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source: trunk/GSASIIphsGUI.py @ 1071

Last change on this file since 1071 was 1071, checked in by vondreele, 10 years ago
change tolerance on RB atom matching; wasn't big enough
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1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2013-10-01 13:39:32 +0000 (Tue, 01 Oct 2013) $
5	# $Author: vondreele $
6	# $Revision: 1071 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1071 2013-10-01 13:39:32Z vondreele $
9	########### SVN repository information ###################
10	'''
11	GSASIIphsGUI: Phase GUI
12	-------------------------
13
14	Module to create the GUI for display of phase information
15	in the data display window when a phase is selected.
16	Phase information is stored in one or more
17	:ref:`Phase Tree Item <Phase_table>` objects.
18	Note that there are functions
19	that respond to some tabs in the phase GUI in other modules
20	(such as GSASIIddata).
21
22	'''
23	import os.path
24	import wx
25	import wx.grid as wg
26	import wx.lib.gridmovers as wgmove
27	import wx.wizard as wz
28	import matplotlib as mpl
29	import math
30	import copy
31	import time
32	import sys
33	import random as ran
34	import cPickle
35	import GSASIIpath
36	GSASIIpath.SetVersionNumber("$Revision: 1071 $")
37	import GSASIIlattice as G2lat
38	import GSASIIspc as G2spc
39	import GSASIIElem as G2elem
40	import GSASIIElemGUI as G2elemGUI
41	import GSASIIddataGUI as G2ddG
42	import GSASIIplot as G2plt
43	import GSASIIgrid as G2gd
44	import GSASIIIO as G2IO
45	import GSASIIstrMain as G2stMn
46	import GSASIImath as G2mth
47	import GSASIIpwd as G2pwd
48	import numpy as np
49	import numpy.linalg as nl
50	import numpy.ma as ma
51
52	VERY_LIGHT_GREY = wx.Colour(235,235,235)
53	WHITE = wx.Colour(255,255,255)
54	BLACK = wx.Colour(0,0,0)
55	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
56	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
57	# trig functions in degrees
58	sind = lambda x: np.sin(x*np.pi/180.)
59	tand = lambda x: np.tan(x*np.pi/180.)
60	cosd = lambda x: np.cos(x*np.pi/180.)
61	asind = lambda x: 180.*np.arcsin(x)/np.pi
62	acosd = lambda x: 180.*np.arccos(x)/np.pi
63
64	def SetPhaseWindow(mainFrame,phasePage,mainSizer):
65	phasePage.SetSizer(mainSizer)
66	Size = mainSizer.GetMinSize()
67	Size[0] += 40
68	Size[1] = max(Size[1],430) + 35
69	phasePage.SetSize(Size)
70	phasePage.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
71	mainFrame.setSizePosLeft(Size)
72
73	def UpdatePhaseData(G2frame,Item,data,oldPage):
74	'''Create the data display window contents when a phase is clicked on
75	in the man (data tree) window.
76	Called only from :meth:`GSASIIgrid.MovePatternTreeToGrid`,
77	which in turn is called from :meth:`GSASII.GSASII.OnPatternTreeSelChanged`
78	when a tree item is selected.
79
80	:param wx.frame G2frame: the main GSAS-II frame object
81	:param wx.TreeItemId Item: the tree item that was selected
82	:param dict data: all the information on the phase in a dictionary
83	:param int oldPage: This sets a tab to select when moving
84	from one phase to another, in which case the same tab is selected
85	to display first. This is set only when the previous data tree
86	selection is a phase, if not the value is None. The default action
87	is to bring up the General tab.
88
89	'''
90
91	#patch
92	if 'RBModels' not in data:
93	data['RBModels'] = {}
94	if 'MCSA' not in data:
95	data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[0.3,3.],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
96	if isinstance(data['MCSA']['Results'],dict):
97	data['MCSA']['Results'] = []
98	#end patch
99
100	global rbAtmDict
101	rbAtmDict = {}
102	if G2frame.dataDisplay:
103	G2frame.dataDisplay.Destroy()
104	PhaseName = G2frame.PatternTree.GetItemText(Item)
105	G2gd.SetDataMenuBar(G2frame)
106	G2frame.dataFrame.SetLabel('Phase Data for '+PhaseName)
107	G2frame.dataFrame.CreateStatusBar()
108	G2frame.dataDisplay = G2gd.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize())
109	G2frame.dataDisplay.gridList = [] # list of all grids in notebook
110
111	def SetupGeneral():
112	generalData = data['General']
113	atomData = data['Atoms']
114	generalData['AtomTypes'] = []
115	generalData['Isotopes'] = {}
116	# various patches
117	if 'Isotope' not in generalData:
118	generalData['Isotope'] = {}
119	if 'Data plot type' not in generalData:
120	generalData['Data plot type'] = 'Mustrain'
121	if 'POhkl' not in generalData:
122	generalData['POhkl'] = [0,0,1]
123	if 'Map' not in generalData:
124	generalData['Map'] = mapDefault
125	if 'Flip' not in generalData:
126	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
127	'k-factor':0.1,'k-Max':20.}
128	if 'doPawley' not in generalData:
129	generalData['doPawley'] = False
130	if 'Pawley dmin' not in generalData:
131	generalData['Pawley dmin'] = 1.0
132	if 'Pawley neg wt' not in generalData:
133	generalData['Pawley neg wt'] = 0.0
134	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
135	'MCSA controls' not in generalData:
136	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
137	'dmin':2.0,'Algorithm':'fast','Jump coeff':[0.95,0.5],'boltzmann':1.0,
138	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[]}
139	# end of patches
140	generalData['NoAtoms'] = {}
141	generalData['BondRadii'] = []
142	generalData['AngleRadii'] = []
143	generalData['vdWRadii'] = []
144	generalData['AtomMass'] = []
145	generalData['Color'] = []
146	generalData['Mydir'] = G2frame.dirname
147	cx,ct,cs,cia = [3,1,7,9]
148	if generalData['Type'] =='macromolecular':
149	cx,ct,cs,cia = [6,4,10,12]
150	generalData['AtomPtrs'] = [cx,ct,cs,cia]
151	for atom in atomData:
152	atom[ct] = atom[ct].lower().capitalize() #force to standard form
153	if generalData['AtomTypes'].count(atom[ct]):
154	generalData['NoAtoms'][atom[ct]] += atom[cs-1]*float(atom[cs+1])
155	elif atom[ct] != 'UNK':
156	Info = G2elem.GetAtomInfo(atom[ct])
157	generalData['AtomTypes'].append(atom[ct])
158	generalData['Z'] = Info['Z']
159	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
160	generalData['BondRadii'].append(Info['Drad'])
161	generalData['AngleRadii'].append(Info['Arad'])
162	generalData['vdWRadii'].append(Info['Vdrad'])
163	if atom[ct] in generalData['Isotope']:
164	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]][0])
165	else:
166	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
167	generalData['AtomMass'].append(Info['Mass'])
168	generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
169	generalData['Color'].append(Info['Color'])
