Context Navigation

source: trunk/GSASIIphsGUI.py @ 1011

Last change on this file since 1011 was 1011, checked in by vondreele, 10 years ago
fix updates of atom parms when RB parms are modified. Edit Pawley tutorials
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 244.3 KB

Line
1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2013-07-25 23:04:52 +0000 (Thu, 25 Jul 2013) $
5	# $Author: vondreele $
6	# $Revision: 1011 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1011 2013-07-25 23:04:52Z 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 wx
24	import wx.grid as wg
25	import wx.lib.gridmovers as wgmove
26	import wx.wizard as wz
27	import matplotlib as mpl
28	import math
29	import copy
30	import time
31	import sys
32	import random as ran
33	import cPickle
34	import GSASIIpath
35	GSASIIpath.SetVersionNumber("$Revision: 1011 $")
36	import GSASIIlattice as G2lat
37	import GSASIIspc as G2spc
38	import GSASIIElem as G2elem
39	import GSASIIElemGUI as G2elemGUI
40	import GSASIIddataGUI as G2ddG
41	import GSASIIplot as G2plt
42	import GSASIIgrid as G2gd
43	import GSASIIIO as G2IO
44	import GSASIIstrMain as G2stMn
45	import GSASIImath as G2mth
46	import GSASIIpwd as G2pwd
47	import numpy as np
48	import numpy.linalg as nl
49	import numpy.ma as ma
50
51	VERY_LIGHT_GREY = wx.Colour(235,235,235)
52	WHITE = wx.Colour(255,255,255)
53	BLACK = wx.Colour(0,0,0)
54	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
55	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
56	# trig functions in degrees
57	sind = lambda x: np.sin(x*np.pi/180.)
58	tand = lambda x: np.tan(x*np.pi/180.)
59	cosd = lambda x: np.cos(x*np.pi/180.)
60	asind = lambda x: 180.*np.arcsin(x)/np.pi
61	acosd = lambda x: 180.*np.arccos(x)/np.pi
62
63	def SetPhaseWindow(mainFrame,phasePage,mainSizer):
64	phasePage.SetSizer(mainSizer)
65	Size = mainSizer.GetMinSize()
66	Size[0] += 40
67	Size[1] = max(Size[1],430) + 35
68	phasePage.SetSize(Size)
69	phasePage.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
70	mainFrame.setSizePosLeft(Size)
71
72	def UpdatePhaseData(G2frame,Item,data,oldPage):
73	'''Create the data display window contents when a phase is clicked on
74	in the man (data tree) window.
75	Called only from :meth:`GSASIIgrid.MovePatternTreeToGrid`,
76	which in turn is called from :meth:`GSASII.GSASII.OnPatternTreeSelChanged`
77	when a tree item is selected.
78
79	:param wx.frame G2frame: the main GSAS-II frame object
80	:param wx.TreeItemId Item: the tree item that was selected
81	:param dict data: all the information on the phase in a dictionary
82	:param int oldPage: This sets a tab to select when moving
83	from one phase to another, in which case the same tab is selected
84	to display first. This is set only when the previous data tree
85	selection is a phase, if not the value is None. The default action
86	is to bring up the General tab.
87
88	'''
89
90	#patch
91	if 'RBModels' not in data:
92	data['RBModels'] = {}
93	if 'MCSA' not in data:
94	data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[0.3,3.],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
95	if isinstance(data['MCSA']['Results'],dict):
96	data['MCSA']['Results'] = []
97	#end patch
98
99	global rbAtmDict
100	rbAtmDict = {}
101	if G2frame.dataDisplay:
102	G2frame.dataDisplay.Destroy()
103	PhaseName = G2frame.PatternTree.GetItemText(Item)
104	G2gd.SetDataMenuBar(G2frame)
105	G2frame.dataFrame.SetLabel('Phase Data for '+PhaseName)
106	G2frame.dataFrame.CreateStatusBar()
107	G2frame.dataDisplay = G2gd.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize())
108	G2frame.dataDisplay.gridList = [] # list of all grids in notebook
109
110	def SetupGeneral():
111	generalData = data['General']
112	atomData = data['Atoms']
113	generalData['AtomTypes'] = []
114	generalData['Isotopes'] = {}
115	# various patches
116	if 'Isotope' not in generalData:
117	generalData['Isotope'] = {}
118	if 'Data plot type' not in generalData:
119	generalData['Data plot type'] = 'Mustrain'
120	if 'POhkl' not in generalData:
121	generalData['POhkl'] = [0,0,1]
122	if 'Map' not in generalData:
123	generalData['Map'] = mapDefault
124	if 'Flip' not in generalData:
125	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
126	'k-factor':0.1,'k-Max':20.}
127	if 'doPawley' not in generalData:
128	generalData['doPawley'] = False
129	if 'Pawley dmin' not in generalData:
130	generalData['Pawley dmin'] = 1.0
131	if 'Pawley neg wt' not in generalData:
132	generalData['Pawley neg wt'] = 0.0
133	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
134	'MCSA controls' not in generalData:
135	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
136	'dmin':2.0,'Algorithm':'fast','Jump coeff':[0.95,0.5],'boltzmann':1.0,
137	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[]}
138	# end of patches
139	generalData['NoAtoms'] = {}
140	generalData['BondRadii'] = []
141	generalData['AngleRadii'] = []
142	generalData['vdWRadii'] = []
143	generalData['AtomMass'] = []
144	generalData['Color'] = []
145	generalData['Mydir'] = G2frame.dirname
146	cx,ct,cs,cia = [3,1,7,9]
147	if generalData['Type'] =='macromolecular':
148	cx,ct,cs,cia = [6,4,10,12]
149	generalData['AtomPtrs'] = [cx,ct,cs,cia]
150	for atom in atomData:
151	atom[ct] = atom[ct].lower().capitalize() #force to standard form
152	if generalData['AtomTypes'].count(atom[ct]):
153	generalData['NoAtoms'][atom[ct]] += atom[cs-1]*float(atom[cs+1])
154	elif atom[ct] != 'UNK':
155	Info = G2elem.GetAtomInfo(atom[ct])
156	generalData['AtomTypes'].append(atom[ct])
157	generalData['Z'] = Info['Z']
158	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
159	generalData['BondRadii'].append(Info['Drad'])
160	generalData['AngleRadii'].append(Info['Arad'])
161	generalData['vdWRadii'].append(Info['Vdrad'])
162	if atom[ct] in generalData['Isotope']:
163	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]][0])
164	else:
165	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
166	generalData['AtomMass'].append(Info['Mass'])
167	generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
168	generalData['Color'].append(Info['Color'])
169	F000X = 0.
170	F000N = 0.
171	for i,elem in enumerate(generalData['AtomTypes']):
172	F000X += generalData['NoAtoms'][elem]*generalData['Z']
173	isotope = generalData['Isotope'][elem]
174	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope][1]
175	generalData['F000X'] = F000X
176	generalData['F000N'] = F000N
177
178
179	################################################################################
180	##### General phase routines
181	################################################################################
182
183	def UpdateGeneral():
184	'''Draw the controls for the General phase data subpage
185	'''
186
187	""" This is the default dictionary structure for phase data
188	(taken from GSASII.py)
189	'General':{
190	'Name':PhaseName
191	'Type':'nuclear'
192	'SGData':SGData
193	'Cell':[False,10.,10.,10.,90.,90.,90,1000.]
194	'AtomPtrs':[]
195	'Histogram list':['',]
196	'Pawley dmin':1.0,
197	'Pawley neg wt':0.0}
198	'Atoms':[]
199	'Drawing':{}
200	"""
201	# UpdateGeneral execution starts here
202	phaseTypes = ['nuclear','modulated','magnetic','macromolecular']
203	SetupGeneral()
204	generalData = data['General']
205	Map = generalData['Map']
206	Flip = generalData['Flip']
207	MCSA = generalData['MCSA controls']
208	PWDR = any(['PWDR' in item for item in data['Histograms'].keys()])
209	# UpdateGeneral execution continues below
210
211	def NameSizer():
212	def OnPhaseName(event):
213	oldName = generalData['Name']
214	generalData['Name'] = NameTxt.GetValue()
215	G2frame.G2plotNB.Rename(oldName,generalData['Name'])
216	G2frame.dataFrame.SetLabel('Phase Data for '+generalData['Name'])
217	G2frame.PatternTree.SetItemText(Item,generalData['Name'])
218	#Hmm, need to change phase name key in Reflection Lists for each histogram
219
220	def OnPhaseType(event):
221	if not generalData['AtomTypes']: #can change only if no atoms!
222	generalData['Type'] = TypeTxt.GetValue()
223	wx.CallAfter(UpdateGeneral)
224	else:
225	TypeTxt.SetValue(generalData['Type'])
226
227	def OnSpaceGroup(event):
228	SpcGp = SGTxt.GetValue()
229	SGErr,SGData = G2spc.SpcGroup(SpcGp)
230	# try a lookup on the user-supplied name
231	if SGErr:
232	SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
233	if SpGrpNorm:
234	E,SGData = G2spc.SpcGroup(SpGrpNorm)
235	if not E: SGErr = False
236	if SGErr:
237	text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
238	SGTxt.SetValue(generalData['SGData']['SpGrp'])
239	msg = 'Space Group Error'
240	Style = wx.ICON_EXCLAMATION
241	else:
242	text = G2spc.SGPrint(SGData)
243	generalData['SGData'] = SGData
244	msg = 'Space Group Information'
245	Style = wx.ICON_INFORMATION
246	Text = ''
247	for line in text:
248	Text += line+'\n'
249	wx.MessageBox(Text,caption=msg,style=Style)
250	# General.DestroyChildren() #needed to clear away bad cellSizer, etc.
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	MCSA['Data source'] = refList.GetValue()
657
658	def OnDmin(event):
659	try:
660	val = float(dmin.GetValue())
661	if 1.0 <= val < 5.0:
662	MCSA['dmin'] = val
663	except ValueError:
664	pass
665	dmin.SetValue("%.3f"%(MCSA['dmin'])) #reset in case of error
666
667	def OnCycles(event):
668	MCSA['Cycles'] = int(cycles.GetValue())
669
670	def OnAlist(event):
671	MCSA['Algorithm'] = Alist.GetValue()
672	wx.CallAfter(UpdateGeneral)
673
674	def OnSlope(event):
675	try:
676	val = float(slope.GetValue())
677	if .25 <= val < 1.0:
678	MCSA['log slope'] = val
679	except ValueError:
680	pass
681	slope.SetValue("%.3f"%(MCSA['log slope'])) #reset in case of error
682
683	def OnAjump(event):
684	Obj = event.GetEventObject()
685	name,ind = Indx[Obj.GetId()]
686	try:
687	val = float(Obj.GetValue())
688	if .0 <= val <= 1.0:
689	MCSA[name][ind] = val
690	except ValueError:
691	pass
692	Obj.SetValue("%.3f"%(MCSA[name][ind]))
693
694	def OnRanStart(event):
695	MCSA['ranStart'] = ranStart.GetValue()
696
697	def OnAnneal(event):
698	Obj = event.GetEventObject()
699	ind,fmt = Indx[Obj.GetId()]
700	if ind == 2: #No. trials
701	try:
702	val = int(Obj.GetValue())
703	if 1 <= val:
704	MCSA['Annealing'][ind] = val
705	except ValueError:
706	Obj.SetValue(fmt%(MCSA['Annealing'][ind]))
707	else:
708	try:
709	val = float(Obj.GetValue())
710	if .0 <= val:
711	MCSA['Annealing'][ind] = val
712	Obj.SetValue(fmt%(MCSA['Annealing'][ind]))
713	except ValueError:
714	MCSA['Annealing'][ind] = None
715	Obj.SetValue(str(MCSA['Annealing'][ind]))
716
717	refList = []
718	if len(data['Pawley ref']):
719	refList = ['Pawley reflections']
720	for item in data['Histograms'].keys():
721	if 'HKLF' in item or 'PWDR' in item:
722	refList.append(item)
723	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
724	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
725	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
726	refList = wx.ComboBox(General,-1,value=MCSA['Data source'],choices=refList,
727	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
728	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
729	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
730	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,wx.ALIGN_CENTER_VERTICAL)
731	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSA['dmin']),style=wx.TE_PROCESS_ENTER)
732	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
733	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
734	lineSizer.Add(dmin,0,wx.ALIGN_CENTER_VERTICAL)
735	mcsaSizer.Add(lineSizer)
736	mcsaSizer.Add((5,5),)
737	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
738	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,wx.ALIGN_CENTER_VERTICAL)
739	Cchoice = ['1','2','3','6','10','20','30','60','100']
740	cycles = wx.ComboBox(General,-1,value=str(MCSA.get('Cycles',1)),choices=Cchoice,
741	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
742	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
743	line2Sizer.Add(cycles,0,wx.ALIGN_CENTER_VERTICAL)
744	line2Sizer.Add((5,0),)
745	ranStart = wx.CheckBox(General,-1,label=' Random start? (ignored if Start temp = None)')
746	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
747	ranStart.SetValue(MCSA.get('ranStart',True))
748	line2Sizer.Add(ranStart,0,wx.ALIGN_CENTER_VERTICAL)
749	mcsaSizer.Add(line2Sizer)
750	mcsaSizer.Add((5,5),)
751	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
752	Achoice = ['log','fast'] #these work
753	# Achoice = ['log','fast','cauchy','boltzmann','Tremayne']
754	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
755	Alist = wx.ComboBox(General,-1,value=MCSA['Algorithm'],choices=Achoice,
756	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
757	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
758	line3Sizer.Add(Alist,0,wx.ALIGN_CENTER_VERTICAL)
759	if MCSA['Algorithm'] in ['Tremayne','fast','boltzmann','cauchy']:
760	Names = [' A-jump: ',' B-jump: ']
761	parms = 'Jump coeff'
762	if MCSA['Algorithm'] in ['boltzmann','cauchy']:
763	Names = [' A-jump: ']
764	elif 'fast' in MCSA['Algorithm']:
765	Names = [' quench: ',' m-factor: ',' n-factor: ']
766	parms = 'fast parms'
767	for i,name in enumerate(Names):
768	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
769	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSA[parms][i]),style=wx.TE_PROCESS_ENTER)
770	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
771	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
772	Indx[Ajump.GetId()] = [parms,i]
773	line3Sizer.Add(Ajump,0,wx.ALIGN_CENTER_VERTICAL)
774	elif 'log' in MCSA['Algorithm']:
775	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,wx.ALIGN_CENTER_VERTICAL)
776	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSA['log slope']),style=wx.TE_PROCESS_ENTER)
777	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
778	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
779	line3Sizer.Add(slope,0,wx.ALIGN_CENTER_VERTICAL)
780	mcsaSizer.Add(line3Sizer)
781	mcsaSizer.Add((5,5),)
782	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
783	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
784	names = [' Start temp: ',' Final temp: ',' No. trials: ']
785	fmts = ['%.1f','%.5f','%d']
786	for i,[name,fmt] in enumerate(zip(names,fmts)):
787	if MCSA['Annealing'][i]:
788	text = fmt%(MCSA['Annealing'][i])
789	else:
790	text = 'None'
791	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
792	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
793	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
794	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
795	Indx[anneal.GetId()] = [i,fmt]
796	line3Sizer.Add(anneal,0,wx.ALIGN_CENTER_VERTICAL)
797	mcsaSizer.Add(line3Sizer)
798	return mcsaSizer
799
800	# UpdateGeneral execution continues here
801	if General.GetSizer():
802	General.GetSizer().Clear(True)
803	mainSizer = wx.BoxSizer(wx.VERTICAL)
804	mainSizer.Add((5,5),0)
805	mainSizer.Add(NameSizer(),0)
806	mainSizer.Add((5,5),0)
807	mainSizer.Add(CellSizer(),0)
808	mainSizer.Add((5,5),0)
809
810	Indx = {}
811	denSizer = None
812	if len(generalData['AtomTypes']):
813	denSizer = DenSizer()
814	mainSizer.Add(denSizer[0])
815	mainSizer.Add((5,5),0)
816	mainSizer.Add(ElemSizer())
817	G2gd.HorizontalLine(mainSizer,General)
818
819	mainSizer.Add(PawleySizer())
820	G2gd.HorizontalLine(mainSizer,General)
821
822	mainSizer.Add(MapSizer())
823	G2gd.HorizontalLine(mainSizer,General)
824
825	mainSizer.Add(FlipSizer())
826	G2gd.HorizontalLine(mainSizer,General)
827
828	mainSizer.Add(MCSASizer())
829	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
830	G2frame.dataFrame.SetStatusText('')
831
832	################################################################################
833	##### Atom routines
834	################################################################################
835
836	def FillAtomsGrid(Atoms):
837	'''Display the contents of the Atoms tab
838	'''
839	def RefreshAtomGrid(event):
840
841	r,c = event.GetRow(),event.GetCol()
842	if r < 0 and c < 0:
843	for row in range(Atoms.GetNumberRows()):
844	Atoms.SelectRow(row,True)
845	if r < 0: #double click on col label! Change all atoms!
