
12	-------------------------
13
14	Module to create the GUI for display of phase information
15	in the data display window when a phase is selected.
16	Phase information is stored in one or more
17	:ref:`Phase Tree Item <Phase_table>` objects.
18	Note that there are functions
19	that respond to some tabs in the phase GUI in other modules
20	(such as GSASIIddata).
21
22	'''
23	import os.path
24	import wx
25	import wx.grid as wg
26	import wx.lib.gridmovers as wgmove
27	import wx.wizard as wz
28	import wx.lib.scrolledpanel as wxscroll
29	import matplotlib as mpl
30	import math
31	import copy
32	import time
33	import sys
34	import random as ran
35	import cPickle
36	import GSASIIpath
37	GSASIIpath.SetVersionNumber("$Revision: 1489 $")
38	import GSASIIlattice as G2lat
39	import GSASIIspc as G2spc
40	import GSASIIElem as G2elem
41	import GSASIIElemGUI as G2elemGUI
42	import GSASIIddataGUI as G2ddG
43	import GSASIIplot as G2plt
44	import GSASIIgrid as G2gd
45	import GSASIIIO as G2IO
46	import GSASIIstrMain as G2stMn
47	import GSASIImath as G2mth
48	import GSASIIpwd as G2pwd
49	import GSASIIpy3 as G2py3
50	import GSASIIobj as G2obj
51	import numpy as np
52	import numpy.linalg as nl
53	import numpy.ma as ma
54
55	VERY_LIGHT_GREY = wx.Colour(235,235,235)
56	WHITE = wx.Colour(255,255,255)
57	BLACK = wx.Colour(0,0,0)
58	WACV = wx.ALIGN_CENTER_VERTICAL
59	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
60	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
61	# trig functions in degrees
62	sind = lambda x: np.sin(x*np.pi/180.)
63	tand = lambda x: np.tan(x*np.pi/180.)
64	cosd = lambda x: np.cos(x*np.pi/180.)
65	asind = lambda x: 180.*np.arcsin(x)/np.pi
66	acosd = lambda x: 180.*np.arccos(x)/np.pi
67
68	def SetPhaseWindow(mainFrame,phasePage,mainSizer):
69	phasePage.SetSizer(mainSizer)
70	Size = mainSizer.GetMinSize()
71	Size[0] += 40
72	# Size[1] = 500
73	Size[1] = min(Size[1]+ 150,500)
74	phasePage.SetSize(Size)
75	phasePage.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
76	mainFrame.setSizePosLeft(Size)
77
78	def UpdatePhaseData(G2frame,Item,data,oldPage):
79	'''Create the data display window contents when a phase is clicked on
80	in the main (data tree) window.
81	Called only from :meth:`GSASIIgrid.MovePatternTreeToGrid`,
82	which in turn is called from :meth:`GSASII.GSASII.OnPatternTreeSelChanged`
83	when a tree item is selected.
84
85	:param wx.frame G2frame: the main GSAS-II frame object
86	:param wx.TreeItemId Item: the tree item that was selected
87	:param dict data: all the information on the phase in a dictionary
88	:param int oldPage: This sets a tab to select when moving
89	from one phase to another, in which case the same tab is selected
90	to display first. This is set only when the previous data tree
91	selection is a phase, if not the value is None. The default action
92	is to bring up the General tab.
93
94	'''
95
96	# UpdatePhaseData execution continues below
97
98	def SetupGeneral():
99	generalData = data['General']
100	atomData = data['Atoms']
101	generalData['AtomTypes'] = []
102	generalData['Isotopes'] = {}
103	# various patches
104	if 'Isotope' not in generalData:
105	generalData['Isotope'] = {}
106	if 'Data plot type' not in generalData:
107	generalData['Data plot type'] = 'Mustrain'
108	if 'POhkl' not in generalData:
109	generalData['POhkl'] = [0,0,1]
110	if 'Map' not in generalData:
111	generalData['Map'] = mapDefault
112	if 'Flip' not in generalData:
113	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
114	'k-factor':0.1,'k-Max':20.}
115	if 'doPawley' not in generalData:
116	generalData['doPawley'] = False
117	if 'Pawley dmin' not in generalData:
118	generalData['Pawley dmin'] = 1.0
119	if 'Pawley neg wt' not in generalData:
120	generalData['Pawley neg wt'] = 0.0
121	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
122	'MCSA controls' not in generalData:
123	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
124	'dmin':2.0,'Algorithm':'log','Jump coeff':[0.95,0.5],'boltzmann':1.0,
125	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[],'newDmin':True}
126	if 'AtomPtrs' not in generalData:
127	generalData['AtomPtrs'] = [3,1,7,9]
128	if generalData['Type'] =='macromolecular':
129	generalData['AtomPtrs'] = [6,4,10,12]
130	# end of patches
131	cx,ct,cs,cia = generalData['AtomPtrs']
132	generalData['NoAtoms'] = {}
133	generalData['BondRadii'] = []
134	generalData['AngleRadii'] = []
135	generalData['vdWRadii'] = []
136	generalData['AtomMass'] = []
137	generalData['Color'] = []
138	generalData['Mydir'] = G2frame.dirname
139	for atom in atomData:
140	atom[ct] = atom[ct].lower().capitalize() #force to standard form
141	if generalData['AtomTypes'].count(atom[ct]):
142	generalData['NoAtoms'][atom[ct]] += atom[cs-1]*float(atom[cs+1])
143	elif atom[ct] != 'UNK':
144	Info = G2elem.GetAtomInfo(atom[ct])
145	generalData['AtomTypes'].append(atom[ct])
146	generalData['Z'] = Info['Z']
147	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
148	generalData['BondRadii'].append(Info['Drad'])
149	generalData['AngleRadii'].append(Info['Arad'])
150	generalData['vdWRadii'].append(Info['Vdrad'])
151	if atom[ct] in generalData['Isotope']:
152	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass'])
153	else:
154	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
155	generalData['AtomMass'].append(Info['Mass'])
156	generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
157	generalData['Color'].append(Info['Color'])
158	F000X = 0.
159	F000N = 0.
160	for i,elem in enumerate(generalData['AtomTypes']):
161	F000X += generalData['NoAtoms'][elem]*generalData['Z']
162	isotope = generalData['Isotope'][elem]
163	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0]
164	generalData['F000X'] = F000X
165	generalData['F000N'] = F000N
166
167
168	################################################################################
169	##### General phase routines
170	################################################################################
171
172	def UpdateGeneral():
173	'''Draw the controls for the General phase data subpage
174	'''
175
176	""" This is the default dictionary structure for phase data
177	(taken from GSASII.py)
178	'General':{
179	'Name':PhaseName
180	'Type':'nuclear'
181	'SGData':SGData
182	'Cell':[False,10.,10.,10.,90.,90.,90,1000.]
183	'AtomPtrs':[]
184	'Histogram list':['',]
185	'Pawley dmin':1.0,
186	'Pawley neg wt':0.0}
187	'Atoms':[]
188	'Drawing':{}
189	"""
190	# UpdateGeneral execution starts here
191	phaseTypes = ['nuclear','modulated','magnetic','macromolecular']
192	SetupGeneral()
193	generalData = data['General']
194	Map = generalData['Map']
195	Flip = generalData['Flip']
196	MCSAdata = generalData['MCSA controls']
197	PWDR = any(['PWDR' in item for item in data['Histograms'].keys()])
198	# UpdateGeneral execution continues below
199
200	def NameSizer():
201	def OnPhaseName(event):
202	oldName = generalData['Name']
203	generalData['Name'] = NameTxt.GetValue()
204	G2frame.G2plotNB.Rename(oldName,generalData['Name'])
205	G2frame.dataFrame.SetLabel('Phase Data for '+generalData['Name'])
206	G2frame.PatternTree.SetItemText(Item,generalData['Name'])
207	#Hmm, need to change phase name key in Reflection Lists for each histogram
208
209	def OnPhaseType(event):
210	if not generalData['AtomTypes']: #can change only if no atoms!
211	generalData['Type'] = TypeTxt.GetValue()
212	wx.CallAfter(UpdateGeneral)
213	else:
214	TypeTxt.SetValue(generalData['Type'])
215
216	def OnSpaceGroup(event):
217	SpcGp = SGTxt.GetValue()
218	SGErr,SGData = G2spc.SpcGroup(SpcGp)
219	# try a lookup on the user-supplied name
220	if SGErr:
221	SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
222	if SpGrpNorm:
223	E,SGData = G2spc.SpcGroup(SpGrpNorm)
224	if not E: SGErr = False
225	if SGErr:
226	text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
227	SGTxt.SetValue(generalData['SGData']['SpGrp'])
228	msg = 'Space Group Error'
229	Style = wx.ICON_EXCLAMATION
230	else:
231	text = G2spc.SGPrint(SGData)
232	generalData['SGData'] = SGData
233	msg = 'Space Group Information'
234	Style = wx.ICON_INFORMATION
235	Text = ''
236	for line in text:
237	Text += line+'\n'
238	wx.MessageBox(Text,caption=msg,style=Style)
239	wx.CallAfter(UpdateGeneral)
240
241	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
242	nameSizer.Add(wx.StaticText(General,-1,' Phase name: '),0,WACV)
243	NameTxt = wx.TextCtrl(General,-1,value=generalData['Name'],style=wx.TE_PROCESS_ENTER)
244	NameTxt.Bind(wx.EVT_TEXT_ENTER,OnPhaseName)
245	NameTxt.Bind(wx.EVT_KILL_FOCUS,OnPhaseName)
246	nameSizer.Add(NameTxt,0,WACV)
247	nameSizer.Add(wx.StaticText(General,-1,' Phase type: '),0,WACV)
248	TypeTxt = wx.ComboBox(General,-1,value=generalData['Type'],choices=phaseTypes,
249	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
250	TypeTxt.Bind(wx.EVT_COMBOBOX, OnPhaseType)
251	nameSizer.Add(TypeTxt,0,WACV)
252	nameSizer.Add(wx.StaticText(General,-1,' Space group: '),0,WACV)
253	SGTxt = wx.TextCtrl(General,-1,value=generalData['SGData']['SpGrp'],style=wx.TE_PROCESS_ENTER)
254	SGTxt.Bind(wx.EVT_TEXT_ENTER,OnSpaceGroup)
255	nameSizer.Add(SGTxt,0,WACV)
256	return nameSizer
257
258	def CellSizer():
259
260	cellGUIlist = [[['m3','m3m'],4,zip([" Unit cell: a = "," Vol = "],["%.5f","%.3f"],[True,False],[0,0])],
261	[['3R','3mR'],6,zip([" a = "," alpha = "," Vol = "],["%.5f","%.3f","%.3f"],[True,True,False],[0,2,0])],
262	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],6,zip([" a = "," c = "," Vol = "],["%.5f","%.5f","%.3f"],[True,True,False],[0,2,0])],
263	[['mmm'],8,zip([" a = "," b = "," c = "," Vol = "],["%.5f","%.5f","%.5f","%.3f"],
264	[True,True,True,False],[0,1,2,0])],
265	[['2/m'+'a'],10,zip([" a = "," b = "," c = "," alpha = "," Vol = "],
266	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,5,0])],
267	[['2/m'+'b'],10,zip([" a = "," b = "," c = "," beta = "," Vol = "],
268	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
269	[['2/m'+'c'],10,zip([" a = "," b = "," c = "," gamma = "," Vol = "],
270	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,3,0])],
271	[['-1'],8,zip([" a = "," b = "," c = "," Vol = "," alpha = "," beta = "," gamma = "],
272	["%.5f","%.5f","%.5f","%.3f","%.3f","%.3f","%.3f"],
273	[True,True,True,False,True,True,True],[0,1,2,0,3,4,5])]]
274
275	def OnCellRef(event):
276	generalData['Cell'][0] = cellRef.GetValue()
277
278	def OnCellChange(event):
279	SGData = generalData['SGData']
280	laue = SGData['SGLaue']
281	if laue == '2/m':
282	laue += SGData['SGUniq']
283	cell = generalData['Cell']
284	Obj = event.GetEventObject()
285	ObjId = cellList.index(Obj.GetId())
286	try:
287	value = max(1.0,float(Obj.GetValue()))
288	except ValueError:
289	if ObjId < 3: #bad cell edge - reset
290	value = controls[6+ObjId]
291	else: #bad angle
292	value = 90.
293	if laue in ['m3','m3m']:
294	cell[1] = cell[2] = cell[3] = value
295	cell[4] = cell[5] = cell[6] = 90.0
296	Obj.SetValue("%.5f"%(cell[1]))
297	elif laue in ['3R','3mR']:
298	if ObjId == 0:
299	cell[1] = cell[2] = cell[3] = value
300	Obj.SetValue("%.5f"%(cell[1]))
301	else:
302	cell[4] = cell[5] = cell[6] = value
303	Obj.SetValue("%.5f"%(cell[4]))
304	elif laue in ['3','3m1','31m','6/m','6/mmm','4/m','4/mmm']:
305	cell[4] = cell[5] = 90.
306	cell[6] = 120.
307	if laue in ['4/m','4/mmm']:
308	cell[6] = 90.
309	if ObjId == 0:
310	cell[1] = cell[2] = value
311	Obj.SetValue("%.5f"%(cell[1]))
312	else:
313	cell[3] = value
314	Obj.SetValue("%.5f"%(cell[3]))
315	elif laue in ['mmm']:
316	cell[ObjId+1] = value
317	cell[4] = cell[5] = cell[6] = 90.
318	Obj.SetValue("%.5f"%(cell[ObjId+1]))
319	elif laue in ['2/m'+'a']:
320	cell[5] = cell[6] = 90.
321	if ObjId != 3:
322	cell[ObjId+1] = value
323	Obj.SetValue("%.5f"%(cell[ObjId+1]))
324	else:
325	cell[4] = value
326	Obj.SetValue("%.3f"%(cell[4]))
327	elif laue in ['2/m'+'b']:
328	cell[4] = cell[6] = 90.
329	if ObjId != 3:
330	cell[ObjId+1] = value
331	Obj.SetValue("%.5f"%(cell[ObjId+1]))
332	else:
333	cell[5] = value
334	Obj.SetValue("%.3f"%(cell[5]))
335	elif laue in ['2/m'+'c']:
336	cell[5] = cell[6] = 90.
337	if ObjId != 3:
338	cell[ObjId+1] = value
339	Obj.SetValue("%.5f"%(cell[ObjId+1]))
340	else:
341	cell[6] = value
342	Obj.SetValue("%.3f"%(cell[6]))
343	else:
344	cell[ObjId+1] = value
345	if ObjId < 3:
346	Obj.SetValue("%.5f"%(cell[1+ObjId]))
347	else:
348	Obj.SetValue("%.3f"%(cell[1+ObjId]))
349	cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
350	volVal.SetValue("%.3f"%(cell[7]))
351	density,mattCoeff = G2mth.getDensity(generalData)
352	if denSizer:
353	denSizer[1].SetValue('%.3f'%(density))
354	if denSizer[2]:
355	denSizer[2].SetValue('%.3f'%(mattCoeff))
356	generalData['Cell'] = cell
357
358	cell = generalData['Cell']
359	laue = generalData['SGData']['SGLaue']
360	if laue == '2/m':
361	laue += generalData['SGData']['SGUniq']
362	for cellGUI in cellGUIlist:
363	if laue in cellGUI[0]:
364	useGUI = cellGUI
365	cellSizer = wx.FlexGridSizer(0,useGUI[1]+1,5,5)
366	if PWDR:
367	cellRef = wx.CheckBox(General,-1,label='Refine unit cell:')
368	cellSizer.Add(cellRef,0,WACV)
369	cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef)
370	cellRef.SetValue(cell[0])
371	cellList = []
372	for txt,fmt,ifEdit,Id in useGUI[2]:
373	cellSizer.Add(wx.StaticText(General,label=txt),0,WACV)
374	if ifEdit: #a,b,c,etc.
375	cellVal = wx.TextCtrl(General,value=(fmt%(cell[Id+1])),
376	style=wx.TE_PROCESS_ENTER)
377	cellVal.Bind(wx.EVT_TEXT_ENTER,OnCellChange)
378	cellVal.Bind(wx.EVT_KILL_FOCUS,OnCellChange)
379	cellSizer.Add(cellVal,0,WACV)
380	cellList.append(cellVal.GetId())
381	else: #volume
382	volVal = wx.TextCtrl(General,value=(fmt%(cell[7])),style=wx.TE_READONLY)
383	volVal.SetBackgroundColour(VERY_LIGHT_GREY)
384	cellSizer.Add(volVal,0,WACV)
385	return cellSizer
386
387	def ElemSizer():
388
389	def OnIsotope(event): #how can I update Atom weight on isotope change?
390	Obj = event.GetEventObject()
391	item = Indx[Obj.GetId()]
392	isotope = Obj.GetValue()
393	generalData['Isotope'][item] = isotope
394	indx = generalData['AtomTypes'].index(item)
395	data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope]['Mass']
396	density,mattCoeff = G2mth.getDensity(generalData)
397	denSizer[1].SetValue('%.3f'%(density))
398	if denSizer[2]:
399	denSizer[2].SetValue('%.3f'%(mattCoeff))
400
401	elemSizer = wx.FlexGridSizer(0,len(generalData['AtomTypes'])+1,1,1)
402	elemSizer.Add(wx.StaticText(General,label=' Elements'),0,WACV)
403	for elem in generalData['AtomTypes']:
404	typTxt = wx.TextCtrl(General,value=elem,style=wx.TE_READONLY)
405	typTxt.SetBackgroundColour(VERY_LIGHT_GREY)
406	elemSizer.Add(typTxt,0,WACV)
407	elemSizer.Add(wx.StaticText(General,label=' Isotope'),0,WACV)
408	for elem in generalData['AtomTypes']:
409	choices = generalData['Isotopes'][elem].keys()
410	isoSel = wx.ComboBox(General,-1,value=generalData['Isotope'][elem],choices=choices,
411	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
412	isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope)
413	Indx[isoSel.GetId()] = elem
414	elemSizer.Add(isoSel,1,WACV\|wx.EXPAND)
415	elemSizer.Add(wx.StaticText(General,label=' No. per cell'),0,WACV)
416	for elem in generalData['AtomTypes']:
417	numbTxt = wx.TextCtrl(General,value='%.1f'%(generalData['NoAtoms'][elem]),
418	style=wx.TE_READONLY)
419	numbTxt.SetBackgroundColour(VERY_LIGHT_GREY)
420	elemSizer.Add(numbTxt,0,WACV)
421	elemSizer.Add(wx.StaticText(General,label=' Atom weight'),0,WACV)
422	for wt in generalData['AtomMass']:
423	wtTxt = wx.TextCtrl(General,value='%.3f'%(wt),style=wx.TE_READONLY)
424	wtTxt.SetBackgroundColour(VERY_LIGHT_GREY)
425	elemSizer.Add(wtTxt,0,WACV)
426	elemSizer.Add(wx.StaticText(General,label=' Bond radii'),0,WACV)
427	for rad in generalData['BondRadii']:
428	bondRadii = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
429	bondRadii.SetBackgroundColour(VERY_LIGHT_GREY)
430	elemSizer.Add(bondRadii,0,WACV)
431	elemSizer.Add(wx.StaticText(General,label=' Angle radii'),0,WACV)
432	for rad in generalData['AngleRadii']:
433	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
434	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
435	elemSizer.Add(elemTxt,0,WACV)
436	elemSizer.Add(wx.StaticText(General,label=' van der Waals radii'),0,WACV)
437	for rad in generalData['vdWRadii']:
438	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
439	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
440	elemSizer.Add(elemTxt,0,WACV)
441	elemSizer.Add(wx.StaticText(General,label=' Default color'),0,WACV)
442	for R,G,B in generalData['Color']:
443	colorTxt = wx.TextCtrl(General,value='',style=wx.TE_READONLY)
444	colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
445	elemSizer.Add(colorTxt,0,WACV)
446	return elemSizer
447
448	def DenSizer():
449
450	mass = G2mth.getMass(generalData)
451	density,mattCoeff = G2mth.getDensity(generalData)
452	denSizer = wx.BoxSizer(wx.HORIZONTAL)
453	denSizer.Add(wx.StaticText(General,-1,' Density: '),0,WACV)
454	denTxt = wx.TextCtrl(General,-1,'%.3f'%(density),style=wx.TE_READONLY)
455	denTxt.SetBackgroundColour(VERY_LIGHT_GREY)
456	denSizer.Add(denTxt,0,WACV)
457	mattTxt = None
458	if generalData['Type'] == 'macromolecular' and mass > 0.0:
459	denSizer.Add(wx.StaticText(General,-1,' Matthews coeff.: '),
460	0,WACV)
461	mattTxt = wx.TextCtrl(General,-1,'%.3f'%(mattCoeff),style=wx.TE_READONLY)
462	mattTxt.SetBackgroundColour(VERY_LIGHT_GREY)
463	denSizer.Add(mattTxt,0,WACV)
464	return denSizer,denTxt,mattTxt
465
466	def PawleySizer():
467
468	def OnPawleyRef(event):
469	generalData['doPawley'] = pawlRef.GetValue()
470
471	def OnPawleyVal(event):
472	try:
473	dmin = float(pawlVal.GetValue())
474	if 0.25 <= dmin <= 20.:
475	generalData['Pawley dmin'] = dmin
476	except ValueError:
477	pass
478	pawlVal.SetValue("%.5f"%(generalData['Pawley dmin'])) #reset in case of error
479
480	def OnPawleyNegWt(event):
481	try:
482	wt = float(pawlNegWt.GetValue())
483	if 0. <= wt <= 1.:
484	generalData['Pawley neg wt'] = wt
485	except ValueError:
486	pass
487	pawlNegWt.SetValue("%.4f"%(generalData['Pawley neg wt'])) #reset in case of error
488
489	pawleySizer = wx.BoxSizer(wx.HORIZONTAL)
490	pawleySizer.Add(wx.StaticText(General,label=' Pawley controls: '),0,WACV)
491	pawlRef = wx.CheckBox(General,-1,label=' Do Pawley refinement?')
