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source: trunk/GSASIIphsGUI.py @ 1076

Last change on this file since 1076 was 1076, checked in by vondreele, 10 years ago
again fix MC/SA window scroll behavior & small start on dummy histograms
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
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1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2013-10-03 17:52:28 +0000 (Thu, 03 Oct 2013) $
5	# $Author: vondreele $
6	# $Revision: 1076 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1076 2013-10-03 17:52:28Z 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 matplotlib as mpl
29	import math
30	import copy
31	import time
32	import sys
33	import random as ran
34	import cPickle
35	import GSASIIpath
36	GSASIIpath.SetVersionNumber("$Revision: 1076 $")
37	import GSASIIlattice as G2lat
38	import GSASIIspc as G2spc
39	import GSASIIElem as G2elem
40	import GSASIIElemGUI as G2elemGUI
41	import GSASIIddataGUI as G2ddG
42	import GSASIIplot as G2plt
43	import GSASIIgrid as G2gd
44	import GSASIIIO as G2IO
45	import GSASIIstrMain as G2stMn
46	import GSASIImath as G2mth
47	import GSASIIpwd as G2pwd
48	import numpy as np
49	import numpy.linalg as nl
50	import numpy.ma as ma
51
52	VERY_LIGHT_GREY = wx.Colour(235,235,235)
53	WHITE = wx.Colour(255,255,255)
54	BLACK = wx.Colour(0,0,0)
55	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
56	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
57	# trig functions in degrees
58	sind = lambda x: np.sin(x*np.pi/180.)
59	tand = lambda x: np.tan(x*np.pi/180.)
60	cosd = lambda x: np.cos(x*np.pi/180.)
61	asind = lambda x: 180.*np.arcsin(x)/np.pi
62	acosd = lambda x: 180.*np.arccos(x)/np.pi
63
64	def SetPhaseWindow(mainFrame,phasePage,mainSizer):
65	phasePage.SetSizer(mainSizer)
66	Size = mainSizer.GetMinSize()
67	Size[0] += 40
68	Size[1] = max(Size[1],430) + 35
69	phasePage.SetSize(Size)
70	phasePage.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
71	mainFrame.setSizePosLeft(Size)
72
73	def UpdatePhaseData(G2frame,Item,data,oldPage):
74	'''Create the data display window contents when a phase is clicked on
75	in the man (data tree) window.
76	Called only from :meth:`GSASIIgrid.MovePatternTreeToGrid`,
77	which in turn is called from :meth:`GSASII.GSASII.OnPatternTreeSelChanged`
78	when a tree item is selected.
79
80	:param wx.frame G2frame: the main GSAS-II frame object
81	:param wx.TreeItemId Item: the tree item that was selected
82	:param dict data: all the information on the phase in a dictionary
83	:param int oldPage: This sets a tab to select when moving
84	from one phase to another, in which case the same tab is selected
85	to display first. This is set only when the previous data tree
86	selection is a phase, if not the value is None. The default action
87	is to bring up the General tab.
88
89	'''
90
91	#patch
92	if 'RBModels' not in data:
93	data['RBModels'] = {}
94	if 'MCSA' not in data:
95	data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
96	if isinstance(data['MCSA']['Results'],dict):
97	data['MCSA']['Results'] = []
98	#end patch
99
100	global rbAtmDict
101	rbAtmDict = {}
102	if G2frame.dataDisplay:
103	G2frame.dataDisplay.Destroy()
104	PhaseName = G2frame.PatternTree.GetItemText(Item)
105	G2gd.SetDataMenuBar(G2frame)
106	G2frame.dataFrame.SetLabel('Phase Data for '+PhaseName)
107	G2frame.dataFrame.CreateStatusBar()
108	G2frame.dataDisplay = G2gd.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize())
109	G2frame.dataDisplay.gridList = [] # list of all grids in notebook
110
111	def SetupGeneral():
112	generalData = data['General']
113	atomData = data['Atoms']
114	generalData['AtomTypes'] = []
115	generalData['Isotopes'] = {}
116	# various patches
117	if 'Isotope' not in generalData:
118	generalData['Isotope'] = {}
119	if 'Data plot type' not in generalData:
120	generalData['Data plot type'] = 'Mustrain'
121	if 'POhkl' not in generalData:
122	generalData['POhkl'] = [0,0,1]
123	if 'Map' not in generalData:
124	generalData['Map'] = mapDefault
125	if 'Flip' not in generalData:
126	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
127	'k-factor':0.1,'k-Max':20.}
128	if 'doPawley' not in generalData:
129	generalData['doPawley'] = False
130	if 'Pawley dmin' not in generalData:
131	generalData['Pawley dmin'] = 1.0
132	if 'Pawley neg wt' not in generalData:
133	generalData['Pawley neg wt'] = 0.0
134	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
135	'MCSA controls' not in generalData:
136	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
137	'dmin':2.0,'Algorithm':'fast','Jump coeff':[0.95,0.5],'boltzmann':1.0,
138	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[]}
139	# end of patches
140	generalData['NoAtoms'] = {}
141	generalData['BondRadii'] = []
142	generalData['AngleRadii'] = []
143	generalData['vdWRadii'] = []
144	generalData['AtomMass'] = []
145	generalData['Color'] = []
146	generalData['Mydir'] = G2frame.dirname
147	cx,ct,cs,cia = [3,1,7,9]
148	if generalData['Type'] =='macromolecular':
149	cx,ct,cs,cia = [6,4,10,12]
150	generalData['AtomPtrs'] = [cx,ct,cs,cia]
151	for atom in atomData:
152	atom[ct] = atom[ct].lower().capitalize() #force to standard form
153	if generalData['AtomTypes'].count(atom[ct]):
154	generalData['NoAtoms'][atom[ct]] += atom[cs-1]*float(atom[cs+1])
155	elif atom[ct] != 'UNK':
156	Info = G2elem.GetAtomInfo(atom[ct])
157	generalData['AtomTypes'].append(atom[ct])
158	generalData['Z'] = Info['Z']
159	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
160	generalData['BondRadii'].append(Info['Drad'])
161	generalData['AngleRadii'].append(Info['Arad'])
162	generalData['vdWRadii'].append(Info['Vdrad'])
163	if atom[ct] in generalData['Isotope']:
164	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]][0])
165	else:
166	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
167	generalData['AtomMass'].append(Info['Mass'])
168	generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
169	generalData['Color'].append(Info['Color'])
170	F000X = 0.
171	F000N = 0.
172	for i,elem in enumerate(generalData['AtomTypes']):
173	F000X += generalData['NoAtoms'][elem]*generalData['Z']
174	isotope = generalData['Isotope'][elem]
175	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope][1]
176	generalData['F000X'] = F000X
177	generalData['F000N'] = F000N
178
179
180	################################################################################
181	##### General phase routines
182	################################################################################
183
184	def UpdateGeneral():
185	'''Draw the controls for the General phase data subpage
186	'''
187
188	""" This is the default dictionary structure for phase data
189	(taken from GSASII.py)
190	'General':{
191	'Name':PhaseName
192	'Type':'nuclear'
193	'SGData':SGData
194	'Cell':[False,10.,10.,10.,90.,90.,90,1000.]
195	'AtomPtrs':[]
196	'Histogram list':['',]
197	'Pawley dmin':1.0,
198	'Pawley neg wt':0.0}
199	'Atoms':[]
200	'Drawing':{}
201	"""
202	# UpdateGeneral execution starts here
203	phaseTypes = ['nuclear','modulated','magnetic','macromolecular']
204	SetupGeneral()
205	generalData = data['General']
206	Map = generalData['Map']
207	Flip = generalData['Flip']
208	MCSAdata = generalData['MCSA controls']
209	PWDR = any(['PWDR' in item for item in data['Histograms'].keys()])
210	# UpdateGeneral execution continues below
211
212	def NameSizer():
213	def OnPhaseName(event):
214	oldName = generalData['Name']
215	generalData['Name'] = NameTxt.GetValue()
216	G2frame.G2plotNB.Rename(oldName,generalData['Name'])
217	G2frame.dataFrame.SetLabel('Phase Data for '+generalData['Name'])
218	G2frame.PatternTree.SetItemText(Item,generalData['Name'])
219	#Hmm, need to change phase name key in Reflection Lists for each histogram
220
221	def OnPhaseType(event):
222	if not generalData['AtomTypes']: #can change only if no atoms!
223	generalData['Type'] = TypeTxt.GetValue()
224	wx.CallAfter(UpdateGeneral)
225	else:
226	TypeTxt.SetValue(generalData['Type'])
227
228	def OnSpaceGroup(event):
229	SpcGp = SGTxt.GetValue()
230	SGErr,SGData = G2spc.SpcGroup(SpcGp)
231	# try a lookup on the user-supplied name
232	if SGErr:
233	SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
234	if SpGrpNorm:
235	E,SGData = G2spc.SpcGroup(SpGrpNorm)
236	if not E: SGErr = False
237	if SGErr:
238	text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
239	SGTxt.SetValue(generalData['SGData']['SpGrp'])
240	msg = 'Space Group Error'
241	Style = wx.ICON_EXCLAMATION
242	else:
243	text = G2spc.SGPrint(SGData)
244	generalData['SGData'] = SGData
245	msg = 'Space Group Information'
246	Style = wx.ICON_INFORMATION
247	Text = ''
248	for line in text:
249	Text += line+'\n'
250	wx.MessageBox(Text,caption=msg,style=Style)
251	wx.CallAfter(UpdateGeneral)
252
253	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
254	nameSizer.Add(wx.StaticText(General,-1,' Phase name: '),0,wx.ALIGN_CENTER_VERTICAL)
255	NameTxt = wx.TextCtrl(General,-1,value=generalData['Name'],style=wx.TE_PROCESS_ENTER)
256	NameTxt.Bind(wx.EVT_TEXT_ENTER,OnPhaseName)
257	NameTxt.Bind(wx.EVT_KILL_FOCUS,OnPhaseName)
258	nameSizer.Add(NameTxt,0,wx.ALIGN_CENTER_VERTICAL)
259	nameSizer.Add(wx.StaticText(General,-1,' Phase type: '),0,wx.ALIGN_CENTER_VERTICAL)
260	TypeTxt = wx.ComboBox(General,-1,value=generalData['Type'],choices=phaseTypes,
261	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
262	TypeTxt.Bind(wx.EVT_COMBOBOX, OnPhaseType)
263	nameSizer.Add(TypeTxt,0,wx.ALIGN_CENTER_VERTICAL)
264	nameSizer.Add(wx.StaticText(General,-1,' Space group: '),0,wx.ALIGN_CENTER_VERTICAL)
265	SGTxt = wx.TextCtrl(General,-1,value=generalData['SGData']['SpGrp'],style=wx.TE_PROCESS_ENTER)
266	SGTxt.Bind(wx.EVT_TEXT_ENTER,OnSpaceGroup)
267	nameSizer.Add(SGTxt,0,wx.ALIGN_CENTER_VERTICAL)
268	return nameSizer
269
270	def CellSizer():
271
272	cellGUIlist = [[['m3','m3m'],4,zip([" Unit cell: a = "," Vol = "],["%.5f","%.3f"],[True,False],[0,0])],
273	[['3R','3mR'],6,zip([" a = "," alpha = "," Vol = "],["%.5f","%.3f","%.3f"],[True,True,False],[0,2,0])],
274	[['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])],
275	[['mmm'],8,zip([" a = "," b = "," c = "," Vol = "],["%.5f","%.5f","%.5f","%.3f"],
276	[True,True,True,False],[0,1,2,0])],
277	[['2/m'+'a'],10,zip([" a = "," b = "," c = "," alpha = "," Vol = "],
278	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
279	[['2/m'+'b'],10,zip([" a = "," b = "," c = "," beta = "," Vol = "],
280	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
281	[['2/m'+'c'],10,zip([" a = "," b = "," c = "," gamma = "," Vol = "],
282	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
283	[['-1'],8,zip([" a = "," b = "," c = "," Vol = "," alpha = "," beta = "," gamma = "],
284	["%.5f","%.5f","%.5f","%.3f","%.3f","%.3f","%.3f"],
285	[True,True,True,False,True,True,True],[0,1,2,0,3,4,5])]]
286
287	def OnCellRef(event):
288	generalData['Cell'][0] = cellRef.GetValue()
289
290	def OnCellChange(event):
291	SGData = generalData['SGData']
292	laue = SGData['SGLaue']
293	if laue == '2/m':
294	laue += SGData['SGUniq']
295	cell = generalData['Cell']
296	Obj = event.GetEventObject()
297	ObjId = cellList.index(Obj.GetId())
298	try:
299	value = max(1.0,float(Obj.GetValue()))
300	except ValueError:
301	if ObjId < 3: #bad cell edge - reset
302	value = controls[6+ObjId]
303	else: #bad angle
304	value = 90.
305	if laue in ['m3','m3m']:
306	cell[1] = cell[2] = cell[3] = value
307	cell[4] = cell[5] = cell[6] = 90.0
308	Obj.SetValue("%.5f"%(cell[1]))
309	elif laue in ['3R','3mR']:
310	if ObjId == 0:
311	cell[1] = cell[2] = cell[3] = value
312	Obj.SetValue("%.5f"%(cell[1]))
313	else:
314	cell[4] = cell[5] = cell[6] = value
315	Obj.SetValue("%.5f"%(cell[4]))
316	elif laue in ['3','3m1','31m','6/m','6/mmm','4/m','4/mmm']:
317	cell[4] = cell[5] = 90.
318	cell[6] = 120.
319	if laue in ['4/m','4/mmm']:
320	cell[6] = 90.
321	if ObjId == 0:
322	cell[1] = cell[2] = value
323	Obj.SetValue("%.5f"%(cell[1]))
324	else:
325	cell[3] = value
326	Obj.SetValue("%.5f"%(cell[3]))
327	elif laue in ['mmm']:
328	cell[ObjId+1] = value
329	cell[4] = cell[5] = cell[6] = 90.
330	Obj.SetValue("%.5f"%(cell[ObjId+1]))
331	elif laue in ['2/m'+'a']:
332	cell[5] = cell[6] = 90.
333	if ObjId != 3:
334	cell[ObjId+1] = value
335	Obj.SetValue("%.5f"%(cell[ObjId+1]))
336	else:
337	cell[4] = value
338	Obj.SetValue("%.3f"%(cell[4]))
339	elif laue in ['2/m'+'b']:
340	cell[4] = cell[6] = 90.
341	if ObjId != 3:
342	cell[ObjId+1] = value
343	Obj.SetValue("%.5f"%(cell[ObjId+1]))
344	else:
345	cell[5] = value
346	Obj.SetValue("%.3f"%(cell[5]))
347	elif laue in ['2/m'+'c']:
348	cell[5] = cell[6] = 90.
349	if ObjId != 3:
350	cell[ObjId+1] = value
351	Obj.SetValue("%.5f"%(cell[ObjId+1]))
352	else:
353	cell[6] = value
354	Obj.SetValue("%.3f"%(cell[6]))
355	else:
356	cell[ObjId+1] = value
357	if ObjId < 3:
358	Obj.SetValue("%.5f"%(cell[1+ObjId]))
359	else:
360	Obj.SetValue("%.3f"%(cell[1+ObjId]))
361	cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
362	volVal.SetValue("%.3f"%(cell[7]))
363	density,mattCoeff = G2mth.getDensity(generalData)
364	if denSizer:
365	denSizer[1].SetValue('%.3f'%(density))
366	if denSizer[2]:
367	denSizer[2].SetValue('%.3f'%(mattCoeff))
368	generalData['Cell'] = cell
369
370	cell = generalData['Cell']
371	laue = generalData['SGData']['SGLaue']
372	if laue == '2/m':
373	laue += generalData['SGData']['SGUniq']
374	for cellGUI in cellGUIlist:
375	if laue in cellGUI[0]:
376	useGUI = cellGUI
377	cellSizer = wx.FlexGridSizer(2,useGUI[1]+1,5,5)
378	if PWDR:
379	cellRef = wx.CheckBox(General,-1,label='Refine unit cell:')
380	cellSizer.Add(cellRef,0,wx.ALIGN_CENTER_VERTICAL)
381	cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef)
382	cellRef.SetValue(cell[0])
383	cellList = []
384	for txt,fmt,ifEdit,Id in useGUI[2]:
385	cellSizer.Add(wx.StaticText(General,label=txt),0,wx.ALIGN_CENTER_VERTICAL)
386	if ifEdit: #a,b,c,etc.