846	sel = -1
847	noSkip = True
848	if Atoms.GetColLabelValue(c) == 'refine':
849	Type = generalData['Type']
850	if Type in ['nuclear','macromolecular']:
851	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
852	elif Type in ['magnetic',]:
853	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
854	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
855	if dlg.ShowModal() == wx.ID_OK:
856	sel = dlg.GetSelections()
857	parms = ''
858	for x in sel:
859	parms += choice[x][0]
860	dlg.Destroy()
861	elif Atoms.GetColLabelValue(c) == 'I/A':
862	choice = ['Isotropic','Anisotropic']
863	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
864	if dlg.ShowModal() == wx.ID_OK:
865	sel = dlg.GetSelection()
866	parms = choice[sel][0]
867	dlg.Destroy()
868	elif Atoms.GetColLabelValue(c) == 'Type':
869	choice = generalData['AtomTypes']
870	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
871	if dlg.ShowModal() == wx.ID_OK:
872	sel = dlg.GetSelection()
873	parms = choice[sel]
874	noSkip = False
875	Atoms.ClearSelection()
876	for row in range(Atoms.GetNumberRows()):
877	if parms == atomData[row][c]:
878	Atoms.SelectRow(row,True)
879	dlg.Destroy()
880	SetupGeneral()
881	elif Atoms.GetColLabelValue(c) == 'residue':
882	choice = []
883	for r in range(Atoms.GetNumberRows()):
884	if str(atomData[r][c]) not in choice:
885	choice.append(str(atomData[r][c]))
886	choice.sort()
887	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
888	if dlg.ShowModal() == wx.ID_OK:
889	sel = dlg.GetSelection()
890	parms = choice[sel]
891	noSkip = False
892	Atoms.ClearSelection()
893	for row in range(Atoms.GetNumberRows()):
894	if parms == atomData[row][c]:
895	Atoms.SelectRow(row,True)
896	dlg.Destroy()
897	elif Atoms.GetColLabelValue(c) == 'res no':
898	choice = []
899	for r in range(Atoms.GetNumberRows()):
900	if str(atomData[r][c]) not in choice:
901	choice.append(str(atomData[r][c]))
902	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
903	if dlg.ShowModal() == wx.ID_OK:
904	sel = dlg.GetSelection()
905	parms = choice[sel]
906	noSkip = False
907	Atoms.ClearSelection()
908	for row in range(Atoms.GetNumberRows()):
909	if int(parms) == atomData[row][c]:
910	Atoms.SelectRow(row,True)
911	dlg.Destroy()
912	elif Atoms.GetColLabelValue(c) == 'chain':
913	choice = []
914	for r in range(Atoms.GetNumberRows()):
915	if atomData[r][c] not in choice:
916	choice.append(atomData[r][c])
917	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
918	if dlg.ShowModal() == wx.ID_OK:
919	sel = dlg.GetSelection()
920	parms = choice[sel]
921	noSkip = False
922	Atoms.ClearSelection()
923	for row in range(Atoms.GetNumberRows()):
924	if parms == atomData[row][c]:
925	Atoms.SelectRow(row,True)
926	dlg.Destroy()
927	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
928	pass #& then change all 'I' atoms
929	if sel >= 0 and noSkip:
930	ui = colLabels.index('U11')
931	us = colLabels.index('Uiso')
932	ss = colLabels.index('site sym')
933	for r in range(Atoms.GetNumberRows()):
934	ID = atomData[r][-1]
935	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
936	if parms == 'A': #'I' --> 'A'
937	Uiso = float(Atoms.GetCellValue(r,us))
938	sytsym = atomData[r][ss]
939	CSI = G2spc.GetCSuinel(sytsym)
940	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
941	atomData[r][us] = 0.0
942	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
943	for i in range(6):
944	ci = ui+i
945	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
946	if CSI[2][i]:
947	Atoms.SetCellStyle(r,ci,WHITE,False)
948	else: #'A' --> 'I'
949	Uij = atomData[r][ui:ui+6]
950	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
951	atomData[r][us] = Uiso
952	Atoms.SetCellStyle(r,us,WHITE,False)
953	for i in range(6):
954	ci = ui+i
955	atomData[r][ci] = 0.0
956	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
957	if not Atoms.IsReadOnly(r,c):
958	if Atoms.GetColLabelValue(c) == 'refine':
959	rbExcl = rbAtmDict.get(atomData[r][-1],'')
960	if rbExcl:
961	for excl in rbExcl:
962	atomData[r][c] = parms.replace(excl,'')
963	else:
964	atomData[r][c] = parms
965	else:
966	atomData[r][c] = parms
967	if 'Atoms' in data['Drawing']:
968	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
969	wx.CallAfter(Paint)
970
971	def ChangeAtomCell(event):
972
973	def chkUij(Uij,CSI): #needs to do something!!!
974	return Uij
975
976	r,c = event.GetRow(),event.GetCol()
977	if r >= 0 and c >= 0:
978	ID = atomData[r][-1]
979	if Atoms.GetColLabelValue(c) in ['x','y','z']:
980	ci = colLabels.index('x')
981	XYZ = atomData[r][ci:ci+3]
982	if None in XYZ:
983	XYZ = [0,0,0]
984	SScol = colLabels.index('site sym')
985	Mulcol = colLabels.index('mult')
986	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
987	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
988	atomData[r][SScol] = Sytsym
989	atomData[r][Mulcol] = Mult
990	if atomData[r][colLabels.index('I/A')] == 'A':
991	ui = colLabels.index('U11')
992	CSI = G2spc.GetCSuinel(Sytsym)
993	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
994	for i in range(6):
995	ci = i+ui
996	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
997	if CSI[2][i]:
998	Atoms.SetCellStyle(r,ci,WHITE,False)
999	SetupGeneral()
1000	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1001	if atomData[r][c] == 'I':
1002	Uij = atomData[r][c+2:c+8]
1003	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1004	Atoms.SetCellStyle(r,c+1,WHITE,False)
1005	Atoms.SetCellTextColour(r,c+1,BLACK)
1006	for i in range(6):
1007	ci = i+colLabels.index('U11')
1008	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1009	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1010	atomData[r][ci] = 0.0
1011	else:
1012	value = atomData[r][c+1]
1013	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1014	atomData[r][c+1] = 0.0
1015	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1016	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1017	for i in range(6):
1018	ci = i+colLabels.index('U11')
1019	atomData[r][ci] = value*CSI[3][i]
1020	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1021	Atoms.SetCellTextColour(r,ci,BLACK)
1022	if CSI[2][i]:
1023	Atoms.SetCellStyle(r,ci,WHITE,False)
1024	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1025	value = atomData[r][c]
1026	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1027	iUij = CSI[0][c-colLabels.index('U11')]
1028	for i in range(6):
1029	if iUij == CSI[0][i]:
1030	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1031	elif Atoms.GetColLabelValue(c) == 'refine':
1032	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1033	if 'Atoms' in data['Drawing']:
1034	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1035	wx.CallAfter(Paint)
1036
1037	def AtomTypeSelect(event):
1038	r,c = event.GetRow(),event.GetCol()
1039	if Atoms.GetColLabelValue(c) == 'Type':
1040	PE = G2elemGUI.PickElement(G2frame)
1041	if PE.ShowModal() == wx.ID_OK:
1042	if PE.Elem != 'None':
1043	atomData[r][c] = PE.Elem.strip()
1044	name = atomData[r][c]
1045	if len(name) in [2,4]:
1046	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1047	else:
1048	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1049	PE.Destroy()
1050	SetupGeneral()
1051	wx.CallAfter(Paint)
1052	value = Atoms.GetCellValue(r,c)
1053	atomData[r][c] = value
1054	ID = atomData[r][-1]
1055	if 'Atoms' in data['Drawing']:
1056	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1057	SetupGeneral()
1058	else:
1059	event.Skip()
1060
1061	def RowSelect(event):
1062	r,c = event.GetRow(),event.GetCol()
1063	if not event.AltDown():
1064	Atoms.frm = -1
1065	G2frame.dataFrame.SetStatusText('')
1066	if r < 0 and c < 0:
1067	if Atoms.IsSelection():
1068	Atoms.ClearSelection()
1069	elif c < 0: #only row clicks
1070	if event.ControlDown():
1071	if r in Atoms.GetSelectedRows():
1072	Atoms.DeselectRow(r)
1073	else:
1074	Atoms.SelectRow(r,True)
1075	elif event.ShiftDown():
1076	indxs = Atoms.GetSelectedRows()
1077	Atoms.ClearSelection()
1078	ibeg = 0
1079	if indxs:
1080	ibeg = indxs[-1]
1081	for row in range(ibeg,r+1):
1082	Atoms.SelectRow(row,True)
1083	elif event.AltDown():
1084	if atomData[r][-1] in rbAtmDict:
1085	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1086	Atoms.frm = -1
1087	Atoms.ClearSelection()
1088	else:
1089	if Atoms.frm < 0: #pick atom to be moved
1090	Atoms.frm = r
1091	Atoms.SelectRow(r,True)
1092	n = colLabels.index('Name')
1093	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1094	else: #move it
1095	item = atomData.pop(Atoms.frm)
1096	atomData.insert(r,item)
1097	Atoms.frm = -1
1098	G2frame.dataFrame.SetStatusText('')
1099	wx.CallAfter(Paint)
1100	else:
1101	Atoms.ClearSelection()
1102	Atoms.SelectRow(r,True)
1103
1104	def ChangeSelection(event):
1105	r,c = event.GetRow(),event.GetCol()
1106	if r < 0 and c < 0:
1107	Atoms.ClearSelection()
1108	if c < 0:
1109	if r in Atoms.GetSelectedRows():
1110	Atoms.DeselectRow(r)
1111	else:
1112	Atoms.SelectRow(r,True)
1113	if r < 0:
1114	if c in Atoms.GetSelectedCols():
1115	Atoms.DeselectCol(c)
1116	else:
1117	Atoms.SelectCol(c,True)
1118
1119	def Paint():
1120
1121	table = []
1122	rowLabels = []
1123	for i,atom in enumerate(atomData):
1124	table.append(atom)
1125	rowLabels.append(str(i))
1126	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1127	Atoms.SetTable(atomTable, True)
1128	Atoms.frm = -1
1129	colType = colLabels.index('Type')
1130	colR = colLabels.index('refine')
1131	colSS = colLabels.index('site sym')
1132	colX = colLabels.index('x')
1133	colIA = colLabels.index('I/A')
1134	colU11 = colLabels.index('U11')
1135	colUiso = colLabels.index('Uiso')
1136	attr = wx.grid.GridCellAttr()
1137	attr.IncRef() #fix from Jim Hester
1138	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1139	for c in range(colX,colX+3):
1140	Atoms.SetColAttr(c, attr)
1141	for i in range(colU11-1,colU11+6):
1142	Atoms.SetColSize(i,50)
1143	for row in range(Atoms.GetNumberRows()):
1144	atId = atomData[row][-1]
1145	rbExcl = rbAtmDict.get(atId,'')
1146	Atoms.SetReadOnly(row,colSS,True) #site sym
1147	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1148	if Atoms.GetCellValue(row,colIA) == 'A':
1149	CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')])
1150	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1151	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1152	for i in range(6):
1153	ci = colU11+i
1154	Atoms.SetCellTextColour(row,ci,BLACK)
1155	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1156	if CSI[2][i] and 'U' not in rbExcl:
1157	Atoms.SetCellStyle(row,ci,WHITE,False)
1158	else:
1159	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1160	Atoms.SetCellTextColour(row,colUiso,BLACK)
1161	if 'U' in rbExcl:
1162	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1163	for i in range(6):
1164	ci = colU11+i
1165	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1166	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1167	if 'X' in rbExcl:
1168	for c in range(0,colX+3):
1169	if c != colR:
1170	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1171	Atoms.AutoSizeColumns(False)
1172
1173	# FillAtomsGrid executable code starts here
1174	generalData = data['General']
1175	atomData = data['Atoms']
1176	DData = data['Drawing']
1177	resRBData = data['RBModels'].get('Residue',[])
1178	vecRBData = data['RBModels'].get('Vector',[])
1179	rbAtmDict = {}
1180	for rbObj in resRBData+vecRBData:
1181	exclList = ['X' for i in range(len(rbObj['Ids']))]
1182	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1183	if rbObj['ThermalMotion'][0] != 'None':
1184	for id in rbObj['Ids']:
1185	rbAtmDict[id] += 'U'
1186	# exclList will be 'x' or 'xu' if TLS used in RB
1187	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1188	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1189	if atomData:
1190	for item in Items:
1191	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1192	else:
1193	for item in Items:
1194	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1195	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1196	if 'showABC' in data['Drawing']:
1197	for item in Items:
1198	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1199	else:
1200	for item in Items:
1201	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1202
1203	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1204	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1205	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1206	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1207	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1208	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1209	if generalData['Type'] == 'magnetic':
1210	colLabels += ['Mx','My','Mz']
1211	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1212	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1213	elif generalData['Type'] == 'macromolecular':
1214	colLabels = ['res no','residue','chain'] + colLabels
1215	Types = [wg.GRID_VALUE_STRING,
1216	wg.GRID_VALUE_CHOICE+AAchoice,
1217	wg.GRID_VALUE_STRING] + Types
1218	elif generalData['Type'] == 'modulated':
1219	Types += []
1220	colLabels += []
1221	SGData = data['General']['SGData']
1222	G2frame.dataFrame.SetStatusText('')
1223	if SGData['SGPolax']:
1224	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1225	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1226	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1227	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1228	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1229	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1230	Atoms.SetMargins(0,0)
1231
1232	G2frame.dataFrame.setSizePosLeft([700,300])
1233	Paint()
1234
1235	def OnAtomAdd(event):
1236	AtomAdd(0,0,0)
1237	FillAtomsGrid(Atoms)
1238	event.StopPropagation()
1239	G2plt.PlotStructure(G2frame,data)
1240
1241	def OnAtomViewAdd(event):
1242	try:
1243	drawData = data['Drawing']
1244	x,y,z = drawData['viewPoint'][0]
1245	AtomAdd(x,y,z)
1246	except:
1247	AtomAdd(0,0,0)
1248	FillAtomsGrid(Atoms)
1249	event.StopPropagation()
1250	G2plt.PlotStructure(G2frame,data)
1251
1252	def AtomAdd(x,y,z,El='H',Name='UNK'):
1253	atomData = data['Atoms']
1254	generalData = data['General']
1255	Ncol = Atoms.GetNumberCols()
1256	atId = ran.randint(0,sys.maxint)
1257	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1258	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1259	if generalData['Type'] == 'macromolecular':
1260	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1261	elif generalData['Type'] == 'nuclear':
1262	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1263	elif generalData['Type'] == 'magnetic':
1264	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1265	SetupGeneral()
1266	if 'Atoms' in data['Drawing']:
1267	DrawAtomAdd(data['Drawing'],atomData[-1])
1268
1269	def OnAtomInsert(event):
1270	AtomInsert(0,0,0)
1271	FillAtomsGrid(Atoms)
1272	event.StopPropagation()
1273	G2plt.PlotStructure(G2frame,data)
1274
1275	def OnAtomViewInsert(event):
1276	if 'Drawing' in data:
1277	drawData = data['Drawing']
1278	x,y,z = drawData['viewPoint'][0]
1279	AtomAdd(x,y,z)
1280	FillAtomsGrid(Atoms)
1281	event.StopPropagation()
1282
1283	def OnAtomMove(event):
1284	drawData = data['Drawing']
1285	atomData = data['Atoms']
1286	x,y,z = drawData['viewPoint'][0]
1287	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1288	cx = colLabels.index('x')
1289	indx = Atoms.GetSelectedRows()
1290	if len(indx) != 1:
1291	print '** ERROR - only one atom can be moved **'
1292	elif atomData[indx[0]][-1] in rbAtmDict:
1293	print '** ERROR - Atoms in rigid bodies can not be moved **'
1294	else:
1295	atomData[indx[0]][cx:cx+3] = [x,y,z]
1296	SetupGeneral()
1297	FillAtomsGrid(Atoms)
1298	ID = atomData[indx[0]][-1]
1299	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1300	G2plt.PlotStructure(G2frame,data)
1301	event.StopPropagation()
1302
1303	def DrawAtomsReplaceByID(drawingData,atom,ID):
1304	IDs = [ID,]
1305	atomData = drawingData['Atoms']
1306	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1307	for ind in indx:
1308	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1309
1310	def MakeDrawAtom(atom,oldatom=None):
1311	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1312	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1313	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1314	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1315	generalData = data['General']
1316	SGData = generalData['SGData']
1317	if generalData['Type'] == 'nuclear':
1318	if oldatom:
1319	opr = oldatom[5]
1320	if atom[9] == 'A':
1321	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1322	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1323	else:
1324	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1325	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1326	else:
1327	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1328	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1329	ct,cs = [1,8] #type & color
1330	elif generalData['Type'] == 'macromolecular':
1331	try:
1332	oneLetter = AA3letter.index(atom[1])
1333	except ValueError:
1334	oneLetter = -1
1335	atomInfo = [[atom[1].strip()+atom[0],]+
1336	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1337	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1338	ct,cs = [4,11] #type & color
1339	elif generalData['Type'] == 'magnetic':
1340	if oldatom:
1341	atomInfo = [atom[:2]+oldatom[3:]][0]
1342	else:
1343	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1344	ct,cs = [1,8] #type & color
1345	# elif generalData['Type'] == 'modulated':
1346	# ????? for future
1347	atNum = generalData['AtomTypes'].index(atom[ct])
1348	atomInfo[cs] = list(generalData['Color'][atNum])
1349	return atomInfo
1350
1351	def AtomInsert(x,y,z):
1352	indx = Atoms.GetSelectedRows()
1353	if indx:
1354	indx = indx[0]
1355	atomData = data['Atoms']
1356	generalData = data['General']
1357	Ncol = Atoms.GetNumberCols()
1358	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1359	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1360	atId = ran.randint(0,sys.maxint)
1361	if generalData['Type'] == 'macromolecular':
1362	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1363	elif generalData['Type'] == 'nuclear':
1364	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1365	elif generalData['Type'] == 'magnetic':
1366	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])
1367	SetupGeneral()
1368
1369	def AtomDelete(event):
1370	indx = Atoms.GetSelectedRows()
1371	IDs = []
1372	if indx:
1373	atomData = data['Atoms']
1374	indx.reverse()
1375	for ind in indx:
1376	atom = atomData[ind]
1377	if atom[-1] in rbAtmDict:
1378	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1379	else:
1380	IDs.append(atom[-1])
1381	del atomData[ind]
1382	if 'Atoms' in data['Drawing']:
1383	DrawAtomsDeleteByIDs(IDs)
1384	wx.CallAfter(FillAtomsGrid,Atoms)
1385	G2plt.PlotStructure(G2frame,data)
1386	SetupGeneral()
1387	event.StopPropagation()
1388
1389	def AtomRefine(event):
1390	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1391	c = colLabels.index('refine')
1392	indx = Atoms.GetSelectedRows()
1393	if indx:
1394	atomData = data['Atoms']
1395	generalData = data['General']
1396	Type = generalData['Type']
1397	if Type in ['nuclear','macromolecular']:
1398	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1399	elif Type == 'magnetic':
1400	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1401	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1402	if dlg.ShowModal() == wx.ID_OK:
1403	sel = dlg.GetSelections()
1404	parms = ''
1405	for x in sel:
1406	parms += choice[x][0]
1407	for r in indx:
1408	if not Atoms.IsReadOnly(r,c):
1409	atomData[r][c] = parms
1410	Atoms.ForceRefresh()
1411	dlg.Destroy()
1412
1413	def AtomModify(event):
1414	indx = Atoms.GetSelectedRows()
1415	if indx:
1416	atomData = data['Atoms']
1417	generalData = data['General']
1418	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1419	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1420	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1421	parm = ''
1422	if dlg.ShowModal() == wx.ID_OK:
1423	sel = dlg.GetSelection()
1424	parm = choices[sel]
1425	cid = colLabels.index(parm)
1426	dlg.Destroy()
1427	if parm in ['Type']:
1428	dlg = G2elemGUI.PickElement(G2frame)
1429	if dlg.ShowModal() == wx.ID_OK:
1430	if dlg.Elem not in ['None']:
1431	El = dlg.Elem.strip()
1432	for r in indx:
1433	if not Atoms.IsReadOnly(r,cid):
1434	atomData[r][cid] = El
1435	if len(El) in [2,4]:
1436	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1437	else:
1438	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1439	SetupGeneral()
1440	if 'Atoms' in data['Drawing']:
1441	for r in indx:
1442	ID = atomData[r][-1]
1443	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1444	FillAtomsGrid(Atoms)
1445	dlg.Destroy()
1446	elif parm in ['Name',]:
1447	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1448	wx.YES_NO \| wx.ICON_QUESTION)
1449	try:
1450	result = dlg.ShowModal()
1451	if result == wx.ID_YES:
1452	for r in indx:
1453	if not Atoms.IsReadOnly(r,cid+1):
1454	El = atomData[r][cid+1]
1455	if len(El) in [2,4]:
1456	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1457	else:
1458	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1459	FillAtomsGrid(Atoms)
1460	finally:
1461	dlg.Destroy()
1462
1463	elif parm in ['I/A']:
1464	choices = ['Isotropic','Anisotropic']
1465	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1466	if dlg.ShowModal() == wx.ID_OK:
1467	sel = dlg.GetSelection()
1468	parm = choices[sel][0]
1469	for r in indx:
1470	if not Atoms.IsReadOnly(r,cid):
1471	atomData[r][cid] = parm
1472	FillAtomsGrid(Atoms)
1473	dlg.Destroy()
1474	elif parm in ['frac','Uiso']:
1475	limits = [0.,1.]