170	F000X = 0.
171	F000N = 0.
172	for i,elem in enumerate(generalData['AtomTypes']):
173	F000X += generalData['NoAtoms'][elem]*generalData['Z']
174	isotope = generalData['Isotope'][elem]
175	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope][1]
176	generalData['F000X'] = F000X
177	generalData['F000N'] = F000N
178
179
180	################################################################################
181	##### General phase routines
182	################################################################################
183
184	def UpdateGeneral():
185	'''Draw the controls for the General phase data subpage
186	'''
187
188	""" This is the default dictionary structure for phase data
189	(taken from GSASII.py)
190	'General':{
191	'Name':PhaseName
192	'Type':'nuclear'
193	'SGData':SGData
194	'Cell':[False,10.,10.,10.,90.,90.,90,1000.]
195	'AtomPtrs':[]
196	'Histogram list':['',]
197	'Pawley dmin':1.0,
198	'Pawley neg wt':0.0}
199	'Atoms':[]
200	'Drawing':{}
201	"""
202	# UpdateGeneral execution starts here
203	phaseTypes = ['nuclear','modulated','magnetic','macromolecular']
204	SetupGeneral()
205	generalData = data['General']
206	Map = generalData['Map']
207	Flip = generalData['Flip']
208	MCSAdata = generalData['MCSA controls']
209	PWDR = any(['PWDR' in item for item in data['Histograms'].keys()])
210	# UpdateGeneral execution continues below
211
212	def NameSizer():
213	def OnPhaseName(event):
214	oldName = generalData['Name']
215	generalData['Name'] = NameTxt.GetValue()
216	G2frame.G2plotNB.Rename(oldName,generalData['Name'])
217	G2frame.dataFrame.SetLabel('Phase Data for '+generalData['Name'])
218	G2frame.PatternTree.SetItemText(Item,generalData['Name'])
219	#Hmm, need to change phase name key in Reflection Lists for each histogram
220
221	def OnPhaseType(event):
222	if not generalData['AtomTypes']: #can change only if no atoms!
223	generalData['Type'] = TypeTxt.GetValue()
224	wx.CallAfter(UpdateGeneral)
225	else:
226	TypeTxt.SetValue(generalData['Type'])
227
228	def OnSpaceGroup(event):
229	SpcGp = SGTxt.GetValue()
230	SGErr,SGData = G2spc.SpcGroup(SpcGp)
231	# try a lookup on the user-supplied name
232	if SGErr:
233	SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
234	if SpGrpNorm:
235	E,SGData = G2spc.SpcGroup(SpGrpNorm)
236	if not E: SGErr = False
237	if SGErr:
238	text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
239	SGTxt.SetValue(generalData['SGData']['SpGrp'])
240	msg = 'Space Group Error'
241	Style = wx.ICON_EXCLAMATION
242	else:
243	text = G2spc.SGPrint(SGData)
244	generalData['SGData'] = SGData
245	msg = 'Space Group Information'
246	Style = wx.ICON_INFORMATION
247	Text = ''
248	for line in text:
249	Text += line+'\n'
250	wx.MessageBox(Text,caption=msg,style=Style)
251	# General.DestroyChildren() #needed to clear away bad cellSizer, etc.