387	cellVal = wx.TextCtrl(General,value=(fmt%(cell[Id+1])),
388	style=wx.TE_PROCESS_ENTER)
389	cellVal.Bind(wx.EVT_TEXT_ENTER,OnCellChange)
390	cellVal.Bind(wx.EVT_KILL_FOCUS,OnCellChange)
391	cellSizer.Add(cellVal,0,wx.ALIGN_CENTER_VERTICAL)
392	cellList.append(cellVal.GetId())
393	else: #volume
394	volVal = wx.TextCtrl(General,value=(fmt%(cell[7])),style=wx.TE_READONLY)
395	volVal.SetBackgroundColour(VERY_LIGHT_GREY)
396	cellSizer.Add(volVal,0,wx.ALIGN_CENTER_VERTICAL)
397	return cellSizer
398
399	def ElemSizer():
400
401	def OnIsotope(event):
402	Obj = event.GetEventObject()
403	item = Indx[Obj.GetId()]
404	isotope = Obj.GetValue()
405	generalData['Isotope'][item] = isotope
406	indx = generalData['AtomTypes'].index(item)
407	data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope][0]
408	density,mattCoeff = G2mth.getDensity(generalData)
409	denSizer[1].SetValue('%.3f'%(density))
410	if denSizer[2]:
411	denSizer[2].SetValue('%.3f'%(mattCoeff))
412
413	elemSizer = wx.FlexGridSizer(8,len(generalData['AtomTypes'])+1,1,1)
414	elemSizer.Add(wx.StaticText(General,label=' Elements'),0,wx.ALIGN_CENTER_VERTICAL)
415	for elem in generalData['AtomTypes']:
416	typTxt = wx.TextCtrl(General,value=elem,style=wx.TE_READONLY)
417	typTxt.SetBackgroundColour(VERY_LIGHT_GREY)
418	elemSizer.Add(typTxt,0,wx.ALIGN_CENTER_VERTICAL)
419	elemSizer.Add(wx.StaticText(General,label=' Isotope'),0,wx.ALIGN_CENTER_VERTICAL)
420	for elem in generalData['AtomTypes']:
421	choices = generalData['Isotopes'][elem].keys()
422	isoSel = wx.ComboBox(General,-1,value=generalData['Isotope'][elem],choices=choices,
423	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
424	isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope)
425	Indx[isoSel.GetId()] = elem
426	elemSizer.Add(isoSel,1,wx.ALIGN_CENTER_VERTICAL\|wx.EXPAND)
427	elemSizer.Add(wx.StaticText(General,label=' No. per cell'),0,wx.ALIGN_CENTER_VERTICAL)
428	for elem in generalData['AtomTypes']:
429	numbTxt = wx.TextCtrl(General,value='%.1f'%(generalData['NoAtoms'][elem]),
430	style=wx.TE_READONLY)
431	numbTxt.SetBackgroundColour(VERY_LIGHT_GREY)
432	elemSizer.Add(numbTxt,0,wx.ALIGN_CENTER_VERTICAL)
433	elemSizer.Add(wx.StaticText(General,label=' Atom weight'),0,wx.ALIGN_CENTER_VERTICAL)
434	for wt in generalData['AtomMass']:
435	wtTxt = wx.TextCtrl(General,value='%.3f'%(wt),style=wx.TE_READONLY)
436	wtTxt.SetBackgroundColour(VERY_LIGHT_GREY)
437	elemSizer.Add(wtTxt,0,wx.ALIGN_CENTER_VERTICAL)
438	elemSizer.Add(wx.StaticText(General,label=' Bond radii'),0,wx.ALIGN_CENTER_VERTICAL)
439	for rad in generalData['BondRadii']:
440	bondRadii = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
441	bondRadii.SetBackgroundColour(VERY_LIGHT_GREY)
442	elemSizer.Add(bondRadii,0,wx.ALIGN_CENTER_VERTICAL)
443	elemSizer.Add(wx.StaticText(General,label=' Angle radii'),0,wx.ALIGN_CENTER_VERTICAL)
444	for rad in generalData['AngleRadii']:
445	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
446	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
447	elemSizer.Add(elemTxt,0,wx.ALIGN_CENTER_VERTICAL)
448	elemSizer.Add(wx.StaticText(General,label=' van der Waals radii'),0,wx.ALIGN_CENTER_VERTICAL)
449	for rad in generalData['vdWRadii']:
450	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
451	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
452	elemSizer.Add(elemTxt,0,wx.ALIGN_CENTER_VERTICAL)
453	elemSizer.Add(wx.StaticText(General,label=' Default color'),0,wx.ALIGN_CENTER_VERTICAL)
454	for R,G,B in generalData['Color']:
455	colorTxt = wx.TextCtrl(General,value='',style=wx.TE_READONLY)
456	colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
457	elemSizer.Add(colorTxt,0,wx.ALIGN_CENTER_VERTICAL)
458	return elemSizer
459
460	def DenSizer():
461
462	mass = G2mth.getMass(generalData)
463	density,mattCoeff = G2mth.getDensity(generalData)
464	denSizer = wx.BoxSizer(wx.HORIZONTAL)
465	denSizer.Add(wx.StaticText(General,-1,' Density: '),0,wx.ALIGN_CENTER_VERTICAL)
466	denTxt = wx.TextCtrl(General,-1,'%.3f'%(density),style=wx.TE_READONLY)
467	denTxt.SetBackgroundColour(VERY_LIGHT_GREY)
468	denSizer.Add(denTxt,0,wx.ALIGN_CENTER_VERTICAL)
469	mattTxt = None
470	if generalData['Type'] == 'macromolecular' and mass > 0.0:
471	denSizer.Add(wx.StaticText(General,-1,' Matthews coeff.: '),
472	0,wx.ALIGN_CENTER_VERTICAL)
473	mattTxt = wx.TextCtrl(General,-1,'%.3f'%(mattCoeff),style=wx.TE_READONLY)
474	mattTxt.SetBackgroundColour(VERY_LIGHT_GREY)
475	denSizer.Add(mattTxt,0,wx.ALIGN_CENTER_VERTICAL)
476	return denSizer,denTxt,mattTxt
477
478	def PawleySizer():
479
480	def OnPawleyRef(event):
481	generalData['doPawley'] = pawlRef.GetValue()
482
483	def OnPawleyVal(event):
484	try:
485	dmin = float(pawlVal.GetValue())
486	if 0.25 <= dmin <= 20.:
487	generalData['Pawley dmin'] = dmin
488	except ValueError:
489	pass
490	pawlVal.SetValue("%.3f"%(generalData['Pawley dmin'])) #reset in case of error
491
492	def OnPawleyNegWt(event):
493	try:
494	wt = float(pawlNegWt.GetValue())
495	if 0. <= wt <= 1.:
496	generalData['Pawley neg wt'] = wt
497	except ValueError:
498	pass
499	pawlNegWt.SetValue("%.4f"%(generalData['Pawley neg wt'])) #reset in case of error
500
501	pawleySizer = wx.BoxSizer(wx.HORIZONTAL)
502	pawleySizer.Add(wx.StaticText(General,label=' Pawley controls: '),0,wx.ALIGN_CENTER_VERTICAL)
503	pawlRef = wx.CheckBox(General,-1,label=' Do Pawley refinement?')
504	pawlRef.SetValue(generalData['doPawley'])
505	pawlRef.Bind(wx.EVT_CHECKBOX,OnPawleyRef)
506	pawleySizer.Add(pawlRef,0,wx.ALIGN_CENTER_VERTICAL)
507	pawleySizer.Add(wx.StaticText(General,label=' Pawley dmin: '),0,wx.ALIGN_CENTER_VERTICAL)
508	pawlVal = wx.TextCtrl(General,value='%.3f'%(generalData['Pawley dmin']),style=wx.TE_PROCESS_ENTER)
509	pawlVal.Bind(wx.EVT_TEXT_ENTER,OnPawleyVal)
510	pawlVal.Bind(wx.EVT_KILL_FOCUS,OnPawleyVal)
511	pawleySizer.Add(pawlVal,0,wx.ALIGN_CENTER_VERTICAL)
512	pawleySizer.Add(wx.StaticText(General,label=' Pawley neg. wt.: '),0,wx.ALIGN_CENTER_VERTICAL)
513	pawlNegWt = wx.TextCtrl(General,value='%.4f'%(generalData['Pawley neg wt']),style=wx.TE_PROCESS_ENTER)
514	pawlNegWt.Bind(wx.EVT_TEXT_ENTER,OnPawleyNegWt)
515	pawlNegWt.Bind(wx.EVT_KILL_FOCUS,OnPawleyNegWt)
516	pawleySizer.Add(pawlNegWt,0,wx.ALIGN_CENTER_VERTICAL)
517	return pawleySizer
518
519	def MapSizer():
520
521	def OnMapType(event):
522	Map['MapType'] = mapType.GetValue()
523
524	def OnRefList(event):
525	Map['RefList'] = refList.GetValue()
526
527	def OnResVal(event):
528	try:
529	res = float(mapRes.GetValue())
530	if 0.25 <= res <= 20.:
531	Map['Resolution'] = res
532	except ValueError:
533	pass
534	mapRes.SetValue("%.2f"%(Map['Resolution'])) #reset in case of error
535
536	def OnCutOff(event):
537	try:
538	res = float(cutOff.GetValue())
539	if 10.0 <= res <= 100.:
540	Map['cutOff'] = res
541	except ValueError:
542	pass
543	cutOff.SetValue("%.1f"%(Map['cutOff'])) #reset in case of error
544
545	#patch
546	if 'cutOff' not in Map:
547	Map['cutOff'] = 100.0
548	mapTypes = ['Fobs','Fcalc','delt-F','2*Fo-Fc','Omit','Patterson']
549	refList = data['Histograms'].keys()
550	if not generalData['AtomTypes']:
551	mapTypes = ['Patterson',]
552	Map['MapType'] = 'Patterson'
553	mapSizer = wx.BoxSizer(wx.VERTICAL)
554	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
555	lineSizer.Add(wx.StaticText(General,label=' Fourier map controls: Map type: '),0,wx.ALIGN_CENTER_VERTICAL)
556	mapType = wx.ComboBox(General,-1,value=Map['MapType'],choices=mapTypes,
557	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
558	mapType.Bind(wx.EVT_COMBOBOX,OnMapType)
559	lineSizer.Add(mapType,0,wx.ALIGN_CENTER_VERTICAL)
560	lineSizer.Add(wx.StaticText(General,label=' Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
561	refList = wx.ComboBox(General,-1,value=Map['RefList'],choices=refList,
562	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
563	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
564	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
565	mapSizer.Add(lineSizer,0,wx.ALIGN_CENTER_VERTICAL)
566	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
567	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,wx.ALIGN_CENTER_VERTICAL)
568	mapRes = wx.TextCtrl(General,value='%.2f'%(Map['Resolution']),style=wx.TE_PROCESS_ENTER)
569	mapRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
570	mapRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
571	line2Sizer.Add(mapRes,0,wx.ALIGN_CENTER_VERTICAL)
572	line2Sizer.Add(wx.StaticText(General,label=' Peak cutoff %: '),0,wx.ALIGN_CENTER_VERTICAL)
573	cutOff = wx.TextCtrl(General,value='%.1f'%(Map['cutOff']),style=wx.TE_PROCESS_ENTER)
574	cutOff.Bind(wx.EVT_TEXT_ENTER,OnCutOff)
575	cutOff.Bind(wx.EVT_KILL_FOCUS,OnCutOff)
576	line2Sizer.Add(cutOff,0,wx.ALIGN_CENTER_VERTICAL)
577	mapSizer.Add(line2Sizer,0,wx.ALIGN_CENTER_VERTICAL)
578	return mapSizer
579
580	def FlipSizer():
581	if 'k-Max' not in Flip: Flip['k-Max'] = 20.
582
583	def OnRefList(event):
584	Flip['RefList'] = refList.GetValue()
585
586	def OnNormElem(event):
587	PE = G2elemGUI.PickElement(G2frame,ifNone=True)
588	if PE.ShowModal() == wx.ID_OK:
589	Flip['Norm element'] = PE.Elem.strip()
590	normElem.SetLabel(Flip['Norm element'])
591	PE.Destroy()
592
593	def OnResVal(event):
594	try:
595	res = float(flipRes.GetValue())
596	if 0.25 <= res <= 20.:
597	Flip['Resolution'] = res
598	except ValueError:
599	pass
600	flipRes.SetValue("%.2f"%(Flip['Resolution'])) #reset in case of error
601
602	def OnkFactor(event):
603	try:
604	res = float(kFactor.GetValue())
605	if 0.1 <= res <= 1.2:
606	Flip['k-factor'] = res
607	except ValueError:
608	pass
609	kFactor.SetValue("%.3f"%(Flip['k-factor'])) #reset in case of error
610
611	def OnkMax(event):
612	try:
613	res = float(kMax.GetValue())
614	if res >= 10.:
615	Flip['k-Max'] = res
616	except ValueError:
617	pass
618	kMax.SetValue("%.1f"%(Flip['k-Max'])) #reset in case of error
619
620	refList = data['Histograms'].keys()
621	flipSizer = wx.BoxSizer(wx.VERTICAL)
622	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
623	lineSizer.Add(wx.StaticText(General,label=' Charge flip controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
624	refList = wx.ComboBox(General,-1,value=Flip['RefList'],choices=refList,
625	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
626	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
627	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
628	lineSizer.Add(wx.StaticText(General,label=' Normalizing element: '),0,wx.ALIGN_CENTER_VERTICAL)
629	normElem = wx.Button(General,label=Flip['Norm element'],style=wx.TE_READONLY)
630	normElem.Bind(wx.EVT_BUTTON,OnNormElem)
631	lineSizer.Add(normElem,0,wx.ALIGN_CENTER_VERTICAL)
632	flipSizer.Add(lineSizer,0,wx.ALIGN_CENTER_VERTICAL)
633	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
634	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,wx.ALIGN_CENTER_VERTICAL)
635	flipRes = wx.TextCtrl(General,value='%.2f'%(Flip['Resolution']),style=wx.TE_PROCESS_ENTER)
636	flipRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
637	flipRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
638	line2Sizer.Add(flipRes,0,wx.ALIGN_CENTER_VERTICAL)
639	line2Sizer.Add(wx.StaticText(General,label=' k-Factor (0.1-1.2): '),0,wx.ALIGN_CENTER_VERTICAL)
640	kFactor = wx.TextCtrl(General,value='%.3f'%(Flip['k-factor']),style=wx.TE_PROCESS_ENTER)
641	kFactor.Bind(wx.EVT_TEXT_ENTER,OnkFactor)
642	kFactor.Bind(wx.EVT_KILL_FOCUS,OnkFactor)
643	line2Sizer.Add(kFactor,0,wx.ALIGN_CENTER_VERTICAL)
644	line2Sizer.Add(wx.StaticText(General,label=' k-Max (>=10.0): '),0,wx.ALIGN_CENTER_VERTICAL)
645	kMax = wx.TextCtrl(General,value='%.1f'%(Flip['k-Max']),style=wx.TE_PROCESS_ENTER)
646	kMax.Bind(wx.EVT_TEXT_ENTER,OnkMax)
647	kMax.Bind(wx.EVT_KILL_FOCUS,OnkMax)
648	line2Sizer.Add(kMax,0,wx.ALIGN_CENTER_VERTICAL)
649	flipSizer.Add(line2Sizer,0,wx.ALIGN_CENTER_VERTICAL)
650	return flipSizer
651
652	def MCSASizer():
653	Ind = {}
654
655	def OnRefList(event):
656	MCSAdata['Data source'] = refList.GetValue()
657
658	def OnDmin(event):
659	try:
660	val = float(dmin.GetValue())
661	if 1.0 <= val < 5.0:
662	MCSAdata['dmin'] = val
663	except ValueError:
664	pass
665	dmin.SetValue("%.3f"%(MCSAdata['dmin'])) #reset in case of error
666	MCSAdata['newDmin'] = True
667
668	def OnCycles(event):
669	MCSAdata['Cycles'] = int(cycles.GetValue())
670
671	def OnAlist(event):
672	MCSAdata['Algorithm'] = Alist.GetValue()
673	wx.CallAfter(UpdateGeneral)
674
675	def OnSlope(event):
676	try:
677	val = float(slope.GetValue())
678	if .25 <= val < 1.0:
679	MCSAdata['log slope'] = val
680	except ValueError:
681	pass
682	slope.SetValue("%.3f"%(MCSAdata['log slope'])) #reset in case of error
683
684	def OnAjump(event):
685	Obj = event.GetEventObject()
686	name,ind = Indx[Obj.GetId()]
687	try:
688	val = float(Obj.GetValue())
689	if .0 <= val <= 1.0:
690	MCSAdata[name][ind] = val
691	except ValueError:
692	pass
693	Obj.SetValue("%.3f"%(MCSAdata[name][ind]))
694
695	def OnRanStart(event):
696	MCSAdata['ranStart'] = ranStart.GetValue()
697
698	def OnAutoRan(event):
699	MCSAdata['autoRan'] = autoRan.GetValue()
700
701	def OnRanRange(event):
702	try:
703	val = float(ranRange.GetValue())/100
704	if 0.01 <= val <= 0.99:
705	MCSAdata['ranRange'] = val
706	except ValueError:
707	pass
708	ranRange.SetValue('%.1f'%(MCSAdata['ranRange']*100.))
709
710	def OnAnneal(event):
711	Obj = event.GetEventObject()
712	ind,fmt = Indx[Obj.GetId()]
713	if ind == 2: #No. trials
714	try:
715	val = int(Obj.GetValue())
716	if 1 <= val:
717	MCSAdata['Annealing'][ind] = val
718	except ValueError:
719	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
720	else:
721	try:
722	val = float(Obj.GetValue())
723	if .0 <= val:
724	MCSAdata['Annealing'][ind] = val
725	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
726	except ValueError:
727	MCSAdata['Annealing'][ind] = None
728	Obj.SetValue(str(MCSAdata['Annealing'][ind]))
729
730	refList = []
731	if len(data['Pawley ref']):
732	refList = ['Pawley reflections']
733	for item in data['Histograms'].keys():
734	if 'HKLF' in item or 'PWDR' in item:
735	refList.append(item)
736	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
737	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
738	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
739	refList = wx.ComboBox(General,-1,value=MCSAdata['Data source'],choices=refList,
740	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
741	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
742	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
743	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,wx.ALIGN_CENTER_VERTICAL)
744	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['dmin']),style=wx.TE_PROCESS_ENTER)
745	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
746	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
747	lineSizer.Add(dmin,0,wx.ALIGN_CENTER_VERTICAL)
748	mcsaSizer.Add(lineSizer)
749	mcsaSizer.Add((5,5),)
750	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
751	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,wx.ALIGN_CENTER_VERTICAL)
752	Cchoice = ['1','2','3','6','10','20','30','60','100']
753	cycles = wx.ComboBox(General,-1,value=str(MCSAdata.get('Cycles',1)),choices=Cchoice,
754	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
755	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
756	line2Sizer.Add(cycles,0,wx.ALIGN_CENTER_VERTICAL)
757	line2Sizer.Add((5,0),)
758	ranStart = wx.CheckBox(General,-1,label=' MC/SA Refine at ')
759	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
760	ranStart.SetValue(MCSAdata.get('ranStart',False))
761	line2Sizer.Add(ranStart,0,wx.ALIGN_CENTER_VERTICAL)
762	ranRange = wx.TextCtrl(General,-1,value='%.1f'%(MCSAdata.get('ranRange',0.10)*100),style=wx.TE_PROCESS_ENTER)
763	ranRange.Bind(wx.EVT_TEXT_ENTER,OnRanRange)
764	ranRange.Bind(wx.EVT_KILL_FOCUS,OnRanRange)
765	line2Sizer.Add(ranRange,0,wx.ALIGN_CENTER_VERTICAL)
766	line2Sizer.Add(wx.StaticText(General,label='% of ranges. '),0,wx.ALIGN_CENTER_VERTICAL)
767	# autoRan = wx.CheckBox(General,-1,label=' Do auto range reduction? ')
768	# autoRan.Bind(wx.EVT_CHECKBOX, OnAutoRan)
769	# autoRan.SetValue(MCSAdata.get('autoRan',False))
770	# line2Sizer.Add(autoRan,0,wx.ALIGN_CENTER_VERTICAL)
771	mcsaSizer.Add(line2Sizer)
772	mcsaSizer.Add((5,5),)
773	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
774	Achoice = ['log','fast'] #these work
775	# Achoice = ['log','fast','cauchy','boltzmann']
776	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
777	Alist = wx.ComboBox(General,-1,value=MCSAdata['Algorithm'],choices=Achoice,
778	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
779	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
780	line3Sizer.Add(Alist,0,wx.ALIGN_CENTER_VERTICAL)
781	if MCSAdata['Algorithm'] in ['fast','boltzmann','cauchy']:
782	Names = [' A-jump: ',' B-jump: ']
783	parms = 'Jump coeff'
784	if MCSAdata['Algorithm'] in ['boltzmann','cauchy']:
785	Names = [' A-jump: ']
786	elif 'fast' in MCSAdata['Algorithm']:
787	Names = [' quench: ',' m-factor: ',' n-factor: ']
788	parms = 'fast parms'
789	for i,name in enumerate(Names):
790	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
791	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata[parms][i]),style=wx.TE_PROCESS_ENTER)
792	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
793	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
794	Indx[Ajump.GetId()] = [parms,i]
795	line3Sizer.Add(Ajump,0,wx.ALIGN_CENTER_VERTICAL)
796	elif 'log' in MCSAdata['Algorithm']:
797	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,wx.ALIGN_CENTER_VERTICAL)
798	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['log slope']),style=wx.TE_PROCESS_ENTER)
799	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
800	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
801	line3Sizer.Add(slope,0,wx.ALIGN_CENTER_VERTICAL)
802	mcsaSizer.Add(line3Sizer)
803	mcsaSizer.Add((5,5),)
804	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
805	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
806	names = [' Start temp: ',' Final temp: ',' No. trials: ']
807	fmts = ['%.1f','%.5f','%d']
808	for i,[name,fmt] in enumerate(zip(names,fmts)):
809	if MCSAdata['Annealing'][i]:
810	text = fmt%(MCSAdata['Annealing'][i])
811	else:
812	text = 'None'
813	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
814	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
815	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
816	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
817	Indx[anneal.GetId()] = [i,fmt]
818	line3Sizer.Add(anneal,0,wx.ALIGN_CENTER_VERTICAL)
819	mcsaSizer.Add(line3Sizer)
820	return mcsaSizer
821
822	# UpdateGeneral execution continues here
823	if General.GetSizer():
824	General.GetSizer().Clear(True)
825	mainSizer = wx.BoxSizer(wx.VERTICAL)
826	mainSizer.Add((5,5),0)
827	mainSizer.Add(NameSizer(),0)
828	mainSizer.Add((5,5),0)
829	mainSizer.Add(CellSizer(),0)
830	mainSizer.Add((5,5),0)
831
832	Indx = {}
833	denSizer = None
834	if len(generalData['AtomTypes']):
835	denSizer = DenSizer()
836	mainSizer.Add(denSizer[0])
837	mainSizer.Add((5,5),0)
838	mainSizer.Add(ElemSizer())
839	G2gd.HorizontalLine(mainSizer,General)
840
841	mainSizer.Add(PawleySizer())
842	G2gd.HorizontalLine(mainSizer,General)
843
844	mainSizer.Add(MapSizer())
845	G2gd.HorizontalLine(mainSizer,General)
846
847	mainSizer.Add(FlipSizer())
848	G2gd.HorizontalLine(mainSizer,General)
849
850	mainSizer.Add(MCSASizer())
851	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
852	G2frame.dataFrame.SetStatusText('')
853
854	################################################################################
855	##### Atom routines
856	################################################################################
857
858	def FillAtomsGrid(Atoms):
859	'''Display the contents of the Atoms tab
860	'''
861	def RefreshAtomGrid(event):
862
863	r,c = event.GetRow(),event.GetCol()
864	if r < 0 and c < 0:
865	for row in range(Atoms.GetNumberRows()):
866	Atoms.SelectRow(row,True)
867	if r < 0: #double click on col label! Change all atoms!