1476	val = 1.0
1477	if parm in ['Uiso']:
1478	limits = [0.,0.25]
1479	val = 0.01
1480	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1481	if dlg.ShowModal() == wx.ID_OK:
1482	parm = dlg.GetValue()
1483	for r in indx:
1484	if not Atoms.IsReadOnly(r,cid):
1485	atomData[r][cid] = parm
1486	SetupGeneral()
1487	FillAtomsGrid(Atoms)
1488	dlg.Destroy()
1489	elif parm in ['x','y','z']:
1490	limits = [-1.,1.]
1491	val = 0.
1492	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1493	if dlg.ShowModal() == wx.ID_OK:
1494	parm = dlg.GetValue()
1495	for r in indx:
1496	if not Atoms.IsReadOnly(r,cid):
1497	atomData[r][cid] += parm
1498	SetupGeneral()
1499	FillAtomsGrid(Atoms)
1500	dlg.Destroy()
1501
1502	def AtomTransform(event):
1503	indx = Atoms.GetSelectedRows()
1504	if indx:
1505	generalData = data['General']
1506	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1507	cx = colLabels.index('x')
1508	cuia = colLabels.index('I/A')
1509	cuij = colLabels.index('U11')
1510	css = colLabels.index('site sym')
1511	atomData = data['Atoms']
1512	generalData = data['General']
1513	SGData = generalData['SGData']
1514	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1515	New = False
1516	try:
1517	if dlg.ShowModal() == wx.ID_OK:
1518	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1519	Cell = np.array(Cell)
1520	cent = SGData['SGCen'][Cent]
1521	M,T = SGData['SGOps'][Opr]
1522	for ind in indx:
1523	XYZ = np.array(atomData[ind][cx:cx+3])
1524	XYZ = np.inner(M,XYZ)+T
1525	if Inv:
1526	XYZ = -XYZ
1527	XYZ = XYZ+cent+Cell
1528	if Force:
1529	XYZ = G2spc.MoveToUnitCell(XYZ)
1530	if New:
1531	atom = copy.copy(atomData[ind])
1532	else:
1533	atom = atomData[ind]
1534	atom[cx:cx+3] = XYZ
1535	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1536	if atom[cuia] == 'A':
1537	Uij = atom[cuij:cuij+6]
1538	U = G2spc.Uij2U(Uij)
1539	U = np.inner(np.inner(M,U),M)
1540	Uij = G2spc.U2Uij(U)
1541	atom[cuij:cuij+6] = Uij
1542	if New:
1543	atomData.append(atom)
1544	finally:
1545	dlg.Destroy()
1546	Atoms.ClearSelection()
1547	if New:
1548	FillAtomsGrid(Atoms)
1549	else:
1550	Atoms.ForceRefresh()
1551
1552	def OnDistAngle(event):
1553	indx = Atoms.GetSelectedRows()
1554	Oxyz = []
1555	xyz = []
1556	DisAglData = {}
1557	DisAglCtls = {}
1558	if indx:
1559	generalData = data['General']
1560	DisAglData['OrigIndx'] = indx
1561	if 'DisAglCtls' in generalData:
1562	DisAglCtls = generalData['DisAglCtls']
1563	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1564	if dlg.ShowModal() == wx.ID_OK:
1565	DisAglCtls = dlg.GetData()
1566	dlg.Destroy()
1567	generalData['DisAglCtls'] = DisAglCtls
1568	atomData = data['Atoms']
1569	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1570	cx = colLabels.index('x')
1571	cn = colLabels.index('Name')
1572	for i,atom in enumerate(atomData):
1573	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1574	if i in indx:
1575	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1576	DisAglData['OrigAtoms'] = Oxyz
1577	DisAglData['TargAtoms'] = xyz
1578	generalData = data['General']
1579	DisAglData['SGData'] = generalData['SGData']
1580	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1581	if 'pId' in data:
1582	DisAglData['pId'] = data['pId']
1583	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1584	try:
1585	G2stMn.DistAngle(DisAglCtls,DisAglData)
1586	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1587	print '** ERROR - try again but do "Reset" to fill in missing atom types **'
1588
1589	def OnReImport(event):
1590	print 'reimport atoms from file to be developed'
1591	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1592	rdlist = G2frame.OnImportGeneric(reqrdr,
1593	G2frame.ImportPhaseReaderlist,
1594	'phase')
1595	if len(rdlist) == 0: return
1596	# for now rdlist is only expected to have one element
1597	# for now always use the first phase for when multiple phases are ever implemented
1598	# but it would be better to loop until we find a phase that matches the one in data
1599	for rd in rdlist:
1600	# rd contains all info for a phase
1601	PhaseName = rd.Phase['General']['Name']
1602	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1603	print rd.Phase['Atoms']
1604	return
1605
1606	################################################################################
1607	#Structure drawing GUI stuff
1608	################################################################################
1609
1610	def SetupDrawingData():
1611	generalData = data['General']
1612	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1613	atomData = data['Atoms']
1614	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1615	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1616	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1617	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1618	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1619	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1620	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1621	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1622	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1623	'bondList':{},'viewDir':[1,0,0]}
1624	V0 = np.array([0,0,1])
1625	V = np.inner(Amat,V0)
1626	V /= np.sqrt(np.sum(V**2))
1627	A = np.arccos(np.sum(V*V0))
1628	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1629	try:
1630	drawingData = data['Drawing']
1631	except KeyError:
1632	data['Drawing'] = {}
1633	drawingData = data['Drawing']
1634	if not drawingData: #fill with defaults if empty
1635	drawingData.update(defaultDrawing)
1636	if 'Zstep' not in drawingData:
1637	drawingData['Zstep'] = 0.5
1638	if 'contourLevel' not in drawingData:
1639	drawingData['contourLevel'] = 1.
1640	if 'viewDir' not in drawingData:
1641	drawingData['viewDir'] = [0,0,1]
1642	if 'Quaternion' not in drawingData:
1643	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1644	if 'showRigidBodies' not in drawingData:
1645	drawingData['showRigidBodies'] = True
1646	cx,ct,cs,ci = [0,0,0,0]
1647	if generalData['Type'] == 'nuclear':
1648	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1649	elif generalData['Type'] == 'macromolecular':
1650	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1651	elif generalData['Type'] == 'magnetic':
1652	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1653	# elif generalData['Type'] == 'modulated':
1654	# ????? for future
1655	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1656	if not drawingData.get('Atoms'):
1657	for atom in atomData:
1658	DrawAtomAdd(drawingData,atom)
1659	data['Drawing'] = drawingData
1660
1661	def DrawAtomAdd(drawingData,atom):
1662	drawingData['Atoms'].append(MakeDrawAtom(atom))
1663
1664	def OnRestraint(event):
1665	indx = drawAtoms.GetSelectedRows()
1666	restData = G2frame.PatternTree.GetItemPyData(
1667	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1668	drawingData = data['Drawing']
1669	generalData = data['General']
1670	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1671	cx,ct,cs,ci = drawingData['atomPtrs']
1672	atomData = drawingData['Atoms']
1673	atNames = []
1674	atXYZ = []
1675	atSymOp = []
1676	atIndx = []
1677	for item in indx:
1678	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1679	atSymOp.append(atomData[item][cs-1])
1680	atIndx.append(atomData[item][ci])
1681	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1682	try:
1683	bondData = restData[PhaseName]['Bond']
1684	except KeyError:
1685	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1686	restData[PhaseName] = {}
1687	restData[PhaseName]['Bond'] = bondData
1688	dist = G2mth.getRestDist(atXYZ,Amat)
1689	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1690	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1691	try:
1692	angleData = restData[PhaseName]['Angle']
1693	except KeyError:
1694	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1695	restData[PhaseName] = {}
1696	restData[PhaseName]['Angle'] = angleData
1697	angle = G2mth.getRestAngle(atXYZ,Amat)
1698	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1699	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1700	try:
1701	planeData = restData[PhaseName]['Plane']
1702	except KeyError:
1703	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1704	restData[PhaseName] = {}
1705	restData[PhaseName]['Plane'] = planeData
1706	plane = G2mth.getRestPlane(atXYZ,Amat)
1707	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1708	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1709	try:
1710	chiralData = restData[PhaseName]['Chiral']
1711	except KeyError:
1712	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1713	restData[PhaseName] = {}
1714	restData[PhaseName]['Chiral'] = chiralData
1715	volume = G2mth.getRestChiral(atXYZ,Amat)
1716	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1717	else:
1718	print '**** ERROR wrong number of atoms selected for this restraint'
1719	return
1720	G2frame.PatternTree.SetItemPyData(
1721	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1722
1723	def OnDefineRB(event):
1724	indx = drawAtoms.GetSelectedRows()
1725	indx.sort()
1726	RBData = G2frame.PatternTree.GetItemPyData(
1727	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1728	drawingData = data['Drawing']
1729	generalData = data['General']
1730	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1731	cx,ct,cs,ci = drawingData['atomPtrs']
1732	atomData = drawingData['Atoms']
1733	rbXYZ = []
1734	rbType = []
1735	atNames = []
1736	AtInfo = RBData['Residue']['AtInfo']
1737	for i,item in enumerate(indx):
1738	rbtype = atomData[item][ct]
1739	atNames.append(rbtype+str(i))
1740	rbType.append(rbtype)
1741	if rbtype not in AtInfo:
1742	Info = G2elem.GetAtomInfo(rbtype)
1743	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1744	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1745	rbXYZ = np.array(rbXYZ)
1746	rbXYZ -= rbXYZ[0]
1747	rbId = ran.randint(0,sys.maxint)
1748	rbName = 'UNKRB'
1749	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1750	'Edit rigid body name',rbName ,style=wx.OK)
1751	if dlg.ShowModal() == wx.ID_OK:
1752	rbName = dlg.GetValue()
1753	dlg.Destroy()
1754	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1755	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1756	RBData['RBIds']['Residue'].append(rbId)
1757	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1758
1759	################################################################################
1760	##### Atom draw routines
1761	################################################################################
1762
1763	def UpdateDrawAtoms(atomStyle=''):
1764	def RefreshAtomGrid(event):
1765	def SetChoice(name,c,n=0):
1766	choice = []
1767	for r in range(len(atomData)):
1768	if n:
1769	srchStr = str(atomData[r][c][:n])
1770	else:
1771	srchStr = str(atomData[r][c])
1772	if srchStr not in choice:
1773	if n:
1774	choice.append(str(atomData[r][c][:n]))
1775	else:
1776	choice.append(str(atomData[r][c]))
1777	choice.sort()
1778
1779	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
1780	if dlg.ShowModal() == wx.ID_OK:
1781	sel = dlg.GetSelections()
1782	parms = []
1783	for x in sel:
1784	parms.append(choice[x])
1785	noSkip = False
1786	drawAtoms.ClearSelection()
1787	drawingData['selectedAtoms'] = []
1788	for row in range(len(atomData)):
1789	test = atomData[row][c]
1790	if n:
1791	test = test[:n]
1792	if test in parms:
1793	drawAtoms.SelectRow(row,True)
1794	drawingData['selectedAtoms'].append(row)
1795	G2plt.PlotStructure(G2frame,data)
1796	dlg.Destroy()
1797
1798	r,c = event.GetRow(),event.GetCol()
1799	if r < 0 and c < 0:
1800	for row in range(drawAtoms.GetNumberRows()):
1801	drawingData['selectedAtoms'].append(row)
1802	drawAtoms.SelectRow(row,True)
1803	elif r < 0: #dclick on col label
1804	sel = -1
1805	Parms = False
1806	noSkip = True
1807	if drawAtoms.GetColLabelValue(c) == 'Style':
1808	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1809	if dlg.ShowModal() == wx.ID_OK:
1810	sel = dlg.GetSelection()
1811	parms = styleChoice[sel]
1812	for r in range(len(atomData)):
1813	atomData[r][c] = parms
1814	drawAtoms.SetCellValue(r,c,parms)
1815	FindBondsDraw()
1816	G2plt.PlotStructure(G2frame,data)
1817	dlg.Destroy()
1818	elif drawAtoms.GetColLabelValue(c) == 'Label':
1819	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
1820	if dlg.ShowModal() == wx.ID_OK:
1821	sel = dlg.GetSelection()
1822	parms = labelChoice[sel]
1823	for r in range(len(atomData)):
1824	atomData[r][c] = parms
1825	drawAtoms.SetCellValue(r,c,parms)
1826	dlg.Destroy()
1827	elif drawAtoms.GetColLabelValue(c) == 'Color':
1828	dlg = wx.ColourDialog(G2frame)
1829	if dlg.ShowModal() == wx.ID_OK:
1830	color = dlg.GetColourData().GetColour()
1831	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1832	attr.SetReadOnly(True)
1833	attr.SetBackgroundColour(color)
1834	for r in range(len(atomData)):
1835	atomData[r][c] = color
1836	drawingData['Atoms'][r][c] = color
1837	drawAtoms.SetAttr(r,c,attr)
1838	UpdateDrawAtoms()
1839	dlg.Destroy()
1840	elif drawAtoms.GetColLabelValue(c) == 'Residue':
1841	SetChoice('Residue',c,3)
1842	elif drawAtoms.GetColLabelValue(c) == '1-letter':
1843	SetChoice('1-letter',c,1)
1844	elif drawAtoms.GetColLabelValue(c) == 'Chain':
1845	SetChoice('Chain',c)
1846	elif drawAtoms.GetColLabelValue(c) == 'Name':
1847	SetChoice('Name',c)
1848	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
1849	SetChoice('Name',c)
1850	elif drawAtoms.GetColLabelValue(c) == 'Type':
1851	SetChoice('Type',c)
1852	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
1853	drawAtoms.ClearSelection()
1854	else:
1855	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
1856	atomData[r][c] = drawAtoms.GetCellValue(r,c)
1857	FindBondsDraw()
1858	elif drawAtoms.GetColLabelValue(c) == 'Color':
1859	dlg = wx.ColourDialog(G2frame)
1860	if dlg.ShowModal() == wx.ID_OK:
1861	color = dlg.GetColourData().GetColour()
1862	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1863	attr.SetReadOnly(True)
1864	attr.SetBackgroundColour(color)
1865	atomData[r][c] = color
1866	drawingData['Atoms'][r][c] = color
1867	drawAtoms.SetAttr(i,cs+2,attr)
1868	dlg.Destroy()
1869	UpdateDrawAtoms()
1870	G2plt.PlotStructure(G2frame,data)
1871
1872	def RowSelect(event):
1873	r,c = event.GetRow(),event.GetCol()
1874	if r < 0 and c < 0:
1875	if drawAtoms.IsSelection():
1876	drawAtoms.ClearSelection()
1877	elif c < 0: #only row clicks
1878	if event.ControlDown():
1879	if r in drawAtoms.GetSelectedRows():
1880	drawAtoms.DeselectRow(r)
1881	else:
1882	drawAtoms.SelectRow(r,True)
1883	elif event.ShiftDown():
1884	indxs = drawAtoms.GetSelectedRows()
1885	drawAtoms.ClearSelection()
1886	ibeg = 0
1887	if indxs:
1888	ibeg = indxs[-1]
1889	for row in range(ibeg,r+1):
1890	drawAtoms.SelectRow(row,True)
1891	else:
1892	drawAtoms.ClearSelection()
1893	drawAtoms.SelectRow(r,True)
1894	drawingData['selectedAtoms'] = []
1895	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