252	wx.CallAfter(UpdateGeneral)
253
254	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
255	nameSizer.Add(wx.StaticText(General,-1,' Phase name: '),0,wx.ALIGN_CENTER_VERTICAL)
256	NameTxt = wx.TextCtrl(General,-1,value=generalData['Name'],style=wx.TE_PROCESS_ENTER)
257	NameTxt.Bind(wx.EVT_TEXT_ENTER,OnPhaseName)
258	NameTxt.Bind(wx.EVT_KILL_FOCUS,OnPhaseName)
259	nameSizer.Add(NameTxt,0,wx.ALIGN_CENTER_VERTICAL)
260	nameSizer.Add(wx.StaticText(General,-1,' Phase type: '),0,wx.ALIGN_CENTER_VERTICAL)
261	TypeTxt = wx.ComboBox(General,-1,value=generalData['Type'],choices=phaseTypes,
262	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
263	TypeTxt.Bind(wx.EVT_COMBOBOX, OnPhaseType)
264	nameSizer.Add(TypeTxt,0,wx.ALIGN_CENTER_VERTICAL)
265	nameSizer.Add(wx.StaticText(General,-1,' Space group: '),0,wx.ALIGN_CENTER_VERTICAL)
266	SGTxt = wx.TextCtrl(General,-1,value=generalData['SGData']['SpGrp'],style=wx.TE_PROCESS_ENTER)
267	SGTxt.Bind(wx.EVT_TEXT_ENTER,OnSpaceGroup)
268	nameSizer.Add(SGTxt,0,wx.ALIGN_CENTER_VERTICAL)
269	return nameSizer
270
271	def CellSizer():
272
273	cellGUIlist = [[['m3','m3m'],4,zip([" Unit cell: a = "," Vol = "],["%.5f","%.3f"],[True,False],[0,0])],
274	[['3R','3mR'],6,zip([" a = "," alpha = "," Vol = "],["%.5f","%.3f","%.3f"],[True,True,False],[0,2,0])],
275	[['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])],
276	[['mmm'],8,zip([" a = "," b = "," c = "," Vol = "],["%.5f","%.5f","%.5f","%.3f"],
277	[True,True,True,False],[0,1,2,0])],
278	[['2/m'+'a'],10,zip([" a = "," b = "," c = "," alpha = "," Vol = "],
279	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
280	[['2/m'+'b'],10,zip([" a = "," b = "," c = "," beta = "," Vol = "],
281	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
282	[['2/m'+'c'],10,zip([" a = "," b = "," c = "," gamma = "," Vol = "],
283	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
284	[['-1'],8,zip([" a = "," b = "," c = "," Vol = "," alpha = "," beta = "," gamma = "],
285	["%.5f","%.5f","%.5f","%.3f","%.3f","%.3f","%.3f"],
286	[True,True,True,False,True,True,True],[0,1,2,0,3,4,5])]]
287
288	def OnCellRef(event):
289	generalData['Cell'][0] = cellRef.GetValue()
290
291	def OnCellChange(event):
292	SGData = generalData['SGData']
293	laue = SGData['SGLaue']
294	if laue == '2/m':
295	laue += SGData['SGUniq']
296	cell = generalData['Cell']
297	Obj = event.GetEventObject()
298	ObjId = cellList.index(Obj.GetId())
299	try:
300	value = max(1.0,float(Obj.GetValue()))
301	except ValueError:
302	if ObjId < 3: #bad cell edge - reset
303	value = controls[6+ObjId]
304	else: #bad angle
305	value = 90.
306	if laue in ['m3','m3m']:
307	cell[1] = cell[2] = cell[3] = value
308	cell[4] = cell[5] = cell[6] = 90.0
309	Obj.SetValue("%.5f"%(cell[1]))
310	elif laue in ['3R','3mR']:
311	if ObjId == 0:
312	cell[1] = cell[2] = cell[3] = value
313	Obj.SetValue("%.5f"%(cell[1]))
314	else:
315	cell[4] = cell[5] = cell[6] = value
316	Obj.SetValue("%.5f"%(cell[4]))
317	elif laue in ['3','3m1','31m','6/m','6/mmm','4/m','4/mmm']:
318	cell[4] = cell[5] = 90.
319	cell[6] = 120.
320	if laue in ['4/m','4/mmm']:
321	cell[6] = 90.
322	if ObjId == 0:
323	cell[1] = cell[2] = value
324	Obj.SetValue("%.5f"%(cell[1]))
325	else:
326	cell[3] = value
327	Obj.SetValue("%.5f"%(cell[3]))
328	elif laue in ['mmm']:
329	cell[ObjId+1] = value
330	cell[4] = cell[5] = cell[6] = 90.
331	Obj.SetValue("%.5f"%(cell[ObjId+1]))
332	elif laue in ['2/m'+'a']:
333	cell[5] = cell[6] = 90.
334	if ObjId != 3:
335	cell[ObjId+1] = value
336	Obj.SetValue("%.5f"%(cell[ObjId+1]))
337	else:
338	cell[4] = value
339	Obj.SetValue("%.3f"%(cell[4]))
340	elif laue in ['2/m'+'b']:
341	cell[4] = cell[6] = 90.
342	if ObjId != 3:
343	cell[ObjId+1] = value
344	Obj.SetValue("%.5f"%(cell[ObjId+1]))
345	else:
346	cell[5] = value
347	Obj.SetValue("%.3f"%(cell[5]))
348	elif laue in ['2/m'+'c']:
349	cell[5] = cell[6] = 90.
350	if ObjId != 3:
351	cell[ObjId+1] = value
352	Obj.SetValue("%.5f"%(cell[ObjId+1]))
353	else:
354	cell[6] = value
355	Obj.SetValue("%.3f"%(cell[6]))
356	else:
357	cell[ObjId+1] = value
358	if ObjId < 3:
359	Obj.SetValue("%.5f"%(cell[1+ObjId]))
360	else:
361	Obj.SetValue("%.3f"%(cell[1+ObjId]))
362	cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
363	volVal.SetValue("%.3f"%(cell[7]))
364	density,mattCoeff = G2mth.getDensity(generalData)
365	if denSizer:
366	denSizer[1].SetValue('%.3f'%(density))
367	if denSizer[2]:
368	denSizer[2].SetValue('%.3f'%(mattCoeff))
369	generalData['Cell'] = cell
370
371	cell = generalData['Cell']
372	laue = generalData['SGData']['SGLaue']
373	if laue == '2/m':
374	laue += generalData['SGData']['SGUniq']
375	for cellGUI in cellGUIlist:
376	if laue in cellGUI[0]:
377	useGUI = cellGUI
378	cellSizer = wx.FlexGridSizer(2,useGUI[1]+1,5,5)
379	if PWDR:
380	cellRef = wx.CheckBox(General,-1,label='Refine unit cell:')
381	cellSizer.Add(cellRef,0,wx.ALIGN_CENTER_VERTICAL)
382	cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef)
383	cellRef.SetValue(cell[0])
384	cellList = []
385	for txt,fmt,ifEdit,Id in useGUI[2]:
386	cellSizer.Add(wx.StaticText(General,label=txt),0,wx.ALIGN_CENTER_VERTICAL)
387	if ifEdit: #a,b,c,etc.