492	pawlRef.SetValue(generalData['doPawley'])
493	pawlRef.Bind(wx.EVT_CHECKBOX,OnPawleyRef)
494	pawleySizer.Add(pawlRef,0,WACV)
495	pawleySizer.Add(wx.StaticText(General,label=' Pawley dmin: '),0,WACV)
496	pawlVal = wx.TextCtrl(General,value='%.5f'%(generalData['Pawley dmin']),style=wx.TE_PROCESS_ENTER)
497	pawlVal.Bind(wx.EVT_TEXT_ENTER,OnPawleyVal)
498	pawlVal.Bind(wx.EVT_KILL_FOCUS,OnPawleyVal)
499	pawleySizer.Add(pawlVal,0,WACV)
500	pawleySizer.Add(wx.StaticText(General,label=' Pawley neg. wt.: '),0,WACV)
501	pawlNegWt = wx.TextCtrl(General,value='%.4f'%(generalData['Pawley neg wt']),style=wx.TE_PROCESS_ENTER)
502	pawlNegWt.Bind(wx.EVT_TEXT_ENTER,OnPawleyNegWt)
503	pawlNegWt.Bind(wx.EVT_KILL_FOCUS,OnPawleyNegWt)
504	pawleySizer.Add(pawlNegWt,0,WACV)
505	return pawleySizer
506
507	def MapSizer():
508
509	def OnMapType(event):
510	Map['MapType'] = mapType.GetValue()
511
512	def OnRefList(event):
513	Map['RefList'] = refList.GetValue()
514
515	def OnResVal(event):
516	try:
517	res = float(mapRes.GetValue())
518	if 0.25 <= res <= 20.:
519	Map['Resolution'] = res
520	except ValueError:
521	pass
522	mapRes.SetValue("%.2f"%(Map['Resolution'])) #reset in case of error
523
524	def OnCutOff(event):
525	try:
526	res = float(cutOff.GetValue())
527	if 10.0 <= res <= 100.:
528	Map['cutOff'] = res
529	except ValueError:
530	pass
531	cutOff.SetValue("%.1f"%(Map['cutOff'])) #reset in case of error
532
533	#patch
534	if 'cutOff' not in Map:
535	Map['cutOff'] = 100.0
536	mapTypes = ['Fobs','Fcalc','delt-F','2*Fo-Fc','Omit','2Fo-Fc Omit','Patterson']
537	refList = data['Histograms'].keys()
538	if not generalData['AtomTypes']:
539	mapTypes = ['Patterson',]
540	Map['MapType'] = 'Patterson'
541	mapSizer = wx.BoxSizer(wx.VERTICAL)
542	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
543	lineSizer.Add(wx.StaticText(General,label=' Fourier map controls: Map type: '),0,WACV)
544	mapType = wx.ComboBox(General,-1,value=Map['MapType'],choices=mapTypes,
545	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
546	mapType.Bind(wx.EVT_COMBOBOX,OnMapType)
547	lineSizer.Add(mapType,0,WACV)
548	lineSizer.Add(wx.StaticText(General,label=' Reflection set from: '),0,WACV)
549	refList = wx.ComboBox(General,-1,value=Map['RefList'],choices=refList,
550	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
551	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
552	lineSizer.Add(refList,0,WACV)
553	mapSizer.Add(lineSizer,0,WACV)
554	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
555	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,WACV)
556	mapRes = wx.TextCtrl(General,value='%.2f'%(Map['Resolution']),style=wx.TE_PROCESS_ENTER)
557	mapRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
558	mapRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
559	line2Sizer.Add(mapRes,0,WACV)
560	line2Sizer.Add(wx.StaticText(General,label=' Peak cutoff %: '),0,WACV)
561	cutOff = wx.TextCtrl(General,value='%.1f'%(Map['cutOff']),style=wx.TE_PROCESS_ENTER)
562	cutOff.Bind(wx.EVT_TEXT_ENTER,OnCutOff)
563	cutOff.Bind(wx.EVT_KILL_FOCUS,OnCutOff)
564	line2Sizer.Add(cutOff,0,WACV)
565	mapSizer.Add(line2Sizer,0,WACV)
566	return mapSizer
567
568	def FlipSizer():
569	if 'k-Max' not in Flip: Flip['k-Max'] = 20.
570
571	def OnRefList(event):
572	Flip['RefList'] = refList.GetValue()
573
574	def OnNormElem(event):
575	PE = G2elemGUI.PickElement(G2frame,ifNone=True)
576	if PE.ShowModal() == wx.ID_OK:
577	Flip['Norm element'] = PE.Elem.strip()
578	normElem.SetLabel(Flip['Norm element'])
579	PE.Destroy()
580
581	def OnResVal(event):
582	try:
583	res = float(flipRes.GetValue())
584	if 0.25 <= res <= 20.:
585	Flip['Resolution'] = res
586	except ValueError:
587	pass
588	flipRes.SetValue("%.2f"%(Flip['Resolution'])) #reset in case of error
589
590	def OnkFactor(event):
591	try:
592	res = float(kFactor.GetValue())
593	if 0.1 <= res <= 1.2:
594	Flip['k-factor'] = res
595	except ValueError:
596	pass
597	kFactor.SetValue("%.3f"%(Flip['k-factor'])) #reset in case of error
598
599	def OnkMax(event):
600	try:
601	res = float(kMax.GetValue())
602	if res >= 10.:
603	Flip['k-Max'] = res
604	except ValueError:
605	pass
606	kMax.SetValue("%.1f"%(Flip['k-Max'])) #reset in case of error
607
608	refList = data['Histograms'].keys()
609	flipSizer = wx.BoxSizer(wx.VERTICAL)
610	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
611	lineSizer.Add(wx.StaticText(General,label=' Charge flip controls: Reflection set from: '),0,WACV)
612	refList = wx.ComboBox(General,-1,value=Flip['RefList'],choices=refList,
613	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
614	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
615	lineSizer.Add(refList,0,WACV)
616	lineSizer.Add(wx.StaticText(General,label=' Normalizing element: '),0,WACV)
617	normElem = wx.Button(General,label=Flip['Norm element'],style=wx.TE_READONLY)
618	normElem.Bind(wx.EVT_BUTTON,OnNormElem)
619	lineSizer.Add(normElem,0,WACV)
620	flipSizer.Add(lineSizer,0,WACV)
621	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
622	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,WACV)
623	flipRes = wx.TextCtrl(General,value='%.2f'%(Flip['Resolution']),style=wx.TE_PROCESS_ENTER)
624	flipRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
625	flipRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
626	line2Sizer.Add(flipRes,0,WACV)
627	line2Sizer.Add(wx.StaticText(General,label=' k-Factor (0.1-1.2): '),0,WACV)
628	kFactor = wx.TextCtrl(General,value='%.3f'%(Flip['k-factor']),style=wx.TE_PROCESS_ENTER)
629	kFactor.Bind(wx.EVT_TEXT_ENTER,OnkFactor)
630	kFactor.Bind(wx.EVT_KILL_FOCUS,OnkFactor)
631	line2Sizer.Add(kFactor,0,WACV)
632	line2Sizer.Add(wx.StaticText(General,label=' k-Max (>=10.0): '),0,WACV)
633	kMax = wx.TextCtrl(General,value='%.1f'%(Flip['k-Max']),style=wx.TE_PROCESS_ENTER)
634	kMax.Bind(wx.EVT_TEXT_ENTER,OnkMax)
635	kMax.Bind(wx.EVT_KILL_FOCUS,OnkMax)
636	line2Sizer.Add(kMax,0,WACV)
637	flipSizer.Add(line2Sizer,0,WACV)
638	return flipSizer
639
640	def MCSASizer():
641	Ind = {}
642
643	def OnRefList(event):
644	MCSAdata['Data source'] = refList.GetValue()
645
646	def OnDmin(event):
647	try:
648	val = float(dmin.GetValue())
649	if 1.0 <= val < 5.0:
650	MCSAdata['dmin'] = val
651	except ValueError:
652	pass
653	dmin.SetValue("%.3f"%(MCSAdata['dmin'])) #reset in case of error
654	MCSAdata['newDmin'] = True
655
656	def OnCycles(event):
657	MCSAdata['Cycles'] = int(cycles.GetValue())
658
659	def OnAlist(event):
660	MCSAdata['Algorithm'] = Alist.GetValue()
661	wx.CallAfter(UpdateGeneral)
662
663	def OnSlope(event):
664	try:
665	val = float(slope.GetValue())
666	if .25 <= val < 1.0:
667	MCSAdata['log slope'] = val
668	except ValueError:
669	pass
670	slope.SetValue("%.3f"%(MCSAdata['log slope'])) #reset in case of error
671
672	def OnAjump(event):
673	Obj = event.GetEventObject()
674	name,ind = Indx[Obj.GetId()]
675	try:
676	val = float(Obj.GetValue())
677	if .0 <= val <= 1.0:
678	MCSAdata[name][ind] = val
679	except ValueError:
680	pass
681	Obj.SetValue("%.3f"%(MCSAdata[name][ind]))
682
683	def OnRanStart(event):
684	MCSAdata['ranStart'] = ranStart.GetValue()
685
686	def OnAutoRan(event):
687	MCSAdata['autoRan'] = autoRan.GetValue()
688
689	def OnRanRange(event):
690	try:
691	val = float(ranRange.GetValue())/100
692	if 0.01 <= val <= 0.99:
693	MCSAdata['ranRange'] = val
694	except ValueError:
695	pass
696	ranRange.SetValue('%.1f'%(MCSAdata['ranRange']*100.))
697
698	def OnAnneal(event):
699	Obj = event.GetEventObject()
700	ind,fmt = Indx[Obj.GetId()]
701	if ind == 2: #No. trials
702	try:
703	val = int(Obj.GetValue())
704	if 1 <= val:
705	MCSAdata['Annealing'][ind] = val
706	except ValueError:
707	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
708	else:
709	try:
710	val = float(Obj.GetValue())
711	if .0 <= val:
712	MCSAdata['Annealing'][ind] = val
713	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
714	except ValueError:
715	MCSAdata['Annealing'][ind] = None
716	Obj.SetValue(str(MCSAdata['Annealing'][ind]))
717
718	refList = []
719	if len(data['Pawley ref']):
720	refList = ['Pawley reflections']
721	for item in data['Histograms'].keys():
722	if 'HKLF' in item or 'PWDR' in item:
723	refList.append(item)
724	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
725	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
726	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,WACV)
727	refList = wx.ComboBox(General,-1,value=MCSAdata['Data source'],choices=refList,
728	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
729	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
730	lineSizer.Add(refList,0,WACV)
731	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,WACV)
732	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['dmin']),style=wx.TE_PROCESS_ENTER)
733	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
734	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
735	lineSizer.Add(dmin,0,WACV)
736	mcsaSizer.Add(lineSizer)
737	mcsaSizer.Add((5,5),)
738	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
739	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,WACV)
740	Cchoice = ['1','2','4','8','16','32','64','128','256']
741	cycles = wx.ComboBox(General,-1,value=str(MCSAdata.get('Cycles',1)),choices=Cchoice,
742	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
743	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
744	line2Sizer.Add(cycles,0,WACV)
745	line2Sizer.Add((5,0),)
746	ranStart = wx.CheckBox(General,-1,label=' MC/SA Refine at ')
747	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
748	ranStart.SetValue(MCSAdata.get('ranStart',False))
749	line2Sizer.Add(ranStart,0,WACV)
750	ranRange = wx.TextCtrl(General,-1,value='%.1f'%(MCSAdata.get('ranRange',0.10)*100),style=wx.TE_PROCESS_ENTER)
751	ranRange.Bind(wx.EVT_TEXT_ENTER,OnRanRange)
752	ranRange.Bind(wx.EVT_KILL_FOCUS,OnRanRange)
753	line2Sizer.Add(ranRange,0,WACV)
754	line2Sizer.Add(wx.StaticText(General,label='% of ranges. '),0,WACV)
755	# autoRan = wx.CheckBox(General,-1,label=' Do auto range reduction? ')
756	# autoRan.Bind(wx.EVT_CHECKBOX, OnAutoRan)
757	# autoRan.SetValue(MCSAdata.get('autoRan',False))
758	# line2Sizer.Add(autoRan,0,WACV)
759	mcsaSizer.Add(line2Sizer)
760	mcsaSizer.Add((5,5),)
761	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
762	Achoice = ['log','fast'] #these work
763	# Achoice = ['log','fast','cauchy','boltzmann']
764	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,WACV)
765	Alist = wx.ComboBox(General,-1,value=MCSAdata['Algorithm'],choices=Achoice,
766	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
767	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
768	line3Sizer.Add(Alist,0,WACV)
769	if MCSAdata['Algorithm'] in ['fast','boltzmann','cauchy']:
770	Names = [' A-jump: ',' B-jump: ']
771	parms = 'Jump coeff'
772	if MCSAdata['Algorithm'] in ['boltzmann','cauchy']:
773	Names = [' A-jump: ']
774	elif 'fast' in MCSAdata['Algorithm']:
775	Names = [' quench: ',' m-factor: ',' n-factor: ']
776	parms = 'fast parms'
777	for i,name in enumerate(Names):
778	line3Sizer.Add(wx.StaticText(General,label=name),0,WACV)
779	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata[parms][i]),style=wx.TE_PROCESS_ENTER)
780	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
781	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
782	Indx[Ajump.GetId()] = [parms,i]
783	line3Sizer.Add(Ajump,0,WACV)
784	elif 'log' in MCSAdata['Algorithm']:
785	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,WACV)
786	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['log slope']),style=wx.TE_PROCESS_ENTER)
787	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
788	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
789	line3Sizer.Add(slope,0,WACV)
790	mcsaSizer.Add(line3Sizer)
791	mcsaSizer.Add((5,5),)
792	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
793	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,WACV)
794	names = [' Start temp: ',' Final temp: ',' No. trials: ']
795	fmts = ['%.1f','%.5f','%d']
796	for i,[name,fmt] in enumerate(zip(names,fmts)):
797	if MCSAdata['Annealing'][i]:
798	text = fmt%(MCSAdata['Annealing'][i])
799	else:
800	text = 'None'
801	line3Sizer.Add(wx.StaticText(General,label=name),0,WACV)
802	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
803	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
804	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
805	Indx[anneal.GetId()] = [i,fmt]
806	line3Sizer.Add(anneal,0,WACV)
807	mcsaSizer.Add(line3Sizer)
808	return mcsaSizer
809
810	# UpdateGeneral execution continues here
811	if General.GetSizer():
812	General.GetSizer().Clear(True)
813	mainSizer = wx.BoxSizer(wx.VERTICAL)
814	mainSizer.Add((5,5),0)
815	mainSizer.Add(NameSizer(),0)
816	mainSizer.Add((5,5),0)
817	mainSizer.Add(CellSizer(),0)
818	mainSizer.Add((5,5),0)
819
820	Indx = {}
821	denSizer = None
822	if len(generalData['AtomTypes']):
823	denSizer = DenSizer()
824	mainSizer.Add(denSizer[0])
825	mainSizer.Add((5,5),0)
826	mainSizer.Add(ElemSizer())
827	G2gd.HorizontalLine(mainSizer,General)
828
829	mainSizer.Add(PawleySizer())
830	G2gd.HorizontalLine(mainSizer,General)
831
832	mainSizer.Add(MapSizer())
833	G2gd.HorizontalLine(mainSizer,General)
834
835	mainSizer.Add(FlipSizer())
836	G2gd.HorizontalLine(mainSizer,General)
837
838	mainSizer.Add(MCSASizer())
839	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
840	G2frame.dataFrame.SetStatusText('')
841
842	################################################################################
843	##### Atom routines
844	################################################################################
845
846	def FillAtomsGrid(Atoms):
847	'''Display the contents of the Atoms tab
848	'''
849	def RefreshAtomGrid(event):
850
851	r,c = event.GetRow(),event.GetCol()
852	if r < 0 and c < 0:
853	for row in range(Atoms.GetNumberRows()):
854	Atoms.SelectRow(row,True)
855	if r < 0: #double click on col label! Change all atoms!