1896	G2plt.PlotStructure(G2frame,data)
1897
1898	# UpdateDrawAtoms executable code starts here
1899	G2frame.dataFrame.SetStatusText('')
1900	generalData = data['General']
1901	SetupDrawingData()
1902	drawingData = data['Drawing']
1903	cx,ct,cs,ci = drawingData['atomPtrs']
1904	atomData = drawingData['Atoms']
1905	if atomStyle:
1906	for atom in atomData:
1907	atom[cs] = atomStyle
1908	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
1909	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
1910	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
1911	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1912	labelChoice = [' ','type','name','number']
1913	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
1914	if generalData['Type'] == 'macromolecular':
1915	colLabels = ['Residue','1-letter','Chain'] + colLabels
1916	Types = 3*[wg.GRID_VALUE_STRING,]+Types
1917	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
1918	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
1919	labelChoice = [' ','type','name','number','residue','1-letter','chain']
1920	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
1921	# elif generalData['Type'] == 'modulated':
1922	# Types += []
1923	# colLabels += []
1924	table = []
1925	rowLabels = []
1926	for i,atom in enumerate(drawingData['Atoms']):
1927	table.append(atom[:colLabels.index('I/A')+1])
1928	rowLabels.append(str(i))
1929
1930	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1931	drawAtoms.SetTable(atomTable, True)
1932	drawAtoms.SetMargins(0,0)
1933	drawAtoms.AutoSizeColumns(True)
1934	drawAtoms.SetColSize(colLabels.index('Style'),80)
1935	drawAtoms.SetColSize(colLabels.index('Color'),50)
1936	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
1937	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1938	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
1939	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1940	for i,atom in enumerate(drawingData['Atoms']):
1941	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1942	attr.SetReadOnly(True)
1943	attr.SetBackgroundColour(atom[cs+2])
1944	drawAtoms.SetAttr(i,cs+2,attr)
1945	drawAtoms.SetCellValue(i,cs+2,'')
1946	indx = drawingData['selectedAtoms']
1947	if indx:
1948	for r in range(len(atomData)):
1949	if r in indx:
1950	drawAtoms.SelectRow(r)
1951	for c in range(len(colLabels)):
1952	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1953	attr.SetReadOnly(True)
1954	attr.SetBackgroundColour(VERY_LIGHT_GREY)
1955	if colLabels[c] not in ['Style','Label','Color']:
1956	drawAtoms.SetColAttr(c,attr)
1957	G2frame.dataFrame.setSizePosLeft([600,300])
1958
1959	FindBondsDraw()
1960	drawAtoms.ClearSelection()
1961	# G2plt.PlotStructure(G2frame,data)
1962
1963	def DrawAtomStyle(event):
1964	indx = drawAtoms.GetSelectedRows()
1965	if indx:
1966	generalData = data['General']
1967	atomData = data['Drawing']['Atoms']
1968	cx,ct,cs,ci = data['Drawing']['atomPtrs']
1969	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1970	if generalData['Type'] == 'macromolecular':
1971	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
1972	'backbone','ribbons','schematic']
1973	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1974	if dlg.ShowModal() == wx.ID_OK:
1975	sel = dlg.GetSelection()
1976	parms = styleChoice[sel]
1977	for r in indx:
1978	atomData[r][cs] = parms
1979	drawAtoms.SetCellValue(r,cs,parms)
1980	dlg.Destroy()
1981	FindBondsDraw()
1982	drawAtoms.ClearSelection()
1983	G2plt.PlotStructure(G2frame,data)
1984
1985	def DrawAtomLabel(event):
1986	indx = drawAtoms.GetSelectedRows()
1987	if indx:
1988	generalData = data['General']
1989	atomData = data['Drawing']['Atoms']
1990	cx,ct,cs,ci = data['Drawing']['atomPtrs']
1991	styleChoice = [' ','type','name','number']
1992	if generalData['Type'] == 'macromolecular':
1993	styleChoice = [' ','type','name','number','residue','1-letter','chain']
1994	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
1995	if dlg.ShowModal() == wx.ID_OK:
1996	sel = dlg.GetSelection()
1997	parms = styleChoice[sel]
1998	for r in indx:
1999	atomData[r][cs+1] = parms
2000	drawAtoms.SetCellValue(r,cs+1,parms)
2001	dlg.Destroy()
2002	drawAtoms.ClearSelection()
2003	G2plt.PlotStructure(G2frame,data)
2004
2005	def DrawAtomColor(event):
2006
2007	indx = drawAtoms.GetSelectedRows()
2008	if indx:
2009	if len(indx) > 1:
2010	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2011	else:
2012	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2013	generalData = data['General']
2014	atomData = data['Drawing']['Atoms']
2015	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2016	atmColors = []
2017	atmTypes = []
2018	for r in indx:
2019	if atomData[r][cs+2] not in atmColors:
2020	atmColors.append(atomData[r][cs+2])
2021	atmTypes.append(atomData[r][ct])
2022	if len(atmColors) > 16:
2023	break
2024	colors = wx.ColourData()
2025	colors.SetChooseFull(True)
2026	dlg = wx.ColourDialog(G2frame)
2027	if dlg.ShowModal() == wx.ID_OK:
2028	for i in range(len(atmColors)):
2029	atmColors[i] = dlg.GetColourData().GetColour()
2030	colorDict = dict(zip(atmTypes,atmColors))
2031	for r in indx:
2032	color = colorDict[atomData[r][ct]]
2033	atomData[r][cs+2] = color
2034	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2035	attr.SetBackgroundColour(color)
2036	drawAtoms.SetAttr(r,cs+2,attr)
2037	data['Drawing']['Atoms'][r][cs+2] = color
2038	drawAtoms.ClearSelection()
2039	dlg.Destroy()
2040	G2frame.dataFrame.SetStatusText('')
2041	G2plt.PlotStructure(G2frame,data)
2042
2043	def ResetAtomColors(event):
2044	generalData = data['General']
2045	atomData = data['Drawing']['Atoms']
2046	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2047	for atom in atomData:
2048	atNum = generalData['AtomTypes'].index(atom[ct])
2049	atom[cs+2] = list(generalData['Color'][atNum])
2050	UpdateDrawAtoms()
2051	drawAtoms.ClearSelection()
2052	G2plt.PlotStructure(G2frame,data)
2053
2054	def SetViewPoint(event):
2055	indx = drawAtoms.GetSelectedRows()
2056	if indx:
2057	atomData = data['Drawing']['Atoms']
2058	cx = data['Drawing']['atomPtrs'][0]
2059	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2060	drawAtoms.ClearSelection() #do I really want to do this?
2061	G2plt.PlotStructure(G2frame,data)
2062
2063	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2064	cx = data['Drawing']['atomPtrs'][0]
2065	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2066	return False
2067	else:
2068	return True
2069
2070	def AddSymEquiv(event):
2071	indx = drawAtoms.GetSelectedRows()
2072	indx.sort()
2073	if indx:
2074	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2075	cx = colLabels.index('x')
2076	cuia = colLabels.index('I/A')
2077	cuij = cuia+2
2078	atomData = data['Drawing']['Atoms']
2079	generalData = data['General']
2080	SGData = generalData['SGData']
2081	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2082	try:
2083	if dlg.ShowModal() == wx.ID_OK:
2084	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2085	Cell = np.array(Cell)
2086	cent = SGData['SGCen'][Cent]
2087	M,T = SGData['SGOps'][Opr]
2088	for ind in indx:
2089	XYZ = np.array(atomData[ind][cx:cx+3])
2090	XYZ = np.inner(M,XYZ)+T
2091	if Inv:
2092	XYZ = -XYZ
2093	XYZ = XYZ+cent+Cell
2094	if Force:
2095	XYZ = G2spc.MoveToUnitCell(XYZ)
2096	if noDuplicate(XYZ,atomData):
2097	atom = copy.copy(atomData[ind])
2098	atom[cx:cx+3] = XYZ
2099	atomOp = atom[cx+3]
2100	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2101	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2102	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2103	if atom[cuia] == 'A':
2104	Uij = atom[cuij:cuij+6]
2105	U = G2spc.Uij2U(Uij)
2106	U = np.inner(np.inner(M,U),M)
2107	Uij = G2spc.U2Uij(U)
2108	atom[cuij:cuij+6] = Uij
2109	atomData.append(atom)
2110	finally:
2111	dlg.Destroy()
2112	UpdateDrawAtoms()
2113	drawAtoms.ClearSelection()
2114	G2plt.PlotStructure(G2frame,data)
2115
2116	def TransformSymEquiv(event):
2117	indx = drawAtoms.GetSelectedRows()
2118	indx.sort()
2119	if indx:
2120	atomData = data['Drawing']['Atoms']
2121	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2122	cx = colLabels.index('x')
2123	cuia = colLabels.index('I/A')
2124	cuij = cuia+2
2125	atomData = data['Drawing']['Atoms']
2126	generalData = data['General']
2127	SGData = generalData['SGData']
2128	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2129	try:
2130	if dlg.ShowModal() == wx.ID_OK:
2131	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2132	Cell = np.array(Cell)
2133	cent = SGData['SGCen'][Cent]
2134	M,T = SGData['SGOps'][Opr]
2135	for ind in indx:
2136	XYZ = np.array(atomData[ind][cx:cx+3])
2137	XYZ = np.inner(M,XYZ)+T
2138	if Inv:
2139	XYZ = -XYZ
2140	XYZ = XYZ+cent+Cell
2141	if Force:
2142	XYZ = G2spc.MoveToUnitCell(XYZ)
2143	atom = atomData[ind]
2144	atom[cx:cx+3] = XYZ
2145	atomOp = atom[cx+3]
2146	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2147	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2148	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2149	if atom[cuia] == 'A':
2150	Uij = atom[cuij:cuij+6]
2151	U = G2spc.Uij2U(Uij)
2152	U = np.inner(np.inner(M,U),M)
2153	Uij = G2spc.U2Uij(U)
2154	atom[cuij:cuij+6] = Uij
2155	data['Drawing']['Atoms'] = atomData
2156	finally:
2157	dlg.Destroy()
2158	UpdateDrawAtoms()
2159	drawAtoms.ClearSelection()
2160	G2plt.PlotStructure(G2frame,data)
2161
2162	def FillCoordSphere(event):
2163	generalData = data['General']
2164	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2165	radii = generalData['BondRadii']
2166	atomTypes = generalData['AtomTypes']
2167	try:
2168	indH = atomTypes.index('H')
2169	radii[indH] = 0.5
2170	except:
2171	pass
2172	indx = drawAtoms.GetSelectedRows()
2173	if indx:
2174	indx.sort()
2175	atomData = data['Drawing']['Atoms']
2176	numAtoms = len(atomData)
2177	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2178	generalData = data['General']
2179	SGData = generalData['SGData']
2180	cellArray = G2lat.CellBlock(1)
2181	wx.BeginBusyCursor()
2182	try:
2183	for ind in indx:
2184	atomA = atomData[ind]
2185	xyzA = np.array(atomA[cx:cx+3])
2186	indA = atomTypes.index(atomA[ct])
2187	for atomB in atomData[:numAtoms]:
2188	indB = atomTypes.index(atomB[ct])
2189	sumR = radii[indA]+radii[indB]
2190	xyzB = np.array(atomB[cx:cx+3])
2191	for xyz in cellArray+xyzB:
2192	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2193	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2194	if noDuplicate(xyz,atomData):
2195	oprB = atomB[cx+3]
2196	C = xyz-xyzB
2197	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2198	newAtom = atomB[:]
2199	newAtom[cx:cx+3] = xyz
2200	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2201	atomData.append(newAtom)
2202	finally:
2203	wx.EndBusyCursor()
2204	data['Drawing']['Atoms'] = atomData
2205	UpdateDrawAtoms()
2206	drawAtoms.ClearSelection()
2207	G2plt.PlotStructure(G2frame,data)
2208
2209	def FillUnitCell(event):
2210	indx = drawAtoms.GetSelectedRows()
2211	indx.sort()
2212	if indx:
2213	atomData = data['Drawing']['Atoms']
2214	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2215	cx = colLabels.index('x')
2216	cuia = colLabels.index('I/A')
2217	cuij = cuia+2
2218	generalData = data['General']
2219	SGData = generalData['SGData']
2220	wx.BeginBusyCursor()
2221	try:
2222	for ind in indx:
2223	atom = atomData[ind]
2224	XYZ = np.array(atom[cx:cx+3])
2225	if atom[cuia] == 'A':
2226	Uij = atom[cuij:cuij+6]
2227	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2228	for item in result:
2229	atom = copy.copy(atomData[ind])
2230	atom[cx:cx+3] = item[0]
2231	atom[cx+3] = str(item[2])+'+' \
2232	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2233	atom[cuij:cuij+6] = item[1]
2234	Opp = G2spc.Opposite(item[0])
2235	for xyz in Opp:
2236	if noDuplicate(xyz,atomData):
2237	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2238	cell = '1'+'+'+ \
2239	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2240	atom[cx:cx+3] = xyz
2241	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2242	atomData.append(atom[:])
2243	else:
2244	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2245	for item in result:
2246	atom = copy.copy(atomData[ind])
2247	atom[cx:cx+3] = item[0]
2248	atom[cx+3] = str(item[1])+'+' \
2249	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2250	Opp = G2spc.Opposite(item[0])
2251	for xyz in Opp:
2252	if noDuplicate(xyz,atomData):
2253	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2254	cell = '1'+'+'+ \
2255	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2256	atom[cx:cx+3] = xyz
2257	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2258	atomData.append(atom[:])
2259	data['Drawing']['Atoms'] = atomData
2260	finally:
2261	wx.EndBusyCursor()
2262	UpdateDrawAtoms()
2263	drawAtoms.ClearSelection()
2264	G2plt.PlotStructure(G2frame,data)
2265
2266	def FindBondsToo(): #works but slow for large structures - keep as reference
2267	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2268	atomData = data['Drawing']['Atoms']
2269	generalData = data['General']
2270	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2271	radii = generalData['BondRadii']
2272	atomTypes = generalData['AtomTypes']
2273	try:
2274	indH = atomTypes.index('H')
2275	radii[indH] = 0.5
2276	except:
2277	pass
2278	for atom in atomData:
2279	atom[-1] = []
2280	Atoms = []
2281	for i,atom in enumerate(atomData):
2282	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2283	for atomA in Atoms:
2284	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2285	for atomB in Atoms:
2286	Dx = atomB[1]-atomA[1]
2287	DX = np.inner(Amat,Dx)
2288	dist = np.sqrt(np.sum(DX**2))
2289	sumR = atomA[3]+atomB[3]
2290	if 0.5 < dist <= 0.85*sumR:
2291	i = atomA[0]
2292	if atomA[2] == 'polyhedra':
2293	atomData[i][-1].append(DX)
2294	elif atomB[1] != 'polyhedra':
2295	j = atomB[0]
2296	atomData[i][-1].append(Dx*atomA[3]/sumR)
2297	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2298
2299	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2300	import numpy.ma as ma
2301	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2302	hydro = data['Drawing']['showHydrogen']
2303	atomData = data['Drawing']['Atoms']
2304	generalData = data['General']
2305	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2306	radii = generalData['BondRadii']
2307	atomTypes = generalData['AtomTypes']
2308	try:
2309	indH = atomTypes.index('H')
2310	radii[indH] = 0.5
2311	except:
2312	pass
2313	for atom in atomData:
2314	atom[-2] = [] #clear out old bonds/polyhedra
2315	atom[-1] = []
2316	Indx = range(len(atomData))
2317	Atoms = []
2318	Styles = []
2319	Radii = []
2320	for atom in atomData:
2321	Atoms.append(np.array(atom[cx:cx+3]))
2322	Styles.append(atom[cs])
2323	try:
2324	if not hydro and atom[ct] == 'H':
2325	Radii.append(0.0)
2326	else:
2327	Radii.append(radii[atomTypes.index(atom[ct])])
2328	except ValueError: #changed atom type!