388	cellVal = wx.TextCtrl(General,value=(fmt%(cell[Id+1])),
389	style=wx.TE_PROCESS_ENTER)
390	cellVal.Bind(wx.EVT_TEXT_ENTER,OnCellChange)
391	cellVal.Bind(wx.EVT_KILL_FOCUS,OnCellChange)
392	cellSizer.Add(cellVal,0,wx.ALIGN_CENTER_VERTICAL)
393	cellList.append(cellVal.GetId())
394	else: #volume
395	volVal = wx.TextCtrl(General,value=(fmt%(cell[7])),style=wx.TE_READONLY)
396	volVal.SetBackgroundColour(VERY_LIGHT_GREY)
397	cellSizer.Add(volVal,0,wx.ALIGN_CENTER_VERTICAL)
398	return cellSizer
399
400	def ElemSizer():
401
402	def OnIsotope(event):
403	Obj = event.GetEventObject()
404	item = Indx[Obj.GetId()]
405	isotope = Obj.GetValue()
406	generalData['Isotope'][item] = isotope
407	indx = generalData['AtomTypes'].index(item)
408	data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope][0]
409	density,mattCoeff = G2mth.getDensity(generalData)
410	denSizer[1].SetValue('%.3f'%(density))
411	if denSizer[2]:
412	denSizer[2].SetValue('%.3f'%(mattCoeff))
413
414	elemSizer = wx.FlexGridSizer(8,len(generalData['AtomTypes'])+1,1,1)
415	elemSizer.Add(wx.StaticText(General,label=' Elements'),0,wx.ALIGN_CENTER_VERTICAL)
416	for elem in generalData['AtomTypes']:
417	typTxt = wx.TextCtrl(General,value=elem,style=wx.TE_READONLY)
418	typTxt.SetBackgroundColour(VERY_LIGHT_GREY)
419	elemSizer.Add(typTxt,0,wx.ALIGN_CENTER_VERTICAL)
420	elemSizer.Add(wx.StaticText(General,label=' Isotope'),0,wx.ALIGN_CENTER_VERTICAL)
421	for elem in generalData['AtomTypes']:
422	choices = generalData['Isotopes'][elem].keys()
423	isoSel = wx.ComboBox(General,-1,value=generalData['Isotope'][elem],choices=choices,
424	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
425	isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope)
426	Indx[isoSel.GetId()] = elem
427	elemSizer.Add(isoSel,1,wx.ALIGN_CENTER_VERTICAL\|wx.EXPAND)
428	elemSizer.Add(wx.StaticText(General,label=' No. per cell'),0,wx.ALIGN_CENTER_VERTICAL)
429	for elem in generalData['AtomTypes']:
430	numbTxt = wx.TextCtrl(General,value='%.1f'%(generalData['NoAtoms'][elem]),
431	style=wx.TE_READONLY)
432	numbTxt.SetBackgroundColour(VERY_LIGHT_GREY)
433	elemSizer.Add(numbTxt,0,wx.ALIGN_CENTER_VERTICAL)
434	elemSizer.Add(wx.StaticText(General,label=' Atom weight'),0,wx.ALIGN_CENTER_VERTICAL)
435	for wt in generalData['AtomMass']:
436	wtTxt = wx.TextCtrl(General,value='%.3f'%(wt),style=wx.TE_READONLY)
437	wtTxt.SetBackgroundColour(VERY_LIGHT_GREY)
438	elemSizer.Add(wtTxt,0,wx.ALIGN_CENTER_VERTICAL)
439	elemSizer.Add(wx.StaticText(General,label=' Bond radii'),0,wx.ALIGN_CENTER_VERTICAL)
440	for rad in generalData['BondRadii']:
441	bondRadii = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
442	bondRadii.SetBackgroundColour(VERY_LIGHT_GREY)
443	elemSizer.Add(bondRadii,0,wx.ALIGN_CENTER_VERTICAL)
444	elemSizer.Add(wx.StaticText(General,label=' Angle radii'),0,wx.ALIGN_CENTER_VERTICAL)
445	for rad in generalData['AngleRadii']:
446	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
447	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
448	elemSizer.Add(elemTxt,0,wx.ALIGN_CENTER_VERTICAL)
449	elemSizer.Add(wx.StaticText(General,label=' van der Waals radii'),0,wx.ALIGN_CENTER_VERTICAL)
450	for rad in generalData['vdWRadii']:
451	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
452	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
453	elemSizer.Add(elemTxt,0,wx.ALIGN_CENTER_VERTICAL)
454	elemSizer.Add(wx.StaticText(General,label=' Default color'),0,wx.ALIGN_CENTER_VERTICAL)
455	for R,G,B in generalData['Color']:
456	colorTxt = wx.TextCtrl(General,value='',style=wx.TE_READONLY)
457	colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
458	elemSizer.Add(colorTxt,0,wx.ALIGN_CENTER_VERTICAL)
459	return elemSizer
460
461	def DenSizer():
462
463	mass = G2mth.getMass(generalData)
464	density,mattCoeff = G2mth.getDensity(generalData)
465	denSizer = wx.BoxSizer(wx.HORIZONTAL)
466	denSizer.Add(wx.StaticText(General,-1,' Density: '),0,wx.ALIGN_CENTER_VERTICAL)
467	denTxt = wx.TextCtrl(General,-1,'%.3f'%(density),style=wx.TE_READONLY)
468	denTxt.SetBackgroundColour(VERY_LIGHT_GREY)
469	denSizer.Add(denTxt,0,wx.ALIGN_CENTER_VERTICAL)
470	mattTxt = None
471	if generalData['Type'] == 'macromolecular' and mass > 0.0:
472	denSizer.Add(wx.StaticText(General,-1,' Matthews coeff.: '),
473	0,wx.ALIGN_CENTER_VERTICAL)
474	mattTxt = wx.TextCtrl(General,-1,'%.3f'%(mattCoeff),style=wx.TE_READONLY)
475	mattTxt.SetBackgroundColour(VERY_LIGHT_GREY)
476	denSizer.Add(mattTxt,0,wx.ALIGN_CENTER_VERTICAL)
477	return denSizer,denTxt,mattTxt
478
479	def PawleySizer():
480
481	def OnPawleyRef(event):
482	generalData['doPawley'] = pawlRef.GetValue()
483
484	def OnPawleyVal(event):
485	try:
486	dmin = float(pawlVal.GetValue())
487	if 0.25 <= dmin <= 20.:
488	generalData['Pawley dmin'] = dmin
489	except ValueError:
490	pass
491	pawlVal.SetValue("%.3f"%(generalData['Pawley dmin'])) #reset in case of error
492
493	def OnPawleyNegWt(event):
494	try:
495	wt = float(pawlNegWt.GetValue())
496	if 0. <= wt <= 1.:
497	generalData['Pawley neg wt'] = wt
498	except ValueError:
499	pass
500	pawlNegWt.SetValue("%.4f"%(generalData['Pawley neg wt'])) #reset in case of error
501
502	pawleySizer = wx.BoxSizer(wx.HORIZONTAL)
503	pawleySizer.Add(wx.StaticText(General,label=' Pawley controls: '),0,wx.ALIGN_CENTER_VERTICAL)
504	pawlRef = wx.CheckBox(General,-1,label=' Do Pawley refinement?')