856	sel = -1
857	noSkip = True
858	if Atoms.GetColLabelValue(c) == 'refine':
859	Type = generalData['Type']
860	if Type in ['nuclear','macromolecular']:
861	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
862	elif Type in ['magnetic',]:
863	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
864	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
865	if dlg.ShowModal() == wx.ID_OK:
866	sel = dlg.GetSelections()
867	parms = ''
868	for x in sel:
869	parms += choice[x][0]
870	dlg.Destroy()
871	elif Atoms.GetColLabelValue(c) == 'I/A':
872	choice = ['Isotropic','Anisotropic']
873	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
874	if dlg.ShowModal() == wx.ID_OK:
875	sel = dlg.GetSelection()
876	parms = choice[sel][0]
877	dlg.Destroy()
878	elif Atoms.GetColLabelValue(c) == 'Type':
879	choice = generalData['AtomTypes']
880	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
881	if dlg.ShowModal() == wx.ID_OK:
882	sel = dlg.GetSelection()
883	parms = choice[sel]
884	noSkip = False
885	Atoms.ClearSelection()
886	for row in range(Atoms.GetNumberRows()):
887	if parms == atomData[row][c]:
888	Atoms.SelectRow(row,True)
889	dlg.Destroy()
890	SetupGeneral()
891	elif Atoms.GetColLabelValue(c) == 'residue':
892	choice = []
893	for r in range(Atoms.GetNumberRows()):
894	if str(atomData[r][c]) not in choice:
895	choice.append(str(atomData[r][c]))
896	choice.sort()
897	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
898	if dlg.ShowModal() == wx.ID_OK:
899	sel = dlg.GetSelection()
900	parms = choice[sel]
901	noSkip = False
902	Atoms.ClearSelection()
903	for row in range(Atoms.GetNumberRows()):
904	if parms == atomData[row][c]:
905	Atoms.SelectRow(row,True)
906	dlg.Destroy()
907	elif Atoms.GetColLabelValue(c) == 'res no':
908	choice = []
909	for r in range(Atoms.GetNumberRows()):
910	if str(atomData[r][c]) not in choice:
911	choice.append(str(atomData[r][c]))
912	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
913	if dlg.ShowModal() == wx.ID_OK:
914	sel = dlg.GetSelection()
915	parms = choice[sel]
916	noSkip = False
917	Atoms.ClearSelection()
918	for row in range(Atoms.GetNumberRows()):
919	if int(parms) == atomData[row][c]:
920	Atoms.SelectRow(row,True)
921	dlg.Destroy()
922	elif Atoms.GetColLabelValue(c) == 'chain':
923	choice = []
924	for r in range(Atoms.GetNumberRows()):
925	if atomData[r][c] not in choice:
926	choice.append(atomData[r][c])
927	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
928	if dlg.ShowModal() == wx.ID_OK:
929	sel = dlg.GetSelection()
930	parms = choice[sel]
931	noSkip = False
932	Atoms.ClearSelection()
933	for row in range(Atoms.GetNumberRows()):
934	if parms == atomData[row][c]:
935	Atoms.SelectRow(row,True)
936	dlg.Destroy()
937	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
938	pass #& then change all 'I' atoms
939	if sel >= 0 and noSkip:
940	ui = colLabels.index('U11')
941	us = colLabels.index('Uiso')
942	ss = colLabels.index('site sym')
943	for r in range(Atoms.GetNumberRows()):
944	ID = atomData[r][-1]
945	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
946	if parms == 'A': #'I' --> 'A'
947	Uiso = float(Atoms.GetCellValue(r,us))
948	sytsym = atomData[r][ss]
949	CSI = G2spc.GetCSuinel(sytsym)
950	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
951	atomData[r][us] = 0.0
952	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
953	for i in range(6):
954	ci = ui+i
955	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
956	if CSI[2][i]:
957	Atoms.SetCellStyle(r,ci,WHITE,False)
958	else: #'A' --> 'I'
959	Uij = atomData[r][ui:ui+6]
960	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
961	atomData[r][us] = Uiso
962	Atoms.SetCellStyle(r,us,WHITE,False)
963	for i in range(6):
964	ci = ui+i
965	atomData[r][ci] = 0.0
966	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
967	if not Atoms.IsReadOnly(r,c):
968	if Atoms.GetColLabelValue(c) == 'refine':
969	rbExcl = rbAtmDict.get(atomData[r][-1],'')
970	if rbExcl:
971	for excl in rbExcl:
972	atomData[r][c] = parms.replace(excl,'')
973	else:
974	atomData[r][c] = parms
975	else:
976	atomData[r][c] = parms
977	if 'Atoms' in data['Drawing']:
978	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
979	wx.CallAfter(Paint)
980
981	def ChangeAtomCell(event):
982
983	def chkUij(Uij,CSI): #needs to do something!!!
984	return Uij
985
986	r,c = event.GetRow(),event.GetCol()
987	if r >= 0 and c >= 0:
988	ID = atomData[r][-1]
989	if Atoms.GetColLabelValue(c) in ['x','y','z']:
990	ci = colLabels.index('x')
991	XYZ = atomData[r][ci:ci+3]
992	if None in XYZ:
993	XYZ = [0,0,0]
994	SScol = colLabels.index('site sym')
995	Mulcol = colLabels.index('mult')
996	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
997	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
998	atomData[r][SScol] = Sytsym
999	atomData[r][Mulcol] = Mult
1000	if atomData[r][colLabels.index('I/A')] == 'A':
1001	ui = colLabels.index('U11')
1002	CSI = G2spc.GetCSuinel(Sytsym)
1003	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
1004	for i in range(6):
1005	ci = i+ui
1006	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1007	if CSI[2][i]:
1008	Atoms.SetCellStyle(r,ci,WHITE,False)
1009	SetupGeneral()
1010	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1011	if atomData[r][c] == 'I':
1012	Uij = atomData[r][c+2:c+8]
1013	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1014	Atoms.SetCellStyle(r,c+1,WHITE,False)
1015	Atoms.SetCellTextColour(r,c+1,BLACK)
1016	for i in range(6):
1017	ci = i+colLabels.index('U11')
1018	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1019	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1020	atomData[r][ci] = 0.0
1021	else:
1022	value = atomData[r][c+1]
1023	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1024	atomData[r][c+1] = 0.0
1025	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1026	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1027	for i in range(6):
1028	ci = i+colLabels.index('U11')
1029	atomData[r][ci] = value*CSI[3][i]
1030	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1031	Atoms.SetCellTextColour(r,ci,BLACK)
1032	if CSI[2][i]:
1033	Atoms.SetCellStyle(r,ci,WHITE,False)
1034	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1035	value = atomData[r][c]
1036	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1037	iUij = CSI[0][c-colLabels.index('U11')]
1038	for i in range(6):
1039	if iUij == CSI[0][i]:
1040	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1041	elif Atoms.GetColLabelValue(c) == 'refine':
1042	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1043	if 'Atoms' in data['Drawing']:
1044	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1045	wx.CallAfter(Paint)
1046
1047	def AtomTypeSelect(event):
1048	r,c = event.GetRow(),event.GetCol()
1049	if Atoms.GetColLabelValue(c) == 'Type':
1050	PE = G2elemGUI.PickElement(G2frame)
1051	if PE.ShowModal() == wx.ID_OK:
1052	if PE.Elem != 'None':
1053	atomData[r][c] = PE.Elem.strip()
1054	name = atomData[r][c]
1055	if len(name) in [2,4]:
1056	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1057	else:
1058	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1059	PE.Destroy()
1060	SetupGeneral()
1061	wx.CallAfter(Paint)
1062	value = Atoms.GetCellValue(r,c)
1063	atomData[r][c] = value
1064	ID = atomData[r][-1]
1065	if 'Atoms' in data['Drawing']:
1066	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1067	SetupGeneral()
1068	else:
1069	event.Skip()
1070
1071	def RowSelect(event):
1072	r,c = event.GetRow(),event.GetCol()
1073	if not (event.AltDown() or (event.ShiftDown() and event.ControlDown())):
1074	Atoms.frm = -1
1075	G2frame.dataFrame.SetStatusText('')
1076	if r < 0 and c < 0:
1077	if Atoms.IsSelection():
1078	Atoms.ClearSelection()
1079	elif c < 0: #only row clicks
1080	if event.ControlDown() and not event.ShiftDown():
1081	if r in Atoms.GetSelectedRows():
1082	Atoms.DeselectRow(r)
1083	else:
1084	Atoms.SelectRow(r,True)
1085	elif event.ShiftDown() and not event.ControlDown():
1086	indxs = Atoms.GetSelectedRows()
1087	Atoms.ClearSelection()
1088	ibeg = 0
1089	if indxs:
1090	ibeg = indxs[-1]
1091	for row in range(ibeg,r+1):
1092	Atoms.SelectRow(row,True)
1093	elif event.AltDown() or (event.ShiftDown() and event.ControlDown()):
1094	if atomData[r][-1] in rbAtmDict:
1095	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1096	Atoms.frm = -1
1097	Atoms.ClearSelection()
1098	else:
1099	if Atoms.frm < 0: #pick atom to be moved
1100	Atoms.frm = r
1101	Atoms.SelectRow(r,True)
1102	n = colLabels.index('Name')
1103	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1104	else: #move it
1105	item = atomData.pop(Atoms.frm)
1106	atomData.insert(r,item)
1107	Atoms.frm = -1
1108	G2frame.dataFrame.SetStatusText('')
1109	wx.CallAfter(Paint)
1110	else:
1111	Atoms.ClearSelection()
1112	Atoms.SelectRow(r,True)
1113
1114	def ChangeSelection(event):
1115	r,c = event.GetRow(),event.GetCol()
1116	if r < 0 and c < 0:
1117	Atoms.ClearSelection()
1118	if c < 0:
1119	if r in Atoms.GetSelectedRows():
1120	Atoms.DeselectRow(r)
1121	else:
1122	Atoms.SelectRow(r,True)
1123	if r < 0:
1124	if c in Atoms.GetSelectedCols():
1125	Atoms.DeselectCol(c)
1126	else:
1127	Atoms.SelectCol(c,True)
1128
1129	def Paint():
1130
1131	table = []
1132	rowLabels = []
1133	for i,atom in enumerate(atomData):
1134	table.append(atom)
1135	rowLabels.append(str(i))
1136	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1137	Atoms.SetTable(atomTable, True)
1138	Atoms.frm = -1
1139	colType = colLabels.index('Type')
1140	colR = colLabels.index('refine')
1141	colSS = colLabels.index('site sym')
1142	colX = colLabels.index('x')
1143	colIA = colLabels.index('I/A')
1144	colU11 = colLabels.index('U11')
1145	colUiso = colLabels.index('Uiso')
1146	attr = wx.grid.GridCellAttr()
1147	attr.IncRef() #fix from Jim Hester
1148	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1149	for c in range(colX,colX+3):
1150	Atoms.SetColAttr(c, attr)
1151	for i in range(colU11-1,colU11+6):
1152	Atoms.SetColSize(i,50)
1153	for row in range(Atoms.GetNumberRows()):
1154	atId = atomData[row][-1]
1155	rbExcl = rbAtmDict.get(atId,'')
1156	Atoms.SetReadOnly(row,colSS,True) #site sym
1157	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1158	if Atoms.GetCellValue(row,colIA) == 'A':
1159	try: #patch for sytsym name changes
1160	CSI = G2spc.GetCSuinel(atomData[row][colSS])
1161	except KeyError:
1162	Sytsym = G2spc.SytSym(atomData[row][colX:colX+3],SGData)[0]
1163	atomData[row][colSS] = Sytsym
1164	CSI = G2spc.GetCSuinel(Sytsym)
1165	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1166	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1167	for i in range(6):
1168	ci = colU11+i
1169	Atoms.SetCellTextColour(row,ci,BLACK)
1170	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1171	if CSI[2][i] and 'U' not in rbExcl:
1172	Atoms.SetCellStyle(row,ci,WHITE,False)
1173	else:
1174	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1175	Atoms.SetCellTextColour(row,colUiso,BLACK)
1176	if 'U' in rbExcl:
1177	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1178	for i in range(6):
1179	ci = colU11+i
1180	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1181	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1182	if 'X' in rbExcl:
1183	for c in range(0,colX+3):
1184	if c != colR:
1185	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1186	Atoms.AutoSizeColumns(False)
1187
1188	# FillAtomsGrid executable code starts here
1189	generalData = data['General']
1190	atomData = data['Atoms']
1191	DData = data['Drawing']
1192	resRBData = data['RBModels'].get('Residue',[])
1193	vecRBData = data['RBModels'].get('Vector',[])
1194	rbAtmDict = {}
1195	for rbObj in resRBData+vecRBData:
1196	exclList = ['X' for i in range(len(rbObj['Ids']))]
1197	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1198	if rbObj['ThermalMotion'][0] != 'None':
1199	for id in rbObj['Ids']:
1200	rbAtmDict[id] += 'U'
1201	# exclList will be 'x' or 'xu' if TLS used in RB
1202	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1203	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1204	if atomData:
1205	for item in Items:
1206	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1207	else:
1208	for item in Items:
1209	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1210	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1211	if 'showABC' in data['Drawing']:
1212	for item in Items:
1213	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1214	else:
1215	for item in Items:
1216	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1217
1218	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1219	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1220	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1221	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1222	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1223	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1224	if generalData['Type'] == 'magnetic':
1225	colLabels += ['Mx','My','Mz']
1226	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1227	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1228	elif generalData['Type'] == 'macromolecular':
1229	colLabels = ['res no','residue','chain'] + colLabels
1230	Types = [wg.GRID_VALUE_STRING,
1231	wg.GRID_VALUE_CHOICE+AAchoice,
1232	wg.GRID_VALUE_STRING] + Types
1233	elif generalData['Type'] == 'modulated':
1234	Types += []
1235	colLabels += []
1236	SGData = data['General']['SGData']
1237	G2frame.dataFrame.SetStatusText('')
1238	if SGData['SGPolax']:
1239	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1240	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1241	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1242	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1243	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1244	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1245	Atoms.SetMargins(0,0)
1246
1247	G2frame.dataFrame.setSizePosLeft([700,300])
1248	Paint()
1249
1250	def OnAtomAdd(event):
1251	AtomAdd(0,0,0)
1252	FillAtomsGrid(Atoms)
1253	event.StopPropagation()
1254	if data['Drawing']:
1255	G2plt.PlotStructure(G2frame,data)
1256
1257	def OnAtomViewAdd(event):
1258	try:
1259	drawData = data['Drawing']
1260	x,y,z = drawData['viewPoint'][0]
1261	AtomAdd(x,y,z)
1262	except:
1263	AtomAdd(0,0,0)
1264	FillAtomsGrid(Atoms)
1265	event.StopPropagation()
1266	G2plt.PlotStructure(G2frame,data)
1267
1268	def AtomAdd(x,y,z,El='H',Name='UNK'):
1269	atomData = data['Atoms']
1270	generalData = data['General']
1271	Ncol = Atoms.GetNumberCols()
1272	atId = ran.randint(0,sys.maxint)
1273	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1274	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1275	if generalData['Type'] == 'macromolecular':
1276	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1277	elif generalData['Type'] == 'nuclear':
1278	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1279	elif generalData['Type'] == 'magnetic':
1280	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1281	SetupGeneral()
1282	if 'Atoms' in data['Drawing']:
1283	DrawAtomAdd(data['Drawing'],atomData[-1])
1284
1285	def OnAtomInsert(event):
1286	AtomInsert(0,0,0)
1287	FillAtomsGrid(Atoms)
1288	event.StopPropagation()
1289	G2plt.PlotStructure(G2frame,data)
1290
1291	def OnAtomViewInsert(event):
1292	if 'Drawing' in data:
1293	drawData = data['Drawing']
1294	x,y,z = drawData['viewPoint'][0]
1295	AtomAdd(x,y,z)
1296	FillAtomsGrid(Atoms)
1297	event.StopPropagation()
1298
1299	def OnAtomMove(event):
1300	drawData = data['Drawing']
1301	atomData = data['Atoms']
1302	x,y,z = drawData['viewPoint'][0]
1303	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1304	cx = colLabels.index('x')
1305	indx = Atoms.GetSelectedRows()
1306	if len(indx) != 1:
1307	print '** ERROR - only one atom can be moved **'
1308	elif atomData[indx[0]][-1] in rbAtmDict:
1309	print '** ERROR - Atoms in rigid bodies can not be moved **'
1310	else:
1311	atomData[indx[0]][cx:cx+3] = [x,y,z]
1312	SetupGeneral()
1313	FillAtomsGrid(Atoms)
1314	ID = atomData[indx[0]][-1]
1315	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1316	G2plt.PlotStructure(G2frame,data)
1317	event.StopPropagation()
1318
1319	def DrawAtomsReplaceByID(drawingData,atom,ID):
1320	IDs = [ID,]
1321	atomData = drawingData['Atoms']
1322	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1323	for ind in indx:
1324	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1325
1326	def MakeDrawAtom(atom,oldatom=None):
1327	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1328	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1329	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1330	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1331	generalData = data['General']
1332	SGData = generalData['SGData']
1333	if generalData['Type'] == 'nuclear':
1334	if oldatom:
1335	opr = oldatom[5]
1336	if atom[9] == 'A':
1337	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1338	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1339	else:
1340	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1341	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1342	else:
1343	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1344	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1345	ct,cs = [1,8] #type & color
1346	elif generalData['Type'] == 'macromolecular':
1347	try:
1348	oneLetter = AA3letter.index(atom[1])
1349	except ValueError:
1350	oneLetter = -1
1351	atomInfo = [[atom[1].strip()+atom[0],]+
1352	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1353	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1354	ct,cs = [4,11] #type & color
1355	elif generalData['Type'] == 'magnetic':
1356	if oldatom:
1357	atomInfo = [atom[:2]+oldatom[3:]][0]
1358	else:
1359	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1360	ct,cs = [1,8] #type & color
1361	# elif generalData['Type'] == 'modulated':
1362	# ????? for future
1363	atNum = generalData['AtomTypes'].index(atom[ct])
1364	atomInfo[cs] = list(generalData['Color'][atNum])
1365	return atomInfo
1366
1367	def AtomInsert(x,y,z):
1368	indx = Atoms.GetSelectedRows()
1369	if indx:
1370	indx = indx[0]
1371	atomData = data['Atoms']
1372	generalData = data['General']
1373	Ncol = Atoms.GetNumberCols()
1374	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1375	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1376	atId = ran.randint(0,sys.maxint)
1377	if generalData['Type'] == 'macromolecular':
1378	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1379	elif generalData['Type'] == 'nuclear':
1380	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1381	elif generalData['Type'] == 'magnetic':
1382	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1383	SetupGeneral()
1384
1385	def AtomDelete(event):
1386	indx = Atoms.GetSelectedRows()
1387	IDs = []
1388	if indx:
1389	atomData = data['Atoms']
1390	indx.reverse()
1391	for ind in indx:
1392	atom = atomData[ind]
1393	if atom[-1] in rbAtmDict:
1394	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1395	else:
1396	IDs.append(atom[-1])
1397	del atomData[ind]
1398	if 'Atoms' in data['Drawing']:
1399	DrawAtomsDeleteByIDs(IDs)
1400	wx.CallAfter(FillAtomsGrid,Atoms)
1401	G2plt.PlotStructure(G2frame,data)
1402	SetupGeneral()
1403	event.StopPropagation()
1404
1405	def AtomRefine(event):
1406	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1407	c = colLabels.index('refine')
1408	indx = Atoms.GetSelectedRows()
1409	if indx:
1410	atomData = data['Atoms']
1411	generalData = data['General']
1412	Type = generalData['Type']
1413	if Type in ['nuclear','macromolecular']:
1414	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1415	elif Type == 'magnetic':
1416	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1417	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1418	if dlg.ShowModal() == wx.ID_OK:
1419	sel = dlg.GetSelections()
1420	parms = ''
1421	for x in sel:
1422	parms += choice[x][0]
1423	for r in indx:
1424	if not Atoms.IsReadOnly(r,c):
1425	atomData[r][c] = parms
1426	Atoms.ForceRefresh()
1427	dlg.Destroy()
1428
1429	def AtomModify(event):
1430	indx = Atoms.GetSelectedRows()
1431	if indx:
1432	atomData = data['Atoms']
1433	generalData = data['General']
1434	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1435	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1436	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1437	parm = ''
1438	if dlg.ShowModal() == wx.ID_OK:
1439	sel = dlg.GetSelection()
1440	parm = choices[sel]
1441	cid = colLabels.index(parm)
1442	dlg.Destroy()
1443	if parm in ['Type']:
1444	dlg = G2elemGUI.PickElement(G2frame)
1445	if dlg.ShowModal() == wx.ID_OK:
1446	if dlg.Elem not in ['None']:
1447	El = dlg.Elem.strip()
1448	for r in indx:
1449	if not Atoms.IsReadOnly(r,cid):
1450	atomData[r][cid] = El
1451	if len(El) in [2,4]:
1452	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1453	else:
1454	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1455	SetupGeneral()
1456	if 'Atoms' in data['Drawing']:
1457	for r in indx:
1458	ID = atomData[r][-1]
1459	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1460	FillAtomsGrid(Atoms)
1461	dlg.Destroy()
1462	elif parm in ['Name',]:
1463	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1464	wx.YES_NO \| wx.ICON_QUESTION)
1465	try:
1466	result = dlg.ShowModal()
1467	if result == wx.ID_YES:
1468	for r in indx:
1469	if not Atoms.IsReadOnly(r,cid+1):
1470	El = atomData[r][cid+1]
1471	if len(El) in [2,4]:
1472	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1473	else:
1474	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1475	FillAtomsGrid(Atoms)
1476	finally:
1477	dlg.Destroy()
1478
1479	elif parm in ['I/A']:
1480	choices = ['Isotropic','Anisotropic']
1481	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1482	if dlg.ShowModal() == wx.ID_OK:
1483	sel = dlg.GetSelection()
1484	parm = choices[sel][0]
1485	for r in indx:
1486	if not Atoms.IsReadOnly(r,cid):
1487	atomData[r][cid] = parm
1488	FillAtomsGrid(Atoms)
1489	dlg.Destroy()
1490	elif parm in ['frac','Uiso']:
1491	limits = [0.,1.]