2329	Radii.append(0.20)
2330	Atoms = np.array(Atoms)
2331	Radii = np.array(Radii)
2332	IASR = zip(Indx,Atoms,Styles,Radii)
2333	for atomA in IASR:
2334	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2335	Dx = Atoms-atomA[1]
2336	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
2337	sumR = atomA[3]+Radii
2338	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2339	i = atomA[0]
2340	for j in IndB[0]:
2341	if Styles[i] == 'polyhedra':
2342	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2343	elif Styles[j] != 'polyhedra' and j > i:
2344	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2345	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2346	if Styles[i] == 'polyhedra':
2347	Bonds = atomData[i][-2]
2348	Faces = []
2349	if len(Bonds) > 2:
2350	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2351	for face in FaceGen:
2352	vol = nl.det(face)
2353	if abs(vol) > 1. or len(Bonds) == 3:
2354	if vol < 0.:
2355	face = [face[0],face[2],face[1]]
2356	face = np.array(face)
2357	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2358	norm = np.cross(face[1]-face[0],face[2]-face[0])
2359	norm /= np.sqrt(np.sum(norm**2))
2360	Faces.append([face,norm])
2361	atomData[i][-1] = Faces
2362
2363	def DrawAtomsDelete(event):
2364	indx = drawAtoms.GetSelectedRows()
2365	indx.sort()
2366	if indx:
2367	atomData = data['Drawing']['Atoms']
2368	indx.reverse()
2369	for ind in indx:
2370	del atomData[ind]
2371	UpdateDrawAtoms()
2372	drawAtoms.ClearSelection()
2373	G2plt.PlotStructure(G2frame,data)
2374	event.StopPropagation()
2375
2376	def OnReloadDrawAtoms(event):
2377	data['Drawing']['Atoms'] = []
2378	UpdateDrawAtoms()
2379	drawAtoms.ClearSelection()
2380	G2plt.PlotStructure(G2frame,data)
2381	event.StopPropagation()
2382
2383	def DrawAtomsDeleteByIDs(IDs):
2384	atomData = data['Drawing']['Atoms']
2385	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2386	indx.reverse()
2387	for ind in indx:
2388	del atomData[ind]
2389
2390	def ChangeDrawAtomsByIDs(colName,IDs,value):
2391	atomData = data['Drawing']['Atoms']
2392	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2393	if colName == 'Name':
2394	col = ct-1
2395	elif colName == 'Type':
2396	col = ct
2397	elif colName == 'I/A':
2398	col = cs
2399	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2400	for ind in indx:
2401	atomData[ind][col] = value
2402
2403	def OnDrawPlane(event):
2404	indx = drawAtoms.GetSelectedRows()
2405	if len(indx) < 4:
2406	print '**** ERROR - need 4+ atoms for plane calculation'
2407	return
2408	PlaneData = {}
2409	drawingData = data['Drawing']
2410	atomData = drawingData['Atoms']
2411	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2412	cx = colLabels.index('x')
2413	cn = colLabels.index('Name')
2414	xyz = []
2415	for i,atom in enumerate(atomData):
2416	if i in indx:
2417	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2418	generalData = data['General']
2419	PlaneData['Name'] = generalData['Name']
2420	PlaneData['Atoms'] = xyz
2421	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2422	G2stMn.BestPlane(PlaneData)
2423
2424	def OnDrawDistVP(event):
2425	# distance to view point
2426	indx = drawAtoms.GetSelectedRows()
2427	if not indx:
2428	print '***** ERROR - no atoms selected'
2429	return
2430	generalData = data['General']
2431	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2432	drawingData = data['Drawing']
2433	viewPt = np.array(drawingData['viewPoint'][0])
2434	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2435	atomDData = drawingData['Atoms']
2436	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2437	cx = colLabels.index('x')
2438	cn = colLabels.index('Name')
2439	for i in indx:
2440	atom = atomDData[i]
2441	Dx = np.array(atom[cx:cx+3])-viewPt
2442	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2443	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2444
2445	def OnDrawDAT(event):
2446	#distance, angle, torsion
2447	indx = drawAtoms.GetSelectedRows()
2448	if len(indx) not in [2,3,4]:
2449	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2450	return
2451	DATData = {}
2452	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2453	drawingData = data['Drawing']
2454	atomData = data['Atoms']
2455	atomDData = drawingData['Atoms']
2456	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2457	cx = colLabels.index('x')
2458	cn = colLabels.index('Name')
2459	cid = colLabels.index('I/A')+8
2460	xyz = []
2461	Oxyz = []
2462	DATData['Natoms'] = len(indx)
2463	for i in indx:
2464	atom = atomDData[i]
2465	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2466	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2467	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2468	DATData['Datoms'] = xyz
2469	DATData['Oatoms'] = Oxyz
2470	generalData = data['General']
2471	DATData['Name'] = generalData['Name']
2472	DATData['SGData'] = generalData['SGData']
2473	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2474	if 'pId' in data:
2475	DATData['pId'] = data['pId']
2476	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2477	G2stMn.DisAglTor(DATData)
2478
2479	################################################################################
2480	#### Draw Options page
2481	################################################################################
2482
2483	def UpdateDrawOptions():
2484	import copy
2485	import wx.lib.colourselect as wcs
2486	def SlopSizer():
2487	def OnCameraPos(event):
2488	drawingData['cameraPos'] = cameraPos.GetValue()
2489	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2490	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2491	G2plt.PlotStructure(G2frame,data)
2492
2493	def OnZclip(event):
2494	drawingData['Zclip'] = Zclip.GetValue()
2495	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2496	G2plt.PlotStructure(G2frame,data)
2497
2498	def OnZstep(event):
2499	try:
2500	step = float(Zstep.GetValue())
2501	if not (0.01 <= step <= 1.0):
2502	raise ValueError
2503	except ValueError:
2504	step = drawingData['Zstep']
2505	drawingData['Zstep'] = step
2506	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2507
2508	def OnMoveZ(event):
2509	move = MoveZ.GetValue()*drawingData['Zstep']
2510	MoveZ.SetValue(0)
2511	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2512	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2513	VD /= np.sqrt(np.sum(VD**2))
2514	VP += move*VD
2515	VP = np.inner(Bmat,VP)
2516	drawingData['viewPoint'][0] = VP
2517	panel = drawOptions.GetChildren()
2518	names = [child.GetName() for child in panel]
2519	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2520	G2plt.PlotStructure(G2frame,data)
2521
2522	def OnVdWScale(event):
2523	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2524	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2525	G2plt.PlotStructure(G2frame,data)
2526
2527	def OnEllipseProb(event):
2528	drawingData['ellipseProb'] = ellipseProb.GetValue()
2529	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2530	G2plt.PlotStructure(G2frame,data)
2531
2532	def OnBallScale(event):
2533	drawingData['ballScale'] = ballScale.GetValue()/100.
2534	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2535	G2plt.PlotStructure(G2frame,data)
2536
2537	def OnBondRadius(event):
2538	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2539	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2540	G2plt.PlotStructure(G2frame,data)
2541
2542	def OnContourLevel(event):
2543	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2544	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2545	G2plt.PlotStructure(G2frame,data)
2546
2547	def OnMapSize(event):
2548	drawingData['mapSize'] = mapSize.GetValue()/10.
2549	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2550	G2plt.PlotStructure(G2frame,data)
2551
2552
2553	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2554	slideSizer = wx.FlexGridSizer(7,2)
2555	slideSizer.AddGrowableCol(1,1)
2556
2557	cameraPosTxt = wx.StaticText(drawOptions,-1,
2558	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2559	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2560	slideSizer.Add(cameraPosTxt,0,wx.ALIGN_CENTER_VERTICAL)
2561	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2562	cameraPos.SetRange(10,500)
2563	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2564	G2frame.dataDisplay.cameraSlider = cameraPos
2565	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2566
2567	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2568	slideSizer.Add(ZclipTxt,0,wx.ALIGN_CENTER_VERTICAL)
2569	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2570	Zclip.SetRange(1,99)
2571	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2572	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2573
2574	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2575	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,wx.ALIGN_CENTER_VERTICAL)
2576	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2577	style=wx.TE_PROCESS_ENTER)
2578	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2579	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2580	ZstepSizer.Add(Zstep,0,wx.ALIGN_CENTER_VERTICAL)
2581	slideSizer.Add(ZstepSizer)
2582	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2583	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,wx.ALIGN_CENTER_VERTICAL)
2584	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2585	MoveZ.SetValue(0)
2586	MoveZ.SetRange(-1,1)
2587	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2588	MoveSizer.Add(MoveZ)
2589	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2590
2591	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2592	slideSizer.Add(vdwScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2593	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2594	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2595	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2596
2597	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2598	slideSizer.Add(ellipseProbTxt,0,wx.ALIGN_CENTER_VERTICAL)
2599	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2600	ellipseProb.SetRange(1,99)
2601	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2602	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2603
2604	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2605	slideSizer.Add(ballScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2606	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2607	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2608	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2609
2610	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2611	slideSizer.Add(bondRadiusTxt,0,wx.ALIGN_CENTER_VERTICAL)
2612	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2613	bondRadius.SetRange(1,25)
2614	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2615	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2616
2617	if generalData['Map']['rhoMax']:
2618	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2619	slideSizer.Add(contourLevelTxt,0,wx.ALIGN_CENTER_VERTICAL)
2620	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2621	contourLevel.SetRange(1,100)
2622	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2623	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2624	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2625	slideSizer.Add(mapSizeTxt,0,wx.ALIGN_CENTER_VERTICAL)
2626	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2627	mapSize.SetRange(1,100)
2628	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2629	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2630
2631	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2632	slopSizer.Add((10,5),0)
2633	slopSizer.SetMinSize(wx.Size(350,10))
2634	return slopSizer
2635
2636	def ShowSizer():
2637
2638	def OnBackColor(event):
2639	drawingData['backColor'] = event.GetValue()
2640	G2plt.PlotStructure(G2frame,data)
2641
2642	def OnShowABC(event):
2643	drawingData['showABC'] = showABC.GetValue()
2644	G2plt.PlotStructure(G2frame,data)
2645
2646	def OnShowUnitCell(event):
2647	drawingData['unitCellBox'] = unitCellBox.GetValue()
2648	G2plt.PlotStructure(G2frame,data)
2649
2650	def OnShowHyd(event):
2651	drawingData['showHydrogen'] = showHydrogen.GetValue()
2652	FindBondsDraw()
2653	G2plt.PlotStructure(G2frame,data)
2654
2655	def OnShowRB(event):
2656	drawingData['showRigidBodies'] = showRB.GetValue()
2657	FindBondsDraw()
2658	G2plt.PlotStructure(G2frame,data)
2659
2660	def OnViewPoint(event):
2661	Obj = event.GetEventObject()
2662	viewPt = Obj.GetValue().split()
2663	try:
2664	VP = [float(viewPt[i]) for i in range(3)]
2665	except (ValueError,IndexError):
2666	VP = drawingData['viewPoint'][0]
2667	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2668	drawingData['viewPoint'][0] = VP
2669	G2plt.PlotStructure(G2frame,data)
2670
2671	def OnViewDir(event):
2672	Obj = event.GetEventObject()
2673	viewDir = Obj.GetValue().split()
2674	try:
2675	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2676	VD = np.array([float(viewDir[i]) for i in range(3)])
2677	VC = np.inner(Amat,VD)
2678	VC /= np.sqrt(np.sum(VC**2))
2679	V = np.array(drawingData['viewDir'])
2680	VB = np.inner(Amat,V)
2681	VB /= np.sqrt(np.sum(VB**2))
2682	VX = np.cross(VC,VB)
2683	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2684	QV = G2mth.AVdeg2Q(A,VX)
2685	Q = drawingData['Quaternion']
2686	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2687	except (ValueError,IndexError):
2688	VD = drawingData['viewDir']
2689	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2690	drawingData['viewDir'] = VD
2691	G2plt.PlotStructure(G2frame,data)
2692
2693	showSizer = wx.BoxSizer(wx.VERTICAL)
2694	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2695	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,wx.ALIGN_CENTER_VERTICAL)
2696	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2697	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2698	lineSizer.Add(backColor,0,wx.ALIGN_CENTER_VERTICAL)
2699	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,wx.ALIGN_CENTER_VERTICAL)
2700	VD = drawingData['viewDir']
2701	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2702	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2703	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2704	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2705	G2frame.dataDisplay.viewDir = viewDir
2706	lineSizer.Add(viewDir,0,wx.ALIGN_CENTER_VERTICAL)
2707	showSizer.Add(lineSizer)
2708	showSizer.Add((0,5),0)
2709
2710	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2711	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2712	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2713	showABC.SetValue(drawingData['showABC'])
2714	lineSizer.Add(showABC,0,wx.ALIGN_CENTER_VERTICAL)
2715	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,wx.ALIGN_CENTER_VERTICAL)
2716	VP = drawingData['viewPoint'][0]
2717	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2718	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2719	G2frame.dataDisplay.viewPoint = viewPoint
2720	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2721	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2722	lineSizer.Add(viewPoint,0,wx.ALIGN_CENTER_VERTICAL)
2723	showSizer.Add(lineSizer)
2724	showSizer.Add((0,5),0)
2725
2726	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2727
2728	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2729	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2730	unitCellBox.SetValue(drawingData['unitCellBox'])
2731	line2Sizer.Add(unitCellBox,0,wx.ALIGN_CENTER_VERTICAL)
2732
2733	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2734	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2735	showHydrogen.SetValue(drawingData['showHydrogen'])
2736	line2Sizer.Add(showHydrogen,0,wx.ALIGN_CENTER_VERTICAL)
2737
2738	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2739	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2740	showRB.SetValue(drawingData['showRigidBodies'])
2741	line2Sizer.Add(showRB,0,wx.ALIGN_CENTER_VERTICAL)
2742
2743	showSizer.Add(line2Sizer)
2744	return showSizer
2745
2746	def RadSizer():
2747
2748	def OnSizeHatoms(event):
2749	try:
2750	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2751	except ValueError:
2752	value = 0.5
2753	drawingData['sizeH'] = value
2754	sizeH.SetValue("%.2f"%(value))
2755	G2plt.PlotStructure(G2frame,data)
2756
2757	def OnRadFactor(event):
2758	try:
2759	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2760	except ValueError:
2761	value = 0.85
2762	drawingData['radiusFactor'] = value
2763	radFactor.SetValue("%.2f"%(value))
2764	FindBondsDraw()
2765	G2plt.PlotStructure(G2frame,data)
2766
2767	radSizer = wx.BoxSizer(wx.HORIZONTAL)
2768	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,wx.ALIGN_CENTER_VERTICAL)
2769	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2770	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
2771	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
2772	radSizer.Add(sizeH,0,wx.ALIGN_CENTER_VERTICAL)
2773
2774	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,wx.ALIGN_CENTER_VERTICAL)
2775	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2776	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
2777	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
2778	radSizer.Add(radFactor,0,wx.ALIGN_CENTER_VERTICAL)
2779	return radSizer
2780
2781	# UpdateDrawOptions exectable code starts here
2782	generalData = data['General']
2783	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2784	SetupDrawingData()
2785	drawingData = data['Drawing']
2786	if generalData['Type'] == 'nuclear':
2787	pickChoice = ['Atoms','Bonds','Torsions','Planes']
2788	elif generalData['Type'] == 'macromolecular':
2789	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
2790
2791	G2frame.dataFrame.SetStatusText('')
2792	if drawOptions.GetSizer():
2793	drawOptions.GetSizer().Clear(True)
2794	mainSizer = wx.BoxSizer(wx.VERTICAL)
2795	mainSizer.Add((5,5),0)
2796	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,wx.ALIGN_CENTER_VERTICAL)
2797	mainSizer.Add((5,5),0)
2798	mainSizer.Add(SlopSizer(),0)
2799	mainSizer.Add((5,5),0)
2800	mainSizer.Add(ShowSizer(),0,)
2801	mainSizer.Add((5,5),0)
2802	mainSizer.Add(RadSizer(),0,)
2803	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
2804
2805	################################################################################
2806	#### Texture routines
2807	################################################################################
2808
2809	def UpdateTexture():
2810	def SetSHCoef():
2811	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
2812	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
2813	SHCoeff = textureData['SH Coeff'][1]
2814	for cofName in SHCoeff:
2815	if cofName in cofNames:
2816	newSHCoef[cofName] = SHCoeff[cofName]
2817	return newSHCoef
2818
2819	def OnShOrder(event):
2820	Obj = event.GetEventObject()
2821	textureData['Order'] = int(Obj.GetValue())
2822	textureData['SH Coeff'][1] = SetSHCoef()
2823	wx.CallAfter(UpdateTexture)
2824	G2plt.PlotTexture(G2frame,data)
2825
2826	def OnShModel(event):
2827	Obj = event.GetEventObject()
2828	textureData['Model'] = Obj.GetValue()
2829	textureData['SH Coeff'][1] = SetSHCoef()
2830	wx.CallAfter(UpdateTexture)
2831	G2plt.PlotTexture(G2frame,data)
2832
2833	def OnSHRefine(event):
2834	Obj = event.GetEventObject()
2835	textureData['SH Coeff'][0] = Obj.GetValue()
2836
2837	def OnSHShow(event):
2838	Obj = event.GetEventObject()
2839	textureData['SHShow'] = Obj.GetValue()
2840	wx.CallAfter(UpdateTexture)
2841
2842	def OnProjSel(event):
2843	Obj = event.GetEventObject()
2844	G2frame.Projection = Obj.GetValue()
2845	G2plt.PlotTexture(G2frame,data)
2846
2847	def OnColorSel(event):
2848	Obj = event.GetEventObject()
2849	G2frame.ContourColor = Obj.GetValue()
2850	G2plt.PlotTexture(G2frame,data)
2851
2852	def OnAngRef(event):
2853	Obj = event.GetEventObject()
2854	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
2855
2856	def OnAngValue(event):
2857	Obj = event.GetEventObject()
2858	try:
2859	value = float(Obj.GetValue())
2860	except ValueError:
2861	value = textureData[valIndx[Obj.GetId()]][1]
2862	Obj.SetValue('%8.2f'%(value))
2863	textureData[valIndx[Obj.GetId()]][1] = value
2864
2865	def OnODFValue(event):
2866	Obj = event.GetEventObject()
2867	try:
2868	value = float(Obj.GetValue())
2869	except ValueError:
2870	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
2871	Obj.SetValue('%8.3f'%(value))
2872	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
2873	G2plt.PlotTexture(G2frame,data)
2874
2875	def OnPfType(event):
2876	Obj = event.GetEventObject()
2877	textureData['PlotType'] = Obj.GetValue()
2878	wx.CallAfter(UpdateTexture)
2879	G2plt.PlotTexture(G2frame,data)
2880
2881	def OnPFValue(event):
2882	Obj = event.GetEventObject()
2883	Saxis = Obj.GetValue().split()
2884	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2885	try:
2886	hkl = [int(Saxis[i]) for i in range(3)]
2887	except (ValueError,IndexError):
2888	hkl = textureData['PFhkl']
2889	if not np.any(np.array(hkl)): #can't be all zeros!