868	sel = -1
869	noSkip = True
870	if Atoms.GetColLabelValue(c) == 'refine':
871	Type = generalData['Type']
872	if Type in ['nuclear','macromolecular']:
873	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
874	elif Type in ['magnetic',]:
875	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
876	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
877	if dlg.ShowModal() == wx.ID_OK:
878	sel = dlg.GetSelections()
879	parms = ''
880	for x in sel:
881	parms += choice[x][0]
882	dlg.Destroy()
883	elif Atoms.GetColLabelValue(c) == 'I/A':
884	choice = ['Isotropic','Anisotropic']
885	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
886	if dlg.ShowModal() == wx.ID_OK:
887	sel = dlg.GetSelection()
888	parms = choice[sel][0]
889	dlg.Destroy()
890	elif Atoms.GetColLabelValue(c) == 'Type':
891	choice = generalData['AtomTypes']
892	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
893	if dlg.ShowModal() == wx.ID_OK:
894	sel = dlg.GetSelection()
895	parms = choice[sel]
896	noSkip = False
897	Atoms.ClearSelection()
898	for row in range(Atoms.GetNumberRows()):
899	if parms == atomData[row][c]:
900	Atoms.SelectRow(row,True)
901	dlg.Destroy()
902	SetupGeneral()
903	elif Atoms.GetColLabelValue(c) == 'residue':
904	choice = []
905	for r in range(Atoms.GetNumberRows()):
906	if str(atomData[r][c]) not in choice:
907	choice.append(str(atomData[r][c]))
908	choice.sort()
909	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
910	if dlg.ShowModal() == wx.ID_OK:
911	sel = dlg.GetSelection()
912	parms = choice[sel]
913	noSkip = False
914	Atoms.ClearSelection()
915	for row in range(Atoms.GetNumberRows()):
916	if parms == atomData[row][c]:
917	Atoms.SelectRow(row,True)
918	dlg.Destroy()
919	elif Atoms.GetColLabelValue(c) == 'res no':
920	choice = []
921	for r in range(Atoms.GetNumberRows()):
922	if str(atomData[r][c]) not in choice:
923	choice.append(str(atomData[r][c]))
924	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
925	if dlg.ShowModal() == wx.ID_OK:
926	sel = dlg.GetSelection()
927	parms = choice[sel]
928	noSkip = False
929	Atoms.ClearSelection()
930	for row in range(Atoms.GetNumberRows()):
931	if int(parms) == atomData[row][c]:
932	Atoms.SelectRow(row,True)
933	dlg.Destroy()
934	elif Atoms.GetColLabelValue(c) == 'chain':
935	choice = []
936	for r in range(Atoms.GetNumberRows()):
937	if atomData[r][c] not in choice:
938	choice.append(atomData[r][c])
939	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
940	if dlg.ShowModal() == wx.ID_OK:
941	sel = dlg.GetSelection()
942	parms = choice[sel]
943	noSkip = False
944	Atoms.ClearSelection()
945	for row in range(Atoms.GetNumberRows()):
946	if parms == atomData[row][c]:
947	Atoms.SelectRow(row,True)
948	dlg.Destroy()
949	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
950	pass #& then change all 'I' atoms
951	if sel >= 0 and noSkip:
952	ui = colLabels.index('U11')
953	us = colLabels.index('Uiso')
954	ss = colLabels.index('site sym')
955	for r in range(Atoms.GetNumberRows()):
956	ID = atomData[r][-1]
957	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
958	if parms == 'A': #'I' --> 'A'
959	Uiso = float(Atoms.GetCellValue(r,us))
960	sytsym = atomData[r][ss]
961	CSI = G2spc.GetCSuinel(sytsym)
962	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
963	atomData[r][us] = 0.0
964	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
965	for i in range(6):
966	ci = ui+i
967	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
968	if CSI[2][i]:
969	Atoms.SetCellStyle(r,ci,WHITE,False)
970	else: #'A' --> 'I'
971	Uij = atomData[r][ui:ui+6]
972	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
973	atomData[r][us] = Uiso
974	Atoms.SetCellStyle(r,us,WHITE,False)
975	for i in range(6):
976	ci = ui+i
977	atomData[r][ci] = 0.0
978	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
979	if not Atoms.IsReadOnly(r,c):
980	if Atoms.GetColLabelValue(c) == 'refine':
981	rbExcl = rbAtmDict.get(atomData[r][-1],'')
982	if rbExcl:
983	for excl in rbExcl:
984	atomData[r][c] = parms.replace(excl,'')
985	else:
986	atomData[r][c] = parms
987	else:
988	atomData[r][c] = parms
989	if 'Atoms' in data['Drawing']:
990	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
991	wx.CallAfter(Paint)
992
993	def ChangeAtomCell(event):
994
995	def chkUij(Uij,CSI): #needs to do something!!!
996	return Uij
997
998	r,c = event.GetRow(),event.GetCol()
999	if r >= 0 and c >= 0:
1000	ID = atomData[r][-1]
1001	if Atoms.GetColLabelValue(c) in ['x','y','z']:
1002	ci = colLabels.index('x')
1003	XYZ = atomData[r][ci:ci+3]
1004	if None in XYZ:
1005	XYZ = [0,0,0]
1006	SScol = colLabels.index('site sym')
1007	Mulcol = colLabels.index('mult')
1008	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1009	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
1010	atomData[r][SScol] = Sytsym
1011	atomData[r][Mulcol] = Mult
1012	if atomData[r][colLabels.index('I/A')] == 'A':
1013	ui = colLabels.index('U11')
1014	CSI = G2spc.GetCSuinel(Sytsym)
1015	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
1016	for i in range(6):
1017	ci = i+ui
1018	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1019	if CSI[2][i]:
1020	Atoms.SetCellStyle(r,ci,WHITE,False)
1021	SetupGeneral()
1022	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1023	if atomData[r][c] == 'I':
1024	Uij = atomData[r][c+2:c+8]
1025	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1026	Atoms.SetCellStyle(r,c+1,WHITE,False)
1027	Atoms.SetCellTextColour(r,c+1,BLACK)
1028	for i in range(6):
1029	ci = i+colLabels.index('U11')
1030	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1031	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1032	atomData[r][ci] = 0.0
1033	else:
1034	value = atomData[r][c+1]
1035	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1036	atomData[r][c+1] = 0.0
1037	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1038	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1039	for i in range(6):
1040	ci = i+colLabels.index('U11')
1041	atomData[r][ci] = value*CSI[3][i]
1042	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1043	Atoms.SetCellTextColour(r,ci,BLACK)
1044	if CSI[2][i]:
1045	Atoms.SetCellStyle(r,ci,WHITE,False)
1046	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1047	value = atomData[r][c]
1048	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1049	iUij = CSI[0][c-colLabels.index('U11')]
1050	for i in range(6):
1051	if iUij == CSI[0][i]:
1052	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1053	elif Atoms.GetColLabelValue(c) == 'refine':
1054	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1055	if 'Atoms' in data['Drawing']:
1056	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1057	wx.CallAfter(Paint)
1058
1059	def AtomTypeSelect(event):
1060	r,c = event.GetRow(),event.GetCol()
1061	if Atoms.GetColLabelValue(c) == 'Type':
1062	PE = G2elemGUI.PickElement(G2frame)
1063	if PE.ShowModal() == wx.ID_OK:
1064	if PE.Elem != 'None':
1065	atomData[r][c] = PE.Elem.strip()
1066	name = atomData[r][c]
1067	if len(name) in [2,4]:
1068	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1069	else:
1070	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1071	PE.Destroy()
1072	SetupGeneral()
1073	wx.CallAfter(Paint)
1074	value = Atoms.GetCellValue(r,c)
1075	atomData[r][c] = value
1076	ID = atomData[r][-1]
1077	if 'Atoms' in data['Drawing']:
1078	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1079	SetupGeneral()
1080	else:
1081	event.Skip()
1082
1083	def RowSelect(event):
1084	r,c = event.GetRow(),event.GetCol()
1085	if not event.AltDown():
1086	Atoms.frm = -1
1087	G2frame.dataFrame.SetStatusText('')
1088	if r < 0 and c < 0:
1089	if Atoms.IsSelection():
1090	Atoms.ClearSelection()
1091	elif c < 0: #only row clicks
1092	if event.ControlDown():
1093	if r in Atoms.GetSelectedRows():
1094	Atoms.DeselectRow(r)
1095	else:
1096	Atoms.SelectRow(r,True)
1097	elif event.ShiftDown():
1098	indxs = Atoms.GetSelectedRows()
1099	Atoms.ClearSelection()
1100	ibeg = 0
1101	if indxs:
1102	ibeg = indxs[-1]
1103	for row in range(ibeg,r+1):
1104	Atoms.SelectRow(row,True)
1105	elif event.AltDown():
1106	if atomData[r][-1] in rbAtmDict:
1107	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1108	Atoms.frm = -1
1109	Atoms.ClearSelection()
1110	else:
1111	if Atoms.frm < 0: #pick atom to be moved
1112	Atoms.frm = r
1113	Atoms.SelectRow(r,True)
1114	n = colLabels.index('Name')
1115	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1116	else: #move it
1117	item = atomData.pop(Atoms.frm)
1118	atomData.insert(r,item)
1119	Atoms.frm = -1
1120	G2frame.dataFrame.SetStatusText('')
1121	wx.CallAfter(Paint)
1122	else:
1123	Atoms.ClearSelection()
1124	Atoms.SelectRow(r,True)
1125
1126	def ChangeSelection(event):
1127	r,c = event.GetRow(),event.GetCol()
1128	if r < 0 and c < 0:
1129	Atoms.ClearSelection()
1130	if c < 0:
1131	if r in Atoms.GetSelectedRows():
1132	Atoms.DeselectRow(r)
1133	else:
1134	Atoms.SelectRow(r,True)
1135	if r < 0:
1136	if c in Atoms.GetSelectedCols():
1137	Atoms.DeselectCol(c)
1138	else:
1139	Atoms.SelectCol(c,True)
1140
1141	def Paint():
1142
1143	table = []
1144	rowLabels = []
1145	for i,atom in enumerate(atomData):
1146	table.append(atom)
1147	rowLabels.append(str(i))
1148	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1149	Atoms.SetTable(atomTable, True)
1150	Atoms.frm = -1
1151	colType = colLabels.index('Type')
1152	colR = colLabels.index('refine')
1153	colSS = colLabels.index('site sym')
1154	colX = colLabels.index('x')
1155	colIA = colLabels.index('I/A')
1156	colU11 = colLabels.index('U11')
1157	colUiso = colLabels.index('Uiso')
1158	attr = wx.grid.GridCellAttr()
1159	attr.IncRef() #fix from Jim Hester
1160	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1161	for c in range(colX,colX+3):
1162	Atoms.SetColAttr(c, attr)
1163	for i in range(colU11-1,colU11+6):
1164	Atoms.SetColSize(i,50)
1165	for row in range(Atoms.GetNumberRows()):
1166	atId = atomData[row][-1]
1167	rbExcl = rbAtmDict.get(atId,'')
1168	Atoms.SetReadOnly(row,colSS,True) #site sym
1169	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1170	if Atoms.GetCellValue(row,colIA) == 'A':
1171	CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')])
1172	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1173	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1174	for i in range(6):
1175	ci = colU11+i
1176	Atoms.SetCellTextColour(row,ci,BLACK)
1177	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1178	if CSI[2][i] and 'U' not in rbExcl:
1179	Atoms.SetCellStyle(row,ci,WHITE,False)
1180	else:
1181	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1182	Atoms.SetCellTextColour(row,colUiso,BLACK)
1183	if 'U' in rbExcl:
1184	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1185	for i in range(6):
1186	ci = colU11+i
1187	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1188	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1189	if 'X' in rbExcl:
1190	for c in range(0,colX+3):
1191	if c != colR:
1192	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1193	Atoms.AutoSizeColumns(False)
1194
1195	# FillAtomsGrid executable code starts here
1196	generalData = data['General']
1197	atomData = data['Atoms']
1198	DData = data['Drawing']
1199	resRBData = data['RBModels'].get('Residue',[])
1200	vecRBData = data['RBModels'].get('Vector',[])
1201	rbAtmDict = {}
1202	for rbObj in resRBData+vecRBData:
1203	exclList = ['X' for i in range(len(rbObj['Ids']))]
1204	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1205	if rbObj['ThermalMotion'][0] != 'None':
1206	for id in rbObj['Ids']:
1207	rbAtmDict[id] += 'U'
1208	# exclList will be 'x' or 'xu' if TLS used in RB
1209	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1210	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1211	if atomData:
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	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1218	if 'showABC' in data['Drawing']:
1219	for item in Items:
1220	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1221	else:
1222	for item in Items:
1223	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1224
1225	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1226	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1227	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1228	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1229	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1230	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1231	if generalData['Type'] == 'magnetic':
1232	colLabels += ['Mx','My','Mz']
1233	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1234	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1235	elif generalData['Type'] == 'macromolecular':
1236	colLabels = ['res no','residue','chain'] + colLabels
1237	Types = [wg.GRID_VALUE_STRING,
1238	wg.GRID_VALUE_CHOICE+AAchoice,
1239	wg.GRID_VALUE_STRING] + Types
1240	elif generalData['Type'] == 'modulated':
1241	Types += []
1242	colLabels += []
1243	SGData = data['General']['SGData']
1244	G2frame.dataFrame.SetStatusText('')
1245	if SGData['SGPolax']:
1246	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1247	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1248	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1249	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1250	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1251	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1252	Atoms.SetMargins(0,0)
1253
1254	G2frame.dataFrame.setSizePosLeft([700,300])
1255	Paint()
1256
1257	def OnAtomAdd(event):
1258	AtomAdd(0,0,0)
1259	FillAtomsGrid(Atoms)
1260	event.StopPropagation()
1261	if data['Drawing']:
1262	G2plt.PlotStructure(G2frame,data)
1263
1264	def OnAtomViewAdd(event):
1265	try:
1266	drawData = data['Drawing']
1267	x,y,z = drawData['viewPoint'][0]
1268	AtomAdd(x,y,z)
1269	except:
1270	AtomAdd(0,0,0)
1271	FillAtomsGrid(Atoms)
1272	event.StopPropagation()
1273	G2plt.PlotStructure(G2frame,data)
1274
1275	def AtomAdd(x,y,z,El='H',Name='UNK'):
1276	atomData = data['Atoms']
1277	generalData = data['General']
1278	Ncol = Atoms.GetNumberCols()
1279	atId = ran.randint(0,sys.maxint)
1280	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1281	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1282	if generalData['Type'] == 'macromolecular':
1283	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1284	elif generalData['Type'] == 'nuclear':
1285	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1286	elif generalData['Type'] == 'magnetic':
1287	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1288	SetupGeneral()
1289	if 'Atoms' in data['Drawing']:
1290	DrawAtomAdd(data['Drawing'],atomData[-1])
1291
1292	def OnAtomInsert(event):
1293	AtomInsert(0,0,0)
1294	FillAtomsGrid(Atoms)
1295	event.StopPropagation()
1296	G2plt.PlotStructure(G2frame,data)
1297
1298	def OnAtomViewInsert(event):
1299	if 'Drawing' in data:
1300	drawData = data['Drawing']
1301	x,y,z = drawData['viewPoint'][0]
1302	AtomAdd(x,y,z)
1303	FillAtomsGrid(Atoms)
1304	event.StopPropagation()
1305
1306	def OnAtomMove(event):
1307	drawData = data['Drawing']
1308	atomData = data['Atoms']
1309	x,y,z = drawData['viewPoint'][0]
1310	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1311	cx = colLabels.index('x')
1312	indx = Atoms.GetSelectedRows()
1313	if len(indx) != 1:
1314	print '** ERROR - only one atom can be moved **'
1315	elif atomData[indx[0]][-1] in rbAtmDict:
1316	print '** ERROR - Atoms in rigid bodies can not be moved **'
1317	else:
1318	atomData[indx[0]][cx:cx+3] = [x,y,z]
1319	SetupGeneral()
1320	FillAtomsGrid(Atoms)
1321	ID = atomData[indx[0]][-1]
1322	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1323	G2plt.PlotStructure(G2frame,data)
1324	event.StopPropagation()
1325
1326	def DrawAtomsReplaceByID(drawingData,atom,ID):
1327	IDs = [ID,]
1328	atomData = drawingData['Atoms']
1329	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1330	for ind in indx:
1331	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1332
1333	def MakeDrawAtom(atom,oldatom=None):
1334	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1335	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1336	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1337	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1338	generalData = data['General']
1339	SGData = generalData['SGData']
1340	if generalData['Type'] == 'nuclear':
1341	if oldatom:
1342	opr = oldatom[5]
1343	if atom[9] == 'A':
1344	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1345	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1346	else:
1347	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1348	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1349	else:
1350	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1351	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1352	ct,cs = [1,8] #type & color
1353	elif generalData['Type'] == 'macromolecular':
1354	try:
1355	oneLetter = AA3letter.index(atom[1])
1356	except ValueError:
1357	oneLetter = -1
1358	atomInfo = [[atom[1].strip()+atom[0],]+
1359	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1360	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1361	ct,cs = [4,11] #type & color
1362	elif generalData['Type'] == 'magnetic':
1363	if oldatom:
1364	atomInfo = [atom[:2]+oldatom[3:]][0]
1365	else:
1366	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1367	ct,cs = [1,8] #type & color
1368	# elif generalData['Type'] == 'modulated':
1369	# ????? for future
1370	atNum = generalData['AtomTypes'].index(atom[ct])
1371	atomInfo[cs] = list(generalData['Color'][atNum])
1372	return atomInfo
1373
1374	def AtomInsert(x,y,z):
1375	indx = Atoms.GetSelectedRows()
1376	if indx:
1377	indx = indx[0]
1378	atomData = data['Atoms']
1379	generalData = data['General']
1380	Ncol = Atoms.GetNumberCols()
1381	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1382	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1383	atId = ran.randint(0,sys.maxint)
1384	if generalData['Type'] == 'macromolecular':
1385	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1386	elif generalData['Type'] == 'nuclear':
1387	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1388	elif generalData['Type'] == 'magnetic':
1389	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])
1390	SetupGeneral()
1391
1392	def AtomDelete(event):
1393	indx = Atoms.GetSelectedRows()
1394	IDs = []
1395	if indx:
1396	atomData = data['Atoms']
1397	indx.reverse()
1398	for ind in indx:
1399	atom = atomData[ind]
1400	if atom[-1] in rbAtmDict:
1401	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1402	else:
1403	IDs.append(atom[-1])
1404	del atomData[ind]
1405	if 'Atoms' in data['Drawing']:
1406	DrawAtomsDeleteByIDs(IDs)
1407	wx.CallAfter(FillAtomsGrid,Atoms)
1408	G2plt.PlotStructure(G2frame,data)
1409	SetupGeneral()
1410	event.StopPropagation()
1411
1412	def AtomRefine(event):
1413	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1414	c = colLabels.index('refine')
1415	indx = Atoms.GetSelectedRows()
1416	if indx:
1417	atomData = data['Atoms']
1418	generalData = data['General']
1419	Type = generalData['Type']
1420	if Type in ['nuclear','macromolecular']:
1421	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1422	elif Type == 'magnetic':
1423	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1424	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1425	if dlg.ShowModal() == wx.ID_OK:
1426	sel = dlg.GetSelections()
1427	parms = ''
1428	for x in sel:
1429	parms += choice[x][0]
1430	for r in indx:
1431	if not Atoms.IsReadOnly(r,c):
1432	atomData[r][c] = parms
1433	Atoms.ForceRefresh()
1434	dlg.Destroy()
1435
1436	def AtomModify(event):
1437	indx = Atoms.GetSelectedRows()
1438	if indx:
1439	atomData = data['Atoms']
1440	generalData = data['General']
1441	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1442	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1443	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1444	parm = ''
1445	if dlg.ShowModal() == wx.ID_OK:
1446	sel = dlg.GetSelection()
1447	parm = choices[sel]
1448	cid = colLabels.index(parm)
1449	dlg.Destroy()
1450	if parm in ['Type']:
1451	dlg = G2elemGUI.PickElement(G2frame)
1452	if dlg.ShowModal() == wx.ID_OK:
1453	if dlg.Elem not in ['None']:
1454	El = dlg.Elem.strip()
1455	for r in indx:
1456	if not Atoms.IsReadOnly(r,cid):
1457	atomData[r][cid] = El
1458	if len(El) in [2,4]:
1459	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1460	else:
1461	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1462	SetupGeneral()
1463	if 'Atoms' in data['Drawing']:
1464	for r in indx:
1465	ID = atomData[r][-1]
1466	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1467	FillAtomsGrid(Atoms)
1468	dlg.Destroy()
1469	elif parm in ['Name',]:
1470	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1471	wx.YES_NO \| wx.ICON_QUESTION)
1472	try:
1473	result = dlg.ShowModal()
1474	if result == wx.ID_YES:
1475	for r in indx:
1476	if not Atoms.IsReadOnly(r,cid+1):
1477	El = atomData[r][cid+1]
1478	if len(El) in [2,4]:
1479	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1480	else:
1481	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1482	FillAtomsGrid(Atoms)
1483	finally:
1484	dlg.Destroy()
1485
1486	elif parm in ['I/A']:
1487	choices = ['Isotropic','Anisotropic']
1488	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1489	if dlg.ShowModal() == wx.ID_OK:
1490	sel = dlg.GetSelection()
1491	parm = choices[sel][0]
1492	for r in indx:
1493	if not Atoms.IsReadOnly(r,cid):
1494	atomData[r][cid] = parm
1495	FillAtomsGrid(Atoms)
1496	dlg.Destroy()
1497	elif parm in ['frac','Uiso']:
1498	limits = [0.,1.]