1492	val = 1.0
1493	if parm in ['Uiso']:
1494	limits = [0.,0.25]
1495	val = 0.01
1496	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1497	if dlg.ShowModal() == wx.ID_OK:
1498	parm = dlg.GetValue()
1499	for r in indx:
1500	if not Atoms.IsReadOnly(r,cid):
1501	atomData[r][cid] = parm
1502	SetupGeneral()
1503	FillAtomsGrid(Atoms)
1504	dlg.Destroy()
1505	elif parm in ['x','y','z']:
1506	limits = [-1.,1.]
1507	val = 0.
1508	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1509	if dlg.ShowModal() == wx.ID_OK:
1510	parm = dlg.GetValue()
1511	for r in indx:
1512	if not Atoms.IsReadOnly(r,cid):
1513	atomData[r][cid] += parm
1514	SetupGeneral()
1515	FillAtomsGrid(Atoms)
1516	dlg.Destroy()
1517
1518	def AtomTransform(event):
1519	indx = Atoms.GetSelectedRows()
1520	if indx:
1521	generalData = data['General']
1522	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1523	cx = colLabels.index('x')
1524	cuia = colLabels.index('I/A')
1525	cuij = colLabels.index('U11')
1526	css = colLabels.index('site sym')
1527	atomData = data['Atoms']
1528	generalData = data['General']
1529	SGData = generalData['SGData']
1530	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1531	New = False
1532	try:
1533	if dlg.ShowModal() == wx.ID_OK:
1534	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1535	Cell = np.array(Cell)
1536	cent = SGData['SGCen'][Cent]
1537	M,T = SGData['SGOps'][Opr]
1538	for ind in indx:
1539	XYZ = np.array(atomData[ind][cx:cx+3])
1540	XYZ = np.inner(M,XYZ)+T
1541	if Inv:
1542	XYZ = -XYZ
1543	XYZ = XYZ+cent+Cell
1544	if Force:
1545	XYZ = G2spc.MoveToUnitCell(XYZ)
1546	if New:
1547	atom = copy.copy(atomData[ind])
1548	else:
1549	atom = atomData[ind]
1550	atom[cx:cx+3] = XYZ
1551	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1552	if atom[cuia] == 'A':
1553	Uij = atom[cuij:cuij+6]
1554	U = G2spc.Uij2U(Uij)
1555	U = np.inner(np.inner(M,U),M)
1556	Uij = G2spc.U2Uij(U)
1557	atom[cuij:cuij+6] = Uij
1558	if New:
1559	atomData.append(atom)
1560	finally:
1561	dlg.Destroy()
1562	Atoms.ClearSelection()
1563	if New:
1564	FillAtomsGrid(Atoms)
1565	else:
1566	Atoms.ForceRefresh()
1567
1568	def OnDistAnglePrt(event):
1569	'save distances and angles to a file'
1570	fp = file(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile
1571	)[0]+'.disagl'),'w')
1572	OnDistAngle(event,fp=fp)
1573	fp.close()
1574
1575	def OnDistAngle(event,fp=None):
1576	'Compute distances and angles'
1577	indx = Atoms.GetSelectedRows()
1578	Oxyz = []
1579	xyz = []
1580	DisAglData = {}
1581	DisAglCtls = {}
1582	if indx:
1583	generalData = data['General']
1584	DisAglData['OrigIndx'] = indx
1585	if 'DisAglCtls' in generalData:
1586	DisAglCtls = generalData['DisAglCtls']
1587	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1588	if dlg.ShowModal() == wx.ID_OK:
1589	DisAglCtls = dlg.GetData()
1590	else:
1591	dlg.Destroy()
1592	return
1593	dlg.Destroy()
1594	generalData['DisAglCtls'] = DisAglCtls
1595	atomData = data['Atoms']
1596	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1597	cx = colLabels.index('x')
1598	cn = colLabels.index('Name')
1599	for i,atom in enumerate(atomData):
1600	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1601	if i in indx:
1602	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1603	DisAglData['OrigAtoms'] = Oxyz
1604	DisAglData['TargAtoms'] = xyz
1605	generalData = data['General']
1606	DisAglData['SGData'] = generalData['SGData']
1607	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1608	if 'pId' in data:
1609	DisAglData['pId'] = data['pId']
1610	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1611	try:
1612	if fp:
1613	G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
1614	else:
1615	G2stMn.PrintDistAngle(DisAglCtls,DisAglData)
1616	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1617	G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types')
1618	else:
1619	print "select one or more rows of atoms"
1620	G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
1621
1622	def OnIsoDistortCalc(event):
1623	'''Compute the ISODISTORT mode values from the current coordinates.
1624	Called in response to the (Phase/Atoms tab) AtomCompute
1625	"Compute ISODISTORT mode values" menu item, which should be enabled
1626	only when Phase['ISODISTORT'] is defined.
1627	'''
1628	def _onClose(event):
1629	dlg.EndModal(wx.ID_CANCEL)
1630	def fmtHelp(item,fullname):
1631	helptext = "A new variable"
1632	if item[-3]:
1633	helptext += " named "+str(item[-3])
1634	helptext += " is a linear combination of the following parameters:\n"
1635	first = True
1636	for term in item[:-3]:
1637	line = ''
1638	var = str(term[1])
1639	m = term[0]
1640	if first:
1641	first = False
1642	line += ' = '
1643	else:
1644	if m >= 0:
1645	line += ' + '
1646	else:
1647	line += ' - '
1648	m = abs(m)
1649	line += '%.3f*%s '%(m,var)
1650	varMean = G2obj.fmtVarDescr(var)
1651	helptext += "\n" + line + " ("+ varMean + ")"
1652	helptext += '\n\nISODISTORT full name: '+str(fullname)
1653	return helptext
1654
1655	if 'ISODISTORT' not in data:
1656	raise Exception,"Should not happen: 'ISODISTORT' not in data"
1657	if len(data.get('Histograms',[])) == 0:
1658	G2frame.ErrorDialog(
1659	'No data',
1660	'Sorry, this computation requires that a histogram first be added to the phase'
1661	)
1662	return
1663	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() # init for constraint
1664	# make a lookup table for constraints
1665	sub = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Constraints')
1666	Constraints = G2frame.PatternTree.GetItemPyData(sub)
1667	constDict = {}
1668	for item in Constraints:
1669	if item.startswith('_'): continue
1670	for c in Constraints[item]:
1671	if c[-1] != 'f' or not c[-3]: continue
1672	constDict[c[-3]] = c
1673
1674	ISO = data['ISODISTORT']
1675	parmDict,varyList = G2frame.MakeLSParmDict()
1676
1677	dlg = wx.Dialog(G2frame,wx.ID_ANY,'ISODISTORT mode values',#size=(630,400),
1678	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
1679	mainSizer = wx.BoxSizer(wx.VERTICAL)
1680	mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,
1681	'ISODISTORT mode computation for cordinates in phase '+
1682	str(data['General'].get('Name'))))
1683	aSizer = wx.BoxSizer(wx.HORIZONTAL)
1684	panel1 = wxscroll.ScrolledPanel(
1685	dlg, wx.ID_ANY,#size=(100,200),
1686	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
1687	subSizer1 = wx.FlexGridSizer(cols=2,hgap=5,vgap=2)
1688	panel2 = wxscroll.ScrolledPanel(
1689	dlg, wx.ID_ANY,#size=(100,200),
1690	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
1691	subSizer2 = wx.FlexGridSizer(cols=3,hgap=5,vgap=2)
1692	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'Parameter name '))
1693	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
1694	subSizer2.Add((-1,-1))
1695	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'Mode name '))
1696	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
1697
1698	if 'G2VarList' in ISO:
1699	deltaList = []
1700	for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']):
1701	dvar = gv.varname()
1702	var = dvar.replace('::dA','::A')
1703	albl = Ilbl[:Ilbl.rfind('_')]
1704	v = Ilbl[Ilbl.rfind('_')+1:]
1705	pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)]
1706	if var in parmDict:
1707	cval = parmDict[var][0]
1708	else:
1709	dlg.EndModal(wx.ID_CANCEL)
1710	G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var))
1711	return
1712	deltaList.append(cval-pval)
1713	modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList)
1714	for lbl,xyz,var,val,G2var in zip(ISO['IsoVarList'],deltaList,
1715	ISO['IsoModeList'],modeVals,ISO['G2ModeList']):
1716	if G2var in constDict:
1717	ch = G2gd.HelpButton(panel2,fmtHelp(constDict[G2var],var))
1718	subSizer2.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
1719	else:
1720	subSizer2.Add((-1,-1))
1721	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
1722	try:
1723	value = G2py3.FormatSigFigs(xyz)
1724	except TypeError:
1725	value = str(xyz)
1726	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1727	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
1728	try:
1729	value = G2py3.FormatSigFigs(val)
1730	except TypeError:
1731	value = str(val)
1732	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1733	if 'G2OccVarList' in ISO:
1734	deltaList = []
1735	for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']):
1736	var = gv.varname()
1737	albl = Ilbl[:Ilbl.rfind('_')]
1738	#v = Ilbl[Ilbl.rfind('_')+1:]
1739	pval = ISO['BaseOcc'][albl]
1740	if var in parmDict:
1741	cval = parmDict[var][0]
1742	else:
1743	dlg.EndModal(wx.ID_CANCEL)
1744	G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var))
1745	return
1746	deltaList.append(cval-pval)
1747	modeVals = np.inner(ISO['Var2OccMatrix'],deltaList)
1748	for lbl,xyz,var,val,G2var in zip(ISO['OccVarList'],deltaList,
1749	ISO['OccModeList'],modeVals,ISO['G2OccModeList']):
1750	if G2var in constDict:
1751	ch = G2gd.HelpButton(panel2,fmtHelp(constDict[G2var],var))
1752	subSizer2.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
1753	else:
1754	subSizer2.Add((-1,-1))
1755	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
1756	try:
1757	value = G2py3.FormatSigFigs(xyz)
1758	except TypeError:
1759	value = str(xyz)
1760	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1761	#subSizer.Add((10,-1))
1762	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
1763	try:
1764	value = G2py3.FormatSigFigs(val)
1765	except TypeError:
1766	value = str(val)
1767	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1768
1769	# finish up ScrolledPanel
1770	panel1.SetSizer(subSizer1)
1771	panel2.SetSizer(subSizer2)
1772	panel1.SetAutoLayout(1)
1773	panel1.SetupScrolling()
1774	panel2.SetAutoLayout(1)
1775	panel2.SetupScrolling()
1776	# Allow window to be enlarged but not made smaller
1777	dlg.SetSizer(mainSizer)
1778	w1,l1 = subSizer1.GetSize()
1779	w2,l2 = subSizer2.GetSize()
1780	panel1.SetMinSize((w1+10,200))
1781	panel2.SetMinSize((w2+20,200))
1782	aSizer.Add(panel1,1, wx.ALL\|wx.EXPAND,1)
1783	aSizer.Add(panel2,2, wx.ALL\|wx.EXPAND,1)
1784	mainSizer.Add(aSizer,1, wx.ALL\|wx.EXPAND,1)
1785
1786	# make OK button
1787	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
1788	btn = wx.Button(dlg, wx.ID_CLOSE)
1789	btn.Bind(wx.EVT_BUTTON,_onClose)
1790	btnsizer.Add(btn)
1791	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1792
1793	mainSizer.Fit(dlg)
1794	dlg.SetMinSize(dlg.GetSize())
1795	dlg.ShowModal()
1796	dlg.Destroy()
1797
1798	def OnReImport(event):
1799	generalData = data['General']
1800	cx,ct,cs,cia = generalData['AtomPtrs']
1801	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1802	rdlist = G2frame.OnImportGeneric(reqrdr,
1803	G2frame.ImportPhaseReaderlist,'phase')
1804	if len(rdlist) == 0: return
1805	# rdlist is only expected to have one element
1806	rd = rdlist[0]
1807	G2frame.OnFileSave(event)
1808	# rd contains all info for a phase
1809	PhaseName = rd.Phase['General']['Name']
1810	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1811	atomData = data['Atoms']
1812	atomNames = []
1813	for atom in atomData:
1814	atomNames.append(atom[:ct+1])
1815	for atom in rd.Phase['Atoms']:
1816	try:
1817	idx = atomNames.index(atom[:ct+1])
1818	atomData[idx][:-1] = atom[:-1]
1819	except ValueError:
1820	print atom[:ct+1], 'not in Atom array; not updated'
1821	wx.CallAfter(FillAtomsGrid,Atoms)
1822
1823
1824	################################################################################
1825	#Structure drawing GUI stuff
1826	################################################################################
1827
1828	def SetupDrawingData():
1829	generalData = data['General']
1830	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1831	atomData = data['Atoms']
1832	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1833	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1834	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1835	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1836	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1837	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1838	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1839	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1840	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1841	'bondList':{},'viewDir':[1,0,0]}
1842	V0 = np.array([0,0,1])
1843	V = np.inner(Amat,V0)
1844	V /= np.sqrt(np.sum(V**2))
1845	A = np.arccos(np.sum(V*V0))
1846	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1847	try:
1848	drawingData = data['Drawing']
1849	except KeyError:
1850	data['Drawing'] = {}
1851	drawingData = data['Drawing']
1852	if not drawingData: #fill with defaults if empty
1853	drawingData.update(defaultDrawing)
1854	if 'Zstep' not in drawingData:
1855	drawingData['Zstep'] = 0.5
1856	if 'contourLevel' not in drawingData:
1857	drawingData['contourLevel'] = 1.