2890	hkl = textureData['PFhkl']
2891	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
2892	textureData['PFhkl'] = hkl
2893	else:
2894	try:
2895	xyz = [float(Saxis[i]) for i in range(3)]
2896	except (ValueError,IndexError):
2897	xyz = textureData['PFxyz']
2898	if not np.any(np.array(xyz)): #can't be all zeros!
2899	xyz = textureData['PFxyz']
2900	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
2901	textureData['PFxyz'] = xyz
2902	G2plt.PlotTexture(G2frame,data)
2903
2904	# UpdateTexture executable starts here
2905	G2frame.dataFrame.SetStatusText('')
2906	generalData = data['General']
2907	SGData = generalData['SGData']
2908	try:
2909	textureData = generalData['SH Texture']
2910	except KeyError: #fix old files!
2911	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
2912	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
2913	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
2914	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
2915	if 'SHShow' not in textureData: #another fix
2916	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2917	try: #another fix!
2918	x = textureData['PlotType']
2919	except KeyError:
2920	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2921	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
2922	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
2923	if generalData['doPawley'] and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Sequental results'):
2924	G2frame.dataFrame.RefineTexture.Enable(True)
2925	shAngles = ['omega','chi','phi']
2926	if Texture.GetSizer():
2927	Texture.GetSizer().Clear(True)
2928	mainSizer = wx.BoxSizer(wx.VERTICAL)
2929	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
2930	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,wx.ALIGN_CENTER_VERTICAL)
2931	titleSizer.Add(wx.StaticText(Texture,-1,
2932	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
2933	0,wx.ALIGN_CENTER_VERTICAL)
2934	mainSizer.Add(titleSizer,0)
2935	mainSizer.Add((0,5),0)
2936	shSizer = wx.FlexGridSizer(1,6,5,5)
2937	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,wx.ALIGN_CENTER_VERTICAL)
2938	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
2939	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2940	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
2941	shSizer.Add(shModel,0,wx.ALIGN_CENTER_VERTICAL)
2942	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,wx.ALIGN_CENTER_VERTICAL)
2943	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
2944	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2945	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
2946	shSizer.Add(shOrder,0,wx.ALIGN_CENTER_VERTICAL)
2947	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
2948	shRef.SetValue(textureData['SH Coeff'][0])
2949	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
2950	shSizer.Add(shRef,0,wx.ALIGN_CENTER_VERTICAL)
2951	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
2952	shShow.SetValue(textureData['SHShow'])
2953	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
2954	shSizer.Add(shShow,0,wx.ALIGN_CENTER_VERTICAL)
2955	mainSizer.Add(shSizer,0,0)
2956	mainSizer.Add((0,5),0)
2957	PTSizer = wx.FlexGridSizer(2,4,5,5)
2958	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,wx.ALIGN_CENTER_VERTICAL)
2959	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
2960	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
2961	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2962	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
2963	PTSizer.Add(pfType,0,wx.ALIGN_CENTER_VERTICAL)
2964	if 'Axial' not in textureData['PlotType']:
2965	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,wx.ALIGN_CENTER_VERTICAL)
2966	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
2967	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2968	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
2969	PTSizer.Add(projSel,0,wx.ALIGN_CENTER_VERTICAL)
2970	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2971	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,wx.ALIGN_CENTER_VERTICAL)
2972	PH = textureData['PFhkl']
2973	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
2974	else:
2975	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,wx.ALIGN_CENTER_VERTICAL)
2976	PX = textureData['PFxyz']
2977	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
2978	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
2979	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
2980	PTSizer.Add(pfVal,0,wx.ALIGN_CENTER_VERTICAL)
2981	if 'Axial' not in textureData['PlotType']:
2982	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,wx.ALIGN_CENTER_VERTICAL)
2983	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2984	choice.sort()
2985	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
2986	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2987	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
2988	PTSizer.Add(colorSel,0,wx.ALIGN_CENTER_VERTICAL)
2989	mainSizer.Add(PTSizer,0,wx.ALIGN_CENTER_VERTICAL)
2990	mainSizer.Add((0,5),0)
2991	if textureData['SHShow']:
2992	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,wx.ALIGN_CENTER_VERTICAL)
2993	mainSizer.Add((0,5),0)
2994	ODFSizer = wx.FlexGridSizer(2,8,2,2)
2995	ODFIndx = {}
2996	ODFkeys = textureData['SH Coeff'][1].keys()
2997	ODFkeys.sort()
2998	for item in ODFkeys:
2999	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,wx.ALIGN_CENTER_VERTICAL)
3000	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3001	ODFIndx[ODFval.GetId()] = item
3002	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3003	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3004	ODFSizer.Add(ODFval,0,wx.ALIGN_CENTER_VERTICAL)
3005	mainSizer.Add(ODFSizer,0,wx.ALIGN_CENTER_VERTICAL)
3006	mainSizer.Add((0,5),0)
3007	mainSizer.Add((0,5),0)
3008	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,wx.ALIGN_CENTER_VERTICAL)
3009	mainSizer.Add((0,5),0)
3010	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3011	angIndx = {}
3012	valIndx = {}
3013	for item in ['Sample omega','Sample chi','Sample phi']:
3014	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3015	angRef.SetValue(textureData[item][0])
3016	angIndx[angRef.GetId()] = item
3017	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3018	angSizer.Add(angRef,0,wx.ALIGN_CENTER_VERTICAL)
3019	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3020	valIndx[angVal.GetId()] = item
3021	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3022	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3023	angSizer.Add(angVal,0,wx.ALIGN_CENTER_VERTICAL)
3024	angSizer.Add((5,0),0)
3025	mainSizer.Add(angSizer,0,wx.ALIGN_CENTER_VERTICAL)
3026	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3027
3028	################################################################################
3029	##### DData routines - GUI stuff in GSASIIddataGUI.py
3030	################################################################################
3031
3032	def OnHklfAdd(event):
3033	UseList = data['Histograms']
3034	keyList = UseList.keys()
3035	TextList = []
3036	if G2frame.PatternTree.GetCount():
3037	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3038	while item:
3039	name = G2frame.PatternTree.GetItemText(item)
3040	if name not in keyList and 'HKLF' in name:
3041	TextList.append(name)
3042	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3043	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3044	try:
3045	if dlg.ShowModal() == wx.ID_OK:
3046	result = dlg.GetSelections()
3047	for i in result:
3048	histoName = TextList[i]
3049	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3050	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3051	'Extinction':['Lorentzian','None',
3052	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3053	wx.BeginBusyCursor()
3054	UpdateHKLFdata(histoName)
3055	wx.EndBusyCursor()
3056	data['Histograms'] = UseList
3057	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3058	finally:
3059	dlg.Destroy()
3060
3061	def UpdateHKLFdata(histoName):
3062	generalData = data['General']
3063	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3064	reflData = G2frame.PatternTree.GetItemPyData(Id)[1]
3065	SGData = generalData['SGData']
3066	Cell = generalData['Cell'][1:7]
3067	G,g = G2lat.cell2Gmat(Cell)
3068	for ref in reflData:
3069	H = ref[:3]
3070	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3071	iabsnt,ref[3],ref[11],ref[12] = G2spc.GenHKLf(H,SGData)
3072	G2frame.PatternTree.SetItemPyData(Id,[histoName,reflData])
3073
3074	def OnPwdrAdd(event):
3075	generalData = data['General']
3076	SGData = generalData['SGData']
3077	UseList = data['Histograms']
3078	newList = []
3079	NShkl = len(G2spc.MustrainNames(SGData))
3080	NDij = len(G2spc.HStrainNames(SGData))
3081	keyList = UseList.keys()
3082	TextList = ['All PWDR']
3083	if G2frame.PatternTree.GetCount():
3084	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3085	while item:
3086	name = G2frame.PatternTree.GetItemText(item)
3087	if name not in keyList and 'PWDR' in name:
3088	TextList.append(name)
3089	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3090	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3091	try:
3092	if dlg.ShowModal() == wx.ID_OK:
3093	result = dlg.GetSelections()
3094	for i in result: newList.append(TextList[i])
3095	if 'All PWDR' in newList:
3096	newList = TextList[1:]
3097	for histoName in newList:
3098	pId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3099	UseList[histoName] = {'Histogram':histoName,'Show':False,
3100	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3101	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3102	[1.,1.,1.,0.,0.,0.],6*[False,]],
3103	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3104	NShkl[0.01,],NShkl[False,]],
3105	'HStrain':[NDij[0.0,],NDij[False,]],
3106	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3107	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,pId,'Reflection Lists'))
3108	refList[generalData['Name']] = []
3109	data['Histograms'] = UseList
3110	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3111	finally:
3112	dlg.Destroy()
3113
3114	def OnDataDelete(event):
3115	UseList = data['Histograms']
3116	keyList = ['All',]+UseList.keys()
3117	keyList.sort()
3118	DelList = []
3119	if UseList:
3120	DelList = []
3121	dlg = wx.MultiChoiceDialog(G2frame,
3122	'Which histogram to delete from this phase?', 'Delete histogram',
3123	keyList, wx.CHOICEDLG_STYLE)
3124	try:
3125	if dlg.ShowModal() == wx.ID_OK:
3126	result = dlg.GetSelections()
3127	for i in result:
3128	DelList.append(keyList[i])
3129	if 'All' in DelList:
3130	DelList = keyList[1:]
3131	for i in DelList:
3132	del UseList[i]
3133	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3134	finally:
3135	dlg.Destroy()
3136
3137	################################################################################
3138	##### Rigid bodies
3139	################################################################################
3140
3141	def FillRigidBodyGrid(refresh=True):
3142	'''Fill the Rigid Body Phase information tab page.
3143	Note that the page is a ScrolledWindow, not a Grid
3144	'''
3145	def OnThermSel(event): #needs to be seen by VecRbSizer!