1499	val = 1.0
1500	if parm in ['Uiso']:
1501	limits = [0.,0.25]
1502	val = 0.01
1503	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1504	if dlg.ShowModal() == wx.ID_OK:
1505	parm = dlg.GetValue()
1506	for r in indx:
1507	if not Atoms.IsReadOnly(r,cid):
1508	atomData[r][cid] = parm
1509	SetupGeneral()
1510	FillAtomsGrid(Atoms)
1511	dlg.Destroy()
1512	elif parm in ['x','y','z']:
1513	limits = [-1.,1.]
1514	val = 0.
1515	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1516	if dlg.ShowModal() == wx.ID_OK:
1517	parm = dlg.GetValue()
1518	for r in indx:
1519	if not Atoms.IsReadOnly(r,cid):
1520	atomData[r][cid] += parm
1521	SetupGeneral()
1522	FillAtomsGrid(Atoms)
1523	dlg.Destroy()
1524
1525	def AtomTransform(event):
1526	indx = Atoms.GetSelectedRows()
1527	if indx:
1528	generalData = data['General']
1529	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1530	cx = colLabels.index('x')
1531	cuia = colLabels.index('I/A')
1532	cuij = colLabels.index('U11')
1533	css = colLabels.index('site sym')
1534	atomData = data['Atoms']
1535	generalData = data['General']
1536	SGData = generalData['SGData']
1537	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1538	New = False
1539	try:
1540	if dlg.ShowModal() == wx.ID_OK:
1541	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1542	Cell = np.array(Cell)
1543	cent = SGData['SGCen'][Cent]
1544	M,T = SGData['SGOps'][Opr]
1545	for ind in indx:
1546	XYZ = np.array(atomData[ind][cx:cx+3])
1547	XYZ = np.inner(M,XYZ)+T
1548	if Inv:
1549	XYZ = -XYZ
1550	XYZ = XYZ+cent+Cell
1551	if Force:
1552	XYZ = G2spc.MoveToUnitCell(XYZ)
1553	if New:
1554	atom = copy.copy(atomData[ind])
1555	else:
1556	atom = atomData[ind]
1557	atom[cx:cx+3] = XYZ
1558	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1559	if atom[cuia] == 'A':
1560	Uij = atom[cuij:cuij+6]
1561	U = G2spc.Uij2U(Uij)
1562	U = np.inner(np.inner(M,U),M)
1563	Uij = G2spc.U2Uij(U)
1564	atom[cuij:cuij+6] = Uij
1565	if New:
1566	atomData.append(atom)
1567	finally:
1568	dlg.Destroy()
1569	Atoms.ClearSelection()
1570	if New:
1571	FillAtomsGrid(Atoms)
1572	else:
1573	Atoms.ForceRefresh()
1574
1575	def OnDistAnglePrt(event):
1576	fp = file(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile
1577	)[0]+'.disagl'),'w')
1578	OnDistAngle(event,fp=fp)
1579	fp.close()
1580
1581	def OnDistAngle(event,fp=None):
1582	indx = Atoms.GetSelectedRows()
1583	Oxyz = []
1584	xyz = []
1585	DisAglData = {}
1586	DisAglCtls = {}
1587	if indx:
1588	generalData = data['General']
1589	DisAglData['OrigIndx'] = indx
1590	if 'DisAglCtls' in generalData:
1591	DisAglCtls = generalData['DisAglCtls']
1592	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1593	if dlg.ShowModal() == wx.ID_OK:
1594	DisAglCtls = dlg.GetData()
1595	else:
1596	dlg.Destroy()
1597	return
1598	dlg.Destroy()
1599	generalData['DisAglCtls'] = DisAglCtls
1600	atomData = data['Atoms']
1601	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1602	cx = colLabels.index('x')
1603	cn = colLabels.index('Name')
1604	for i,atom in enumerate(atomData):
1605	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1606	if i in indx:
1607	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1608	DisAglData['OrigAtoms'] = Oxyz
1609	DisAglData['TargAtoms'] = xyz
1610	generalData = data['General']
1611	DisAglData['SGData'] = generalData['SGData']
1612	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1613	if 'pId' in data:
1614	DisAglData['pId'] = data['pId']
1615	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1616	try:
1617	if fp:
1618	G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
1619	else:
1620	G2stMn.PrintDistAngle(DisAglCtls,DisAglData)
1621	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1622	G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types')
1623	else:
1624	print "select one or more rows of atoms"
1625	G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
1626
1627	def OnReImport(event):
1628	print 'reimport atoms from file to be developed'
1629	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1630	rdlist = G2frame.OnImportGeneric(reqrdr,
1631	G2frame.ImportPhaseReaderlist,
1632	'phase')
1633	if len(rdlist) == 0: return
1634	# for now rdlist is only expected to have one element
1635	# for now always use the first phase for when multiple phases are ever implemented
1636	# but it would be better to loop until we find a phase that matches the one in data
1637	for rd in rdlist:
1638	# rd contains all info for a phase
1639	PhaseName = rd.Phase['General']['Name']
1640	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1641	print rd.Phase['Atoms']
1642	return
1643
1644	################################################################################
1645	#Structure drawing GUI stuff
1646	################################################################################
1647
1648	def SetupDrawingData():
1649	generalData = data['General']
1650	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1651	atomData = data['Atoms']
1652	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1653	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1654	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1655	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1656	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1657	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1658	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1659	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1660	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1661	'bondList':{},'viewDir':[1,0,0]}
1662	V0 = np.array([0,0,1])
1663	V = np.inner(Amat,V0)
1664	V /= np.sqrt(np.sum(V**2))
1665	A = np.arccos(np.sum(V*V0))
1666	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1667	try:
1668	drawingData = data['Drawing']
1669	except KeyError:
1670	data['Drawing'] = {}
1671	drawingData = data['Drawing']
1672	if not drawingData: #fill with defaults if empty
1673	drawingData.update(defaultDrawing)
1674	if 'Zstep' not in drawingData:
1675	drawingData['Zstep'] = 0.5
1676	if 'contourLevel' not in drawingData:
1677	drawingData['contourLevel'] = 1.
1678	if 'viewDir' not in drawingData:
1679	drawingData['viewDir'] = [0,0,1]
1680	if 'Quaternion' not in drawingData:
1681	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1682	if 'showRigidBodies' not in drawingData:
1683	drawingData['showRigidBodies'] = True
1684	cx,ct,cs,ci = [0,0,0,0]
1685	if generalData['Type'] == 'nuclear':
1686	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1687	elif generalData['Type'] == 'macromolecular':
1688	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1689	elif generalData['Type'] == 'magnetic':
1690	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1691	# elif generalData['Type'] == 'modulated':
1692	# ????? for future
1693	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1694	if not drawingData.get('Atoms'):
1695	for atom in atomData:
1696	DrawAtomAdd(drawingData,atom)
1697	data['Drawing'] = drawingData
1698
1699	def DrawAtomAdd(drawingData,atom):
1700	drawingData['Atoms'].append(MakeDrawAtom(atom))
1701
1702	def OnRestraint(event):
1703	indx = drawAtoms.GetSelectedRows()
1704	restData = G2frame.PatternTree.GetItemPyData(
1705	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1706	drawingData = data['Drawing']
1707	generalData = data['General']
1708	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1709	cx,ct,cs,ci = drawingData['atomPtrs']
1710	atomData = drawingData['Atoms']
1711	atNames = []
1712	atXYZ = []
1713	atSymOp = []
1714	atIndx = []
1715	for item in indx:
1716	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1717	atSymOp.append(atomData[item][cs-1])
1718	atIndx.append(atomData[item][ci])
1719	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1720	try:
1721	bondData = restData[PhaseName]['Bond']
1722	except KeyError:
1723	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1724	restData[PhaseName] = {}
1725	restData[PhaseName]['Bond'] = bondData
1726	dist = G2mth.getRestDist(atXYZ,Amat)
1727	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1728	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1729	try:
1730	angleData = restData[PhaseName]['Angle']
1731	except KeyError:
1732	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1733	restData[PhaseName] = {}
1734	restData[PhaseName]['Angle'] = angleData
1735	angle = G2mth.getRestAngle(atXYZ,Amat)
1736	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1737	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1738	try:
1739	planeData = restData[PhaseName]['Plane']
1740	except KeyError:
1741	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1742	restData[PhaseName] = {}
1743	restData[PhaseName]['Plane'] = planeData
1744	plane = G2mth.getRestPlane(atXYZ,Amat)
1745	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1746	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1747	try:
1748	chiralData = restData[PhaseName]['Chiral']
1749	except KeyError:
1750	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1751	restData[PhaseName] = {}
1752	restData[PhaseName]['Chiral'] = chiralData
1753	volume = G2mth.getRestChiral(atXYZ,Amat)
1754	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1755	else:
1756	print '**** ERROR wrong number of atoms selected for this restraint'
1757	return
1758	G2frame.PatternTree.SetItemPyData(
1759	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1760
1761	def OnDefineRB(event):
1762	indx = drawAtoms.GetSelectedRows()
1763	indx.sort()
1764	RBData = G2frame.PatternTree.GetItemPyData(
1765	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1766	drawingData = data['Drawing']
1767	generalData = data['General']
1768	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1769	cx,ct,cs,ci = drawingData['atomPtrs']
1770	atomData = drawingData['Atoms']
1771	rbXYZ = []
1772	rbType = []
1773	atNames = []
1774	AtInfo = RBData['Residue']['AtInfo']
1775	for i,item in enumerate(indx):
1776	rbtype = atomData[item][ct]
1777	atNames.append(rbtype+str(i))
1778	rbType.append(rbtype)
1779	if rbtype not in AtInfo:
1780	Info = G2elem.GetAtomInfo(rbtype)
1781	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1782	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1783	rbXYZ = np.array(rbXYZ)
1784	rbXYZ -= rbXYZ[0]
1785	rbId = ran.randint(0,sys.maxint)
1786	rbName = 'UNKRB'
1787	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1788	'Edit rigid body name',rbName ,style=wx.OK)
1789	if dlg.ShowModal() == wx.ID_OK:
1790	rbName = dlg.GetValue()
1791	dlg.Destroy()
1792	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1793	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1794	RBData['RBIds']['Residue'].append(rbId)
1795	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1796
1797	################################################################################
1798	##### Atom draw routines
1799	################################################################################
1800
1801	def UpdateDrawAtoms(atomStyle=''):
1802	def RefreshAtomGrid(event):
1803	def SetChoice(name,c,n=0):
1804	choice = []
1805	for r in range(len(atomData)):
1806	if n:
1807	srchStr = str(atomData[r][c][:n])
1808	else:
1809	srchStr = str(atomData[r][c])
1810	if srchStr not in choice:
1811	if n:
1812	choice.append(str(atomData[r][c][:n]))
1813	else:
1814	choice.append(str(atomData[r][c]))
1815	choice.sort()
1816
1817	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
1818	if dlg.ShowModal() == wx.ID_OK:
1819	sel = dlg.GetSelections()
1820	parms = []
1821	for x in sel:
1822	parms.append(choice[x])
1823	noSkip = False
1824	drawAtoms.ClearSelection()
1825	drawingData['selectedAtoms'] = []
1826	for row in range(len(atomData)):
1827	test = atomData[row][c]
1828	if n:
1829	test = test[:n]
1830	if test in parms:
1831	drawAtoms.SelectRow(row,True)
1832	drawingData['selectedAtoms'].append(row)
1833	G2plt.PlotStructure(G2frame,data)
1834	dlg.Destroy()
1835
1836	r,c = event.GetRow(),event.GetCol()
1837	if r < 0 and c < 0:
1838	for row in range(drawAtoms.GetNumberRows()):
1839	drawingData['selectedAtoms'].append(row)
1840	drawAtoms.SelectRow(row,True)
1841	elif r < 0: #dclick on col label
1842	sel = -1
1843	Parms = False
1844	noSkip = True
1845	if drawAtoms.GetColLabelValue(c) == 'Style':
1846	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1847	if dlg.ShowModal() == wx.ID_OK:
1848	sel = dlg.GetSelection()
1849	parms = styleChoice[sel]
1850	for r in range(len(atomData)):
1851	atomData[r][c] = parms
1852	drawAtoms.SetCellValue(r,c,parms)
1853	FindBondsDraw()
1854	G2plt.PlotStructure(G2frame,data)
1855	dlg.Destroy()
1856	elif drawAtoms.GetColLabelValue(c) == 'Label':
1857	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
1858	if dlg.ShowModal() == wx.ID_OK:
1859	sel = dlg.GetSelection()
1860	parms = labelChoice[sel]
1861	for r in range(len(atomData)):
1862	atomData[r][c] = parms
1863	drawAtoms.SetCellValue(r,c,parms)
1864	dlg.Destroy()
1865	elif drawAtoms.GetColLabelValue(c) == 'Color':
1866	dlg = wx.ColourDialog(G2frame)
1867	if dlg.ShowModal() == wx.ID_OK:
1868	color = dlg.GetColourData().GetColour()
1869	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1870	attr.SetReadOnly(True)
1871	attr.SetBackgroundColour(color)
1872	for r in range(len(atomData)):
1873	atomData[r][c] = color
1874	drawingData['Atoms'][r][c] = color
1875	drawAtoms.SetAttr(r,c,attr)
1876	UpdateDrawAtoms()
1877	dlg.Destroy()
1878	elif drawAtoms.GetColLabelValue(c) == 'Residue':
1879	SetChoice('Residue',c,3)
1880	elif drawAtoms.GetColLabelValue(c) == '1-letter':
1881	SetChoice('1-letter',c,1)
1882	elif drawAtoms.GetColLabelValue(c) == 'Chain':
1883	SetChoice('Chain',c)
1884	elif drawAtoms.GetColLabelValue(c) == 'Name':
1885	SetChoice('Name',c)
1886	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
1887	SetChoice('Name',c)
1888	elif drawAtoms.GetColLabelValue(c) == 'Type':
1889	SetChoice('Type',c)
1890	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
1891	drawAtoms.ClearSelection()
1892	else:
1893	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
1894	atomData[r][c] = drawAtoms.GetCellValue(r,c)
1895	FindBondsDraw()
1896	elif drawAtoms.GetColLabelValue(c) == 'Color':
1897	dlg = wx.ColourDialog(G2frame)
1898	if dlg.ShowModal() == wx.ID_OK:
1899	color = dlg.GetColourData().GetColour()
1900	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1901	attr.SetReadOnly(True)
1902	attr.SetBackgroundColour(color)
1903	atomData[r][c] = color
1904	drawingData['Atoms'][r][c] = color
1905	drawAtoms.SetAttr(i,cs+2,attr)
1906	dlg.Destroy()
1907	UpdateDrawAtoms()
1908	G2plt.PlotStructure(G2frame,data)
1909
1910	def RowSelect(event):
1911	r,c = event.GetRow(),event.GetCol()
1912	if r < 0 and c < 0:
1913	if drawAtoms.IsSelection():
1914	drawAtoms.ClearSelection()
1915	elif c < 0: #only row clicks
1916	if event.ControlDown():
1917	if r in drawAtoms.GetSelectedRows():
1918	drawAtoms.DeselectRow(r)
1919	else:
1920	drawAtoms.SelectRow(r,True)
1921	elif event.ShiftDown():
1922	indxs = drawAtoms.GetSelectedRows()
1923	drawAtoms.ClearSelection()
1924	ibeg = 0
1925	if indxs:
1926	ibeg = indxs[-1]
1927	for row in range(ibeg,r+1):
1928	drawAtoms.SelectRow(row,True)
1929	else:
1930	drawAtoms.ClearSelection()
1931	drawAtoms.SelectRow(r,True)
1932	drawingData['selectedAtoms'] = []
1933	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
1934	G2plt.PlotStructure(G2frame,data)
1935
1936	# UpdateDrawAtoms executable code starts here
1937	G2frame.dataFrame.SetStatusText('')
1938	generalData = data['General']
1939	SetupDrawingData()
1940	drawingData = data['Drawing']
1941	cx,ct,cs,ci = drawingData['atomPtrs']
1942	atomData = drawingData['Atoms']
1943	if atomStyle:
1944	for atom in atomData:
1945	atom[cs] = atomStyle
1946	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
1947	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
1948	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
1949	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1950	labelChoice = [' ','type','name','number']
1951	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
1952	if generalData['Type'] == 'macromolecular':
1953	colLabels = ['Residue','1-letter','Chain'] + colLabels
1954	Types = 3*[wg.GRID_VALUE_STRING,]+Types
1955	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
1956	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
1957	labelChoice = [' ','type','name','number','residue','1-letter','chain']
1958	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
1959	# elif generalData['Type'] == 'modulated':
1960	# Types += []
1961	# colLabels += []
1962	table = []
1963	rowLabels = []
1964	for i,atom in enumerate(drawingData['Atoms']):
1965	table.append(atom[:colLabels.index('I/A')+1])
1966	rowLabels.append(str(i))
1967
1968	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1969	drawAtoms.SetTable(atomTable, True)
1970	drawAtoms.SetMargins(0,0)
1971	drawAtoms.AutoSizeColumns(True)
1972	drawAtoms.SetColSize(colLabels.index('Style'),80)
1973	drawAtoms.SetColSize(colLabels.index('Color'),50)
1974	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
1975	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1976	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
1977	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1978	for i,atom in enumerate(drawingData['Atoms']):
1979	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1980	attr.SetReadOnly(True)
1981	attr.SetBackgroundColour(atom[cs+2])
1982	drawAtoms.SetAttr(i,cs+2,attr)
1983	drawAtoms.SetCellValue(i,cs+2,'')
1984	indx = drawingData['selectedAtoms']
1985	if indx:
1986	for r in range(len(atomData)):
1987	if r in indx:
1988	drawAtoms.SelectRow(r)
1989	for c in range(len(colLabels)):
1990	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1991	attr.SetReadOnly(True)
1992	attr.SetBackgroundColour(VERY_LIGHT_GREY)
1993	if colLabels[c] not in ['Style','Label','Color']:
1994	drawAtoms.SetColAttr(c,attr)
1995	G2frame.dataFrame.setSizePosLeft([600,300])
1996
1997	FindBondsDraw()
1998	drawAtoms.ClearSelection()
1999	# G2plt.PlotStructure(G2frame,data)
2000
2001	def DrawAtomStyle(event):
2002	indx = drawAtoms.GetSelectedRows()
2003	if indx:
2004	generalData = data['General']
2005	atomData = data['Drawing']['Atoms']
2006	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2007	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2008	if generalData['Type'] == 'macromolecular':
2009	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
2010	'backbone','ribbons','schematic']
2011	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2012	if dlg.ShowModal() == wx.ID_OK:
2013	sel = dlg.GetSelection()
2014	parms = styleChoice[sel]
2015	for r in indx:
2016	atomData[r][cs] = parms
2017	drawAtoms.SetCellValue(r,cs,parms)
2018	dlg.Destroy()
2019	FindBondsDraw()
2020	drawAtoms.ClearSelection()
2021	G2plt.PlotStructure(G2frame,data)
2022
2023	def DrawAtomLabel(event):
2024	indx = drawAtoms.GetSelectedRows()
2025	if indx:
2026	generalData = data['General']
2027	atomData = data['Drawing']['Atoms']
2028	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2029	styleChoice = [' ','type','name','number']
2030	if generalData['Type'] == 'macromolecular':
2031	styleChoice = [' ','type','name','number','residue','1-letter','chain']
2032	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
2033	if dlg.ShowModal() == wx.ID_OK:
2034	sel = dlg.GetSelection()
2035	parms = styleChoice[sel]
2036	for r in indx:
2037	atomData[r][cs+1] = parms
2038	drawAtoms.SetCellValue(r,cs+1,parms)
2039	dlg.Destroy()
2040	drawAtoms.ClearSelection()
2041	G2plt.PlotStructure(G2frame,data)
2042
2043	def DrawAtomColor(event):
2044
2045	indx = drawAtoms.GetSelectedRows()
2046	if indx:
2047	if len(indx) > 1:
2048	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2049	else:
2050	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2051	generalData = data['General']
2052	atomData = data['Drawing']['Atoms']
2053	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2054	atmColors = []
2055	atmTypes = []
2056	for r in indx:
2057	if atomData[r][cs+2] not in atmColors:
2058	atmColors.append(atomData[r][cs+2])
2059	atmTypes.append(atomData[r][ct])
2060	if len(atmColors) > 16:
2061	break
2062	colors = wx.ColourData()
2063	colors.SetChooseFull(True)
2064	dlg = wx.ColourDialog(G2frame)
2065	if dlg.ShowModal() == wx.ID_OK:
2066	for i in range(len(atmColors)):
2067	atmColors[i] = dlg.GetColourData().GetColour()
2068	colorDict = dict(zip(atmTypes,atmColors))
2069	for r in indx:
2070	color = colorDict[atomData[r][ct]]
2071	atomData[r][cs+2] = color
2072	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2073	attr.SetBackgroundColour(color)
2074	drawAtoms.SetAttr(r,cs+2,attr)
2075	data['Drawing']['Atoms'][r][cs+2] = color
2076	drawAtoms.ClearSelection()
2077	dlg.Destroy()
2078	G2frame.dataFrame.SetStatusText('')
2079	G2plt.PlotStructure(G2frame,data)
2080
2081	def ResetAtomColors(event):
2082	generalData = data['General']
2083	atomData = data['Drawing']['Atoms']
2084	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2085	for atom in atomData:
2086	atNum = generalData['AtomTypes'].index(atom[ct])
2087	atom[cs+2] = list(generalData['Color'][atNum])
2088	UpdateDrawAtoms()
2089	drawAtoms.ClearSelection()
2090	G2plt.PlotStructure(G2frame,data)
2091
2092	def SetViewPoint(event):
2093	indx = drawAtoms.GetSelectedRows()
2094	if indx:
2095	atomData = data['Drawing']['Atoms']
2096	cx = data['Drawing']['atomPtrs'][0]
2097	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2098	drawAtoms.ClearSelection() #do I really want to do this?