1858	if 'viewDir' not in drawingData:
1859	drawingData['viewDir'] = [0,0,1]
1860	if 'Quaternion' not in drawingData:
1861	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1862	if 'showRigidBodies' not in drawingData:
1863	drawingData['showRigidBodies'] = True
1864	cx,ct,cs,ci = [0,0,0,0]
1865	if generalData['Type'] == 'nuclear':
1866	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1867	elif generalData['Type'] == 'macromolecular':
1868	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1869	elif generalData['Type'] == 'magnetic':
1870	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1871	# elif generalData['Type'] == 'modulated':
1872	# ????? for future
1873	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1874	if not drawingData.get('Atoms'):
1875	for atom in atomData:
1876	DrawAtomAdd(drawingData,atom)
1877	data['Drawing'] = drawingData
1878
1879	def DrawAtomAdd(drawingData,atom):
1880	drawingData['Atoms'].append(MakeDrawAtom(atom))
1881
1882	def OnRestraint(event):
1883	indx = drawAtoms.GetSelectedRows()
1884	restData = G2frame.PatternTree.GetItemPyData(
1885	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1886	drawingData = data['Drawing']
1887	generalData = data['General']
1888	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1889	cx,ct,cs,ci = drawingData['atomPtrs']
1890	atomData = drawingData['Atoms']
1891	atNames = []
1892	atXYZ = []
1893	atSymOp = []
1894	atIndx = []
1895	for item in indx:
1896	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1897	atSymOp.append(atomData[item][cs-1])
1898	atIndx.append(atomData[item][ci])
1899	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1900	try:
1901	bondData = restData[PhaseName]['Bond']
1902	except KeyError:
1903	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1904	restData[PhaseName] = {}
1905	restData[PhaseName]['Bond'] = bondData
1906	dist = G2mth.getRestDist(atXYZ,Amat)
1907	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1908	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1909	try:
1910	angleData = restData[PhaseName]['Angle']
1911	except KeyError:
1912	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1913	restData[PhaseName] = {}
1914	restData[PhaseName]['Angle'] = angleData
1915	angle = G2mth.getRestAngle(atXYZ,Amat)
1916	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1917	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1918	try:
1919	planeData = restData[PhaseName]['Plane']
1920	except KeyError:
1921	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1922	restData[PhaseName] = {}
1923	restData[PhaseName]['Plane'] = planeData
1924	plane = G2mth.getRestPlane(atXYZ,Amat)
1925	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1926	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1927	try:
1928	chiralData = restData[PhaseName]['Chiral']
1929	except KeyError:
1930	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1931	restData[PhaseName] = {}
1932	restData[PhaseName]['Chiral'] = chiralData
1933	volume = G2mth.getRestChiral(atXYZ,Amat)
1934	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1935	else:
1936	print '**** ERROR wrong number of atoms selected for this restraint'
1937	return
1938	G2frame.PatternTree.SetItemPyData(
1939	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1940
1941	def OnDefineRB(event):
1942	indx = drawAtoms.GetSelectedRows()
1943	indx.sort()
1944	RBData = G2frame.PatternTree.GetItemPyData(
1945	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1946	drawingData = data['Drawing']
1947	generalData = data['General']
1948	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1949	cx,ct,cs,ci = drawingData['atomPtrs']
1950	atomData = drawingData['Atoms']
1951	rbXYZ = []
1952	rbType = []
1953	atNames = []
1954	AtInfo = RBData['Residue']['AtInfo']
1955	for i,item in enumerate(indx):
1956	rbtype = atomData[item][ct]
1957	atNames.append(rbtype+str(i))
1958	rbType.append(rbtype)
1959	if rbtype not in AtInfo:
1960	Info = G2elem.GetAtomInfo(rbtype)
1961	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1962	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1963	rbXYZ = np.array(rbXYZ)
1964	rbXYZ -= rbXYZ[0]
1965	rbId = ran.randint(0,sys.maxint)
1966	rbName = 'UNKRB'
1967	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1968	'Edit rigid body name',rbName ,style=wx.OK)
1969	if dlg.ShowModal() == wx.ID_OK:
1970	rbName = dlg.GetValue()
1971	dlg.Destroy()
1972	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1973	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1974	RBData['RBIds']['Residue'].append(rbId)
1975	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1976
1977	################################################################################
1978	##### Atom draw routines
1979	################################################################################
1980
1981	def UpdateDrawAtoms(atomStyle=''):
1982	def RefreshAtomGrid(event):
1983	def SetChoice(name,c,n=0):
1984	choice = []
1985	for r in range(len(atomData)):
1986	if n:
1987	srchStr = str(atomData[r][c][:n])
1988	else:
1989	srchStr = str(atomData[r][c])
1990	if srchStr not in choice:
1991	if n:
1992	choice.append(str(atomData[r][c][:n]))
1993	else:
1994	choice.append(str(atomData[r][c]))
1995	choice.sort()
1996
1997	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
1998	if dlg.ShowModal() == wx.ID_OK:
1999	sel = dlg.GetSelections()
2000	parms = []
2001	for x in sel:
2002	parms.append(choice[x])
2003	noSkip = False
2004	drawAtoms.ClearSelection()
2005	drawingData['selectedAtoms'] = []
2006	for row in range(len(atomData)):
2007	test = atomData[row][c]
2008	if n:
2009	test = test[:n]
2010	if test in parms:
2011	drawAtoms.SelectRow(row,True)
2012	drawingData['selectedAtoms'].append(row)
2013	G2plt.PlotStructure(G2frame,data)
2014	dlg.Destroy()
2015
2016	r,c = event.GetRow(),event.GetCol()
2017	if r < 0 and c < 0:
2018	for row in range(drawAtoms.GetNumberRows()):
2019	drawingData['selectedAtoms'].append(row)
2020	drawAtoms.SelectRow(row,True)
2021	elif r < 0: #dclick on col label
2022	sel = -1
2023	Parms = False
2024	noSkip = True
2025	if drawAtoms.GetColLabelValue(c) == 'Style':
2026	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2027	if dlg.ShowModal() == wx.ID_OK:
2028	sel = dlg.GetSelection()
2029	parms = styleChoice[sel]
2030	for r in range(len(atomData)):
2031	atomData[r][c] = parms
2032	drawAtoms.SetCellValue(r,c,parms)
2033	FindBondsDraw()
2034	G2plt.PlotStructure(G2frame,data)
2035	dlg.Destroy()
2036	elif drawAtoms.GetColLabelValue(c) == 'Label':
2037	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
2038	if dlg.ShowModal() == wx.ID_OK:
2039	sel = dlg.GetSelection()
2040	parms = labelChoice[sel]
2041	for r in range(len(atomData)):
2042	atomData[r][c] = parms
2043	drawAtoms.SetCellValue(r,c,parms)
2044	dlg.Destroy()
2045	elif drawAtoms.GetColLabelValue(c) == 'Color':
2046	dlg = wx.ColourDialog(G2frame)
2047	if dlg.ShowModal() == wx.ID_OK:
2048	color = dlg.GetColourData().GetColour()
2049	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2050	attr.SetReadOnly(True)
2051	attr.SetBackgroundColour(color)
2052	for r in range(len(atomData)):
2053	atomData[r][c] = color
2054	drawingData['Atoms'][r][c] = color
2055	drawAtoms.SetAttr(r,c,attr)
2056	UpdateDrawAtoms()
2057	dlg.Destroy()
2058	elif drawAtoms.GetColLabelValue(c) == 'Residue':
2059	SetChoice('Residue',c,3)
2060	elif drawAtoms.GetColLabelValue(c) == '1-letter':
2061	SetChoice('1-letter',c,1)
2062	elif drawAtoms.GetColLabelValue(c) == 'Chain':
2063	SetChoice('Chain',c)
2064	elif drawAtoms.GetColLabelValue(c) == 'Name':
2065	SetChoice('Name',c)
2066	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
2067	SetChoice('Name',c)
2068	elif drawAtoms.GetColLabelValue(c) == 'Type':
2069	SetChoice('Type',c)
2070	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
2071	drawAtoms.ClearSelection()
2072	else:
2073	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
2074	atomData[r][c] = drawAtoms.GetCellValue(r,c)
2075	FindBondsDraw()
2076	elif drawAtoms.GetColLabelValue(c) == 'Color':
2077	dlg = wx.ColourDialog(G2frame)
2078	if dlg.ShowModal() == wx.ID_OK:
2079	color = dlg.GetColourData().GetColour()
2080	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2081	attr.SetReadOnly(True)
2082	attr.SetBackgroundColour(color)
2083	atomData[r][c] = color
2084	drawingData['Atoms'][r][c] = color
2085	drawAtoms.SetAttr(i,cs+2,attr)
2086	dlg.Destroy()
2087	UpdateDrawAtoms()
2088	G2plt.PlotStructure(G2frame,data)
2089
2090	def RowSelect(event):
2091	r,c = event.GetRow(),event.GetCol()
2092	if r < 0 and c < 0:
2093	if drawAtoms.IsSelection():
2094	drawAtoms.ClearSelection()
2095	elif c < 0: #only row clicks
2096	if event.ControlDown():
2097	if r in drawAtoms.GetSelectedRows():
2098	drawAtoms.DeselectRow(r)
2099	else:
2100	drawAtoms.SelectRow(r,True)
2101	elif event.ShiftDown():
2102	indxs = drawAtoms.GetSelectedRows()
2103	drawAtoms.ClearSelection()
2104	ibeg = 0
2105	if indxs:
2106	ibeg = indxs[-1]
2107	for row in range(ibeg,r+1):
2108	drawAtoms.SelectRow(row,True)
2109	else:
2110	drawAtoms.ClearSelection()
2111	drawAtoms.SelectRow(r,True)
2112	drawingData['selectedAtoms'] = []
2113	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
2114	G2plt.PlotStructure(G2frame,data)
2115
2116	# UpdateDrawAtoms executable code starts here
2117	G2frame.dataFrame.SetStatusText('')
2118	generalData = data['General']
2119	SetupDrawingData()
2120	drawingData = data['Drawing']
2121	cx,ct,cs,ci = drawingData['atomPtrs']
2122	atomData = drawingData['Atoms']
2123	if atomStyle:
2124	for atom in atomData:
2125	atom[cs] = atomStyle
2126	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
2127	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
2128	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
2129	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2130	labelChoice = [' ','type','name','number']
2131	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
2132	if generalData['Type'] == 'macromolecular':
2133	colLabels = ['Residue','1-letter','Chain'] + colLabels
2134	Types = 3*[wg.GRID_VALUE_STRING,]+Types
2135	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
2136	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
2137	labelChoice = [' ','type','name','number','residue','1-letter','chain']
2138	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
2139	# elif generalData['Type'] == 'modulated':
2140	# Types += []
2141	# colLabels += []
2142	table = []
2143	rowLabels = []
2144	for i,atom in enumerate(drawingData['Atoms']):
2145	table.append(atom[:colLabels.index('I/A')+1])
2146	rowLabels.append(str(i))
2147
2148	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
2149	drawAtoms.SetTable(atomTable, True)
2150	drawAtoms.SetMargins(0,0)
2151	drawAtoms.AutoSizeColumns(True)
2152	drawAtoms.SetColSize(colLabels.index('Style'),80)
2153	drawAtoms.SetColSize(colLabels.index('Color'),50)
2154	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
2155	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
2156	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
2157	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
2158	for i,atom in enumerate(drawingData['Atoms']):
2159	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2160	attr.SetReadOnly(True)
2161	attr.SetBackgroundColour(atom[cs+2])
2162	drawAtoms.SetAttr(i,cs+2,attr)
2163	drawAtoms.SetCellValue(i,cs+2,'')
2164	indx = drawingData['selectedAtoms']
2165	if indx:
2166	for r in range(len(atomData)):
2167	if r in indx:
2168	drawAtoms.SelectRow(r)
2169	for c in range(len(colLabels)):
2170	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2171	attr.SetReadOnly(True)
2172	attr.SetBackgroundColour(VERY_LIGHT_GREY)
2173	if colLabels[c] not in ['Style','Label','Color']:
2174	drawAtoms.SetColAttr(c,attr)
2175	G2frame.dataFrame.setSizePosLeft([600,300])
2176
2177	FindBondsDraw()
2178	drawAtoms.ClearSelection()
2179	# G2plt.PlotStructure(G2frame,data)
2180
2181	def DrawAtomStyle(event):
2182	indx = drawAtoms.GetSelectedRows()
2183	if indx:
2184	generalData = data['General']
2185	atomData = data['Drawing']['Atoms']
2186	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2187	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2188	if generalData['Type'] == 'macromolecular':
2189	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
2190	'backbone','ribbons','schematic']
2191	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2192	if dlg.ShowModal() == wx.ID_OK:
2193	sel = dlg.GetSelection()
2194	parms = styleChoice[sel]
2195	for r in indx:
2196	atomData[r][cs] = parms
2197	drawAtoms.SetCellValue(r,cs,parms)
2198	dlg.Destroy()
2199	FindBondsDraw()
2200	drawAtoms.ClearSelection()
2201	G2plt.PlotStructure(G2frame,data)
2202
2203	def DrawAtomLabel(event):
2204	indx = drawAtoms.GetSelectedRows()
2205	if indx:
2206	generalData = data['General']
2207	atomData = data['Drawing']['Atoms']
2208	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2209	styleChoice = [' ','type','name','number']
2210	if generalData['Type'] == 'macromolecular':
2211	styleChoice = [' ','type','name','number','residue','1-letter','chain']
2212	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
2213	if dlg.ShowModal() == wx.ID_OK:
2214	sel = dlg.GetSelection()
2215	parms = styleChoice[sel]
2216	for r in indx:
2217	atomData[r][cs+1] = parms
2218	drawAtoms.SetCellValue(r,cs+1,parms)
2219	dlg.Destroy()
2220	drawAtoms.ClearSelection()
2221	G2plt.PlotStructure(G2frame,data)
2222
2223	def DrawAtomColor(event):
2224
2225	indx = drawAtoms.GetSelectedRows()
2226	if indx:
2227	if len(indx) > 1:
2228	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2229	else:
2230	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2231	generalData = data['General']
2232	atomData = data['Drawing']['Atoms']
2233	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2234	atmColors = []
2235	atmTypes = []
2236	for r in indx:
2237	if atomData[r][cs+2] not in atmColors:
2238	atmColors.append(atomData[r][cs+2])
2239	atmTypes.append(atomData[r][ct])
2240	if len(atmColors) > 16:
2241	break
2242	colors = wx.ColourData()
2243	colors.SetChooseFull(True)
2244	dlg = wx.ColourDialog(G2frame)
2245	if dlg.ShowModal() == wx.ID_OK:
2246	for i in range(len(atmColors)):
2247	atmColors[i] = dlg.GetColourData().GetColour()
2248	colorDict = dict(zip(atmTypes,atmColors))
2249	for r in indx:
2250	color = colorDict[atomData[r][ct]]
2251	atomData[r][cs+2] = color
2252	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2253	attr.SetBackgroundColour(color)
2254	drawAtoms.SetAttr(r,cs+2,attr)
2255	data['Drawing']['Atoms'][r][cs+2] = color
2256	drawAtoms.ClearSelection()
2257	dlg.Destroy()
2258	G2frame.dataFrame.SetStatusText('')
2259	G2plt.PlotStructure(G2frame,data)
2260
2261	def ResetAtomColors(event):
2262	generalData = data['General']
2263	atomData = data['Drawing']['Atoms']
2264	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2265	for atom in atomData:
2266	atNum = generalData['AtomTypes'].index(atom[ct])
2267	atom[cs+2] = list(generalData['Color'][atNum])
2268	UpdateDrawAtoms()
2269	drawAtoms.ClearSelection()
2270	G2plt.PlotStructure(G2frame,data)
2271
2272	def SetViewPoint(event):
2273	indx = drawAtoms.GetSelectedRows()
2274	if indx:
2275	atomData = data['Drawing']['Atoms']
2276	cx = data['Drawing']['atomPtrs'][0]
2277	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2278	drawAtoms.ClearSelection() #do I really want to do this?
2279	G2plt.PlotStructure(G2frame,data)
2280
2281	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2282	cx = data['Drawing']['atomPtrs'][0]
2283	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2284	return False
2285	else:
2286	return True
2287
2288	def AddSymEquiv(event):
2289	indx = drawAtoms.GetSelectedRows()
2290	indx.sort()
2291	if indx:
2292	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2293	cx = colLabels.index('x')
2294	cuia = colLabels.index('I/A')
2295	cuij = cuia+2
2296	atomData = data['Drawing']['Atoms']
2297	generalData = data['General']
2298	SGData = generalData['SGData']
2299	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2300	try:
2301	if dlg.ShowModal() == wx.ID_OK:
2302	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2303	Cell = np.array(Cell)
2304	cent = SGData['SGCen'][Cent]
2305	M,T = SGData['SGOps'][Opr]
2306	for ind in indx:
2307	XYZ = np.array(atomData[ind][cx:cx+3])
2308	XYZ = np.inner(M,XYZ)+T
2309	if Inv:
2310	XYZ = -XYZ
2311	XYZ = XYZ+cent+Cell
2312	if Force:
2313	XYZ = G2spc.MoveToUnitCell(XYZ)
2314	if noDuplicate(XYZ,atomData):
2315	atom = copy.copy(atomData[ind])
2316	atom[cx:cx+3] = XYZ
2317	atomOp = atom[cx+3]
2318	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2319	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2320	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2321	if atom[cuia] == 'A':
2322	Uij = atom[cuij:cuij+6]
2323	U = G2spc.Uij2U(Uij)
2324	U = np.inner(np.inner(M,U),M)
2325	Uij = G2spc.U2Uij(U)
2326	atom[cuij:cuij+6] = Uij
2327	atomData.append(atom)
2328	finally:
2329	dlg.Destroy()
2330	UpdateDrawAtoms()
2331	drawAtoms.ClearSelection()
2332	G2plt.PlotStructure(G2frame,data)
2333
2334	def TransformSymEquiv(event):
2335	indx = drawAtoms.GetSelectedRows()
2336	indx.sort()
2337	if indx:
2338	atomData = data['Drawing']['Atoms']
2339	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2340	cx = colLabels.index('x')
2341	cuia = colLabels.index('I/A')
2342	cuij = cuia+2
2343	atomData = data['Drawing']['Atoms']
2344	generalData = data['General']
2345	SGData = generalData['SGData']
2346	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2347	try:
2348	if dlg.ShowModal() == wx.ID_OK:
2349	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2350	Cell = np.array(Cell)
2351	cent = SGData['SGCen'][Cent]
2352	M,T = SGData['SGOps'][Opr]
2353	for ind in indx:
2354	XYZ = np.array(atomData[ind][cx:cx+3])
2355	XYZ = np.inner(M,XYZ)+T
2356	if Inv:
2357	XYZ = -XYZ
2358	XYZ = XYZ+cent+Cell
2359	if Force:
2360	XYZ = G2spc.MoveToUnitCell(XYZ)
2361	atom = atomData[ind]
2362	atom[cx:cx+3] = XYZ
2363	atomOp = atom[cx+3]
2364	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2365	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2366	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2367	if atom[cuia] == 'A':
2368	Uij = atom[cuij:cuij+6]
2369	U = G2spc.Uij2U(Uij)
2370	U = np.inner(np.inner(M,U),M)
2371	Uij = G2spc.U2Uij(U)
2372	atom[cuij:cuij+6] = Uij
2373	data['Drawing']['Atoms'] = atomData
2374	finally:
2375	dlg.Destroy()
2376	UpdateDrawAtoms()
2377	drawAtoms.ClearSelection()
2378	G2plt.PlotStructure(G2frame,data)
2379
2380	def FillCoordSphere(event):
2381	generalData = data['General']
2382	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2383	radii = generalData['BondRadii']
2384	atomTypes = generalData['AtomTypes']
2385	try:
2386	indH = atomTypes.index('H')
2387	radii[indH] = 0.5
2388	except:
2389	pass
2390	indx = drawAtoms.GetSelectedRows()
2391	if indx:
2392	indx.sort()
2393	atomData = data['Drawing']['Atoms']
2394	numAtoms = len(atomData)
2395	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2396	generalData = data['General']
2397	SGData = generalData['SGData']
2398	cellArray = G2lat.CellBlock(1)
2399	wx.BeginBusyCursor()
2400	try:
2401	for ind in indx:
2402	atomA = atomData[ind]
2403	xyzA = np.array(atomA[cx:cx+3])
2404	indA = atomTypes.index(atomA[ct])
2405	for atomB in atomData[:numAtoms]:
2406	indB = atomTypes.index(atomB[ct])
2407	sumR = radii[indA]+radii[indB]
2408	xyzB = np.array(atomB[cx:cx+3])
2409	for xyz in cellArray+xyzB:
2410	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2411	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2412	if noDuplicate(xyz,atomData):
2413	oprB = atomB[cx+3]
2414	C = xyz-xyzB
2415	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2416	newAtom = atomB[:]
2417	newAtom[cx:cx+3] = xyz
2418	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2419	atomData.append(newAtom)
2420	finally:
2421	wx.EndBusyCursor()
2422	data['Drawing']['Atoms'] = atomData
2423	UpdateDrawAtoms()
2424	drawAtoms.ClearSelection()
2425	G2plt.PlotStructure(G2frame,data)
2426
2427	def FillUnitCell(event):
2428	indx = drawAtoms.GetSelectedRows()
2429	indx.sort()
2430	if indx:
2431	atomData = data['Drawing']['Atoms']
2432	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2433	cx = colLabels.index('x')
2434	cuia = colLabels.index('I/A')
2435	cuij = cuia+2
2436	generalData = data['General']
2437	SGData = generalData['SGData']
2438	wx.BeginBusyCursor()
2439	try:
2440	for ind in indx:
2441	atom = atomData[ind]
2442	XYZ = np.array(atom[cx:cx+3])
2443	if atom[cuia] == 'A':
2444	Uij = atom[cuij:cuij+6]
2445	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2446	for item in result:
2447	atom = copy.copy(atomData[ind])
2448	atom[cx:cx+3] = item[0]
2449	atom[cx+3] = str(item[2])+'+' \
2450	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2451	atom[cuij:cuij+6] = item[1]
2452	Opp = G2spc.Opposite(item[0])
2453	for xyz in Opp:
2454	if noDuplicate(xyz,atomData):
2455	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2456	cell = '1'+'+'+ \
2457	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2458	atom[cx:cx+3] = xyz
2459	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2460	atomData.append(atom[:])
2461	else:
2462	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2463	for item in result:
2464	atom = copy.copy(atomData[ind])
2465	atom[cx:cx+3] = item[0]
2466	atom[cx+3] = str(item[1])+'+' \
2467	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2468	Opp = G2spc.Opposite(item[0])
2469	for xyz in Opp:
2470	if noDuplicate(xyz,atomData):
2471	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2472	cell = '1'+'+'+ \
2473	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2474	atom[cx:cx+3] = xyz
2475	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2476	atomData.append(atom[:])
2477	data['Drawing']['Atoms'] = atomData
2478	finally:
2479	wx.EndBusyCursor()
2480	UpdateDrawAtoms()
2481	drawAtoms.ClearSelection()
2482	G2plt.PlotStructure(G2frame,data)
2483
2484	def FindBondsToo(): #works but slow for large structures - keep as reference
2485	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2486	atomData = data['Drawing']['Atoms']
2487	generalData = data['General']
2488	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2489	radii = generalData['BondRadii']
2490	atomTypes = generalData['AtomTypes']
2491	try:
2492	indH = atomTypes.index('H')
2493	radii[indH] = 0.5
2494	except:
2495	pass
2496	for atom in atomData:
2497	atom[-1] = []
2498	Atoms = []
2499	for i,atom in enumerate(atomData):
2500	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2501	for atomA in Atoms:
2502	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2503	for atomB in Atoms:
2504	Dx = atomB[1]-atomA[1]
2505	DX = np.inner(Amat,Dx)
2506	dist = np.sqrt(np.sum(DX**2))
2507	sumR = atomA[3]+atomB[3]
2508	if 0.5 < dist <= 0.85*sumR:
2509	i = atomA[0]
2510	if atomA[2] == 'polyhedra':
2511	atomData[i][-1].append(DX)
2512	elif atomB[1] != 'polyhedra':
2513	j = atomB[0]
2514	atomData[i][-1].append(Dx*atomA[3]/sumR)
2515	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2516
2517	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2518	import numpy.ma as ma
2519	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2520	hydro = data['Drawing']['showHydrogen']
2521	atomData = data['Drawing']['Atoms']
2522	generalData = data['General']
2523	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2524	radii = generalData['BondRadii']
2525	atomTypes = generalData['AtomTypes']
2526	try:
2527	indH = atomTypes.index('H')
2528	radii[indH] = 0.5
2529	except:
2530	pass
2531	for atom in atomData:
2532	atom[-2] = [] #clear out old bonds/polyhedra
2533	atom[-1] = []
2534	Indx = range(len(atomData))
2535	Atoms = []
2536	Styles = []
2537	Radii = []
2538	for atom in atomData:
2539	Atoms.append(np.array(atom[cx:cx+3]))
2540	Styles.append(atom[cs])
2541	try:
2542	if not hydro and atom[ct] == 'H':
2543	Radii.append(0.0)
2544	else:
2545	Radii.append(radii[atomTypes.index(atom[ct])])
2546	except ValueError: #changed atom type!