3146	Obj = event.GetEventObject()
3147	RBObj = Indx[Obj.GetId()]
3148	val = Obj.GetValue()
3149	Ttype = 'A'
3150	if val == 'Uiso':
3151	Ttype = 'I'
3152	RBObj['ThermalMotion'][0] = 'Uiso'
3153	elif val == 'T':
3154	RBObj['ThermalMotion'][0] = 'T'
3155	elif val == 'TL':
3156	RBObj['ThermalMotion'][0] = 'TL'
3157	elif val == 'TLS':
3158	RBObj['ThermalMotion'][0] = 'TLS'
3159	wx.CallAfter(FillRigidBodyGrid,True)
3160	if val != 'None':
3161	cia = data['General']['AtomPtrs'][3]
3162	for i,id in enumerate(RBObj['Ids']):
3163	data['Atoms'][AtLookUp[id]][cia] = Ttype
3164	G2plt.PlotStructure(G2frame,data)
3165
3166	def ThermDataSizer(RBObj,rbType):
3167
3168	def OnThermval(event):
3169	Obj = event.GetEventObject()
3170	item = Indx[Obj.GetId()]
3171	try:
3172	val = float(Obj.GetValue())
3173	RBObj['ThermalMotion'][1][item] = val
3174	except ValueError:
3175	pass
3176	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3177	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3178	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3179	cia = data['General']['AtomPtrs'][3]
3180	for i,id in enumerate(RBObj['Ids']):
3181	if Uout[i][0] == 'I':
3182	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3183	else:
3184	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3185	G2plt.PlotStructure(G2frame,data)
3186
3187	def OnTLSRef(event):
3188	Obj = event.GetEventObject()
3189	item = Indx[Obj.GetId()]
3190	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3191
3192	thermSizer = wx.FlexGridSizer(1,9,5,5)
3193	model = RBObj['ThermalMotion']
3194	if model[0] == 'Uiso':
3195	names = ['Uiso',]
3196	elif 'T' in model[0]:
3197	names = ['T11','T22','T33','T12','T13','T23']
3198	if 'L' in model[0]:
3199	names += ['L11','L22','L33','L12','L13','L23']
3200	if 'S' in model[0]:
3201	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3202	for i,name in enumerate(names):
3203	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,wx.ALIGN_CENTER_VERTICAL)
3204	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3205	style=wx.TE_PROCESS_ENTER)
3206	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3207	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3208	Indx[thermVal.GetId()] = i
3209	thermSizer.Add(thermVal)
3210	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3211	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3212	Tcheck.SetValue(model[2][i])
3213	Indx[Tcheck.GetId()] = i
3214	thermSizer.Add(Tcheck,0,wx.ALIGN_CENTER_VERTICAL)
3215	return thermSizer
3216
3217	def LocationSizer(RBObj,rbType):
3218
3219	def OnOrigRef(event):
3220	RBObj['Orig'][1] = Ocheck.GetValue()
3221
3222	def OnOrienRef(event):
3223	RBObj['Orient'][1] = Qcheck.GetValue()
3224
3225	def OnOrigX(event):
3226	Obj = event.GetEventObject()
3227	item = Indx[Obj.GetId()]
3228	try:
3229	val = float(Obj.GetValue())
3230	RBObj['Orig'][0][item] = val
3231	Obj.SetValue('%8.5f'%(val))
3232	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3233	for i,id in enumerate(RBObj['Ids']):
3234	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3235	data['Drawing']['Atoms'] = []
3236	UpdateDrawAtoms(atomStyle)
3237	G2plt.PlotStructure(G2frame,data)
3238	except ValueError:
3239	pass
3240
3241	def OnOrien(event):
3242	Obj = event.GetEventObject()
3243	item = Indx[Obj.GetId()]
3244	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3245	V = np.inner(Bmat,V)
3246	try:
3247	val = float(Obj.GetValue())
3248	if item:
3249	V[item-1] = val
3250	else:
3251	A = val
3252	Obj.SetValue('%8.5f'%(val))
3253	V = np.inner(Amat,V)
3254	Q = G2mth.AVdeg2Q(A,V)
3255	if not any(Q):
3256	raise ValueError
3257	RBObj['Orient'][0] = Q
3258	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3259	for i,id in enumerate(RBObj['Ids']):
3260	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3261	data['Drawing']['Atoms'] = []
3262	UpdateDrawAtoms(atomStyle)
3263	G2plt.PlotStructure(G2frame,data)
3264	except ValueError:
3265	pass
3266
3267	topSizer = wx.FlexGridSizer(2,6,5,5)
3268	Orig = RBObj['Orig'][0]
3269	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3270	Orien = [Orien,]
3271	Orien.extend(OrienV/nl.norm(OrienV))
3272	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,wx.ALIGN_CENTER_VERTICAL)
3273	for ix,x in enumerate(Orig):
3274	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3275	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3276	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3277	Indx[origX.GetId()] = ix
3278	topSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3279	topSizer.Add((5,0),)
3280	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3281	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3282	Ocheck.SetValue(RBObj['Orig'][1])
3283	topSizer.Add(Ocheck,0,wx.ALIGN_CENTER_VERTICAL)
3284	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,wx.ALIGN_CENTER_VERTICAL)
3285	for ix,x in enumerate(Orien):
3286	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3287	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3288	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3289	Indx[orien.GetId()] = ix
3290	topSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3291	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3292	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3293	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3294	Qcheck.SetValue(RBObj['Orient'][1])
3295	topSizer.Add(Qcheck)
3296	return topSizer
3297
3298	def ResrbSizer(RBObj):
3299	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3300
3301	def OnTorsionRef(event):
3302	Obj = event.GetEventObject()
3303	item = Indx[Obj.GetId()]
3304	RBObj['Torsions'][item][1] = Obj.GetValue()
3305
3306	def OnTorsion(event):
3307	Obj = event.GetEventObject()
3308	item = Indx[Obj.GetId()]
3309	try:
3310	val = float(Obj.GetValue())
3311	RBObj['Torsions'][item][0] = val
3312	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3313	for i,id in enumerate(RBObj['Ids']):
3314	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3315	except ValueError:
3316	pass
3317	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3318	data['Drawing']['Atoms'] = []
3319	UpdateDrawAtoms(atomStyle)
3320	drawAtoms.ClearSelection()
3321	G2plt.PlotStructure(G2frame,data)
3322
3323	def OnDelResRB(event):
3324	Obj = event.GetEventObject()
3325	RBId = Indx[Obj.GetId()]
3326	RBData['Residue'][RBId]['useCount'] -= 1
3327	RBObjs = data['RBModels']['Residue']
3328	for rbObj in RBObjs:
3329	if RBId == rbObj['RBId']:
3330	data['RBModels']['Residue'].remove(rbObj)
3331	G2plt.PlotStructure(G2frame,data)
3332	wx.CallAfter(FillRigidBodyGrid,True)
3333
3334	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3335	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3336	topLine = wx.BoxSizer(wx.HORIZONTAL)
3337	topLine.Add(wx.StaticText(RigidBodies,-1,
3338	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3339	rbId = RBObj['RBId']
3340	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3341	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3342	Indx[delRB.GetId()] = rbId
3343	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3344	resrbSizer.Add(topLine)
3345	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3346	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,wx.ALIGN_CENTER_VERTICAL)
3347	torSizer = wx.FlexGridSizer(1,6,5,5)
3348	for itors,tors in enumerate(RBObj['Torsions']):
3349	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,wx.ALIGN_CENTER_VERTICAL)
3350	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3351	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3352	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3353	Indx[torsTxt.GetId()] = itors
3354	torSizer.Add(torsTxt)
3355	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3356	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3357	torCheck.SetValue(tors[1])
3358	Indx[torCheck.GetId()] = itors
3359	torSizer.Add(torCheck,0,wx.ALIGN_CENTER_VERTICAL)
3360	resrbSizer.Add(torSizer)
3361	tchoice = ['None','Uiso','T','TL','TLS']
3362	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3363	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3364	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3365	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3366	Indx[thermSel.GetId()] = RBObj
3367	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3368	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3369	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3370	resrbSizer.Add(thermSizer)
3371	if RBObj['ThermalMotion'][0] != 'None':
3372	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3373	return resrbSizer
3374
3375	def VecrbSizer(RBObj):
3376	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3377
3378	def OnDelVecRB(event):
3379	Obj = event.GetEventObject()
3380	RBId = Indx[Obj.GetId()]
3381	RBData['Vector'][RBId]['useCount'] -= 1
3382	RBObjs = data['RBModels']['Vector']
3383	for rbObj in RBObjs:
3384	if RBId == rbObj['RBId']:
3385	data['RBModels']['Vector'].remove(rbObj)
3386	G2plt.PlotStructure(G2frame,data)
3387	wx.CallAfter(FillRigidBodyGrid,True)
3388
3389	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3390	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3391	topLine = wx.BoxSizer(wx.HORIZONTAL)
3392	topLine.Add(wx.StaticText(RigidBodies,-1,
3393	'Name: '+RBObj['RBname']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3394	rbId = RBObj['RBId']
3395	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3396	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3397	Indx[delRB.GetId()] = rbId
3398	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3399	vecrbSizer.Add(topLine)
3400	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3401	tchoice = ['None','Uiso','T','TL','TLS']
3402	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3403	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3404	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3405	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3406	Indx[thermSel.GetId()] = RBObj
3407	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3408	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3409	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3410	vecrbSizer.Add(thermSizer)
3411	if RBObj['ThermalMotion'][0] != 'None':
3412	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3413	return vecrbSizer
3414
3415	# FillRigidBodyGrid executable code starts here
3416	if refresh:
3417	RigidBodies.DestroyChildren()
3418	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3419	general = data['General']
3420	cx = general['AtomPtrs'][0]
3421	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3422	RBData = G2frame.PatternTree.GetItemPyData(
3423	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3424	Indx = {}
3425	atomStyle = 'balls & sticks'
3426	if 'macro' in general['Type']:
3427	atomStyle = 'sticks'
3428	G2frame.dataFrame.SetStatusText('')
3429	mainSizer = wx.BoxSizer(wx.VERTICAL)
3430	if not data['RBModels']:
3431	mainSizer.Add((5,5),0)
3432	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,wx.ALIGN_CENTER_VERTICAL)
3433	mainSizer.Add((5,5),0)
3434	if 'Residue' in data['RBModels']:
3435	mainSizer.Add((5,5),0)
3436	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3437	mainSizer.Add((5,5),0)
3438	for RBObj in data['RBModels']['Residue']:
3439	mainSizer.Add(ResrbSizer(RBObj))
3440	if 'Vector' in data['RBModels']:
3441	mainSizer.Add((5,5),0)
3442	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3443	mainSizer.Add((5,5),0)
3444	for RBObj in data['RBModels']['Vector']:
3445	mainSizer.Add(VecrbSizer(RBObj))
3446
3447	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3448
3449	def OnRBCopyParms(event):
3450	RBObjs = []
3451	for rbType in ['Vector','Residue']:
3452	RBObjs += data['RBModels'].get(rbType,[])
3453	if not len(RBObjs):
3454	print '** ERROR - no rigid bodies defined **'
3455	return
3456	if len(RBObjs) == 1:
3457	print '** INFO - only one rigid body defined; nothing to copy to **'
3458	return
3459	Source = []
3460	sourceRB = {}
3461	for RBObj in RBObjs:
3462	Source.append(RBObj['RBname'])
3463	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3464	if dlg.ShowModal() == wx.ID_OK:
3465	sel = dlg.GetSelection()
3466	name = Source[sel]
3467	for item in ['Orig','Orient','ThermalMotion']:
3468	sourceRB.update({item:RBObjs[sel][item],})
3469	dlg.Destroy()
3470	if not sourceRB:
3471	return
3472	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3473	if dlg.ShowModal() == wx.ID_OK:
3474	sel = dlg.GetSelections()
3475	for x in sel:
3476	RBObjs[x].update(copy.copy(sourceRB))
3477	G2plt.PlotStructure(G2frame,data)
3478	wx.CallAfter(FillRigidBodyGrid(True))
3479
3480	def OnRBAssign(event):
3481
3482	G2frame.dataFrame.SetStatusText('')
3483	RBData = G2frame.PatternTree.GetItemPyData(
3484	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3485	rbNames = {}
3486	for rbVec in RBData['Vector']:
3487	if rbVec != 'AtInfo':
3488	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3489	for rbRes in RBData['Residue']:
3490	if rbRes != 'AtInfo':
3491	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3492	if not rbNames:
3493	print '** ERROR - no rigid bodies defined **'
3494	return
3495	general = data['General']
3496	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3497	cx,ct = general['AtomPtrs'][:2]
3498	atomData = data['Atoms']
3499	Indx = {}
3500	atInd = [-1,-1,-1]
3501	data['testRBObj'] = {}
3502
3503	def Draw():
3504
3505	def OnOk(event):
3506	rbType = data['testRBObj']['rbType']
3507	RBObjs = data['RBModels'].get(rbType,[])
3508	rbObj = data['testRBObj']['rbObj']
3509	rbId = rbObj['RBId']
3510	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3511	Ids = []
3512	dmax = 0.0
3513	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3514	for xyz in newXYZ:
3515	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3516	dmax = max(dmax,np.min(dist))
3517	id = np.argmin(dist)
3518	Ids.append(atomData[id][-1])
3519	atomData[id][cx:cx+3] = xyz
3520	if dmax > 0.5:
3521	print '** WARNING - some atoms not found or misidentified **'
3522	print '** check torsion angles & try again **'
3523	OkBtn.SetLabel('Not Ready')
3524	OkBtn.Enable(False)
3525	return
3526	rbObj['Ids'] = Ids
3527	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3528	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3529	RBObjs.append(rbObj)
3530	data['RBModels'][rbType] = RBObjs
3531	RBData[rbType][rbId]['useCount'] += 1
3532	del data['testRBObj']
3533	G2plt.PlotStructure(G2frame,data)
3534	FillRigidBodyGrid(True)
3535
3536	def OnCancel(event):
3537	del data['testRBObj']
3538	FillRigidBodyGrid(True)
3539
3540	def OnRBSel(event):
3541	selection = rbSel.GetValue()
3542	rbType,rbId = rbNames[selection]
3543	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3544	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3545	data['testRBObj']['rbType'] = rbType
3546	data['testRBObj']['rbData'] = RBData
3547	data['testRBObj']['Sizers'] = {}
3548	rbRef = RBData[rbType][rbId]['rbRef']
3549	data['testRBObj']['rbRef'] = rbRef
3550	refType = []
3551	refName = []
3552	for ref in rbRef[:3]:
3553	reftype = data['testRBObj']['rbAtTypes'][ref]
3554	refType.append(reftype)
3555	refName.append(reftype+' '+str(rbRef[0]))
3556	atNames,AtNames = fillAtNames(refType,atomData,ct)
3557	data['testRBObj']['atNames'] = atNames
3558	data['testRBObj']['AtNames'] = AtNames
3559	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3560	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3561	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3562	data['testRBObj']['torAtms'] = []
3563	for item in RBData[rbType][rbId].get('rbSeq',[]):
3564	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3565	data['testRBObj']['torAtms'].append([-1,-1,-1])
3566	Draw()
3567
3568	def fillAtNames(refType,atomData,ct):
3569	atNames = [{},{},{}]
3570	AtNames = {}
3571	for iatm,atom in enumerate(atomData):
3572	AtNames[atom[ct-1]] = iatm
3573	for i,reftype in enumerate(refType):
3574	if atom[ct] == reftype:
3575	atNames[i][atom[ct-1]] = iatm
3576	return atNames,AtNames
3577
3578	def OnAtOrigPick(event):
3579	Obj = event.GetEventObject()
3580	item = Indx[Obj.GetId()]
3581	atName = Obj.GetValue()
3582	rbType = data['testRBObj']['rbType']
3583	atInd[0] = atNames[item][atName]
3584	if 'Vector' in rbType:
3585	rbObj = data['testRBObj']['rbObj']
3586	rbId = rbObj['RBId']
3587	rbRef = data['testRBObj']['rbRef']
3588	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3589	nref = atNames[item][atName]
3590	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3591	Nxyz = np.array(atomData[nref][cx:cx+3])
3592	Orig = Nxyz-Oxyz
3593	data['testRBObj']['rbObj']['Orig'][0] = Orig
3594	else:
3595	Orig = atomData[atNames[item][atName]][cx:cx+3]
3596	data['testRBObj']['rbObj']['Orig'][0] = Orig
3597	for x,item in zip(Orig,Xsizers):
3598	item.SetLabel('%10.5f'%(x))
3599	G2plt.PlotStructure(G2frame,data)
3600
3601	def OnAtQPick(event):
3602	Obj = event.GetEventObject()
3603	item = Indx[Obj.GetId()]
3604	atName = Obj.GetValue()
3605	atInd[item] = atNames[item][atName]
3606	if any([x<0 for x in atInd]):
3607	return
3608	OkBtn.SetLabel('OK')
3609	OkBtn.Enable(True)
3610	rbType = data['testRBObj']['rbType']
3611	rbObj = data['testRBObj']['rbObj']
3612	rbId = rbObj['RBId']
3613	rbRef = data['testRBObj']['rbRef']
3614	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3615	rbOrig = rbXYZ[rbRef[0]]
3616	VAR = rbXYZ[rbRef[1]]-rbOrig
3617	VBR = rbXYZ[rbRef[2]]-rbOrig
3618	if rbType == 'Vector':
3619	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3620	else:
3621	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3622	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3623	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3624	VCC = np.cross(VAR,VAC)
3625	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3626	VAR = G2mth.prodQVQ(QuatA,VAR)
3627	VBR = G2mth.prodQVQ(QuatA,VBR)
3628	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3629	QuatC = G2mth.prodQQ(QuatB,QuatA)
3630	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3631	for x,item in zip(QuatC,Osizers):
3632	item.SetLabel('%10.4f'%(x))
3633	if rbType == 'Vector':
3634	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3635	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3636	Orig = Nxyz-Oxyz
3637	data['testRBObj']['rbObj']['Orig'][0] = Orig
3638	for x,item in zip(Orig,Xsizers):
3639	item.SetLabel('%10.5f'%(x))
3640	G2plt.PlotStructure(G2frame,data)
3641
3642	def OnTorAngle(event):
3643	OkBtn.SetLabel('OK')
3644	OkBtn.Enable(True)
3645	Obj = event.GetEventObject()
3646	[tor,torSlide] = Indx[Obj.GetId()]
3647	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3648	try:
3649	value = float(Obj.GetValue())
3650	except ValueError:
3651	value = Tors[0]
3652	Tors[0] = value
3653	Obj.SetValue('%8.3f'%(value))
3654	torSlide.SetValue(int(value*10))
3655	G2plt.PlotStructure(G2frame,data)
3656
3657	def OnTorSlide(event):
3658	OkBtn.SetLabel('OK')
3659	OkBtn.Enable(True)
3660	Obj = event.GetEventObject()
3661	tor,ang = Indx[Obj.GetId()]
3662	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3663	val = float(Obj.GetValue())/10.