2099	G2plt.PlotStructure(G2frame,data)
2100
2101	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2102	cx = data['Drawing']['atomPtrs'][0]
2103	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2104	return False
2105	else:
2106	return True
2107
2108	def AddSymEquiv(event):
2109	indx = drawAtoms.GetSelectedRows()
2110	indx.sort()
2111	if indx:
2112	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2113	cx = colLabels.index('x')
2114	cuia = colLabels.index('I/A')
2115	cuij = cuia+2
2116	atomData = data['Drawing']['Atoms']
2117	generalData = data['General']
2118	SGData = generalData['SGData']
2119	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2120	try:
2121	if dlg.ShowModal() == wx.ID_OK:
2122	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2123	Cell = np.array(Cell)
2124	cent = SGData['SGCen'][Cent]
2125	M,T = SGData['SGOps'][Opr]
2126	for ind in indx:
2127	XYZ = np.array(atomData[ind][cx:cx+3])
2128	XYZ = np.inner(M,XYZ)+T
2129	if Inv:
2130	XYZ = -XYZ
2131	XYZ = XYZ+cent+Cell
2132	if Force:
2133	XYZ = G2spc.MoveToUnitCell(XYZ)
2134	if noDuplicate(XYZ,atomData):
2135	atom = copy.copy(atomData[ind])
2136	atom[cx:cx+3] = XYZ
2137	atomOp = atom[cx+3]
2138	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2139	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2140	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2141	if atom[cuia] == 'A':
2142	Uij = atom[cuij:cuij+6]
2143	U = G2spc.Uij2U(Uij)
2144	U = np.inner(np.inner(M,U),M)
2145	Uij = G2spc.U2Uij(U)
2146	atom[cuij:cuij+6] = Uij
2147	atomData.append(atom)
2148	finally:
2149	dlg.Destroy()
2150	UpdateDrawAtoms()
2151	drawAtoms.ClearSelection()
2152	G2plt.PlotStructure(G2frame,data)
2153
2154	def TransformSymEquiv(event):
2155	indx = drawAtoms.GetSelectedRows()
2156	indx.sort()
2157	if indx:
2158	atomData = data['Drawing']['Atoms']
2159	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2160	cx = colLabels.index('x')
2161	cuia = colLabels.index('I/A')
2162	cuij = cuia+2
2163	atomData = data['Drawing']['Atoms']
2164	generalData = data['General']
2165	SGData = generalData['SGData']
2166	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2167	try:
2168	if dlg.ShowModal() == wx.ID_OK:
2169	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2170	Cell = np.array(Cell)
2171	cent = SGData['SGCen'][Cent]
2172	M,T = SGData['SGOps'][Opr]
2173	for ind in indx:
2174	XYZ = np.array(atomData[ind][cx:cx+3])
2175	XYZ = np.inner(M,XYZ)+T
2176	if Inv:
2177	XYZ = -XYZ
2178	XYZ = XYZ+cent+Cell
2179	if Force:
2180	XYZ = G2spc.MoveToUnitCell(XYZ)
2181	atom = atomData[ind]
2182	atom[cx:cx+3] = XYZ
2183	atomOp = atom[cx+3]
2184	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2185	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2186	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2187	if atom[cuia] == 'A':
2188	Uij = atom[cuij:cuij+6]
2189	U = G2spc.Uij2U(Uij)
2190	U = np.inner(np.inner(M,U),M)
2191	Uij = G2spc.U2Uij(U)
2192	atom[cuij:cuij+6] = Uij
2193	data['Drawing']['Atoms'] = atomData
2194	finally:
2195	dlg.Destroy()
2196	UpdateDrawAtoms()
2197	drawAtoms.ClearSelection()
2198	G2plt.PlotStructure(G2frame,data)
2199
2200	def FillCoordSphere(event):
2201	generalData = data['General']
2202	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2203	radii = generalData['BondRadii']
2204	atomTypes = generalData['AtomTypes']
2205	try:
2206	indH = atomTypes.index('H')
2207	radii[indH] = 0.5
2208	except:
2209	pass
2210	indx = drawAtoms.GetSelectedRows()
2211	if indx:
2212	indx.sort()
2213	atomData = data['Drawing']['Atoms']
2214	numAtoms = len(atomData)
2215	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2216	generalData = data['General']
2217	SGData = generalData['SGData']
2218	cellArray = G2lat.CellBlock(1)
2219	wx.BeginBusyCursor()
2220	try:
2221	for ind in indx:
2222	atomA = atomData[ind]
2223	xyzA = np.array(atomA[cx:cx+3])
2224	indA = atomTypes.index(atomA[ct])
2225	for atomB in atomData[:numAtoms]:
2226	indB = atomTypes.index(atomB[ct])
2227	sumR = radii[indA]+radii[indB]
2228	xyzB = np.array(atomB[cx:cx+3])
2229	for xyz in cellArray+xyzB:
2230	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2231	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2232	if noDuplicate(xyz,atomData):
2233	oprB = atomB[cx+3]
2234	C = xyz-xyzB
2235	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2236	newAtom = atomB[:]
2237	newAtom[cx:cx+3] = xyz
2238	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2239	atomData.append(newAtom)
2240	finally:
2241	wx.EndBusyCursor()
2242	data['Drawing']['Atoms'] = atomData
2243	UpdateDrawAtoms()
2244	drawAtoms.ClearSelection()
2245	G2plt.PlotStructure(G2frame,data)
2246
2247	def FillUnitCell(event):
2248	indx = drawAtoms.GetSelectedRows()
2249	indx.sort()
2250	if indx:
2251	atomData = data['Drawing']['Atoms']
2252	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2253	cx = colLabels.index('x')
2254	cuia = colLabels.index('I/A')
2255	cuij = cuia+2
2256	generalData = data['General']
2257	SGData = generalData['SGData']
2258	wx.BeginBusyCursor()
2259	try:
2260	for ind in indx:
2261	atom = atomData[ind]
2262	XYZ = np.array(atom[cx:cx+3])
2263	if atom[cuia] == 'A':
2264	Uij = atom[cuij:cuij+6]
2265	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2266	for item in result:
2267	atom = copy.copy(atomData[ind])
2268	atom[cx:cx+3] = item[0]
2269	atom[cx+3] = str(item[2])+'+' \
2270	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2271	atom[cuij:cuij+6] = item[1]
2272	Opp = G2spc.Opposite(item[0])
2273	for xyz in Opp:
2274	if noDuplicate(xyz,atomData):
2275	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2276	cell = '1'+'+'+ \
2277	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2278	atom[cx:cx+3] = xyz
2279	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2280	atomData.append(atom[:])
2281	else:
2282	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2283	for item in result:
2284	atom = copy.copy(atomData[ind])
2285	atom[cx:cx+3] = item[0]
2286	atom[cx+3] = str(item[1])+'+' \
2287	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2288	Opp = G2spc.Opposite(item[0])
2289	for xyz in Opp:
2290	if noDuplicate(xyz,atomData):
2291	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2292	cell = '1'+'+'+ \
2293	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2294	atom[cx:cx+3] = xyz
2295	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2296	atomData.append(atom[:])
2297	data['Drawing']['Atoms'] = atomData
2298	finally:
2299	wx.EndBusyCursor()
2300	UpdateDrawAtoms()
2301	drawAtoms.ClearSelection()
2302	G2plt.PlotStructure(G2frame,data)
2303
2304	def FindBondsToo(): #works but slow for large structures - keep as reference
2305	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2306	atomData = data['Drawing']['Atoms']
2307	generalData = data['General']
2308	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2309	radii = generalData['BondRadii']
2310	atomTypes = generalData['AtomTypes']
2311	try:
2312	indH = atomTypes.index('H')
2313	radii[indH] = 0.5
2314	except:
2315	pass
2316	for atom in atomData:
2317	atom[-1] = []
2318	Atoms = []
2319	for i,atom in enumerate(atomData):
2320	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2321	for atomA in Atoms:
2322	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2323	for atomB in Atoms:
2324	Dx = atomB[1]-atomA[1]
2325	DX = np.inner(Amat,Dx)
2326	dist = np.sqrt(np.sum(DX**2))
2327	sumR = atomA[3]+atomB[3]
2328	if 0.5 < dist <= 0.85*sumR:
2329	i = atomA[0]
2330	if atomA[2] == 'polyhedra':
2331	atomData[i][-1].append(DX)
2332	elif atomB[1] != 'polyhedra':
2333	j = atomB[0]
2334	atomData[i][-1].append(Dx*atomA[3]/sumR)
2335	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2336
2337	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2338	import numpy.ma as ma
2339	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2340	hydro = data['Drawing']['showHydrogen']
2341	atomData = data['Drawing']['Atoms']
2342	generalData = data['General']
2343	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2344	radii = generalData['BondRadii']
2345	atomTypes = generalData['AtomTypes']
2346	try:
2347	indH = atomTypes.index('H')
2348	radii[indH] = 0.5
2349	except:
2350	pass
2351	for atom in atomData:
2352	atom[-2] = [] #clear out old bonds/polyhedra
2353	atom[-1] = []
2354	Indx = range(len(atomData))
2355	Atoms = []
2356	Styles = []
2357	Radii = []
2358	for atom in atomData:
2359	Atoms.append(np.array(atom[cx:cx+3]))
2360	Styles.append(atom[cs])
2361	try:
2362	if not hydro and atom[ct] == 'H':
2363	Radii.append(0.0)
2364	else:
2365	Radii.append(radii[atomTypes.index(atom[ct])])
2366	except ValueError: #changed atom type!
2367	Radii.append(0.20)
2368	Atoms = np.array(Atoms)
2369	Radii = np.array(Radii)
2370	IASR = zip(Indx,Atoms,Styles,Radii)
2371	for atomA in IASR:
2372	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2373	Dx = Atoms-atomA[1]
2374	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
2375	sumR = atomA[3]+Radii
2376	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2377	i = atomA[0]
2378	for j in IndB[0]:
2379	if Styles[i] == 'polyhedra':
2380	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2381	elif Styles[j] != 'polyhedra' and j > i:
2382	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2383	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2384	if Styles[i] == 'polyhedra':
2385	Bonds = atomData[i][-2]
2386	Faces = []
2387	if len(Bonds) > 2:
2388	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2389	for face in FaceGen:
2390	vol = nl.det(face)
2391	if abs(vol) > 1. or len(Bonds) == 3:
2392	if vol < 0.:
2393	face = [face[0],face[2],face[1]]
2394	face = np.array(face)
2395	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2396	norm = np.cross(face[1]-face[0],face[2]-face[0])
2397	norm /= np.sqrt(np.sum(norm**2))
2398	Faces.append([face,norm])
2399	atomData[i][-1] = Faces
2400
2401	def DrawAtomsDelete(event):
2402	indx = drawAtoms.GetSelectedRows()
2403	indx.sort()
2404	if indx:
2405	atomData = data['Drawing']['Atoms']
2406	indx.reverse()
2407	for ind in indx:
2408	del atomData[ind]
2409	UpdateDrawAtoms()
2410	drawAtoms.ClearSelection()
2411	G2plt.PlotStructure(G2frame,data)
2412	event.StopPropagation()
2413
2414	def OnReloadDrawAtoms(event):
2415	data['Drawing']['Atoms'] = []
2416	UpdateDrawAtoms()
2417	drawAtoms.ClearSelection()
2418	G2plt.PlotStructure(G2frame,data)
2419	event.StopPropagation()
2420
2421	def DrawAtomsDeleteByIDs(IDs):
2422	atomData = data['Drawing']['Atoms']
2423	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2424	indx.reverse()
2425	for ind in indx:
2426	del atomData[ind]
2427
2428	def ChangeDrawAtomsByIDs(colName,IDs,value):
2429	atomData = data['Drawing']['Atoms']
2430	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2431	if colName == 'Name':
2432	col = ct-1
2433	elif colName == 'Type':
2434	col = ct
2435	elif colName == 'I/A':
2436	col = cs
2437	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2438	for ind in indx:
2439	atomData[ind][col] = value
2440
2441	def OnDrawPlane(event):
2442	indx = drawAtoms.GetSelectedRows()
2443	if len(indx) < 4:
2444	print '**** ERROR - need 4+ atoms for plane calculation'
2445	return
2446	PlaneData = {}
2447	drawingData = data['Drawing']
2448	atomData = drawingData['Atoms']
2449	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2450	cx = colLabels.index('x')
2451	cn = colLabels.index('Name')
2452	xyz = []
2453	for i,atom in enumerate(atomData):
2454	if i in indx:
2455	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2456	generalData = data['General']
2457	PlaneData['Name'] = generalData['Name']
2458	PlaneData['Atoms'] = xyz
2459	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2460	G2stMn.BestPlane(PlaneData)
2461
2462	def OnDrawDistVP(event):
2463	# distance to view point
2464	indx = drawAtoms.GetSelectedRows()
2465	if not indx:
2466	print '***** ERROR - no atoms selected'
2467	return
2468	generalData = data['General']
2469	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2470	drawingData = data['Drawing']
2471	viewPt = np.array(drawingData['viewPoint'][0])
2472	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2473	atomDData = drawingData['Atoms']
2474	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2475	cx = colLabels.index('x')
2476	cn = colLabels.index('Name')
2477	for i in indx:
2478	atom = atomDData[i]
2479	Dx = np.array(atom[cx:cx+3])-viewPt
2480	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2481	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2482
2483	def OnDrawDAT(event):
2484	#distance, angle, torsion
2485	indx = drawAtoms.GetSelectedRows()
2486	if len(indx) not in [2,3,4]:
2487	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2488	return
2489	DATData = {}
2490	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2491	drawingData = data['Drawing']
2492	atomData = data['Atoms']
2493	atomDData = drawingData['Atoms']
2494	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2495	cx = colLabels.index('x')
2496	cn = colLabels.index('Name')
2497	cid = colLabels.index('I/A')+8
2498	xyz = []
2499	Oxyz = []
2500	DATData['Natoms'] = len(indx)
2501	for i in indx:
2502	atom = atomDData[i]
2503	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2504	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2505	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2506	DATData['Datoms'] = xyz
2507	DATData['Oatoms'] = Oxyz
2508	generalData = data['General']
2509	DATData['Name'] = generalData['Name']
2510	DATData['SGData'] = generalData['SGData']
2511	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2512	if 'pId' in data:
2513	DATData['pId'] = data['pId']
2514	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2515	G2stMn.DisAglTor(DATData)
2516
2517	################################################################################
2518	#### Draw Options page
2519	################################################################################
2520
2521	def UpdateDrawOptions():
2522	import copy
2523	import wx.lib.colourselect as wcs
2524	def SlopSizer():
2525	def OnCameraPos(event):
2526	drawingData['cameraPos'] = cameraPos.GetValue()
2527	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2528	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2529	G2plt.PlotStructure(G2frame,data)
2530
2531	def OnZclip(event):
2532	drawingData['Zclip'] = Zclip.GetValue()
2533	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2534	G2plt.PlotStructure(G2frame,data)
2535
2536	def OnZstep(event):
2537	try:
2538	step = float(Zstep.GetValue())
2539	if not (0.01 <= step <= 1.0):
2540	raise ValueError
2541	except ValueError:
2542	step = drawingData['Zstep']
2543	drawingData['Zstep'] = step
2544	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2545
2546	def OnMoveZ(event):
2547	move = MoveZ.GetValue()*drawingData['Zstep']
2548	MoveZ.SetValue(0)
2549	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2550	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2551	VD /= np.sqrt(np.sum(VD**2))
2552	VP += move*VD
2553	VP = np.inner(Bmat,VP)
2554	drawingData['viewPoint'][0] = VP
2555	panel = drawOptions.GetChildren()
2556	names = [child.GetName() for child in panel]
2557	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2558	G2plt.PlotStructure(G2frame,data)
2559
2560	def OnVdWScale(event):
2561	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2562	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2563	G2plt.PlotStructure(G2frame,data)
2564
2565	def OnEllipseProb(event):
2566	drawingData['ellipseProb'] = ellipseProb.GetValue()
2567	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2568	G2plt.PlotStructure(G2frame,data)
2569
2570	def OnBallScale(event):
2571	drawingData['ballScale'] = ballScale.GetValue()/100.