2547	Radii.append(0.20)
2548	Atoms = np.array(Atoms)
2549	Radii = np.array(Radii)
2550	IASR = zip(Indx,Atoms,Styles,Radii)
2551	for atomA in IASR:
2552	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2553	Dx = Atoms-atomA[1]
2554	dist = ma.masked_less(np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)),0.5) #gets rid of G2frame & disorder "bonds" < 0.5A
2555	sumR = atomA[3]+Radii
2556	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2557	i = atomA[0]
2558	for j in IndB[0]:
2559	if Styles[i] == 'polyhedra':
2560	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2561	elif Styles[j] != 'polyhedra' and j > i:
2562	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2563	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2564	if Styles[i] == 'polyhedra':
2565	Bonds = atomData[i][-2]
2566	Faces = []
2567	if len(Bonds) > 2:
2568	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2569	for face in FaceGen:
2570	vol = nl.det(face)
2571	if abs(vol) > 1. or len(Bonds) == 3:
2572	if vol < 0.:
2573	face = [face[0],face[2],face[1]]
2574	face = np.array(face)
2575	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2576	norm = np.cross(face[1]-face[0],face[2]-face[0])
2577	norm /= np.sqrt(np.sum(norm**2))
2578	Faces.append([face,norm])
2579	atomData[i][-1] = Faces
2580
2581	def DrawAtomsDelete(event):
2582	indx = drawAtoms.GetSelectedRows()
2583	indx.sort()
2584	if indx:
2585	atomData = data['Drawing']['Atoms']
2586	indx.reverse()
2587	for ind in indx:
2588	del atomData[ind]
2589	UpdateDrawAtoms()
2590	drawAtoms.ClearSelection()
2591	G2plt.PlotStructure(G2frame,data)
2592	event.StopPropagation()
2593
2594	def OnReloadDrawAtoms(event):
2595	data['Drawing']['Atoms'] = []
2596	UpdateDrawAtoms()
2597	drawAtoms.ClearSelection()
2598	G2plt.PlotStructure(G2frame,data)
2599	event.StopPropagation()
2600
2601	def DrawAtomsDeleteByIDs(IDs):
2602	atomData = data['Drawing']['Atoms']
2603	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2604	indx.reverse()
2605	for ind in indx:
2606	del atomData[ind]
2607
2608	def ChangeDrawAtomsByIDs(colName,IDs,value):
2609	atomData = data['Drawing']['Atoms']
2610	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2611	if colName == 'Name':
2612	col = ct-1
2613	elif colName == 'Type':
2614	col = ct
2615	elif colName == 'I/A':
2616	col = cs
2617	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2618	for ind in indx:
2619	atomData[ind][col] = value
2620
2621	def OnDrawPlane(event):
2622	indx = drawAtoms.GetSelectedRows()
2623	if len(indx) < 4:
2624	print '**** ERROR - need 4+ atoms for plane calculation'
2625	return
2626	PlaneData = {}
2627	drawingData = data['Drawing']
2628	atomData = drawingData['Atoms']
2629	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2630	cx = colLabels.index('x')
2631	cn = colLabels.index('Name')
2632	xyz = []
2633	for i,atom in enumerate(atomData):
2634	if i in indx:
2635	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2636	generalData = data['General']
2637	PlaneData['Name'] = generalData['Name']
2638	PlaneData['Atoms'] = xyz
2639	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2640	G2stMn.BestPlane(PlaneData)
2641
2642	def OnDrawDistVP(event):
2643	# distance to view point
2644	indx = drawAtoms.GetSelectedRows()
2645	if not indx:
2646	print '***** ERROR - no atoms selected'
2647	return
2648	generalData = data['General']
2649	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2650	drawingData = data['Drawing']
2651	viewPt = np.array(drawingData['viewPoint'][0])
2652	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2653	atomDData = drawingData['Atoms']
2654	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2655	cx = colLabels.index('x')
2656	cn = colLabels.index('Name')
2657	for i in indx:
2658	atom = atomDData[i]
2659	Dx = np.array(atom[cx:cx+3])-viewPt
2660	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2661	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2662
2663	def OnDrawDAT(event):
2664	#distance, angle, torsion
2665	indx = drawAtoms.GetSelectedRows()
2666	if len(indx) not in [2,3,4]:
2667	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2668	return
2669	DATData = {}
2670	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2671	drawingData = data['Drawing']
2672	atomData = data['Atoms']
2673	atomDData = drawingData['Atoms']
2674	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2675	cx = colLabels.index('x')
2676	cn = colLabels.index('Name')
2677	cid = colLabels.index('I/A')+8
2678	xyz = []
2679	Oxyz = []
2680	DATData['Natoms'] = len(indx)
2681	for i in indx:
2682	atom = atomDData[i]
2683	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2684	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2685	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2686	DATData['Datoms'] = xyz
2687	DATData['Oatoms'] = Oxyz
2688	generalData = data['General']
2689	DATData['Name'] = generalData['Name']
2690	DATData['SGData'] = generalData['SGData']
2691	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2692	if 'pId' in data:
2693	DATData['pId'] = data['pId']
2694	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2695	G2stMn.DisAglTor(DATData)
2696
2697	################################################################################
2698	#### Draw Options page
2699	################################################################################
2700
2701	def UpdateDrawOptions():
2702	import copy
2703	import wx.lib.colourselect as wcs
2704	def SlopSizer():
2705	def OnCameraPos(event):
2706	drawingData['cameraPos'] = cameraPos.GetValue()
2707	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2708	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2709	G2plt.PlotStructure(G2frame,data)
2710
2711	def OnZclip(event):
2712	drawingData['Zclip'] = Zclip.GetValue()
2713	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2714	G2plt.PlotStructure(G2frame,data)
2715
2716	def OnZstep(event):
2717	try:
2718	step = float(Zstep.GetValue())
2719	if not (0.01 <= step <= 1.0):
2720	raise ValueError
2721	except ValueError:
2722	step = drawingData['Zstep']
2723	drawingData['Zstep'] = step
2724	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2725
2726	def OnMoveZ(event):
2727	move = MoveZ.GetValue()*drawingData['Zstep']
2728	MoveZ.SetValue(0)
2729	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2730	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2731	VD /= np.sqrt(np.sum(VD**2))
2732	VP += move*VD
2733	VP = np.inner(Bmat,VP)
2734	drawingData['viewPoint'][0] = VP
2735	panel = drawOptions.GetChildren()
2736	names = [child.GetName() for child in panel]
2737	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2738	G2plt.PlotStructure(G2frame,data)
2739
2740	def OnVdWScale(event):
2741	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2742	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2743	G2plt.PlotStructure(G2frame,data)
2744
2745	def OnEllipseProb(event):
2746	drawingData['ellipseProb'] = ellipseProb.GetValue()
2747	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2748	G2plt.PlotStructure(G2frame,data)
2749
2750	def OnBallScale(event):
2751	drawingData['ballScale'] = ballScale.GetValue()/100.
2752	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2753	G2plt.PlotStructure(G2frame,data)
2754
2755	def OnBondRadius(event):
2756	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2757	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2758	G2plt.PlotStructure(G2frame,data)
2759
2760	def OnContourLevel(event):
2761	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2762	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2763	G2plt.PlotStructure(G2frame,data)
2764
2765	def OnMapSize(event):
2766	drawingData['mapSize'] = mapSize.GetValue()/10.
2767	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2768	G2plt.PlotStructure(G2frame,data)
2769
2770
2771	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2772	slideSizer = wx.FlexGridSizer(0,2)
2773	slideSizer.AddGrowableCol(1,1)
2774
2775	cameraPosTxt = wx.StaticText(drawOptions,-1,
2776	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2777	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2778	slideSizer.Add(cameraPosTxt,0,WACV)
2779	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2780	cameraPos.SetRange(10,500)
2781	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2782	G2frame.dataDisplay.cameraSlider = cameraPos
2783	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2784
2785	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2786	slideSizer.Add(ZclipTxt,0,WACV)
2787	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2788	Zclip.SetRange(1,99)
2789	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2790	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2791
2792	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2793	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,WACV)
2794	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2795	style=wx.TE_PROCESS_ENTER)
2796	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2797	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2798	ZstepSizer.Add(Zstep,0,WACV)
2799	slideSizer.Add(ZstepSizer)
2800	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2801	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,WACV)
2802	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2803	MoveZ.SetValue(0)
2804	MoveZ.SetRange(-1,1)
2805	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2806	MoveSizer.Add(MoveZ)
2807	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2808
2809	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2810	slideSizer.Add(vdwScaleTxt,0,WACV)
2811	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2812	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2813	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2814
2815	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2816	slideSizer.Add(ellipseProbTxt,0,WACV)
2817	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2818	ellipseProb.SetRange(1,99)
2819	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2820	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2821
2822	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2823	slideSizer.Add(ballScaleTxt,0,WACV)
2824	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2825	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2826	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2827
2828	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2829	slideSizer.Add(bondRadiusTxt,0,WACV)
2830	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2831	bondRadius.SetRange(1,25)
2832	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2833	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2834
2835	if generalData['Map']['rhoMax']:
2836	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2837	slideSizer.Add(contourLevelTxt,0,WACV)
2838	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2839	contourLevel.SetRange(1,100)
2840	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2841	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2842	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2843	slideSizer.Add(mapSizeTxt,0,WACV)
2844	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2845	mapSize.SetRange(1,100)
2846	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2847	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2848
2849	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2850	slopSizer.Add((10,5),0)
2851	slopSizer.SetMinSize(wx.Size(350,10))
2852	return slopSizer
2853
2854	def ShowSizer():
2855
2856	def OnBackColor(event):
2857	drawingData['backColor'] = event.GetValue()
2858	G2plt.PlotStructure(G2frame,data)
2859
2860	def OnShowABC(event):
2861	drawingData['showABC'] = showABC.GetValue()
2862	G2plt.PlotStructure(G2frame,data)
2863
2864	def OnShowUnitCell(event):
2865	drawingData['unitCellBox'] = unitCellBox.GetValue()
2866	G2plt.PlotStructure(G2frame,data)
2867
2868	def OnShowHyd(event):
2869	drawingData['showHydrogen'] = showHydrogen.GetValue()
2870	FindBondsDraw()
2871	G2plt.PlotStructure(G2frame,data)
2872
2873	def OnShowRB(event):
2874	drawingData['showRigidBodies'] = showRB.GetValue()
2875	FindBondsDraw()
2876	G2plt.PlotStructure(G2frame,data)
2877
2878	def OnViewPoint(event):
2879	Obj = event.GetEventObject()
2880	viewPt = Obj.GetValue().split()
2881	try:
2882	VP = [float(viewPt[i]) for i in range(3)]
2883	except (ValueError,IndexError):
2884	VP = drawingData['viewPoint'][0]
2885	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2886	drawingData['viewPoint'][0] = VP
2887	G2plt.PlotStructure(G2frame,data)
2888
2889	def OnViewDir(event):
2890	Obj = event.GetEventObject()
2891	viewDir = Obj.GetValue().split()
2892	try:
2893	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2894	VD = np.array([float(viewDir[i]) for i in range(3)])
2895	VC = np.inner(Amat,VD)
2896	VC /= np.sqrt(np.sum(VC**2))
2897	V = np.array(drawingData['viewDir'])
2898	VB = np.inner(Amat,V)
2899	VB /= np.sqrt(np.sum(VB**2))
2900	VX = np.cross(VC,VB)
2901	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2902	QV = G2mth.AVdeg2Q(A,VX)
2903	Q = drawingData['Quaternion']
2904	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2905	except (ValueError,IndexError):
2906	VD = drawingData['viewDir']
2907	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2908	drawingData['viewDir'] = VD
2909	G2plt.PlotStructure(G2frame,data)
2910
2911	showSizer = wx.BoxSizer(wx.VERTICAL)
2912	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2913	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,WACV)
2914	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2915	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2916	lineSizer.Add(backColor,0,WACV)
2917	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,WACV)
2918	VD = drawingData['viewDir']
2919	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2920	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2921	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2922	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2923	G2frame.dataDisplay.viewDir = viewDir
2924	lineSizer.Add(viewDir,0,WACV)
2925	showSizer.Add(lineSizer)
2926	showSizer.Add((0,5),0)
2927
2928	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2929	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2930	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2931	showABC.SetValue(drawingData['showABC'])
2932	lineSizer.Add(showABC,0,WACV)
2933	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,WACV)
2934	VP = drawingData['viewPoint'][0]
2935	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2936	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2937	G2frame.dataDisplay.viewPoint = viewPoint
2938	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2939	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2940	lineSizer.Add(viewPoint,0,WACV)
2941	showSizer.Add(lineSizer)
2942	showSizer.Add((0,5),0)
2943
2944	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2945
2946	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2947	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2948	unitCellBox.SetValue(drawingData['unitCellBox'])
2949	line2Sizer.Add(unitCellBox,0,WACV)
2950
2951	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2952	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2953	showHydrogen.SetValue(drawingData['showHydrogen'])
2954	line2Sizer.Add(showHydrogen,0,WACV)
2955
2956	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2957	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2958	showRB.SetValue(drawingData['showRigidBodies'])
2959	line2Sizer.Add(showRB,0,WACV)
2960
2961	showSizer.Add(line2Sizer)
2962	return showSizer
2963
2964	def RadSizer():
2965
2966	def OnSizeHatoms(event):
2967	try:
2968	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2969	except ValueError:
2970	value = 0.5
2971	drawingData['sizeH'] = value
2972	sizeH.SetValue("%.2f"%(value))
2973	G2plt.PlotStructure(G2frame,data)
2974
2975	def OnRadFactor(event):
2976	try:
2977	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2978	except ValueError:
2979	value = 0.85
2980	drawingData['radiusFactor'] = value
2981	radFactor.SetValue("%.2f"%(value))
2982	FindBondsDraw()
2983	G2plt.PlotStructure(G2frame,data)
2984
2985	radSizer = wx.BoxSizer(wx.HORIZONTAL)
2986	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,WACV)
2987	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2988	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
2989	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
2990	radSizer.Add(sizeH,0,WACV)
2991
2992	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,WACV)
2993	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2994	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
2995	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
2996	radSizer.Add(radFactor,0,WACV)
2997	return radSizer
2998
2999	# UpdateDrawOptions exectable code starts here
3000	generalData = data['General']
3001	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
3002	SetupDrawingData()
3003	drawingData = data['Drawing']
3004	if generalData['Type'] == 'nuclear':
3005	pickChoice = ['Atoms','Bonds','Torsions','Planes']
3006	elif generalData['Type'] == 'macromolecular':
3007	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
3008
3009	G2frame.dataFrame.SetStatusText('')
3010	if drawOptions.GetSizer():
3011	drawOptions.GetSizer().Clear(True)
3012	mainSizer = wx.BoxSizer(wx.VERTICAL)
3013	mainSizer.Add((5,5),0)
3014	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,WACV)
3015	mainSizer.Add((5,5),0)
3016	mainSizer.Add(SlopSizer(),0)
3017	mainSizer.Add((5,5),0)
3018	mainSizer.Add(ShowSizer(),0,)
3019	mainSizer.Add((5,5),0)
3020	mainSizer.Add(RadSizer(),0,)
3021	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
3022
3023	################################################################################
3024	#### Texture routines
3025	################################################################################
3026
3027	def UpdateTexture():
3028	def SetSHCoef():
3029	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
3030	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
3031	SHCoeff = textureData['SH Coeff'][1]
3032	for cofName in SHCoeff:
3033	if cofName in cofNames:
3034	newSHCoef[cofName] = SHCoeff[cofName]
3035	return newSHCoef
3036
3037	def OnShOrder(event):
3038	Obj = event.GetEventObject()
3039	textureData['Order'] = int(Obj.GetValue())
3040	textureData['SH Coeff'][1] = SetSHCoef()
3041	wx.CallAfter(UpdateTexture)
3042	G2plt.PlotTexture(G2frame,data)
3043
3044	def OnShModel(event):
3045	Obj = event.GetEventObject()
3046	textureData['Model'] = Obj.GetValue()
3047	textureData['SH Coeff'][1] = SetSHCoef()
3048	wx.CallAfter(UpdateTexture)
3049	G2plt.PlotTexture(G2frame,data)
3050
3051	def OnSHRefine(event):
3052	Obj = event.GetEventObject()
3053	textureData['SH Coeff'][0] = Obj.GetValue()
3054
3055	def OnSHShow(event):
3056	Obj = event.GetEventObject()
3057	textureData['SHShow'] = Obj.GetValue()
3058	wx.CallAfter(UpdateTexture)
3059
3060	def OnProjSel(event):
3061	Obj = event.GetEventObject()
3062	G2frame.Projection = Obj.GetValue()
3063	G2plt.PlotTexture(G2frame,data)
3064
3065	def OnColorSel(event):
3066	Obj = event.GetEventObject()
3067	G2frame.ContourColor = Obj.GetValue()
3068	G2plt.PlotTexture(G2frame,data)
3069
3070	def OnAngRef(event):
3071	Obj = event.GetEventObject()
3072	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
3073
3074	def OnAngValue(event):
3075	Obj = event.GetEventObject()
3076	try:
3077	value = float(Obj.GetValue())
3078	except ValueError:
3079	value = textureData[valIndx[Obj.GetId()]][1]
3080	Obj.SetValue('%8.2f'%(value))
3081	textureData[valIndx[Obj.GetId()]][1] = value
3082
3083	def OnODFValue(event):
3084	Obj = event.GetEventObject()
3085	try:
3086	value = float(Obj.GetValue())
3087	except ValueError:
3088	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
3089	Obj.SetValue('%8.3f'%(value))
3090	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
3091	G2plt.PlotTexture(G2frame,data)
3092
3093	def OnPfType(event):
3094	Obj = event.GetEventObject()
3095	textureData['PlotType'] = Obj.GetValue()
3096	wx.CallAfter(UpdateTexture)
3097	G2plt.PlotTexture(G2frame,data)
3098
3099	def OnPFValue(event):
3100	Obj = event.GetEventObject()
3101	Saxis = Obj.GetValue().split()
3102	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3103	try:
3104	hkl = [int(Saxis[i]) for i in range(3)]
3105	except (ValueError,IndexError):
3106	hkl = textureData['PFhkl']
3107	if not np.any(np.array(hkl)): #can't be all zeros!