3664	Tors[0] = val
3665	ang.SetValue('%8.3f'%(val))
3666	G2plt.PlotStructure(G2frame,data)
3667
3668	if len(data['testRBObj']):
3669	G2plt.PlotStructure(G2frame,data)
3670
3671	RigidBodies.DestroyChildren()
3672	mainSizer = wx.BoxSizer(wx.VERTICAL)
3673	mainSizer.Add((5,5),0)
3674	if data['testRBObj']:
3675	Xsizers = []
3676	Osizers = []
3677	rbObj = data['testRBObj']['rbObj']
3678	rbName = rbObj['RBname']
3679	rbId = rbObj['RBId']
3680	Orig = rbObj['Orig'][0]
3681	Orien = rbObj['Orient'][0]
3682	rbRef = data['testRBObj']['rbRef']
3683	Torsions = rbObj['Torsions']
3684	refName = []
3685	for ref in rbRef:
3686	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3687	atNames = data['testRBObj']['atNames']
3688	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3689	0,wx.ALIGN_CENTER_VERTICAL)
3690	mainSizer.Add((5,5),0)
3691	OriSizer = wx.FlexGridSizer(1,5,5,5)
3692	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,wx.ALIGN_CENTER_VERTICAL)
3693	for ix,x in enumerate(Orig):
3694	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3695	OriSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3696	Xsizers.append(origX)
3697	OriSizer.Add((5,0),)
3698	if len(atomData):
3699	choice = atNames[0].keys()
3700	choice.sort()
3701	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3702	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,wx.ALIGN_CENTER_VERTICAL)
3703	for ix,x in enumerate(Orien):
3704	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3705	OriSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3706	Osizers.append(orien)
3707	data['testRBObj']['Sizers']['Osizers'] = Osizers
3708	mainSizer.Add(OriSizer)
3709	mainSizer.Add((5,5),0)
3710	RefSizer = wx.FlexGridSizer(1,7,5,5)
3711	if len(atomData):
3712	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,wx.ALIGN_CENTER_VERTICAL)
3713	for i in [0,1,2]:
3714	choice = ['',]+atNames[i].keys()
3715	choice.sort()
3716	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,wx.ALIGN_CENTER_VERTICAL)
3717	atPick = wx.ComboBox(RigidBodies,-1,value='',
3718	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3719	if i:
3720	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3721	else:
3722	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3723	Indx[atPick.GetId()] = i
3724	RefSizer.Add(atPick,0,wx.ALIGN_CENTER_VERTICAL)
3725	mainSizer.Add(RefSizer)
3726	mainSizer.Add((5,5),0)
3727	if Torsions:
3728	AtNames = data['testRBObj']['AtNames']
3729	rbAtTypes = data['testRBObj']['rbAtTypes']
3730	rbSeq = RBData['Residue'][rbId]['rbSeq']
3731	TorSizer = wx.FlexGridSizer(1,4)
3732	TorSizer.AddGrowableCol(1,1)
3733	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3734	torName = ''
3735	for item in [seq[0],seq[1],seq[3][0]]:
3736	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3737	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,wx.ALIGN_CENTER_VERTICAL)
3738	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3739	torSlide.SetRange(0,3600)
3740	torSlide.SetValue(int(torsion[0]*10.))
3741	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3742	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3743	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,wx.ALIGN_CENTER_VERTICAL)
3744	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
3745	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
3746	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
3747	Indx[torSlide.GetId()] = [t,ang]
3748	Indx[ang.GetId()] = [t,torSlide]
3749	TorSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
3750	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
3751	else:
3752	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,wx.ALIGN_CENTER_VERTICAL)
3753	else:
3754	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,wx.ALIGN_CENTER_VERTICAL)
3755	mainSizer.Add((5,5),0)
3756	topSizer = wx.BoxSizer(wx.HORIZONTAL)
3757	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,wx.ALIGN_CENTER_VERTICAL)
3758	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
3759	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3760	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
3761	topSizer.Add((5,5),0)
3762	topSizer.Add(rbSel,0,wx.ALIGN_CENTER_VERTICAL)
3763	mainSizer.Add(topSizer)
3764
3765	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
3766	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
3767	OkBtn.Enable(False)
3768	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
3769	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
3770	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
3771	btnSizer.Add((20,20),1)
3772	btnSizer.Add(OkBtn)
3773	btnSizer.Add(CancelBtn)
3774	btnSizer.Add((20,20),1)
3775	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
3776	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3777	Draw()
3778
3779	def OnAutoFindResRB(event):
3780	RBData = G2frame.PatternTree.GetItemPyData(
3781	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3782	rbKeys = RBData['Residue'].keys()
3783	rbKeys.remove('AtInfo')
3784	if not len(rbKeys):
3785	print '** ERROR - no residue rigid bodies are defined **'
3786	return
3787	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
3788	RBIds = dict(zip(RBNames,rbKeys))
3789	general = data['General']
3790	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3791	Atoms = data['Atoms']
3792	AtLookUp = G2mth.FillAtomLookUp(Atoms)
3793	if 'macro' not in general['Type']:
3794	print '** ERROR - this phase is not a macromolecule **'
3795	return
3796	if not len(Atoms):
3797	print '** ERROR - this phase has no atoms **'
3798	return
3799	RBObjs = []
3800	cx,ct = general['AtomPtrs'][:2]
3801	iatm = 0
3802	wx.BeginBusyCursor()
3803	try:
3804	while iatm < len(Atoms):
3805	atom = Atoms[iatm]
3806	res = atom[1].strip()
3807	numChain = ' %s %s'%(atom[0],atom[2])
3808	if res not in RBIds or atom[ct-1] == 'OXT':
3809	iatm += 1
3810	continue #skip for OXT, water molecules, etc.
3811	rbRes = RBData['Residue'][RBIds[res]]
3812	rbRef = rbRes['rbRef']
3813	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
3814	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
3815	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
3816	rbAtoms = []
3817	rbIds = []
3818	for iratm in range(len(rbRes['atNames'])):
3819	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
3820	rbIds.append(Atoms[iatm][20])
3821	iatm += 1 #puts this at beginning of next residue?
3822	Orig = rbAtoms[rbRef[0]]
3823	rbObj['RBId'] = RBIds[res]
3824	rbObj['Ids'] = rbIds
3825	rbObj['Orig'] = [Orig,False]
3826	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
3827	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
3828	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
3829	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
3830	VCC = np.cross(VAR,VAC)
3831	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3832	VAR = G2mth.prodQVQ(QuatA,VAR)
3833	VBR = G2mth.prodQVQ(QuatA,VBR)
3834	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3835	QuatC = G2mth.prodQQ(QuatB,QuatA)
3836	rbObj['Orient'] = [QuatC,' ']
3837	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3838	SXYZ = []
3839	TXYZ = []
3840	rbObj['Torsions'] = []
3841	for i,xyz in enumerate(rbRes['rbXYZ']):
3842	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
3843	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
3844	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
3845	VBR = SXYZ[Oatm]-SXYZ[Patm]
3846	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
3847	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
3848	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
3849	ang = 180.*D/np.pi
3850	rbObj['Torsions'].append([ang,False])
3851	for ride in Riders:
3852	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
3853	rbRes['useCount'] += 1
3854	RBObjs.append(rbObj)
3855	data['RBModels']['Residue'] = RBObjs
3856	for RBObj in RBObjs:
3857	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3858	for i,id in enumerate(RBObj['Ids']):
3859	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3860	finally:
3861	wx.EndBusyCursor()
3862	wx.CallAfter(FillRigidBodyGrid,True)
3863
3864	def OnRBRemoveAll(event):
3865	data['RBModels']['Residue'] = []
3866	data['RBModels']['Vector'] = []
3867	RBData = G2frame.PatternTree.GetItemPyData(
3868	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3869	for RBType in ['Vector','Residue']:
3870	for rbId in RBData[RBType]:
3871	RBData[RBType][rbId]['useCount'] = 0
3872	FillRigidBodyGrid(True)
3873
3874	def OnGlobalResRBTherm(event):
3875	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3876	RBObjs = data['RBModels']['Residue']
3877	names = ['None','Uiso','T','TL','TLS']
3878	cia = data['General']['AtomPtrs'][3]
3879	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
3880	if dlg.ShowModal() == wx.ID_OK:
3881	sel = dlg.GetSelection()
3882	parm = names[sel]
3883	Ttype = 'A'
3884	if parm == 'Uiso':
3885	Ttype = 'I'
3886	for rbObj in RBObjs:
3887	rbObj['ThermalMotion'][0] = parm
3888	if parm != 'None':
3889	for i,id in enumerate(rbObj['Ids']):
3890	data['Atoms'][AtLookUp[id]][cia] = Ttype
3891	dlg.Destroy()
3892	wx.CallAfter(FillRigidBodyGrid,True)
3893
3894	def OnGlobalResRBRef(event):
3895	RBObjs = data['RBModels']['Residue']
3896	names = ['Origin','Orient. angle','Full Orient.']
3897	nTor = 0
3898	for rbObj in RBObjs:
3899	nTor = max(nTor,len(rbObj['Torsions']))
3900	names += ['Torsion '+str(i) for i in range(nTor)]
3901	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
3902	names += ['Uiso',]
3903	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
3904	names += ['Tii','Tij','Lii','Lij','Sij']
3905	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
3906	names += ['Tii','Tij','Lii','Lij']
3907	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
3908	names += ['Tii','Tij']
3909
3910	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
3911	if dlg.ShowModal() == wx.ID_OK:
3912	sel = dlg.GetSelections()
3913	parms = []
3914	for x in sel:
3915	parms.append(names[x])
3916	wx.BeginBusyCursor()
3917	try:
3918	for rbObj in RBObjs:
3919	if 'Origin' in parms:
3920	rbObj['Orig'][1] = True
3921	else:
3922	rbObj['Orig'][1] = False
3923	if 'Full Orient.' in parms:
3924	rbObj['Orient'][1] = 'AV'
3925	elif 'Orient. angle' in parms:
3926	rbObj['Orient'][1] = 'A'
3927	else:
3928	rbObj['Orient'][1] = ' '
3929	for i in range(len(rbObj['Torsions'])):
3930	if 'Torsion '+str(i) in parms:
3931	rbObj['Torsions'][i][1] = True
3932	else:
3933	rbObj['Torsions'][i][1] = False
3934	if rbObj['ThermalMotion'][0] == 'Uiso':
3935	if 'Uiso' in parms:
3936	rbObj['ThermalMotion'][2][0] = True
3937	else:
3938	rbObj['ThermalMotion'][2][0] = False
3939	elif 'T' in rbObj['ThermalMotion'][0]:
3940	if 'Tii' in parms:
3941	rbObj['ThermalMotion'][2][0:2] = [True,True,True]
3942	else:
3943	rbObj['ThermalMotion'][2][0:2] = [False,False,False]
3944	if 'Tij' in parms:
3945	rbObj['ThermalMotion'][2][3:6] = [True,True,True]
3946	else:
3947	rbObj['ThermalMotion'][2][3:6] = [False,False,False]
3948	elif 'L' in rbObj['ThermalMotion'][0]:
3949	if 'Lii' in parms:
3950	rbObj['ThermalMotion'][2][6:9] = [True,True,True]
3951	else:
3952	rbObj['ThermalMotion'][2][6:9] = [False,False,False]
3953	if 'Lij' in parms:
3954	rbObj['ThermalMotion'][2][9:12] = [True,True,True]
3955	else:
3956	rbObj['ThermalMotion'][2][9:12] = [False,False,False]
3957	elif 'S' in rbObj['ThermalMotion'][0]:
3958	if 'Sij' in parms:
3959	rbObj['ThermalMotion'][2][12:20] = [True,True,True,True,True,True,True,True]
3960	else:
3961	rbObj['ThermalMotion'][2][12:20] = [False,False,False,False,False,False,False,False]
3962	finally:
3963	wx.EndBusyCursor()
3964	FillRigidBodyGrid()
3965
3966	################################################################################
3967	##### MC/SA routines
3968	################################################################################
3969
3970	def UpdateMCSA(refresh=True):
3971	Indx = {}
3972
3973	def OnPosRef(event):
3974	Obj = event.GetEventObject()
3975	model,item,ix = Indx[Obj.GetId()]
3976	model[item][1][ix] = Obj.GetValue()
3977
3978	def OnPosVal(event):
3979	Obj = event.GetEventObject()
3980	model,item,ix = Indx[Obj.GetId()]
3981	try:
3982	model[item][0][ix] = float(Obj.GetValue())
3983	except ValueError:
3984	pass
3985	Obj.SetValue("%.4f"%(model[item][0][ix]))
3986	G2plt.PlotStructure(G2frame,data)
3987
3988	def OnPosRange(event):
3989	Obj = event.GetEventObject()
3990	model,item,ix = Indx[Obj.GetId()]
3991	Range = Obj.GetValue().split()
3992	try:
3993	rmin,rmax = [float(Range[i]) for i in range(2)]
3994	if rmin >= rmax:
3995	raise ValueError
3996	except (ValueError,IndexError):
3997	rmin,rmax = model[item][2][ix]
3998	model[item][2][ix] = [rmin,rmax]
3999	Obj.SetValue('%.3f %.3f'%(rmin,rmax))
4000
4001	def atomSizer(model):
4002
4003	atomsizer = wx.FlexGridSizer(1,7,5,5)
4004	atomsizer.Add(wx.StaticText(MCSA,-1,' Atom: '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4005	for ix,item in enumerate(['x','y','z']):
4006	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4007	posRef.SetValue(model['Pos'][1][ix])
4008	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4009	Indx[posRef.GetId()] = [model,'Pos',ix]
4010	atomsizer.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4011	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4012	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4013	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4014	Indx[posVal.GetId()] = [model,'Pos',ix]
4015	atomsizer.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4016	atomsizer.Add((5,5),0)
4017	for ix,item in enumerate(['x','y','z']):
4018	atomsizer.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4019	rmin,rmax = model['Pos'][2][ix]
4020	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4021	Indx[posRange.GetId()] = [model,'Pos',ix]
4022	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4023	posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4024	atomsizer.Add(posRange,0,wx.ALIGN_CENTER_VERTICAL)
4025	return atomsizer
4026
4027	def rbSizer(model):
4028
4029	def OnOrVar(event):
4030	Obj = event.GetEventObject()
4031	model = Indx[Obj.GetId()]
4032	model['Ovar'] = Obj.GetValue()
4033
4034	def OnOriVal(event):
4035	Obj = event.GetEventObject()
4036	model,ix = Indx[Obj.GetId()]
4037	A,V = G2mth.Q2AVdeg(model['Ori'][0])
4038	if ix:
4039	Anew = A
4040	Vec = Obj.GetValue().split()
4041	try:
4042	Vnew = [float(Vec[i]) for i in range(3)]
4043	except ValueError:
4044	Vnew = V
4045	else:
4046	Vnew = V
4047	try:
4048	Anew = float(Obj.GetValue())
4049	except ValueError:
4050	Anew = A
4051	model['Ori'][0] = G2mth.AVdeg2Q(Anew,Vnew)
4052	G2plt.PlotStructure(G2frame,data)
4053	UpdateMCSA()
4054
4055	def OnMolCent(event):
4056	Obj = event.GetEventObject()
4057	model = Indx[Obj.GetId()]
4058	model['MolCent'][1] = Obj.GetValue()
4059	if model['MolCent'][1]:
4060	G2mth.SetMolCent(model,RBData)
4061	G2plt.PlotStructure(G2frame,data)
4062
4063	rbsizer = wx.BoxSizer(wx.VERTICAL)
4064	rbsizer1 = wx.FlexGridSizer(1,7,5,5)
4065	rbsizer1.Add(wx.StaticText(MCSA,-1,model['Type']+': '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4066	for ix,item in enumerate(['x','y','z']):
4067	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4068	posRef.SetValue(model['Pos'][1][ix])
4069	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4070	Indx[posRef.GetId()] = [model,'Pos',ix]
4071	rbsizer1.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4072	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4073	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4074	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4075	Indx[posVal.GetId()] = [model,'Pos',ix]
4076	rbsizer1.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4077	molcent = wx.CheckBox(MCSA,-1,label=' Use mol. center? ')
4078	molcent.SetValue(model['MolCent'][1])
4079	molcent.Bind(wx.EVT_CHECKBOX,OnMolCent)
4080	Indx[molcent.GetId()] = model
4081	rbsizer1.Add(molcent,0,wx.ALIGN_CENTER_VERTICAL)
4082	for ix,item in enumerate(['x','y','z']):
4083	rbsizer1.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4084	rmin,rmax = model['Pos'][2][ix]
4085	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4086	Indx[posRange.GetId()] = [model,'Pos',ix]
4087	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4088	posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4089	rbsizer1.Add(posRange,0,wx.ALIGN_CENTER_VERTICAL)
4090
4091	rbsizer2 = wx.FlexGridSizer(1,6,5,5)
4092	Orien,OrienV = G2mth.Q2AVdeg(model['Ori'][0])
4093	Ori = [Orien,]+list(OrienV)
4094	rbsizer2.Add(wx.StaticText(MCSA,-1,'Oa: '),0,wx.ALIGN_CENTER_VERTICAL)
4095	angVal = wx.TextCtrl(MCSA,-1,'%.5f'%(Ori[0]),style=wx.TE_PROCESS_ENTER)
4096	angVal.Bind(wx.EVT_TEXT_ENTER,OnOriVal)
4097	angVal.Bind(wx.EVT_KILL_FOCUS,OnOriVal)
4098	Indx[angVal.GetId()] = [model,0]
4099	