2572	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2573	G2plt.PlotStructure(G2frame,data)
2574
2575	def OnBondRadius(event):
2576	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2577	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2578	G2plt.PlotStructure(G2frame,data)
2579
2580	def OnContourLevel(event):
2581	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2582	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2583	G2plt.PlotStructure(G2frame,data)
2584
2585	def OnMapSize(event):
2586	drawingData['mapSize'] = mapSize.GetValue()/10.
2587	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2588	G2plt.PlotStructure(G2frame,data)
2589
2590
2591	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2592	slideSizer = wx.FlexGridSizer(7,2)
2593	slideSizer.AddGrowableCol(1,1)
2594
2595	cameraPosTxt = wx.StaticText(drawOptions,-1,
2596	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2597	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2598	slideSizer.Add(cameraPosTxt,0,wx.ALIGN_CENTER_VERTICAL)
2599	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2600	cameraPos.SetRange(10,500)
2601	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2602	G2frame.dataDisplay.cameraSlider = cameraPos
2603	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2604
2605	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2606	slideSizer.Add(ZclipTxt,0,wx.ALIGN_CENTER_VERTICAL)
2607	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2608	Zclip.SetRange(1,99)
2609	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2610	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2611
2612	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2613	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,wx.ALIGN_CENTER_VERTICAL)
2614	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2615	style=wx.TE_PROCESS_ENTER)
2616	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2617	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2618	ZstepSizer.Add(Zstep,0,wx.ALIGN_CENTER_VERTICAL)
2619	slideSizer.Add(ZstepSizer)
2620	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2621	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,wx.ALIGN_CENTER_VERTICAL)
2622	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2623	MoveZ.SetValue(0)
2624	MoveZ.SetRange(-1,1)
2625	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2626	MoveSizer.Add(MoveZ)
2627	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2628
2629	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2630	slideSizer.Add(vdwScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2631	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2632	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2633	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2634
2635	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2636	slideSizer.Add(ellipseProbTxt,0,wx.ALIGN_CENTER_VERTICAL)
2637	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2638	ellipseProb.SetRange(1,99)
2639	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2640	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2641
2642	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2643	slideSizer.Add(ballScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2644	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2645	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2646	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2647
2648	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2649	slideSizer.Add(bondRadiusTxt,0,wx.ALIGN_CENTER_VERTICAL)
2650	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2651	bondRadius.SetRange(1,25)
2652	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2653	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2654
2655	if generalData['Map']['rhoMax']:
2656	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2657	slideSizer.Add(contourLevelTxt,0,wx.ALIGN_CENTER_VERTICAL)
2658	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2659	contourLevel.SetRange(1,100)
2660	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2661	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2662	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2663	slideSizer.Add(mapSizeTxt,0,wx.ALIGN_CENTER_VERTICAL)
2664	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2665	mapSize.SetRange(1,100)
2666	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2667	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2668
2669	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2670	slopSizer.Add((10,5),0)
2671	slopSizer.SetMinSize(wx.Size(350,10))
2672	return slopSizer
2673
2674	def ShowSizer():
2675
2676	def OnBackColor(event):
2677	drawingData['backColor'] = event.GetValue()
2678	G2plt.PlotStructure(G2frame,data)
2679
2680	def OnShowABC(event):
2681	drawingData['showABC'] = showABC.GetValue()
2682	G2plt.PlotStructure(G2frame,data)
2683
2684	def OnShowUnitCell(event):
2685	drawingData['unitCellBox'] = unitCellBox.GetValue()
2686	G2plt.PlotStructure(G2frame,data)
2687
2688	def OnShowHyd(event):
2689	drawingData['showHydrogen'] = showHydrogen.GetValue()
2690	FindBondsDraw()
2691	G2plt.PlotStructure(G2frame,data)
2692
2693	def OnShowRB(event):
2694	drawingData['showRigidBodies'] = showRB.GetValue()
2695	FindBondsDraw()
2696	G2plt.PlotStructure(G2frame,data)
2697
2698	def OnViewPoint(event):
2699	Obj = event.GetEventObject()
2700	viewPt = Obj.GetValue().split()
2701	try:
2702	VP = [float(viewPt[i]) for i in range(3)]
2703	except (ValueError,IndexError):
2704	VP = drawingData['viewPoint'][0]
2705	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2706	drawingData['viewPoint'][0] = VP
2707	G2plt.PlotStructure(G2frame,data)
2708
2709	def OnViewDir(event):
2710	Obj = event.GetEventObject()
2711	viewDir = Obj.GetValue().split()
2712	try:
2713	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2714	VD = np.array([float(viewDir[i]) for i in range(3)])
2715	VC = np.inner(Amat,VD)
2716	VC /= np.sqrt(np.sum(VC**2))
2717	V = np.array(drawingData['viewDir'])
2718	VB = np.inner(Amat,V)
2719	VB /= np.sqrt(np.sum(VB**2))
2720	VX = np.cross(VC,VB)
2721	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2722	QV = G2mth.AVdeg2Q(A,VX)
2723	Q = drawingData['Quaternion']
2724	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2725	except (ValueError,IndexError):
2726	VD = drawingData['viewDir']
2727	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2728	drawingData['viewDir'] = VD
2729	G2plt.PlotStructure(G2frame,data)
2730
2731	showSizer = wx.BoxSizer(wx.VERTICAL)
2732	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2733	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,wx.ALIGN_CENTER_VERTICAL)
2734	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2735	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2736	lineSizer.Add(backColor,0,wx.ALIGN_CENTER_VERTICAL)
2737	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,wx.ALIGN_CENTER_VERTICAL)
2738	VD = drawingData['viewDir']
2739	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2740	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2741	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2742	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2743	G2frame.dataDisplay.viewDir = viewDir
2744	lineSizer.Add(viewDir,0,wx.ALIGN_CENTER_VERTICAL)
2745	showSizer.Add(lineSizer)
2746	showSizer.Add((0,5),0)
2747
2748	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2749	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2750	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2751	showABC.SetValue(drawingData['showABC'])
2752	lineSizer.Add(showABC,0,wx.ALIGN_CENTER_VERTICAL)
2753	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,wx.ALIGN_CENTER_VERTICAL)
2754	VP = drawingData['viewPoint'][0]
2755	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2756	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2757	G2frame.dataDisplay.viewPoint = viewPoint
2758	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2759	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2760	lineSizer.Add(viewPoint,0,wx.ALIGN_CENTER_VERTICAL)
2761	showSizer.Add(lineSizer)
2762	showSizer.Add((0,5),0)
2763
2764	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2765
2766	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2767	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2768	unitCellBox.SetValue(drawingData['unitCellBox'])
2769	line2Sizer.Add(unitCellBox,0,wx.ALIGN_CENTER_VERTICAL)
2770
2771	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2772	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2773	showHydrogen.SetValue(drawingData['showHydrogen'])
2774	line2Sizer.Add(showHydrogen,0,wx.ALIGN_CENTER_VERTICAL)
2775
2776	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2777	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2778	showRB.SetValue(drawingData['showRigidBodies'])
2779	line2Sizer.Add(showRB,0,wx.ALIGN_CENTER_VERTICAL)
2780
2781	showSizer.Add(line2Sizer)
2782	return showSizer
2783
2784	def RadSizer():
2785
2786	def OnSizeHatoms(event):
2787	try:
2788	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2789	except ValueError:
2790	value = 0.5
2791	drawingData['sizeH'] = value
2792	sizeH.SetValue("%.2f"%(value))
2793	G2plt.PlotStructure(G2frame,data)
2794
2795	def OnRadFactor(event):
2796	try:
2797	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2798	except ValueError:
2799	value = 0.85
2800	drawingData['radiusFactor'] = value
2801	radFactor.SetValue("%.2f"%(value))
2802	FindBondsDraw()
2803	G2plt.PlotStructure(G2frame,data)
2804
2805	radSizer = wx.BoxSizer(wx.HORIZONTAL)
2806	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,wx.ALIGN_CENTER_VERTICAL)
2807	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2808	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
2809	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
2810	radSizer.Add(sizeH,0,wx.ALIGN_CENTER_VERTICAL)
2811
2812	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,wx.ALIGN_CENTER_VERTICAL)
2813	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2814	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
2815	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
2816	radSizer.Add(radFactor,0,wx.ALIGN_CENTER_VERTICAL)
2817	return radSizer
2818
2819	# UpdateDrawOptions exectable code starts here
2820	generalData = data['General']
2821	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2822	SetupDrawingData()
2823	drawingData = data['Drawing']
2824	if generalData['Type'] == 'nuclear':
2825	pickChoice = ['Atoms','Bonds','Torsions','Planes']
2826	elif generalData['Type'] == 'macromolecular':
2827	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
2828
2829	G2frame.dataFrame.SetStatusText('')
2830	if drawOptions.GetSizer():
2831	drawOptions.GetSizer().Clear(True)
2832	mainSizer = wx.BoxSizer(wx.VERTICAL)
2833	mainSizer.Add((5,5),0)
2834	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,wx.ALIGN_CENTER_VERTICAL)
2835	mainSizer.Add((5,5),0)
2836	mainSizer.Add(SlopSizer(),0)
2837	mainSizer.Add((5,5),0)
2838	mainSizer.Add(ShowSizer(),0,)
2839	mainSizer.Add((5,5),0)
2840	mainSizer.Add(RadSizer(),0,)
2841	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
2842
2843	################################################################################
2844	#### Texture routines
2845	################################################################################
2846
2847	def UpdateTexture():
2848	def SetSHCoef():
2849	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
2850	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
2851	SHCoeff = textureData['SH Coeff'][1]
2852	for cofName in SHCoeff:
2853	if cofName in cofNames:
2854	newSHCoef[cofName] = SHCoeff[cofName]
2855	return newSHCoef
2856
2857	def OnShOrder(event):
2858	Obj = event.GetEventObject()
2859	textureData['Order'] = int(Obj.GetValue())
2860	textureData['SH Coeff'][1] = SetSHCoef()
2861	wx.CallAfter(UpdateTexture)
2862	G2plt.PlotTexture(G2frame,data)
2863
2864	def OnShModel(event):
2865	Obj = event.GetEventObject()
2866	textureData['Model'] = Obj.GetValue()
2867	textureData['SH Coeff'][1] = SetSHCoef()
2868	wx.CallAfter(UpdateTexture)
2869	G2plt.PlotTexture(G2frame,data)
2870
2871	def OnSHRefine(event):
2872	Obj = event.GetEventObject()
2873	textureData['SH Coeff'][0] = Obj.GetValue()
2874
2875	def OnSHShow(event):
2876	Obj = event.GetEventObject()
2877	textureData['SHShow'] = Obj.GetValue()
2878	wx.CallAfter(UpdateTexture)
2879
2880	def OnProjSel(event):
2881	Obj = event.GetEventObject()
2882	G2frame.Projection = Obj.GetValue()
2883	G2plt.PlotTexture(G2frame,data)
2884
2885	def OnColorSel(event):
2886	Obj = event.GetEventObject()
2887	G2frame.ContourColor = Obj.GetValue()
2888	G2plt.PlotTexture(G2frame,data)
2889
2890	def OnAngRef(event):
2891	Obj = event.GetEventObject()
2892	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
2893
2894	def OnAngValue(event):
2895	Obj = event.GetEventObject()
2896	try:
2897	value = float(Obj.GetValue())
2898	except ValueError:
2899	value = textureData[valIndx[Obj.GetId()]][1]
2900	Obj.SetValue('%8.2f'%(value))
2901	textureData[valIndx[Obj.GetId()]][1] = value
2902
2903	def OnODFValue(event):
2904	Obj = event.GetEventObject()
2905	try:
2906	value = float(Obj.GetValue())
2907	except ValueError:
2908	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
2909	Obj.SetValue('%8.3f'%(value))
2910	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
2911	G2plt.PlotTexture(G2frame,data)
2912
2913	def OnPfType(event):
2914	Obj = event.GetEventObject()
2915	textureData['PlotType'] = Obj.GetValue()
2916	wx.CallAfter(UpdateTexture)
2917	G2plt.PlotTexture(G2frame,data)
2918
2919	def OnPFValue(event):
2920	Obj = event.GetEventObject()
2921	Saxis = Obj.GetValue().split()
2922	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2923	try:
2924	hkl = [int(Saxis[i]) for i in range(3)]
2925	except (ValueError,IndexError):
2926	hkl = textureData['PFhkl']
2927	if not np.any(np.array(hkl)): #can't be all zeros!
2928	hkl = textureData['PFhkl']
2929	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
2930	textureData['PFhkl'] = hkl
2931	else:
2932	try:
2933	xyz = [float(Saxis[i]) for i in range(3)]
2934	except (ValueError,IndexError):
2935	xyz = textureData['PFxyz']
2936	if not np.any(np.array(xyz)): #can't be all zeros!
2937	xyz = textureData['PFxyz']
2938	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
2939	textureData['PFxyz'] = xyz
2940	G2plt.PlotTexture(G2frame,data)
2941
2942	# UpdateTexture executable starts here
2943	G2frame.dataFrame.SetStatusText('')
2944	generalData = data['General']
2945	SGData = generalData['SGData']
2946	try:
2947	textureData = generalData['SH Texture']
2948	except KeyError: #fix old files!
2949	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
2950	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
2951	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
2952	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
2953	if 'SHShow' not in textureData: #another fix
2954	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2955	try: #another fix!
2956	x = textureData['PlotType']
2957	except KeyError:
2958	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2959	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
2960	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
2961	if generalData['doPawley'] and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Sequental results'):
2962	G2frame.dataFrame.RefineTexture.Enable(True)
2963	shAngles = ['omega','chi','phi']
2964	if Texture.GetSizer():
2965	Texture.GetSizer().Clear(True)
2966	mainSizer = wx.BoxSizer(wx.VERTICAL)
2967	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
2968	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,wx.ALIGN_CENTER_VERTICAL)
2969	titleSizer.Add(wx.StaticText(Texture,-1,
2970	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
2971	0,wx.ALIGN_CENTER_VERTICAL)
2972	mainSizer.Add(titleSizer,0)
2973	mainSizer.Add((0,5),0)
2974	shSizer = wx.FlexGridSizer(1,6,5,5)
2975	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,wx.ALIGN_CENTER_VERTICAL)
2976	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
2977	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2978	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
2979	shSizer.Add(shModel,0,wx.ALIGN_CENTER_VERTICAL)
2980	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,wx.ALIGN_CENTER_VERTICAL)
2981	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
2982	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2983	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
2984	shSizer.Add(shOrder,0,wx.ALIGN_CENTER_VERTICAL)
2985	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
2986	shRef.SetValue(textureData['SH Coeff'][0])
2987	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
2988	shSizer.Add(shRef,0,wx.ALIGN_CENTER_VERTICAL)
2989	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
2990	shShow.SetValue(textureData['SHShow'])
2991	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
2992	shSizer.Add(shShow,0,wx.ALIGN_CENTER_VERTICAL)
2993	mainSizer.Add(shSizer,0,0)
2994	mainSizer.Add((0,5),0)
2995	PTSizer = wx.FlexGridSizer(2,4,5,5)
2996	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,wx.ALIGN_CENTER_VERTICAL)
2997	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
2998	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
2999	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3000	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
3001	PTSizer.Add(pfType,0,wx.ALIGN_CENTER_VERTICAL)
3002	if 'Axial' not in textureData['PlotType']:
3003	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,wx.ALIGN_CENTER_VERTICAL)
3004	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
3005	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3006	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
3007	PTSizer.Add(projSel,0,wx.ALIGN_CENTER_VERTICAL)
3008	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3009	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,wx.ALIGN_CENTER_VERTICAL)
3010	PH = textureData['PFhkl']
3011	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
3012	else:
3013	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,wx.ALIGN_CENTER_VERTICAL)
3014	PX = textureData['PFxyz']
3015	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
3016	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
3017	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
3018	PTSizer.Add(pfVal,0,wx.ALIGN_CENTER_VERTICAL)
3019	if 'Axial' not in textureData['PlotType']:
3020	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,wx.ALIGN_CENTER_VERTICAL)
3021	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3022	choice.sort()
3023	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
3024	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3025	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
3026	PTSizer.Add(colorSel,0,wx.ALIGN_CENTER_VERTICAL)
3027	mainSizer.Add(PTSizer,0,wx.ALIGN_CENTER_VERTICAL)
3028	mainSizer.Add((0,5),0)
3029	if textureData['SHShow']:
3030	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,wx.ALIGN_CENTER_VERTICAL)
3031	mainSizer.Add((0,5),0)
3032	ODFSizer = wx.FlexGridSizer(2,8,2,2)
3033	ODFIndx = {}
3034	ODFkeys = textureData['SH Coeff'][1].keys()
3035	ODFkeys.sort()
3036	for item in ODFkeys:
3037	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,wx.ALIGN_CENTER_VERTICAL)
3038	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3039	ODFIndx[ODFval.GetId()] = item
3040	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3041	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3042	ODFSizer.Add(ODFval,0,wx.ALIGN_CENTER_VERTICAL)
3043	mainSizer.Add(ODFSizer,0,wx.ALIGN_CENTER_VERTICAL)
3044	mainSizer.Add((0,5),0)
3045	mainSizer.Add((0,5),0)
3046	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,wx.ALIGN_CENTER_VERTICAL)
3047	mainSizer.Add((0,5),0)
3048	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3049	angIndx = {}
3050	valIndx = {}
3051	for item in ['Sample omega','Sample chi','Sample phi']:
3052	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3053	angRef.SetValue(textureData[item][0])
3054	angIndx[angRef.GetId()] = item
3055	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3056	angSizer.Add(angRef,0,wx.ALIGN_CENTER_VERTICAL)
3057	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3058	valIndx[angVal.GetId()] = item
3059	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3060	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3061	angSizer.Add(angVal,0,wx.ALIGN_CENTER_VERTICAL)
3062	angSizer.Add((5,0),0)
3063	mainSizer.Add(angSizer,0,wx.ALIGN_CENTER_VERTICAL)
3064	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3065
3066	################################################################################
3067	##### DData routines - GUI stuff in GSASIIddataGUI.py
3068	################################################################################
3069
3070	def OnHklfAdd(event):
3071	UseList = data['Histograms']
3072	keyList = UseList.keys()
3073	TextList = []
3074	if G2frame.PatternTree.GetCount():
3075	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3076	while item:
3077	name = G2frame.PatternTree.GetItemText(item)
3078	if name not in keyList and 'HKLF' in name:
3079	TextList.append(name)
3080	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3081	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3082	try:
3083	if dlg.ShowModal() == wx.ID_OK:
3084	result = dlg.GetSelections()
3085	for i in result:
3086	histoName = TextList[i]
3087	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3088	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3089	'Extinction':['Lorentzian','None',
3090	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3091	wx.BeginBusyCursor()
3092	UpdateHKLFdata(histoName)
3093	wx.EndBusyCursor()
3094	data['Histograms'] = UseList
3095	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3096	finally:
3097	dlg.Destroy()
3098
3099	def UpdateHKLFdata(histoName):
3100	generalData = data['General']
3101	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3102	refDict,reflData = G2frame.PatternTree.GetItemPyData(Id)
3103	SGData = generalData['SGData']
3104	Cell = generalData['Cell'][1:7]
3105	G,g = G2lat.cell2Gmat(Cell)
3106	for ref in reflData:
3107	H = ref[:3]
3108	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3109	iabsnt,ref[3],ref[11],ref[12] = G2spc.GenHKLf(H,SGData)
3110	G2frame.PatternTree.SetItemPyData(Id,[refDict,reflData])
3111
3112	def OnPwdrAdd(event):
3113	generalData = data['General']
3114	SGData = generalData['SGData']
3115	UseList = data['Histograms']
3116	newList = []
3117	NShkl = len(G2spc.MustrainNames(SGData))
3118	NDij = len(G2spc.HStrainNames(SGData))
3119	keyList = UseList.keys()
3120	TextList = ['All PWDR']
3121	if G2frame.PatternTree.GetCount():
3122	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3123	while item:
3124	name = G2frame.PatternTree.GetItemText(item)
3125	if name not in keyList and 'PWDR' in name:
3126	TextList.append(name)
3127	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3128	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3129	try:
3130	if dlg.ShowModal() == wx.ID_OK:
3131	result = dlg.GetSelections()
3132	for i in result: newList.append(TextList[i])
3133	if 'All PWDR' in newList:
3134	newList = TextList[1:]
3135	for histoName in newList:
3136	pId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3137	UseList[histoName] = {'Histogram':histoName,'Show':False,
3138	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3139	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3140	[1.,1.,1.,0.,0.,0.],6*[False,]],
3141	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3142	NShkl[0.01,],NShkl[False,]],
3143	'HStrain':[NDij[0.0,],NDij[False,]],
3144	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3145	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,pId,'Reflection Lists'))
3146	refList[generalData['Name']] = []
3147	data['Histograms'] = UseList
3148	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3149	finally:
3150	dlg.Destroy()
3151
3152	def OnDataDelete(event):
3153	UseList = data['Histograms']
3154	keyList = ['All',]+UseList.keys()
3155	keyList.sort()
3156	DelList = []
3157	if UseList:
3158	DelList = []
3159	dlg = wx.MultiChoiceDialog(G2frame,
3160	'Which histogram to delete from this phase?', 'Delete histogram',
3161	keyList, wx.CHOICEDLG_STYLE)
3162	try:
3163	if dlg.ShowModal() == wx.ID_OK:
3164	result = dlg.GetSelections()
3165	for i in result:
3166	DelList.append(keyList[i])
3167	if 'All' in DelList:
3168	DelList = keyList[1:]
3169	for i in DelList:
3170	del UseList[i]
3171	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3172	finally:
3173	dlg.Destroy()
3174
3175	################################################################################
3176	##### Rigid bodies
3177	################################################################################
3178
3179	def FillRigidBodyGrid(refresh=True):
3180	'''Fill the Rigid Body Phase information tab page.