3108	hkl = textureData['PFhkl']
3109	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
3110	textureData['PFhkl'] = hkl
3111	else:
3112	try:
3113	xyz = [float(Saxis[i]) for i in range(3)]
3114	except (ValueError,IndexError):
3115	xyz = textureData['PFxyz']
3116	if not np.any(np.array(xyz)): #can't be all zeros!
3117	xyz = textureData['PFxyz']
3118	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
3119	textureData['PFxyz'] = xyz
3120	G2plt.PlotTexture(G2frame,data)
3121
3122	# UpdateTexture executable starts here
3123	G2frame.dataFrame.SetStatusText('')
3124	generalData = data['General']
3125	SGData = generalData['SGData']
3126	try:
3127	textureData = generalData['SH Texture']
3128	except KeyError: #fix old files!
3129	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
3130	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
3131	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
3132	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
3133	if 'SHShow' not in textureData: #another fix
3134	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
3135	try: #another fix!
3136	x = textureData['PlotType']
3137	except KeyError:
3138	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
3139	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
3140	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
3141	shAngles = ['omega','chi','phi']
3142	if Texture.GetSizer():
3143	Texture.GetSizer().Clear(True)
3144	mainSizer = wx.BoxSizer(wx.VERTICAL)
3145	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
3146	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,WACV)
3147	titleSizer.Add(wx.StaticText(Texture,-1,
3148	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
3149	0,WACV)
3150	mainSizer.Add(titleSizer,0)
3151	mainSizer.Add((0,5),0)
3152	shSizer = wx.FlexGridSizer(0,6,5,5)
3153	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,WACV)
3154	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
3155	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3156	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
3157	shSizer.Add(shModel,0,WACV)
3158	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,WACV)
3159	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
3160	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3161	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
3162	shSizer.Add(shOrder,0,WACV)
3163	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
3164	shRef.SetValue(textureData['SH Coeff'][0])
3165	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
3166	shSizer.Add(shRef,0,WACV)
3167	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
3168	shShow.SetValue(textureData['SHShow'])
3169	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
3170	shSizer.Add(shShow,0,WACV)
3171	mainSizer.Add(shSizer,0,0)
3172	mainSizer.Add((0,5),0)
3173	PTSizer = wx.FlexGridSizer(0,4,5,5)
3174	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,WACV)
3175	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
3176	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
3177	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3178	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
3179	PTSizer.Add(pfType,0,WACV)
3180	if 'Axial' not in textureData['PlotType']:
3181	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,WACV)
3182	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
3183	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3184	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
3185	PTSizer.Add(projSel,0,WACV)
3186	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3187	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,WACV)
3188	PH = textureData['PFhkl']
3189	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
3190	else:
3191	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,WACV)
3192	PX = textureData['PFxyz']
3193	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
3194	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
3195	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
3196	PTSizer.Add(pfVal,0,WACV)
3197	if 'Axial' not in textureData['PlotType']:
3198	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,WACV)
3199	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3200	choice.sort()
3201	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
3202	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3203	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
3204	PTSizer.Add(colorSel,0,WACV)
3205	mainSizer.Add(PTSizer,0,WACV)
3206	mainSizer.Add((0,5),0)
3207	if textureData['SHShow']:
3208	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,WACV)
3209	mainSizer.Add((0,5),0)
3210	ODFSizer = wx.FlexGridSizer(0,8,2,2)
3211	ODFIndx = {}
3212	ODFkeys = textureData['SH Coeff'][1].keys()
3213	ODFkeys.sort()
3214	for item in ODFkeys:
3215	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,WACV)
3216	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3217	ODFIndx[ODFval.GetId()] = item
3218	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3219	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3220	ODFSizer.Add(ODFval,0,WACV)
3221	mainSizer.Add(ODFSizer,0,WACV)
3222	mainSizer.Add((0,5),0)
3223	mainSizer.Add((0,5),0)
3224	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,WACV)
3225	mainSizer.Add((0,5),0)
3226	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3227	angIndx = {}
3228	valIndx = {}
3229	for item in ['Sample omega','Sample chi','Sample phi']:
3230	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3231	angRef.SetValue(textureData[item][0])
3232	angIndx[angRef.GetId()] = item
3233	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3234	angSizer.Add(angRef,0,WACV)
3235	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3236	valIndx[angVal.GetId()] = item
3237	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3238	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3239	angSizer.Add(angVal,0,WACV)
3240	angSizer.Add((5,0),0)
3241	mainSizer.Add(angSizer,0,WACV)
3242	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3243
3244	################################################################################
3245	##### DData routines - GUI stuff in GSASIIddataGUI.py
3246	################################################################################
3247
3248	def OnHklfAdd(event):
3249	UseList = data['Histograms']
3250	keyList = UseList.keys()
3251	TextList = []
3252	if not G2frame.PatternTree.GetCount():
3253	return
3254
3255	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3256	while item:
3257	name = G2frame.PatternTree.GetItemText(item)
3258	if name not in keyList and 'HKLF' in name:
3259	TextList.append(name)
3260	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3261	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3262	try:
3263	if dlg.ShowModal() == wx.ID_OK:
3264	result = dlg.GetSelections()
3265	else:
3266	return
3267	finally:
3268	dlg.Destroy()
3269
3270	# get the histograms used in other phases
3271	phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree()
3272	usedHKLFhists = [] # used single-crystal histograms
3273	for p in usedHistograms:
3274	for h in usedHistograms[p]:
3275	if h.startswith('HKLF ') and h not in usedHKLFhists:
3276	usedHKLFhists.append(h)
3277	# check that selected single crystal histograms are not already in use!
3278	for i in result:
3279	used = [TextList[i] for i in result if TextList[i] in usedHKLFhists]
3280	if used:
3281	msg = 'The following single crystal histogram(s) are already in use'
3282	for i in used:
3283	msg += '\n '+str(i)
3284	msg += '\nAre you sure you want to add them to this phase? '
3285	msg += 'Associating a single crystal dataset to >1 histogram is usually an error, '
3286	msg += 'so No is suggested here.'
3287	if G2frame.ErrorDialog('Likely error',msg,G2frame,wtype=wx.YES_NO) != wx.ID_YES: return
3288
3289	wx.BeginBusyCursor()
3290	for i in result:
3291	histoName = TextList[i]
3292	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3293	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3294	'Extinction':['Lorentzian','None',
3295	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3296	UpdateHKLFdata(histoName)
3297	data['Histograms'] = UseList
3298	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3299	wx.EndBusyCursor()
3300
3301	def UpdateHKLFdata(histoName):
3302	generalData = data['General']
3303	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3304	refDict,reflData = G2frame.PatternTree.GetItemPyData(Id)
3305	SGData = generalData['SGData']
3306	Cell = generalData['Cell'][1:7]
3307	G,g = G2lat.cell2Gmat(Cell)
3308	for iref,ref in enumerate(reflData['RefList']):
3309	H = list(ref[:3])
3310	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3311	iabsnt,ref[3],Uniq,phi = G2spc.GenHKLf(H,SGData)
3312	#G2frame.PatternTree.SetItemPyData(Id,[refDict,reflData]) #removed by BHT -- not needed!
3313
3314	def OnPwdrAdd(event):
3315	generalData = data['General']
3316	SGData = generalData['SGData']
3317	UseList = data['Histograms']
3318	newList = []
3319	NShkl = len(G2spc.MustrainNames(SGData))
3320	NDij = len(G2spc.HStrainNames(SGData))
3321	keyList = UseList.keys()
3322	TextList = ['All PWDR']
3323	if G2frame.PatternTree.GetCount():
3324	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3325	while item:
3326	name = G2frame.PatternTree.GetItemText(item)
3327	if name not in keyList and 'PWDR' in name:
3328	TextList.append(name)
3329	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3330	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3331	try:
3332	if dlg.ShowModal() == wx.ID_OK:
3333	result = dlg.GetSelections()
3334	for i in result: newList.append(TextList[i])
3335	if 'All PWDR' in newList:
3336	newList = TextList[1:]
3337	for histoName in newList:
3338	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3339	UseList[histoName] = {'Histogram':histoName,'Show':False,
3340	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3341	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3342	[1.,1.,1.,0.,0.,0.],6*[False,]],
3343	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3344	NShkl[0.01,],NShkl[False,]],
3345	'HStrain':[NDij[0.0,],NDij[False,]],
3346	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3347	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Reflection Lists'))
3348	refList[generalData['Name']] = []
3349	data['Histograms'] = UseList
3350	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3351	finally:
3352	dlg.Destroy()
3353
3354	def OnDataDelete(event):
3355	UseList = data['Histograms']
3356	keyList = ['All',]+UseList.keys()
3357	keyList.sort()
3358	DelList = []
3359	if UseList:
3360	DelList = []
3361	dlg = wx.MultiChoiceDialog(G2frame,
3362	'Which histogram to delete from this phase?', 'Delete histogram',
3363	keyList, wx.CHOICEDLG_STYLE)
3364	try:
3365	if dlg.ShowModal() == wx.ID_OK:
3366	result = dlg.GetSelections()
3367	for i in result:
3368	DelList.append(keyList[i])
3369	if 'All' in DelList:
3370	DelList = keyList[1:]
3371	for i in DelList:
3372	del UseList[i]
3373	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3374	finally:
3375	dlg.Destroy()
3376
3377	################################################################################
3378	##### Rigid bodies
3379	################################################################################
3380
3381	def FillRigidBodyGrid(refresh=True):
3382	'''Fill the Rigid Body Phase information tab page.
3383	Note that the page is a ScrolledWindow, not a Grid
3384	'''
3385	def OnThermSel(event): #needs to be seen by VecRbSizer!
3386	Obj = event.GetEventObject()
3387	RBObj = Indx[Obj.GetId()]
3388	val = Obj.GetValue()
3389	Ttype = 'A'
3390	if val == 'Uiso':
3391	Ttype = 'I'
3392	RBObj['ThermalMotion'][0] = 'Uiso'
3393	elif val == 'T':
3394	RBObj['ThermalMotion'][0] = 'T'
3395	elif val == 'TL':
3396	RBObj['ThermalMotion'][0] = 'TL'
3397	elif val == 'TLS':
3398	RBObj['ThermalMotion'][0] = 'TLS'
3399	wx.CallAfter(FillRigidBodyGrid,True)
3400	if val != 'None':
3401	cia = data['General']['AtomPtrs'][3]
3402	for i,id in enumerate(RBObj['Ids']):
3403	data['Atoms'][AtLookUp[id]][cia] = Ttype
3404	G2plt.PlotStructure(G2frame,data)
3405
3406	def ThermDataSizer(RBObj,rbType):
3407
3408	def OnThermval(event):
3409	Obj = event.GetEventObject()
3410	item = Indx[Obj.GetId()]
3411	try:
3412	val = float(Obj.GetValue())
3413	RBObj['ThermalMotion'][1][item] = val
3414	except ValueError:
3415	pass
3416	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3417	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3418	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3419	cia = data['General']['AtomPtrs'][3]
3420	for i,id in enumerate(RBObj['Ids']):
3421	if Uout[i][0] == 'I':
3422	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3423	else:
3424	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3425	G2plt.PlotStructure(G2frame,data)
3426
3427	def OnTLSRef(event):
3428	Obj = event.GetEventObject()
3429	item = Indx[Obj.GetId()]
3430	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3431
3432	thermSizer = wx.FlexGridSizer(0,9,5,5)
3433	model = RBObj['ThermalMotion']
3434	if model[0] == 'Uiso':
3435	names = ['Uiso',]
3436	elif 'T' in model[0]:
3437	names = ['T11','T22','T33','T12','T13','T23']
3438	if 'L' in model[0]:
3439	names += ['L11','L22','L33','L12','L13','L23']
3440	if 'S' in model[0]:
3441	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3442	for i,name in enumerate(names):
3443	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,WACV)
3444	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3445	style=wx.TE_PROCESS_ENTER)
3446	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3447	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3448	Indx[thermVal.GetId()] = i
3449	thermSizer.Add(thermVal)
3450	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3451	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3452	Tcheck.SetValue(model[2][i])
3453	Indx[Tcheck.GetId()] = i
3454	thermSizer.Add(Tcheck,0,WACV)
3455	return thermSizer
3456
3457	def LocationSizer(RBObj,rbType):
3458
3459	def OnOrigRef(event):
3460	RBObj['Orig'][1] = Ocheck.GetValue()
3461
3462	def OnOrienRef(event):
3463	RBObj['Orient'][1] = Qcheck.GetValue()
3464
3465	def OnOrigX(event):
3466	Obj = event.GetEventObject()
3467	item = Indx[Obj.GetId()]
3468	try:
3469	val = float(Obj.GetValue())
3470	RBObj['Orig'][0][item] = val
3471	Obj.SetValue('%8.5f'%(val))
3472	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3473	for i,id in enumerate(RBObj['Ids']):
3474	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3475	data['Drawing']['Atoms'] = []
3476	UpdateDrawAtoms(atomStyle)
3477	G2plt.PlotStructure(G2frame,data)
3478	except ValueError:
3479	pass
3480
3481	def OnOrien(event):
3482	Obj = event.GetEventObject()
3483	item = Indx[Obj.GetId()]
3484	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3485	V = np.inner(Bmat,V)
3486	try:
3487	val = float(Obj.GetValue())
3488	if item:
3489	V[item-1] = val
3490	else:
3491	A = val
3492	Obj.SetValue('%8.5f'%(val))
3493	V = np.inner(Amat,V)
3494	Q = G2mth.AVdeg2Q(A,V)
3495	if not any(Q):
3496	raise ValueError
3497	RBObj['Orient'][0] = Q
3498	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3499	for i,id in enumerate(RBObj['Ids']):
3500	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3501	data['Drawing']['Atoms'] = []
3502	UpdateDrawAtoms(atomStyle)
3503	G2plt.PlotStructure(G2frame,data)
3504	except ValueError:
3505	pass
3506
3507	topSizer = wx.FlexGridSizer(0,6,5,5)
3508	Orig = RBObj['Orig'][0]
3509	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3510	Orien = [Orien,]
3511	Orien.extend(OrienV/nl.norm(OrienV))
3512	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,WACV)
3513	for ix,x in enumerate(Orig):
3514	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3515	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3516	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3517	Indx[origX.GetId()] = ix
3518	topSizer.Add(origX,0,WACV)
3519	topSizer.Add((5,0),)
3520	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3521	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3522	Ocheck.SetValue(RBObj['Orig'][1])
3523	topSizer.Add(Ocheck,0,WACV)
3524	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,WACV)
3525	for ix,x in enumerate(Orien):
3526	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3527	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3528	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3529	Indx[orien.GetId()] = ix
3530	topSizer.Add(orien,0,WACV)
3531	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3532	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3533	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3534	Qcheck.SetValue(RBObj['Orient'][1])
3535	topSizer.Add(Qcheck)
3536	return topSizer
3537
3538	def ResrbSizer(RBObj):
3539	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3540
3541	def OnTorsionRef(event):
3542	Obj = event.GetEventObject()
3543	item = Indx[Obj.GetId()]
3544	RBObj['Torsions'][item][1] = Obj.GetValue()
3545
3546	def OnTorsion(event):
3547	Obj = event.GetEventObject()
3548	item = Indx[Obj.GetId()]
3549	try:
3550	val = float(Obj.GetValue())
3551	RBObj['Torsions'][item][0] = val
3552	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3553	for i,id in enumerate(RBObj['Ids']):
3554	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3555	except ValueError:
3556	pass
3557	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3558	data['Drawing']['Atoms'] = []
3559	UpdateDrawAtoms(atomStyle)
3560	drawAtoms.ClearSelection()
3561	G2plt.PlotStructure(G2frame,data)
3562
3563	def OnDelResRB(event):
3564	Obj = event.GetEventObject()
3565	RBId = Indx[Obj.GetId()]
3566	RBData['Residue'][RBId]['useCount'] -= 1
3567	RBObjs = data['RBModels']['Residue']
3568	for rbObj in RBObjs:
3569	if RBId == rbObj['RBId']:
3570	data['RBModels']['Residue'].remove(rbObj)
3571	G2plt.PlotStructure(G2frame,data)
3572	wx.CallAfter(FillRigidBodyGrid,True)
3573
3574	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3575	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3576	topLine = wx.BoxSizer(wx.HORIZONTAL)
3577	topLine.Add(wx.StaticText(RigidBodies,-1,
3578	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,WACV)
3579	rbId = RBObj['RBId']
3580	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3581	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3582	Indx[delRB.GetId()] = rbId
3583	topLine.Add(delRB,0,WACV)
3584	resrbSizer.Add(topLine)
3585	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3586	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,WACV)
3587	torSizer = wx.FlexGridSizer(0,6,5,5)
3588	for itors,tors in enumerate(RBObj['Torsions']):
3589	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,WACV)
3590	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3591	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3592	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3593	Indx[torsTxt.GetId()] = itors
3594	torSizer.Add(torsTxt)
3595	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3596	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3597	torCheck.SetValue(tors[1])
3598	Indx[torCheck.GetId()] = itors
3599	torSizer.Add(torCheck,0,WACV)
3600	resrbSizer.Add(torSizer)
3601	tchoice = ['None','Uiso','T','TL','TLS']
3602	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3603	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,WACV)
3604	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3605	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3606	Indx[thermSel.GetId()] = RBObj
3607	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3608	thermSizer.Add(thermSel,0,WACV)
3609	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,WACV)
3610	resrbSizer.Add(thermSizer)
3611	if RBObj['ThermalMotion'][0] != 'None':
3612	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3613	return resrbSizer
3614
3615	def VecrbSizer(RBObj):
3616	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3617
3618	def OnDelVecRB(event):
3619	Obj = event.GetEventObject()
3620	RBId = Indx[Obj.GetId()]
3621	RBData['Vector'][RBId]['useCount'] -= 1
3622	RBObjs = data['RBModels']['Vector']