505	pawlRef.SetValue(generalData['doPawley'])
506	pawlRef.Bind(wx.EVT_CHECKBOX,OnPawleyRef)
507	pawleySizer.Add(pawlRef,0,wx.ALIGN_CENTER_VERTICAL)
508	pawleySizer.Add(wx.StaticText(General,label=' Pawley dmin: '),0,wx.ALIGN_CENTER_VERTICAL)
509	pawlVal = wx.TextCtrl(General,value='%.3f'%(generalData['Pawley dmin']),style=wx.TE_PROCESS_ENTER)
510	pawlVal.Bind(wx.EVT_TEXT_ENTER,OnPawleyVal)
511	pawlVal.Bind(wx.EVT_KILL_FOCUS,OnPawleyVal)
512	pawleySizer.Add(pawlVal,0,wx.ALIGN_CENTER_VERTICAL)
513	pawleySizer.Add(wx.StaticText(General,label=' Pawley neg. wt.: '),0,wx.ALIGN_CENTER_VERTICAL)
514	pawlNegWt = wx.TextCtrl(General,value='%.4f'%(generalData['Pawley neg wt']),style=wx.TE_PROCESS_ENTER)
515	pawlNegWt.Bind(wx.EVT_TEXT_ENTER,OnPawleyNegWt)
516	pawlNegWt.Bind(wx.EVT_KILL_FOCUS,OnPawleyNegWt)
517	pawleySizer.Add(pawlNegWt,0,wx.ALIGN_CENTER_VERTICAL)
518	return pawleySizer
519
520	def MapSizer():
521
522	def OnMapType(event):
523	Map['MapType'] = mapType.GetValue()
524
525	def OnRefList(event):
526	Map['RefList'] = refList.GetValue()
527
528	def OnResVal(event):
529	try:
530	res = float(mapRes.GetValue())
531	if 0.25 <= res <= 20.:
532	Map['Resolution'] = res
533	except ValueError:
534	pass
535	mapRes.SetValue("%.2f"%(Map['Resolution'])) #reset in case of error
536
537	def OnCutOff(event):
538	try:
539	res = float(cutOff.GetValue())
540	if 10.0 <= res <= 100.:
541	Map['cutOff'] = res
542	except ValueError:
543	pass
544	cutOff.SetValue("%.1f"%(Map['cutOff'])) #reset in case of error
545
546	#patch
547	if 'cutOff' not in Map:
548	Map['cutOff'] = 100.0
549	mapTypes = ['Fobs','Fcalc','delt-F','2*Fo-Fc','Omit','Patterson']
550	refList = data['Histograms'].keys()
551	if not generalData['AtomTypes']:
552	mapTypes = ['Patterson',]
553	Map['MapType'] = 'Patterson'
554	mapSizer = wx.BoxSizer(wx.VERTICAL)
555	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
556	lineSizer.Add(wx.StaticText(General,label=' Fourier map controls: Map type: '),0,wx.ALIGN_CENTER_VERTICAL)
557	mapType = wx.ComboBox(General,-1,value=Map['MapType'],choices=mapTypes,
558	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
559	mapType.Bind(wx.EVT_COMBOBOX,OnMapType)
560	lineSizer.Add(mapType,0,wx.ALIGN_CENTER_VERTICAL)
561	lineSizer.Add(wx.StaticText(General,label=' Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
562	refList = wx.ComboBox(General,-1,value=Map['RefList'],choices=refList,
563	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
564	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
565	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
566	mapSizer.Add(lineSizer,0,wx.ALIGN_CENTER_VERTICAL)
567	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
568	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,wx.ALIGN_CENTER_VERTICAL)
569	mapRes = wx.TextCtrl(General,value='%.2f'%(Map['Resolution']),style=wx.TE_PROCESS_ENTER)
570	mapRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
571	mapRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
572	line2Sizer.Add(mapRes,0,wx.ALIGN_CENTER_VERTICAL)
573	line2Sizer.Add(wx.StaticText(General,label=' Peak cutoff %: '),0,wx.ALIGN_CENTER_VERTICAL)
574	cutOff = wx.TextCtrl(General,value='%.1f'%(Map['cutOff']),style=wx.TE_PROCESS_ENTER)
575	cutOff.Bind(wx.EVT_TEXT_ENTER,OnCutOff)
576	cutOff.Bind(wx.EVT_KILL_FOCUS,OnCutOff)
577	line2Sizer.Add(cutOff,0,wx.ALIGN_CENTER_VERTICAL)
578	mapSizer.Add(line2Sizer,0,wx.ALIGN_CENTER_VERTICAL)
579	return mapSizer
580
581	def FlipSizer():
582	if 'k-Max' not in Flip: Flip['k-Max'] = 20.