3181	Note that the page is a ScrolledWindow, not a Grid
3182	'''
3183	def OnThermSel(event): #needs to be seen by VecRbSizer!
3184	Obj = event.GetEventObject()
3185	RBObj = Indx[Obj.GetId()]
3186	val = Obj.GetValue()
3187	Ttype = 'A'
3188	if val == 'Uiso':
3189	Ttype = 'I'
3190	RBObj['ThermalMotion'][0] = 'Uiso'
3191	elif val == 'T':
3192	RBObj['ThermalMotion'][0] = 'T'
3193	elif val == 'TL':
3194	RBObj['ThermalMotion'][0] = 'TL'
3195	elif val == 'TLS':
3196	RBObj['ThermalMotion'][0] = 'TLS'
3197	wx.CallAfter(FillRigidBodyGrid,True)
3198	if val != 'None':
3199	cia = data['General']['AtomPtrs'][3]
3200	for i,id in enumerate(RBObj['Ids']):
3201	data['Atoms'][AtLookUp[id]][cia] = Ttype
3202	G2plt.PlotStructure(G2frame,data)
3203
3204	def ThermDataSizer(RBObj,rbType):
3205
3206	def OnThermval(event):
3207	Obj = event.GetEventObject()
3208	item = Indx[Obj.GetId()]
3209	try:
3210	val = float(Obj.GetValue())
3211	RBObj['ThermalMotion'][1][item] = val
3212	except ValueError:
3213	pass
3214	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3215	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3216	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3217	cia = data['General']['AtomPtrs'][3]
3218	for i,id in enumerate(RBObj['Ids']):
3219	if Uout[i][0] == 'I':
3220	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3221	else:
3222	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3223	G2plt.PlotStructure(G2frame,data)
3224
3225	def OnTLSRef(event):
3226	Obj = event.GetEventObject()
3227	item = Indx[Obj.GetId()]
3228	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3229
3230	thermSizer = wx.FlexGridSizer(1,9,5,5)
3231	model = RBObj['ThermalMotion']
3232	if model[0] == 'Uiso':
3233	names = ['Uiso',]
3234	elif 'T' in model[0]:
3235	names = ['T11','T22','T33','T12','T13','T23']
3236	if 'L' in model[0]:
3237	names += ['L11','L22','L33','L12','L13','L23']
3238	if 'S' in model[0]:
3239	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3240	for i,name in enumerate(names):
3241	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,wx.ALIGN_CENTER_VERTICAL)
3242	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3243	style=wx.TE_PROCESS_ENTER)
3244	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3245	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3246	Indx[thermVal.GetId()] = i
3247	thermSizer.Add(thermVal)
3248	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3249	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3250	Tcheck.SetValue(model[2][i])
3251	Indx[Tcheck.GetId()] = i
3252	thermSizer.Add(Tcheck,0,wx.ALIGN_CENTER_VERTICAL)
3253	return thermSizer
3254
3255	def LocationSizer(RBObj,rbType):
3256
3257	def OnOrigRef(event):
3258	RBObj['Orig'][1] = Ocheck.GetValue()
3259
3260	def OnOrienRef(event):
3261	RBObj['Orient'][1] = Qcheck.GetValue()
3262
3263	def OnOrigX(event):
3264	Obj = event.GetEventObject()
3265	item = Indx[Obj.GetId()]
3266	try:
3267	val = float(Obj.GetValue())
3268	RBObj['Orig'][0][item] = val
3269	Obj.SetValue('%8.5f'%(val))
3270	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3271	for i,id in enumerate(RBObj['Ids']):
3272	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3273	data['Drawing']['Atoms'] = []
3274	UpdateDrawAtoms(atomStyle)
3275	G2plt.PlotStructure(G2frame,data)
3276	except ValueError:
3277	pass
3278
3279	def OnOrien(event):
3280	Obj = event.GetEventObject()
3281	item = Indx[Obj.GetId()]
3282	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3283	V = np.inner(Bmat,V)
3284	try:
3285	val = float(Obj.GetValue())
3286	if item:
3287	V[item-1] = val
3288	else:
3289	A = val
3290	Obj.SetValue('%8.5f'%(val))
3291	V = np.inner(Amat,V)
3292	Q = G2mth.AVdeg2Q(A,V)
3293	if not any(Q):
3294	raise ValueError
3295	RBObj['Orient'][0] = Q
3296	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3297	for i,id in enumerate(RBObj['Ids']):
3298	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3299	data['Drawing']['Atoms'] = []
3300	UpdateDrawAtoms(atomStyle)
3301	G2plt.PlotStructure(G2frame,data)
3302	except ValueError:
3303	pass
3304
3305	topSizer = wx.FlexGridSizer(2,6,5,5)
3306	Orig = RBObj['Orig'][0]
3307	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3308	Orien = [Orien,]
3309	Orien.extend(OrienV/nl.norm(OrienV))
3310	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,wx.ALIGN_CENTER_VERTICAL)
3311	for ix,x in enumerate(Orig):
3312	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3313	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3314	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3315	Indx[origX.GetId()] = ix
3316	topSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3317	topSizer.Add((5,0),)
3318	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3319	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3320	Ocheck.SetValue(RBObj['Orig'][1])
3321	topSizer.Add(Ocheck,0,wx.ALIGN_CENTER_VERTICAL)
3322	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,wx.ALIGN_CENTER_VERTICAL)
3323	for ix,x in enumerate(Orien):
3324	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3325	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3326	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3327	Indx[orien.GetId()] = ix
3328	topSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3329	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3330	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3331	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3332	Qcheck.SetValue(RBObj['Orient'][1])
3333	topSizer.Add(Qcheck)
3334	return topSizer
3335
3336	def ResrbSizer(RBObj):
3337	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3338
3339	def OnTorsionRef(event):
3340	Obj = event.GetEventObject()
3341	item = Indx[Obj.GetId()]
3342	RBObj['Torsions'][item][1] = Obj.GetValue()
3343
3344	def OnTorsion(event):
3345	Obj = event.GetEventObject()
3346	item = Indx[Obj.GetId()]
3347	try:
3348	val = float(Obj.GetValue())
3349	RBObj['Torsions'][item][0] = val
3350	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3351	for i,id in enumerate(RBObj['Ids']):
3352	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3353	except ValueError:
3354	pass
3355	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3356	data['Drawing']['Atoms'] = []
3357	UpdateDrawAtoms(atomStyle)
3358	drawAtoms.ClearSelection()
3359	G2plt.PlotStructure(G2frame,data)
3360
3361	def OnDelResRB(event):
3362	Obj = event.GetEventObject()
3363	RBId = Indx[Obj.GetId()]
3364	RBData['Residue'][RBId]['useCount'] -= 1
3365	RBObjs = data['RBModels']['Residue']
3366	for rbObj in RBObjs:
3367	if RBId == rbObj['RBId']:
3368	data['RBModels']['Residue'].remove(rbObj)
3369	G2plt.PlotStructure(G2frame,data)
3370	wx.CallAfter(FillRigidBodyGrid,True)
3371
3372	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3373	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3374	topLine = wx.BoxSizer(wx.HORIZONTAL)
3375	topLine.Add(wx.StaticText(RigidBodies,-1,
3376	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3377	rbId = RBObj['RBId']
3378	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3379	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3380	Indx[delRB.GetId()] = rbId
3381	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3382	resrbSizer.Add(topLine)
3383	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3384	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,wx.ALIGN_CENTER_VERTICAL)
3385	torSizer = wx.FlexGridSizer(1,6,5,5)
3386	for itors,tors in enumerate(RBObj['Torsions']):
3387	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,wx.ALIGN_CENTER_VERTICAL)
3388	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3389	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3390	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3391	Indx[torsTxt.GetId()] = itors
3392	torSizer.Add(torsTxt)
3393	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3394	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3395	torCheck.SetValue(tors[1])
3396	Indx[torCheck.GetId()] = itors
3397	torSizer.Add(torCheck,0,wx.ALIGN_CENTER_VERTICAL)
3398	resrbSizer.Add(torSizer)
3399	tchoice = ['None','Uiso','T','TL','TLS']
3400	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3401	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3402	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3403	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3404	Indx[thermSel.GetId()] = RBObj
3405	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3406	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3407	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3408	resrbSizer.Add(thermSizer)
3409	if RBObj['ThermalMotion'][0] != 'None':
3410	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3411	return resrbSizer
3412
3413	def VecrbSizer(RBObj):
3414	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3415
3416	def OnDelVecRB(event):
3417	Obj = event.GetEventObject()
3418	RBId = Indx[Obj.GetId()]
3419	RBData['Vector'][RBId]['useCount'] -= 1
3420	RBObjs = data['RBModels']['Vector']
3421	for rbObj in RBObjs:
3422	if RBId == rbObj['RBId']:
3423	data['RBModels']['Vector'].remove(rbObj)
3424	G2plt.PlotStructure(G2frame,data)
3425	wx.CallAfter(FillRigidBodyGrid,True)
3426
3427	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3428	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3429	topLine = wx.BoxSizer(wx.HORIZONTAL)
3430	topLine.Add(wx.StaticText(RigidBodies,-1,
3431	'Name: '+RBObj['RBname']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3432	rbId = RBObj['RBId']
3433	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3434	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3435	Indx[delRB.GetId()] = rbId
3436	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3437	vecrbSizer.Add(topLine)
3438	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3439	tchoice = ['None','Uiso','T','TL','TLS']
3440	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3441	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3442	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3443	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3444	Indx[thermSel.GetId()] = RBObj
3445	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3446	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3447	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3448	vecrbSizer.Add(thermSizer)
3449	if RBObj['ThermalMotion'][0] != 'None':
3450	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3451	return vecrbSizer
3452
3453	# FillRigidBodyGrid executable code starts here
3454	if refresh:
3455	RigidBodies.DestroyChildren()
3456	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3457	general = data['General']
3458	cx = general['AtomPtrs'][0]
3459	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3460	RBData = G2frame.PatternTree.GetItemPyData(
3461	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3462	Indx = {}
3463	atomStyle = 'balls & sticks'
3464	if 'macro' in general['Type']:
3465	atomStyle = 'sticks'
3466	G2frame.dataFrame.SetStatusText('')
3467	mainSizer = wx.BoxSizer(wx.VERTICAL)
3468	if not data['RBModels']:
3469	mainSizer.Add((5,5),0)
3470	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,wx.ALIGN_CENTER_VERTICAL)
3471	mainSizer.Add((5,5),0)
3472	if 'Residue' in data['RBModels']:
3473	mainSizer.Add((5,5),0)
3474	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3475	mainSizer.Add((5,5),0)
3476	for RBObj in data['RBModels']['Residue']:
3477	mainSizer.Add(ResrbSizer(RBObj))
3478	if 'Vector' in data['RBModels']:
3479	mainSizer.Add((5,5),0)
3480	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3481	mainSizer.Add((5,5),0)
3482	for RBObj in data['RBModels']['Vector']:
3483	mainSizer.Add(VecrbSizer(RBObj))
3484
3485	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3486
3487	def OnRBCopyParms(event):
3488	RBObjs = []
3489	for rbType in ['Vector','Residue']:
3490	RBObjs += data['RBModels'].get(rbType,[])
3491	if not len(RBObjs):
3492	print '** ERROR - no rigid bodies defined **'
3493	return
3494	if len(RBObjs) == 1:
3495	print '** INFO - only one rigid body defined; nothing to copy to **'
3496	return
3497	Source = []
3498	sourceRB = {}
3499	for RBObj in RBObjs:
3500	Source.append(RBObj['RBname'])
3501	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3502	if dlg.ShowModal() == wx.ID_OK:
3503	sel = dlg.GetSelection()
3504	name = Source[sel]
3505	for item in ['Orig','Orient','ThermalMotion']:
3506	sourceRB.update({item:RBObjs[sel][item],})
3507	dlg.Destroy()
3508	if not sourceRB:
3509	return
3510	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3511	if dlg.ShowModal() == wx.ID_OK:
3512	sel = dlg.GetSelections()
3513	for x in sel:
3514	RBObjs[x].update(copy.copy(sourceRB))
3515	G2plt.PlotStructure(G2frame,data)
3516	wx.CallAfter(FillRigidBodyGrid(True))
3517
3518	def OnRBAssign(event):
3519
3520	G2frame.dataFrame.SetStatusText('')
3521	RBData = G2frame.PatternTree.GetItemPyData(
3522	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3523	rbNames = {}
3524	for rbVec in RBData['Vector']:
3525	if rbVec != 'AtInfo':
3526	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3527	for rbRes in RBData['Residue']:
3528	if rbRes != 'AtInfo':
3529	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3530	if not rbNames:
3531	print '** ERROR - no rigid bodies defined **'
3532	return
3533	general = data['General']
3534	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3535	cx,ct = general['AtomPtrs'][:2]
3536	atomData = data['Atoms']
3537	Indx = {}
3538	atInd = [-1,-1,-1]
3539	data['testRBObj'] = {}
3540
3541	def Draw():
3542
3543	def OnOk(event):
3544	rbType = data['testRBObj']['rbType']
3545	RBObjs = data['RBModels'].get(rbType,[])
3546	rbObj = data['testRBObj']['rbObj']
3547	rbId = rbObj['RBId']
3548	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3549	Ids = []
3550	dmax = 0.0
3551	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3552	for xyz in newXYZ:
3553	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3554	dmax = max(dmax,np.min(dist))
3555	id = np.argmin(dist)
3556	Ids.append(atomData[id][-1])
3557	atomData[id][cx:cx+3] = xyz
3558	if dmax > 1.0:
3559	print '** WARNING - some atoms not found or misidentified **'
3560	print '** check torsion angles & try again **'
3561	OkBtn.SetLabel('Not Ready')
3562	OkBtn.Enable(False)
3563	return
3564	rbObj['Ids'] = Ids
3565	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3566	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3567	RBObjs.append(rbObj)
3568	data['RBModels'][rbType] = RBObjs
3569	RBData[rbType][rbId]['useCount'] += 1
3570	del data['testRBObj']
3571	G2plt.PlotStructure(G2frame,data)
3572	FillRigidBodyGrid(True)
3573
3574	def OnCancel(event):
3575	del data['testRBObj']
3576	FillRigidBodyGrid(True)
3577
3578	def OnRBSel(event):
3579	selection = rbSel.GetValue()
3580	rbType,rbId = rbNames[selection]
3581	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3582	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3583	data['testRBObj']['rbType'] = rbType
3584	data['testRBObj']['rbData'] = RBData
3585	data['testRBObj']['Sizers'] = {}
3586	rbRef = RBData[rbType][rbId]['rbRef']
3587	data['testRBObj']['rbRef'] = rbRef
3588	refType = []
3589	refName = []
3590	for ref in rbRef[:3]:
3591	reftype = data['testRBObj']['rbAtTypes'][ref]
3592	refType.append(reftype)
3593	refName.append(reftype+' '+str(rbRef[0]))
3594	atNames,AtNames = fillAtNames(refType,atomData,ct)
3595	data['testRBObj']['atNames'] = atNames
3596	data['testRBObj']['AtNames'] = AtNames
3597	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3598	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3599	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3600	data['testRBObj']['torAtms'] = []
3601	for item in RBData[rbType][rbId].get('rbSeq',[]):
3602	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3603	data['testRBObj']['torAtms'].append([-1,-1,-1])
3604	Draw()
3605
3606	def fillAtNames(refType,atomData,ct):
3607	atNames = [{},{},{}]
3608	AtNames = {}
3609	for iatm,atom in enumerate(atomData):
3610	AtNames[atom[ct-1]] = iatm
3611	for i,reftype in enumerate(refType):
3612	if atom[ct] == reftype:
3613	atNames[i][atom[ct-1]] = iatm
3614	return atNames,AtNames
3615
3616	def OnAtOrigPick(event):
3617	Obj = event.GetEventObject()
3618	item = Indx[Obj.GetId()]
3619	atName = Obj.GetValue()
3620	rbType = data['testRBObj']['rbType']
3621	atInd[0] = atNames[item][atName]
3622	if 'Vector' in rbType:
3623	rbObj = data['testRBObj']['rbObj']
3624	rbId = rbObj['RBId']
3625	rbRef = data['testRBObj']['rbRef']
3626	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3627	nref = atNames[item][atName]
3628	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3629	Nxyz = np.array(atomData[nref][cx:cx+3])
3630	Orig = Nxyz-Oxyz
3631	data['testRBObj']['rbObj']['Orig'][0] = Orig
3632	else:
3633	Orig = atomData[atNames[item][atName]][cx:cx+3]
3634	data['testRBObj']['rbObj']['Orig'][0] = Orig
3635	for x,item in zip(Orig,Xsizers):
3636	item.SetLabel('%10.5f'%(x))
3637	G2plt.PlotStructure(G2frame,data)
3638
3639	def OnAtQPick(event):
3640	Obj = event.GetEventObject()
3641	item = Indx[Obj.GetId()]
3642	atName = Obj.GetValue()
3643	atInd[item] = atNames[item][atName]
3644	if any([x<0 for x in atInd]):
3645	return
3646	OkBtn.SetLabel('OK')
3647	OkBtn.Enable(True)
3648	rbType = data['testRBObj']['rbType']
3649	rbObj = data['testRBObj']['rbObj']
3650	rbId = rbObj['RBId']
3651	rbRef = data['testRBObj']['rbRef']
3652	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3653	rbOrig = rbXYZ[rbRef[0]]
3654	VAR = rbXYZ[rbRef[1]]-rbOrig
3655	VBR = rbXYZ[rbRef[2]]-rbOrig
3656	if rbType == 'Vector':
3657	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3658	else:
3659	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3660	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3661	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3662	VCC = np.cross(VAR,VAC)
3663	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3664	VAR = G2mth.prodQVQ(QuatA,VAR)
3665	VBR = G2mth.prodQVQ(QuatA,VBR)
3666	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3667	QuatC = G2mth.prodQQ(QuatB,QuatA)
3668	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3669	for x,item in zip(QuatC,Osizers):
3670	item.SetLabel('%10.4f'%(x))
3671	if rbType == 'Vector':
3672	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3673	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3674	Orig = Nxyz-Oxyz
3675	data['testRBObj']['rbObj']['Orig'][0] = Orig
3676	for x,item in zip(Orig,Xsizers):
3677	item.SetLabel('%10.5f'%(x))
3678	G2plt.PlotStructure(G2frame,data)
3679
3680	def OnTorAngle(event):
3681	OkBtn.SetLabel('OK')
3682	OkBtn.Enable(True)
3683	Obj = event.GetEventObject()
3684	[tor,torSlide] = Indx[Obj.GetId()]
3685	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3686	try:
3687	value = float(Obj.GetValue())
3688	except ValueError:
3689	value = Tors[0]
3690	Tors[0] = value
3691	Obj.SetValue('%8.3f'%(value))
3692	torSlide.SetValue(int(value*10))
3693	G2plt.PlotStructure(G2frame,data)
3694
3695	def OnTorSlide(event):
3696	OkBtn.SetLabel('OK')
3697	OkBtn.Enable(True)
3698	Obj = event.GetEventObject()
3699	tor,ang = Indx[Obj.GetId()]
3700	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3701	val = float(Obj.GetValue())/10.