3623	for rbObj in RBObjs:
3624	if RBId == rbObj['RBId']:
3625	data['RBModels']['Vector'].remove(rbObj)
3626	G2plt.PlotStructure(G2frame,data)
3627	wx.CallAfter(FillRigidBodyGrid,True)
3628
3629	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3630	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3631	topLine = wx.BoxSizer(wx.HORIZONTAL)
3632	topLine.Add(wx.StaticText(RigidBodies,-1,
3633	'Name: '+RBObj['RBname']+' '),0,WACV)
3634	rbId = RBObj['RBId']
3635	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3636	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3637	Indx[delRB.GetId()] = rbId
3638	topLine.Add(delRB,0,WACV)
3639	vecrbSizer.Add(topLine)
3640	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3641	tchoice = ['None','Uiso','T','TL','TLS']
3642	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3643	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,WACV)
3644	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3645	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3646	Indx[thermSel.GetId()] = RBObj
3647	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3648	thermSizer.Add(thermSel,0,WACV)
3649	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,WACV)
3650	vecrbSizer.Add(thermSizer)
3651	if RBObj['ThermalMotion'][0] != 'None':
3652	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3653	return vecrbSizer
3654
3655	# FillRigidBodyGrid executable code starts here
3656	if refresh:
3657	RigidBodies.DestroyChildren()
3658	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3659	general = data['General']
3660	cx = general['AtomPtrs'][0]
3661	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3662	RBData = G2frame.PatternTree.GetItemPyData(
3663	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3664	Indx = {}
3665	atomStyle = 'balls & sticks'
3666	if 'macro' in general['Type']:
3667	atomStyle = 'sticks'
3668	G2frame.dataFrame.SetStatusText('')
3669	mainSizer = wx.BoxSizer(wx.VERTICAL)
3670	if not data['RBModels']:
3671	mainSizer.Add((5,5),0)
3672	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,WACV)
3673	mainSizer.Add((5,5),0)
3674	if 'Residue' in data['RBModels']:
3675	mainSizer.Add((5,5),0)
3676	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,WACV)
3677	mainSizer.Add((5,5),0)
3678	for RBObj in data['RBModels']['Residue']:
3679	mainSizer.Add(ResrbSizer(RBObj))
3680	if 'Vector' in data['RBModels']:
3681	mainSizer.Add((5,5),0)
3682	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,WACV)
3683	mainSizer.Add((5,5),0)
3684	for RBObj in data['RBModels']['Vector']:
3685	mainSizer.Add(VecrbSizer(RBObj))
3686
3687	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3688
3689	def OnRBCopyParms(event):
3690	RBObjs = []
3691	for rbType in ['Vector','Residue']:
3692	RBObjs += data['RBModels'].get(rbType,[])
3693	if not len(RBObjs):
3694	print '** ERROR - no rigid bodies defined **'
3695	return
3696	if len(RBObjs) == 1:
3697	print '** INFO - only one rigid body defined; nothing to copy to **'
3698	return
3699	Source = []
3700	sourceRB = {}
3701	for RBObj in RBObjs:
3702	Source.append(RBObj['RBname'])
3703	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3704	if dlg.ShowModal() == wx.ID_OK:
3705	sel = dlg.GetSelection()
3706	name = Source[sel]
3707	for item in ['Orig','Orient','ThermalMotion']:
3708	sourceRB.update({item:RBObjs[sel][item],})
3709	dlg.Destroy()
3710	if not sourceRB:
3711	return
3712	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3713	if dlg.ShowModal() == wx.ID_OK:
3714	sel = dlg.GetSelections()
3715	for x in sel:
3716	RBObjs[x].update(copy.copy(sourceRB))
3717	G2plt.PlotStructure(G2frame,data)
3718	wx.CallAfter(FillRigidBodyGrid(True))
3719
3720	def OnRBAssign(event):
3721
3722	G2frame.dataFrame.SetStatusText('')
3723	RBData = G2frame.PatternTree.GetItemPyData(
3724	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3725	rbNames = {}
3726	for rbVec in RBData['Vector']:
3727	if rbVec != 'AtInfo':
3728	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3729	for rbRes in RBData['Residue']:
3730	if rbRes != 'AtInfo':
3731	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3732	if not rbNames:
3733	print '** ERROR - no rigid bodies defined **'
3734	return
3735	general = data['General']
3736	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3737	cx,ct = general['AtomPtrs'][:2]
3738	atomData = data['Atoms']
3739	Indx = {}
3740	atInd = [-1,-1,-1]
3741	data['testRBObj'] = {}
3742
3743	def Draw():
3744
3745	def OnOk(event):
3746	rbType = data['testRBObj']['rbType']
3747	RBObjs = data['RBModels'].get(rbType,[])
3748	rbObj = data['testRBObj']['rbObj']
3749	rbId = rbObj['RBId']
3750	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3751	Ids = []
3752	dmax = 0.0
3753	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3754	for xyz in newXYZ:
3755	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3756	dmax = max(dmax,np.min(dist))
3757	id = np.argmin(dist)
3758	Ids.append(atomData[id][-1])
3759	atomData[id][cx:cx+3] = xyz
3760	if dmax > 1.0:
3761	print '** WARNING - some atoms not found or misidentified **'
3762	print '** check torsion angles & try again **'
3763	OkBtn.SetLabel('Not Ready')
3764	OkBtn.Enable(False)
3765	return
3766	rbObj['Ids'] = Ids
3767	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3768	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3769	RBObjs.append(rbObj)
3770	data['RBModels'][rbType] = RBObjs
3771	RBData[rbType][rbId]['useCount'] += 1
3772	del data['testRBObj']
3773	G2plt.PlotStructure(G2frame,data)
3774	FillRigidBodyGrid(True)
3775
3776	def OnCancel(event):
3777	del data['testRBObj']
3778	FillRigidBodyGrid(True)
3779
3780	def OnRBSel(event):
3781	selection = rbSel.GetValue()
3782	rbType,rbId = rbNames[selection]
3783	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3784	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3785	data['testRBObj']['rbType'] = rbType
3786	data['testRBObj']['rbData'] = RBData
3787	data['testRBObj']['Sizers'] = {}
3788	rbRef = RBData[rbType][rbId]['rbRef']
3789	data['testRBObj']['rbRef'] = rbRef
3790	refType = []
3791	refName = []
3792	for ref in rbRef[:3]:
3793	reftype = data['testRBObj']['rbAtTypes'][ref]
3794	refType.append(reftype)
3795	refName.append(reftype+' '+str(rbRef[0]))
3796	atNames,AtNames = fillAtNames(refType,atomData,ct)
3797	data['testRBObj']['atNames'] = atNames
3798	data['testRBObj']['AtNames'] = AtNames
3799	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3800	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3801	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3802	data['testRBObj']['torAtms'] = []
3803	for item in RBData[rbType][rbId].get('rbSeq',[]):
3804	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3805	data['testRBObj']['torAtms'].append([-1,-1,-1])
3806	Draw()
3807
3808	def fillAtNames(refType,atomData,ct):
3809	atNames = [{},{},{}]
3810	AtNames = {}
3811	for iatm,atom in enumerate(atomData):
3812	AtNames[atom[ct-1]] = iatm
3813	for i,reftype in enumerate(refType):
3814	if atom[ct] == reftype:
3815	atNames[i][atom[ct-1]] = iatm
3816	return atNames,AtNames
3817
3818	def OnAtOrigPick(event):
3819	Obj = event.GetEventObject()
3820	item = Indx[Obj.GetId()]
3821	atName = Obj.GetValue()
3822	rbType = data['testRBObj']['rbType']
3823	atInd[0] = atNames[item][atName]
3824	if 'Vector' in rbType:
3825	rbObj = data['testRBObj']['rbObj']
3826	rbId = rbObj['RBId']
3827	rbRef = data['testRBObj']['rbRef']
3828	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3829	nref = atNames[item][atName]
3830	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3831	Nxyz = np.array(atomData[nref][cx:cx+3])
3832	Orig = Nxyz-Oxyz
3833	data['testRBObj']['rbObj']['Orig'][0] = Orig
3834	else:
3835	Orig = atomData[atNames[item][atName]][cx:cx+3]
3836	data['testRBObj']['rbObj']['Orig'][0] = Orig
3837	for x,item in zip(Orig,Xsizers):
3838	item.SetLabel('%10.5f'%(x))
3839	G2plt.PlotStructure(G2frame,data)
3840
3841	def OnAtQPick(event):
3842	Obj = event.GetEventObject()
3843	item = Indx[Obj.GetId()]
3844	atName = Obj.GetValue()
3845	atInd[item] = atNames[item][atName]
3846	if any([x<0 for x in atInd]):
3847	return
3848	OkBtn.SetLabel('OK')
3849	OkBtn.Enable(True)
3850	rbType = data['testRBObj']['rbType']
3851	rbObj = data['testRBObj']['rbObj']
3852	rbId = rbObj['RBId']
3853	rbRef = data['testRBObj']['rbRef']
3854	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3855	rbOrig = rbXYZ[rbRef[0]]
3856	VAR = rbXYZ[rbRef[1]]-rbOrig
3857	VBR = rbXYZ[rbRef[2]]-rbOrig
3858	if rbType == 'Vector':
3859	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3860	else:
3861	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3862	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3863	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3864	VCC = np.cross(VAR,VAC)
3865	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3866	VAR = G2mth.prodQVQ(QuatA,VAR)
3867	VBR = G2mth.prodQVQ(QuatA,VBR)
3868	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3869	QuatC = G2mth.prodQQ(QuatB,QuatA)
3870	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3871	for x,item in zip(QuatC,Osizers):
3872	item.SetLabel('%10.4f'%(x))
3873	if rbType == 'Vector':
3874	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3875	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3876	Orig = Nxyz-Oxyz
3877	data['testRBObj']['rbObj']['Orig'][0] = Orig
3878	for x,item in zip(Orig,Xsizers):
3879	item.SetLabel('%10.5f'%(x))
3880	G2plt.PlotStructure(G2frame,data)
3881
3882	def OnTorAngle(event):
3883	OkBtn.SetLabel('OK')
3884	OkBtn.Enable(True)
3885	Obj = event.GetEventObject()
3886	[tor,torSlide] = Indx[Obj.GetId()]
3887	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3888	try:
3889	value = float(Obj.GetValue())
3890	except ValueError:
3891	value = Tors[0]
3892	Tors[0] = value
3893	Obj.SetValue('%8.3f'%(value))
3894	torSlide.SetValue(int(value*10))
3895	G2plt.PlotStructure(G2frame,data)
3896
3897	def OnTorSlide(event):
3898	OkBtn.SetLabel('OK')
3899	OkBtn.Enable(True)
3900	Obj = event.GetEventObject()
3901	tor,ang = Indx[Obj.GetId()]
3902	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3903	val = float(Obj.GetValue())/10.
3904	Tors[0] = val
3905	ang.SetValue('%8.3f'%(val))
3906	G2plt.PlotStructure(G2frame,data)
3907
3908	if len(data['testRBObj']):
3909	G2plt.PlotStructure(G2frame,data)
3910
3911	RigidBodies.DestroyChildren()
3912	mainSizer = wx.BoxSizer(wx.VERTICAL)
3913	mainSizer.Add((5,5),0)
3914	if data['testRBObj']:
3915	Xsizers = []
3916	Osizers = []
3917	rbObj = data['testRBObj']['rbObj']
3918	rbName = rbObj['RBname']
3919	rbId = rbObj['RBId']
3920	Orig = rbObj['Orig'][0]
3921	Orien = rbObj['Orient'][0]
3922	rbRef = data['testRBObj']['rbRef']
3923	Torsions = rbObj['Torsions']
3924	refName = []
3925	for ref in rbRef:
3926	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3927	atNames = data['testRBObj']['atNames']
3928	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3929	0,WACV)
3930	mainSizer.Add((5,5),0)
3931	OriSizer = wx.FlexGridSizer(0,5,5,5)
3932	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,WACV)
3933	for ix,x in enumerate(Orig):
3934	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3935	OriSizer.Add(origX,0,WACV)
3936	Xsizers.append(origX)
3937	OriSizer.Add((5,0),)
3938	if len(atomData):
3939	choice = atNames[0].keys()
3940	choice.sort()
3941	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3942	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,WACV)
3943	for ix,x in enumerate(Orien):
3944	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3945	OriSizer.Add(orien,0,WACV)
3946	Osizers.append(orien)
3947	data['testRBObj']['Sizers']['Osizers'] = Osizers
3948	mainSizer.Add(OriSizer)
3949	mainSizer.Add((5,5),0)
3950	RefSizer = wx.FlexGridSizer(0,7,5,5)
3951	if len(atomData):
3952	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,WACV)
3953	for i in [0,1,2]:
3954	choice = ['',]+atNames[i].keys()
3955	choice.sort()
3956	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,WACV)
3957	atPick = wx.ComboBox(RigidBodies,-1,value='',
3958	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3959	if i:
3960	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3961	else:
3962	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3963	Indx[atPick.GetId()] = i
3964	RefSizer.Add(atPick,0,WACV)
3965	mainSizer.Add(RefSizer)
3966	mainSizer.Add((5,5),0)
3967	if Torsions:
3968	AtNames = data['testRBObj']['AtNames']
3969	rbAtTypes = data['testRBObj']['rbAtTypes']
3970	rbSeq = RBData['Residue'][rbId]['rbSeq']
3971	TorSizer = wx.FlexGridSizer(0,4)
3972	TorSizer.AddGrowableCol(1,1)
3973	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3974	torName = ''
3975	for item in [seq[0],seq[1],seq[3][0]]:
3976	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3977	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,WACV)
3978	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3979	torSlide.SetRange(0,3600)
3980	torSlide.SetValue(int(torsion[0]*10.))
3981	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3982	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3983	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,WACV)
3984	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
3985	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
3986	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
3987	Indx[torSlide.GetId()] = [t,ang]
3988	Indx[ang.GetId()] = [t,torSlide]
3989	TorSizer.Add(ang,0,WACV)
3990	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
3991	else:
3992	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,WACV)
3993	else:
3994	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,WACV)
3995	mainSizer.Add((5,5),0)
3996	topSizer = wx.BoxSizer(wx.HORIZONTAL)
3997	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,WACV)
3998	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
3999	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
4000	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
4001	topSizer.Add((5,5),0)
4002	topSizer.Add(rbSel,0,WACV)
4003	mainSizer.Add(topSizer)
4004
4005	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
4006	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
4007	OkBtn.Enable(False)
4008	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
4009	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
4010	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
4011	btnSizer.Add((20,20),1)
4012	btnSizer.Add(OkBtn)
4013	btnSizer.Add(CancelBtn)
4014	btnSizer.Add((20,20),1)
4015	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
4016	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
4017	Draw()
4018
4019	def OnAutoFindResRB(event):
4020	RBData = G2frame.PatternTree.GetItemPyData(
4021	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4022	rbKeys = RBData['Residue'].keys()
4023	rbKeys.remove('AtInfo')
4024	if not len(rbKeys):
4025	print '** ERROR - no residue rigid bodies are defined **'
4026	return
4027	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
4028	RBIds = dict(zip(RBNames,rbKeys))
4029	general = data['General']
4030	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
4031	Atoms = data['Atoms']
4032	AtLookUp = G2mth.FillAtomLookUp(Atoms)
4033	if 'macro' not in general['Type']:
4034	print '** ERROR - this phase is not a macromolecule **'
4035	return
4036	if not len(Atoms):
4037	print '** ERROR - this phase has no atoms **'
4038	return
4039	RBObjs = []
4040	cx,ct = general['AtomPtrs'][:2]
4041	iatm = 0
4042	wx.BeginBusyCursor()
4043	try:
4044	while iatm < len(Atoms):
4045	atom = Atoms[iatm]
4046	res = atom[1].strip()
4047	numChain = ' %s %s'%(atom[0],atom[2])
4048	if res not in RBIds or atom[ct-1] == 'OXT':
4049	iatm += 1
4050	continue #skip for OXT, water molecules, etc.
4051	rbRes = RBData['Residue'][RBIds[res]]
4052	rbRef = rbRes['rbRef']
4053	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
4054	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
4055	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
4056	rbAtoms = []
4057	rbIds = []
4058	for iratm in range(len(rbRes['atNames'])):
4059	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
4060	rbIds.append(Atoms[iatm][20])
4061	iatm += 1 #puts this at beginning of next residue?
4062	Orig = rbAtoms[rbRef[0]]
4063	rbObj['RBId'] = RBIds[res]
4064	rbObj['Ids'] = rbIds
4065	rbObj['Orig'] = [Orig,False]
4066	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
4067	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
4068	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
4069	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
4070	VCC = np.cross(VAR,VAC)
4071	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
4072	VAR = G2mth.prodQVQ(QuatA,VAR)
4073	VBR = G2mth.prodQVQ(QuatA,VBR)
4074	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
4075	QuatC = G2mth.prodQQ(QuatB,QuatA)
4076	rbObj['Orient'] = [QuatC,' ']
4077	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
4078	SXYZ = []
4079	TXYZ = []
4080	rbObj['Torsions'] = []
4081	for i,xyz in enumerate(rbRes['rbXYZ']):
4082	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
4083	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
4084	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
4085	VBR = SXYZ[Oatm]-SXYZ[Patm]
4086	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
4087	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
4088	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
4089	ang = 180.*D/np.pi
4090	rbObj['Torsions'].append([ang,False])
4091	for ride in Riders:
4092	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
4093	rbRes['useCount'] += 1
4094	RBObjs.append(rbObj)
4095	data['RBModels']['Residue'] = RBObjs
4096	for RBObj in RBObjs:
4097	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
4098	for i,id in enumerate(RBObj['Ids']):
4099	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
4100	finally:
4101	wx.EndBusyCursor()
4102	wx.CallAfter(FillRigidBodyGrid,True)
4103
4104	def OnRBRemoveAll(event):
4105	data['RBModels']['Residue'] = []
4106	data['RBModels']['Vector'] = []
4107	RBData = G2frame.PatternTree.GetItemPyData(
4108	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4109	for RBType in ['Vector','Residue']:
4110	for rbId in RBData[RBType]:
4111	RBData[RBType][rbId]['useCount'] = 0
4112	FillRigidBodyGrid(True)
4113
4114	def OnGlobalResRBTherm(event):
4115	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
4116	RBObjs = data['RBModels']['Residue']
4117	names = ['None','Uiso','T','TL','TLS']
4118	cia = data['General']['AtomPtrs'][3]
4119	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
4120	if dlg.ShowModal() == wx.ID_OK:
4121	sel = dlg.GetSelection()
4122	parm = names[sel]
4123	Ttype = 'A'
4124	if parm == 'Uiso':
4125	Ttype = 'I'
4126	for rbObj in RBObjs:
4127	rbObj['ThermalMotion'][0] = parm
4128	if parm != 'None':
4129	for i,id in enumerate(rbObj['Ids']):
4130	data['Atoms'][AtLookUp[id]][cia] = Ttype
4131	dlg.Destroy()
4132	wx.CallAfter(FillRigidBodyGrid,True)
4133
4134	def OnGlobalResRBRef(event):
4135	RBObjs = data['RBModels']['Residue']
4136	names = ['Origin','Orient. angle','Full Orient.']
4137	nTor = 0
4138	for rbObj in RBObjs:
4139	nTor = max(nTor,len(rbObj['Torsions']))
4140	names += ['Torsion '+str(i) for i in range(nTor)]
4141	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
4142	names += ['Uiso',]
4143	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
4144	names += ['Tii','Tij','Lii','Lij','Sij']
4145	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
4146	names += ['Tii','Tij','Lii','Lij']
4147	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
4148	names += ['Tii','Tij']
4149
4150	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
4151	if dlg.ShowModal() == wx.ID_OK:
4152	sel = dlg.GetSelections()
4153	parms = []
4154	for x in sel:
4155	parms.append(names[x])
4156	wx.BeginBusyCursor()
4157	try:
4158	for rbObj in RBObjs:
4159	if 'Origin' in parms:
4160	rbObj['Orig'][1] = True
4161	else:
4162	rbObj['Orig'][1] = False
4163	if 'Full Orient.' in parms:
4164	rbObj['Orient'][1] = 'AV'
4165	elif 'Orient. angle' in parms:
4166	rbObj['Orient'][1] = 'A'
4167	else:
4168	rbObj