583
584	def OnRefList(event):
585	Flip['RefList'] = refList.GetValue()
586
587	def OnNormElem(event):
588	PE = G2elemGUI.PickElement(G2frame,ifNone=True)
589	if PE.ShowModal() == wx.ID_OK:
590	Flip['Norm element'] = PE.Elem.strip()
591	normElem.SetLabel(Flip['Norm element'])
592	PE.Destroy()
593
594	def OnResVal(event):
595	try:
596	res = float(flipRes.GetValue())
597	if 0.25 <= res <= 20.:
598	Flip['Resolution'] = res
599	except ValueError:
600	pass
601	flipRes.SetValue("%.2f"%(Flip['Resolution'])) #reset in case of error
602
603	def OnkFactor(event):
604	try:
605	res = float(kFactor.GetValue())
606	if 0.1 <= res <= 1.2:
607	Flip['k-factor'] = res
608	except ValueError:
609	pass
610	kFactor.SetValue("%.3f"%(Flip['k-factor'])) #reset in case of error
611
612	def OnkMax(event):
613	try:
614	res = float(kMax.GetValue())
615	if res >= 10.:
616	Flip['k-Max'] = res
617	except ValueError:
618	pass
619	kMax.SetValue("%.1f"%(Flip['k-Max'])) #reset in case of error
620
621	refList = data['Histograms'].keys()
622	flipSizer = wx.BoxSizer(wx.VERTICAL)
623	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
624	lineSizer.Add(wx.StaticText(General,label=' Charge flip controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
625	refList = wx.ComboBox(General,-1,value=Flip['RefList'],choices=refList,
626	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
627	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
628	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
629	lineSizer.Add(wx.StaticText(General,label=' Normalizing element: '),0,wx.ALIGN_CENTER_VERTICAL)
630	normElem = wx.Button(General,label=Flip['Norm element'],style=wx.TE_READONLY)
631	normElem.Bind(wx.EVT_BUTTON,OnNormElem)
632	lineSizer.Add(normElem,0,wx.ALIGN_CENTER_VERTICAL)
633	flipSizer.Add(lineSizer,0,wx.ALIGN_CENTER_VERTICAL)
634	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
635	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,wx.ALIGN_CENTER_VERTICAL)
636	flipRes = wx.TextCtrl(General,value='%.2f'%(Flip['Resolution']),style=wx.TE_PROCESS_ENTER)
637	flipRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
638	flipRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
639	line2Sizer.Add(flipRes,0,wx.ALIGN_CENTER_VERTICAL)
640	line2Sizer.Add(wx.StaticText(General,label=' k-Factor (0.1-1.2): '),0,wx.ALIGN_CENTER_VERTICAL)
641	kFactor = wx.TextCtrl(General,value='%.3f'%(Flip['k-factor']),style=wx.TE_PROCESS_ENTER)
642	kFactor.Bind(wx.EVT_TEXT_ENTER,OnkFactor)
643	kFactor.Bind(wx.EVT_KILL_FOCUS,OnkFactor)
644	line2Sizer.Add(kFactor,0,wx.ALIGN_CENTER_VERTICAL)
645	line2Sizer.Add(wx.StaticText(General,label=' k-Max (>=10.0): '),0,wx.ALIGN_CENTER_VERTICAL)
646	kMax = wx.TextCtrl(General,value='%.1f'%(Flip['k-Max']),style=wx.TE_PROCESS_ENTER)
647	kMax.Bind(wx.EVT_TEXT_ENTER,OnkMax)
648	kMax.Bind(wx.EVT_KILL_FOCUS,OnkMax)
649	line2Sizer.Add(kMax,0,wx.ALIGN_CENTER_VERTICAL)
650	flipSizer.Add(line2Sizer,0,wx.ALIGN_CENTER_VERTICAL)
651	return flipSizer
652
653	def MCSASizer():
654	Ind = {}
655
656	def OnRefList(event):
657	MCSAdata['Data source'] = refList.GetValue()
658
659	def OnDmin(event):
660	try:
661	val = float(dmin.GetValue())
662	if 1.0 <= val < 5.0:
663	MCSAdata['dmin'] = val
664	except ValueError:
665	pass
666	dmin.SetValue("%.3f"%(MCSAdata['dmin'])) #reset in case of error
667	MCSAdata['newDmin'] = True
668
669	def OnCycles(event):
670	MCSAdata['Cycles'] = int(cycles.GetValue())
671
672	def OnAlist(event):
673	MCSAdata['Algorithm'] = Alist.GetValue()
674	wx.CallAfter(UpdateGeneral)
675
676	def OnSlope(event):
677	try:
678	val = float(slope.GetValue())
679	if .25 <= val < 1.0:
680	MCSAdata['log slope'] = val
681	except ValueError:
682	pass
683	slope.SetValue("%.3f"%(MCSAdata['log slope'])) #reset in case of error
684
685	def OnAjump(event):
686	Obj = event.GetEventObject()
687	name,ind = Indx[Obj.GetId()]
688	try:
689	val = float(Obj.GetValue())
690	if .0 <= val <= 1.0:
691	MCSAdata[name][ind] = val
692	except ValueError:
693	pass
694	Obj.SetValue("%.3f"%(MCSAdata[name][ind]))
695
696	def OnRanStart(event):
697	MCSAdata['ranStart'] = ranStart.GetValue()
698
699	def OnAutoRan(event):
700	MCSAdata['autoRan'] = autoRan.GetValue()
701
702	def OnRanRange(event):
703	try:
704	val = float(ranRange.GetValue())/100
705	if 0.01 <= val <= 0.99:
706	MCSAdata['ranRange'] = val
707	except ValueError:
708	pass
709	ranRange.SetValue('%.1f'%(MCSAdata['ranRange']*100.))