3702	Tors[0] = val
3703	ang.SetValue('%8.3f'%(val))
3704	G2plt.PlotStructure(G2frame,data)
3705
3706	if len(data['testRBObj']):
3707	G2plt.PlotStructure(G2frame,data)
3708
3709	RigidBodies.DestroyChildren()
3710	mainSizer = wx.BoxSizer(wx.VERTICAL)
3711	mainSizer.Add((5,5),0)
3712	if data['testRBObj']:
3713	Xsizers = []
3714	Osizers = []
3715	rbObj = data['testRBObj']['rbObj']
3716	rbName = rbObj['RBname']
3717	rbId = rbObj['RBId']
3718	Orig = rbObj['Orig'][0]
3719	Orien = rbObj['Orient'][0]
3720	rbRef = data['testRBObj']['rbRef']
3721	Torsions = rbObj['Torsions']
3722	refName = []
3723	for ref in rbRef:
3724	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3725	atNames = data['testRBObj']['atNames']
3726	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3727	0,wx.ALIGN_CENTER_VERTICAL)
3728	mainSizer.Add((5,5),0)
3729	OriSizer = wx.FlexGridSizer(1,5,5,5)
3730	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,wx.ALIGN_CENTER_VERTICAL)
3731	for ix,x in enumerate(Orig):
3732	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3733	OriSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3734	Xsizers.append(origX)
3735	OriSizer.Add((5,0),)
3736	if len(atomData):
3737	choice = atNames[0].keys()
3738	choice.sort()
3739	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3740	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,wx.ALIGN_CENTER_VERTICAL)
3741	for ix,x in enumerate(Orien):
3742	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3743	OriSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3744	Osizers.append(orien)
3745	data['testRBObj']['Sizers']['Osizers'] = Osizers
3746	mainSizer.Add(OriSizer)
3747	mainSizer.Add((5,5),0)
3748	RefSizer = wx.FlexGridSizer(1,7,5,5)
3749	if len(atomData):
3750	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,wx.ALIGN_CENTER_VERTICAL)
3751	for i in [0,1,2]:
3752	choice = ['',]+atNames[i].keys()
3753	choice.sort()
3754	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,wx.ALIGN_CENTER_VERTICAL)
3755	atPick = wx.ComboBox(RigidBodies,-1,value='',
3756	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3757	if i:
3758	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3759	else:
3760	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3761	Indx[atPick.GetId()] = i
3762	RefSizer.Add(atPick,0,wx.ALIGN_CENTER_VERTICAL)
3763	mainSizer.Add(RefSizer)
3764	mainSizer.Add((5,5),0)
3765	if Torsions:
3766	AtNames = data['testRBObj']['AtNames']
3767	rbAtTypes = data['testRBObj']['rbAtTypes']
3768	rbSeq = RBData['Residue'][rbId]['rbSeq']
3769	TorSizer = wx.FlexGridSizer(1,4)
3770	TorSizer.AddGrowableCol(1,1)
3771	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3772	torName = ''
3773	for item in [seq[0],seq[1],seq[3][0]]:
3774	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3775	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,wx.ALIGN_CENTER_VERTICAL)
3776	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3777	torSlide.SetRange(0,3600)
3778	torSlide.SetValue(int(torsion[0]*10.))
3779	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3780	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3781	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,wx.ALIGN_CENTER_VERTICAL)
3782	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
3783	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
3784	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
3785	Indx[torSlide.GetId()] = [t,ang]
3786	Indx[ang.GetId()] = [t,torSlide]
3787	TorSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
3788	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
3789	else:
3790	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,wx.ALIGN_CENTER_VERTICAL)
3791	else:
3792	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,wx.ALIGN_CENTER_VERTICAL)
3793	mainSizer.Add((5,5),0)
3794	topSizer = wx.BoxSizer(wx.HORIZONTAL)
3795	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,wx.ALIGN_CENTER_VERTICAL)
3796	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
3797	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3798	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
3799	topSizer.Add((5,5),0)
3800	topSizer.Add(rbSel,0,wx.ALIGN_CENTER_VERTICAL)
3801	mainSizer.Add(topSizer)
3802
3803	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
3804	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
3805	OkBtn.Enable(False)
3806	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
3807	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
3808	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
3809	btnSizer.Add((20,20),1)
3810	btnSizer.Add(OkBtn)
3811	btnSizer.Add(CancelBtn)
3812	btnSizer.Add((20,20),1)
3813	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
3814	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3815	Draw()
3816
3817	def OnAutoFindResRB(event):
3818	RBData = G2frame.PatternTree.GetItemPyData(
3819	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3820	rbKeys = RBData['Residue'].keys()
3821	rbKeys.remove('AtInfo')
3822	if not len(rbKeys):
3823	print '** ERROR - no residue rigid bodies are defined **'
3824	return
3825	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
3826	RBIds = dict(zip(RBNames,rbKeys))
3827	general = data['General']
3828	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3829	Atoms = data['Atoms']
3830	AtLookUp = G2mth.FillAtomLookUp(Atoms)
3831	if 'macro' not in general['Type']:
3832	print '** ERROR - this phase is not a macromolecule **'
3833	return
3834	if not len(Atoms):
3835	print '** ERROR - this phase has no atoms **'
3836	return
3837	RBObjs = []
3838	cx,ct = general['AtomPtrs'][:2]
3839	iatm = 0
3840	wx.BeginBusyCursor()
3841	try:
3842	while iatm < len(Atoms):
3843	atom = Atoms[iatm]
3844	res = atom[1].strip()
3845	numChain = ' %s %s'%(atom[0],atom[2])
3846	if res not in RBIds or atom[ct-1] == 'OXT':
3847	iatm += 1
3848	continue #skip for OXT, water molecules, etc.
3849	rbRes = RBData['Residue'][RBIds[res]]
3850	rbRef = rbRes['rbRef']
3851	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
3852	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
3853	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
3854	rbAtoms = []
3855	rbIds = []
3856	for iratm in range(len(rbRes['atNames'])):
3857	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
3858	rbIds.append(Atoms[iatm][20])
3859	iatm += 1 #puts this at beginning of next residue?
3860	Orig = rbAtoms[rbRef[0]]
3861	rbObj['RBId'] = RBIds[res]
3862	rbObj['Ids'] = rbIds
3863	rbObj['Orig'] = [Orig,False]
3864	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
3865	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
3866	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
3867	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
3868	VCC = np.cross(VAR,VAC)
3869	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3870	VAR = G2mth.prodQVQ(QuatA,VAR)
3871	VBR = G2mth.prodQVQ(QuatA,VBR)
3872	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3873	QuatC = G2mth.prodQQ(QuatB,QuatA)
3874	rbObj['Orient'] = [QuatC,' ']
3875	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3876	SXYZ = []
3877	TXYZ = []
3878	rbObj['Torsions'] = []
3879	for i,xyz in enumerate(rbRes['rbXYZ']):
3880	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
3881	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
3882	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
3883	VBR = SXYZ[Oatm]-SXYZ[Patm]
3884	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
3885	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
3886	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
3887	ang = 180.*D/np.pi
3888	rbObj['Torsions'].append([ang,False])
3889	for ride in Riders:
3890	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
3891	rbRes['useCount'] += 1
3892	RBObjs.append(rbObj)
3893	data['RBModels']['Residue'] = RBObjs
3894	for RBObj in RBObjs:
3895	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3896	for i,id in enumerate(RBObj['Ids']):
3897	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3898	finally:
3899	wx.EndBusyCursor()
3900	wx.CallAfter(FillRigidBodyGrid,True)
3901
3902	def OnRBRemoveAll(event):
3903	data['RBModels']['Residue'] = []
3904	data['RBModels']['Vector'] = []
3905	RBData = G2frame.PatternTree.GetItemPyData(
3906	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3907	for RBType in ['Vector','Residue']:
3908	for rbId in RBData[RBType]:
3909	RBData[RBType][rbId]['useCount'] = 0
3910	FillRigidBodyGrid(True)
3911
3912	def OnGlobalResRBTherm(event):
3913	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3914	RBObjs = data['RBModels']['Residue']
3915	names = ['None','Uiso','T','TL','TLS']
3916	cia = data['General']['AtomPtrs'][3]
3917	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
3918	if dlg.ShowModal() == wx.ID_OK:
3919	sel = dlg.GetSelection()
3920	parm = names[sel]
3921	Ttype = 'A'
3922	if parm == 'Uiso':
3923	Ttype = 'I'
3924	for rbObj in RBObjs:
3925	rbObj['ThermalMotion'][0] = parm
3926	if parm != 'None':
3927	for i,id in enumerate(rbObj['Ids']):
3928	data['Atoms'][AtLookUp[id]][cia] = Ttype
3929	dlg.Destroy()
3930	wx.CallAfter(FillRigidBodyGrid,True)
3931
3932	def OnGlobalResRBRef(event):
3933	RBObjs = data['RBModels']['Residue']
3934	names = ['Origin','Orient. angle','Full Orient.']
3935	nTor = 0
3936	for rbObj in RBObjs:
3937	nTor = max(nTor,len(rbObj['Torsions']))
3938	names += ['Torsion '+str(i) for i in range(nTor)]
3939	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
3940	names += ['Uiso',]
3941	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
3942	names += ['Tii','Tij','Lii','Lij','Sij']
3943	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
3944	names += ['Tii','Tij','Lii','Lij']
3945	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
3946	names += ['Tii','Tij']
3947
3948	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
3949	if dlg.ShowModal() == wx.ID_OK:
3950	sel = dlg.GetSelections()
3951	parms = []
3952	for x in sel:
3953	parms.append(names[x])
3954	wx.BeginBusyCursor()
3955	try:
3956	for rbObj in RBObjs:
3957	if 'Origin' in parms:
3958	rbObj['Orig'][1] = True
3959	else:
3960	rbObj['Orig'][1] = False
3961	if 'Full Orient.' in parms:
3962	rbObj['Orient'][1] = 'AV'
3963	elif 'Orient. angle' in parms:
3964	rbObj['Orient'][1] = 'A'
3965	else:
3966	rbObj['Orient'][1] = ' '
3967	for i in range(len(rbObj['Torsions'])):
3968	if 'Torsion '+str(i) in parms:
3969	rbObj['Torsions'][i][1] = True
3970	else:
3971	rbObj['Torsions'][i][1] = False
3972	if rbObj['ThermalMotion'][0] == 'Uiso':
3973	if 'Uiso' in parms:
3974	rbObj['ThermalMotion'][2][0] = True
3975	else:
3976	rbObj['ThermalMotion'][2][0] = False
3977	elif 'T' in rbObj['ThermalMotion'][0]:
3978	if 'Tii' in parms:
3979	rbObj['ThermalMotion'][2][0:2] = [True,True,True]
3980	else:
3981	rbObj['ThermalMotion'][2][0:2] = [False,False,False]
3982	if 'Tij' in parms:
3983	rbObj['ThermalMotion'][2][3:6] = [True,True,True]
3984	else:
3985	rbObj['ThermalMotion'][2][3:6] = [False,False,False]
3986	elif 'L' in rbObj['ThermalMotion'][0]:
3987	if 'Lii' in parms:
3988	rbObj['ThermalMotion'][2][6:9] = [True,True,True]
3989	else:
3990	rbObj['ThermalMotion'][2][6:9] = [False,False,False]
3991	if 'Lij' in parms:
3992	rbObj['ThermalMotion'][2][9:12] = [True,True,True]
3993	else:
3994	rbObj['ThermalMotion'][2][9:12] = [False,False,False]
3995	elif 'S' in rbObj['ThermalMotion'][0]:
3996	if 'Sij' in parms:
3997	rbObj['ThermalMotion'][2][12:20] = [True,True,True,True,True,True,True,True]
3998	else:
3999	rbObj['ThermalMotion'][2][12:20] = [False,False,False,False,False,False,False,False]
4000	finally:
4001	wx.EndBusyCursor()
4002	FillRigidBodyGrid()
4003
4004	################################################################################
4005	##### MC/SA routines
4006	################################################################################
4007
4008	def UpdateMCSA(Scroll=0):
4009	Indx = {}
4010
4011	def OnPosRef(event):
4012	Obj = event.GetEventObject()
4013	model,item,ix = Indx[Obj.GetId()]
4014	model[item][1][ix] = Obj.GetValue()
4015
4016	def OnPosVal(event):
4017	Obj = event.GetEventObject()
4018	model,item,ix = Indx[Obj.GetId()]
4019	try:
4020	model[item][0][ix] = float(Obj.GetValue())
4021	except ValueError:
4022	pass
4023	Obj.SetValue("%.4f"%(model[item][0][ix]))
4024	G2plt.PlotStructure(G2frame,data)
4025
4026	def OnPosRange(event):
4027	Obj = event.GetEventObject()
4028	model,item,ix = Indx[Obj.GetId()]
4029	Range = Obj.GetValue().split()
4030	try:
4031	rmin,rmax = [float(Range[i]) for i in range(2)]
4032	if rmin >= rmax:
4033	raise ValueError
4034	except (ValueError,IndexError):
4035	rmin,rmax = model[item][2][ix]
4036	model[item][2][ix] = [rmin,rmax]
4037	Obj.SetValue('%.3f %.3f'%(rmin,rmax))
4038
4039	def atomSizer(model):
4040
4041	atomsizer = wx.FlexGridSizer(1,7,5,5)
4042	atomsizer.Add(wx.StaticText(MCSA,-1,' Atom: '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4043	for ix,item in enumerate(['x','y','z']):
4044	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4045	posRef.SetValue(model['Pos'][1][ix])
4046	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4047	Indx[posRef.GetId()] = [model,'Pos',ix]
4048	atomsizer.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4049	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4050	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4051	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4052	Indx[posVal.GetId()] = [model,'Pos',ix]
4053	atomsizer.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4054	atomsizer.Add((5,5),0)
4055	for ix,item in enumerate(['x','y','z']):
4056	atomsizer.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4057	rmin,rmax = model['Pos'][2][ix]
4058	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4059	Indx[posRange.GetId()] = [model,'Pos',ix]
4060	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4061	posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4062	atomsizer.Add(posRange,0,wx.ALIGN_CENTER_VERTICAL)
4063	return atomsizer
4064
4065	def rbSizer(model):
4066
4067	def OnOrVar(event):
4068	Obj = event.GetEventObject()
4069	model = Indx[Obj.GetId()]
4070	model['Ovar'] = Obj.GetValue()
4071
4072	def OnOriVal(event):
4073	Obj = event.GetEventObject()
4074	model,ix,ObjA,ObjV = Indx[Obj.GetId()]
4075	A = model['Ori'][0][0]
4076	V = model['Ori'][0][1:]
4077	if ix:
4078	Anew = A
4079	Vec = ObjV.GetValue().split()
4080	try:
4081	Vnew = [float(Vec[i]) for i in range(3)]
4082	except ValueError:
4083	Vnew = V
4084	else:
4085	Vnew = V
4086	try:
4087	Anew = float(ObjA.GetValue())
4088	if not Anew: #==0.0!
4089	Anew = 360.
4090	except ValueError:
4091	Anew = A
4092	Q = G2mth.AVdeg2Q(Anew,Vnew)
4093	A,V = G2mth.Q2AVdeg(Q)
4094	model['Ori'][0][0] = A
4095	model['Ori'][0][1:] = V
4096	if ix:
4097	ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2]))
4098	else:
4099	ObjA.SetValue('%.5f'%(A))
4100	ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2]))
4101	G2plt.PlotStructure(G2frame,data)
4102	# UpdateMCSA()
4103
4104	def OnMolCent(event):
4105	Obj = event.GetEventObject()
4106	model = Indx[Obj.GetId()]
4107	model['MolCent'][1] = Obj.GetValue()
4108	if model['MolCent'][1]:
4109	G2mth.SetMolCent(model,RBData)
4110	G2plt.PlotStructure(G2frame,data)
4111
4112	rbsizer = wx.BoxSizer(wx.VERTICAL)
4113	rbsizer1 = wx.FlexGridSizer(1,7,5,