710
711	def OnAnneal(event):
712	Obj = event.GetEventObject()
713	ind,fmt = Indx[Obj.GetId()]
714	if ind == 2: #No. trials
715	try:
716	val = int(Obj.GetValue())
717	if 1 <= val:
718	MCSAdata['Annealing'][ind] = val
719	except ValueError:
720	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
721	else:
722	try:
723	val = float(Obj.GetValue())
724	if .0 <= val:
725	MCSAdata['Annealing'][ind] = val
726	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
727	except ValueError:
728	MCSAdata['Annealing'][ind] = None
729	Obj.SetValue(str(MCSAdata['Annealing'][ind]))
730
731	refList = []
732	if len(data['Pawley ref']):
733	refList = ['Pawley reflections']
734	for item in data['Histograms'].keys():
735	if 'HKLF' in item or 'PWDR' in item:
736	refList.append(item)
737	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
738	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
739	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
740	refList = wx.ComboBox(General,-1,value=MCSAdata['Data source'],choices=refList,
741	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
742	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
743	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
744	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,wx.ALIGN_CENTER_VERTICAL)
745	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['dmin']),style=wx.TE_PROCESS_ENTER)
746	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
747	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
748	lineSizer.Add(dmin,0,wx.ALIGN_CENTER_VERTICAL)
749	mcsaSizer.Add(lineSizer)
750	mcsaSizer.Add((5,5),)
751	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
752	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,wx.ALIGN_CENTER_VERTICAL)
753	Cchoice = ['1','2','3','6','10','20','30','60','100']
754	cycles = wx.ComboBox(General,-1,value=str(MCSAdata.get('Cycles',1)),choices=Cchoice,
755	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
756	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
757	line2Sizer.Add(cycles,0,wx.ALIGN_CENTER_VERTICAL)
758	line2Sizer.Add((5,0),)
759	ranStart = wx.CheckBox(General,-1,label=' MC/SA Refine at ')
760	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
761	ranStart.SetValue(MCSAdata.get('ranStart',False))
762	line2Sizer.Add(ranStart,0,wx.ALIGN_CENTER_VERTICAL)
763	ranRange = wx.TextCtrl(General,-1,value='%.1f'%(MCSAdata.get('ranRange',0.10)*100),style=wx.TE_PROCESS_ENTER)
764	ranRange.Bind(wx.EVT_TEXT_ENTER,OnRanRange)
765	ranRange.Bind(wx.EVT_KILL_FOCUS,OnRanRange)
766	line2Sizer.Add(ranRange,0,wx.ALIGN_CENTER_VERTICAL)
767	line2Sizer.Add(wx.StaticText(General,label='% of ranges. '),0,wx.ALIGN_CENTER_VERTICAL)
768	# autoRan = wx.CheckBox(General,-1,label=' Do auto range reduction? ')
769	# autoRan.Bind(wx.EVT_CHECKBOX, OnAutoRan)
770	# autoRan.SetValue(MCSAdata.get('autoRan',False))
771	# line2Sizer.Add(autoRan,0,wx.ALIGN_CENTER_VERTICAL)
772	mcsaSizer.Add(line2Sizer)
773	mcsaSizer.Add((5,5),)
774	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
775	Achoice = ['log','fast'] #these work
776	# Achoice = ['log','fast','cauchy','boltzmann']
777	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
778	Alist = wx.ComboBox(General,-1,value=MCSAdata['Algorithm'],choices=Achoice,
779	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
780	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
781	line3Sizer.Add(Alist,0,wx.ALIGN_CENTER_VERTICAL)
782	if MCSAdata['Algorithm'] in ['fast','boltzmann','cauchy']:
783	Names = [' A-jump: ',' B-jump: ']
784	parms = 'Jump coeff'
785	if MCSAdata['Algorithm'] in ['boltzmann','cauchy']:
786	Names = [' A-jump: ']
787	elif 'fast' in MCSAdata['Algorithm']:
788	Names = [' quench: ',' m-factor: ',' n-factor: ']
789	parms = 'fast parms'
790	for i,name in enumerate(Names):
791	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
792	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata[parms][i]),style=wx.TE_PROCESS_ENTER)
793	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
794	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
795	Indx[Ajump.GetId()] = [parms,i]
796	line3Sizer.Add(Ajump,0,wx.ALIGN_CENTER_VERTICAL)
797	elif 'log' in MCSAdata['Algorithm']:
798	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,wx.ALIGN_CENTER_VERTICAL)
799	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['log slope']),style=wx.TE_PROCESS_ENTER)
800	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
801	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
802	line3Sizer.Add(slope,0,wx.ALIGN_CENTER_VERTICAL)
803	mcsaSizer.Add(line3Sizer)
804	mcsaSizer.Add((5,5),)
805	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
806	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
807	names = [' Start temp: ',' Final temp: ',' No. trials: ']
808	fmts = ['%.1f','%.5f','%d']
809	for i,[name,fmt] in enumerate(zip(names,fmts)):
810	if MCSAdata['Annealing'][i]:
811	text = fmt%(MCSAdata['Annealing'][i])
812	else:
813	text = 'None'
814	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
815	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
816	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
817	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
818	Indx[anneal.GetId()] = [i,fmt]
819	line3Sizer.Add(anneal,0,wx.ALIGN_CENTER_VERTICAL)
820	mcsaSizer.Add(line3Sizer)
821	return mcsaSizer
822
823	# UpdateGeneral execution continues here
824	if General.GetSizer():
825	General.GetSizer().Clear(True)
826	mainSizer = wx.BoxSizer(wx.VERTICAL)
827	mainSizer.Add((5,5),0)
828	mainSizer.Add(NameSizer(),0)
829	mainSizer.Add((5,5),0)
830	mainSizer.Add(CellSizer(),0)
831	mainSizer.Add((5,5),0)
832
833	Indx = {}
834	denSizer = None
835	if len(generalData['AtomTypes']):
836	denSizer = DenSizer()
837	mainSizer.Add(denSizer[0])
838	mainSizer.Add((5,5),0)
839	mainSizer.Add(ElemSizer())
840	G2gd.HorizontalLine(mainSizer,General)
841
842	mainSizer.Add(PawleySizer())
843	G2gd.HorizontalLine(mainSizer,General)
844
845	mainSizer.Add(MapSizer())
846	G2gd.HorizontalLine(mainSizer,General)
847
848	mainSizer.Add(FlipSizer())
849	G2gd.HorizontalLine(mainSizer,General)
850
851	mainSizer.Add(MCSASizer())
852	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
853	G2frame.dataFrame.SetStatusText('')
854
855	################################################################################
856	##### Atom routines
857	################################################################################
858
859	def FillAtomsGrid(Atoms):
860	'''Display the contents of the Atoms tab
861	'''
862	def RefreshAtomGrid(event):
863
864	r,c = event.GetRow(),event.GetCol()
865	if r < 0 and c < 0:
866	for row in range(Atoms.GetNumberRows()):
867	Atoms.SelectRow(row,True)
868	if r < 0: #double click on col label! Change all atoms!
869	sel = -1
870	noSkip = True
871	if Atoms.GetColLabelValue(c) == 'refine':
872	Type = generalData['Type']
873	if Type in ['nuclear','macromolecular']:
874	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
875	elif Type in ['magnetic',]:
876	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
877	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
878	if dlg.ShowModal() == wx.ID_OK:
879	sel = dlg.GetSelections()
880	parms = ''
881	for x in sel:
882	parms += choice[x][0]
883	dlg.Destroy()
884	elif Atoms.GetColLabelValue(c) == 'I/A':
885	choice = ['Isotropic','Anisotropic']
886	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
887	if dlg.ShowModal() == wx.ID_OK:
888	sel = dlg.GetSelection()
889	parms = choice[sel][0]
890	dlg.Destroy()
891	elif Atoms.GetColLabelValue(c) == 'Type':
892	choice = generalData['AtomTypes']
893	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
894	if dlg.ShowModal() == wx.ID_OK:
895	sel = dlg.GetSelection()
896	parms = choice[sel]
897	noSkip = False
898	Atoms.ClearSelection()
899	for row in range(Atoms.GetNumberRows()):
900	if parms == atomData[row][c]:
901	Atoms.SelectRow(row,True)
902	dlg.Destroy()
903	SetupGeneral()
904	elif Atoms.GetColLabelValue(c) == 'residue':
905	choice = []
906	for r in range(Atoms.GetNumberRows()):
907	if str(atomData[r][c]) not in choice:
908	choice.append(str(atomData[r][c]))
909	choice.sort()
910	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
911	if dlg.ShowModal() == wx.ID_OK:
912	sel = dlg.GetSelection()
913	parms = choice[sel]
914	noSkip = False
915	Atoms.ClearSelection()
916	for row in range(Atoms.GetNumberRows()):
917	if parms == atomData[row][c]:
918	Atoms.SelectRow(row,True)
919	dlg.Destroy()
920	elif Atoms.GetColLabelValue(c) == 'res no':
921	choice = []
922	for r in range(Atoms.GetNumberRows()):
923	if str(atomData[r][c]) not in choice:
924	choice.append(str(atomData[r][c]))
925	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
926	if dlg.ShowModal() == wx.ID_OK:
927	sel = dlg.GetSelection()
928	parms = choice[sel]
929	noSkip = False
930	Atoms.ClearSelection()
931	for row in range(Atoms.GetNumberRows()):
932	if int(parms) == atomData[row][c]:
933	Atoms.SelectRow(row,True)
934	dlg.Destroy()
935	elif Atoms.GetColLabelValue(c) == 'chain':
936	choice = []
937	for r in range(Atoms.GetNumberRows()):
938	if atomData[r][c] not in choice:
939	choice.append(atomData[r][c])
940	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
941	if dlg.ShowModal() == wx.ID_OK:
942	sel = dlg.GetSelection()
943	parms = choice[sel]
944	noSkip = False
945	Atoms.ClearSelection()
946	for row in range(Atoms.GetNumberRows()):
947	if parms == atomData[row][c]:
948	Atoms.SelectRow(row,True)
949	dlg.Destroy()
950	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
951	pass #& then change all 'I' atoms
952	if sel >= 0 and noSkip:
953	ui = colLabels.index('U11')
954	us = colLabels.index('Uiso')
955	ss = colLabels.index('site sym')
956	for r in range(Atoms.GetNumberRows()):
957	ID = atomData[r][-1]
958	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
959	if parms == 'A': #'I' --> 'A'
960	Uiso = float(Atoms.GetCellValue(r,us))
961	sytsym = atomData[r][ss]
962	CSI = G2spc.GetCSuinel(sytsym)
963	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
964	atomData[r][us] = 0.0
965	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
966	for i in range(6):
967	ci = ui+i
968	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
969	if CSI[2][i]:
970	Atoms.SetCellStyle(r,ci,WHITE,False)
971	else: #'A' --> 'I'
972	Uij = atomData[r][ui:ui+6]
973	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
974	atomData[r][us] = Uiso
975	Atoms.SetCellStyle(r,us,WHITE,False)
976	for i in range(6):
977	ci = ui+i
978	atomData[r][ci] = 0.0
979	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
980	if not Atoms.IsReadOnly(r,c):
981	if Atoms.GetColLabelValue(c) == 'refine':
982	rbExcl = rbAtmDict.get(atomData[r][-1],'')
983	if rbExcl:
984	for excl in rbExcl:
985	atomData[r][c] = parms.replace(excl,'')
986	else:
987	atomData[r][c] = parms
988	else:
989	atomData[r][c] = parms
990	if 'Atoms' in data['Drawing']:
991	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
992	wx.CallAfter(Paint)
993
994	def ChangeAtomCell(event):
995
996	def chkUij(Uij,CSI): #needs to do something!!!
997	return Uij
998
999	r,c = event.GetRow(),event.GetCol()
1000	if r >= 0 and c >= 0:
1001	ID = atomData[r][-1]
1002	if Atoms.GetColLabelValue(c) in ['x','y','z']:
1003	ci = colLabels.index('x')
1004	XYZ = atomData[r][ci:ci+3]
1005	if None in XYZ:
1006	XYZ = [0,0,0]
1007	SScol = colLabels.index('site sym')
1008	Mulcol = colLabels.index('mult')
1009	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1010	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
1011	atomData[r][SScol] = Sytsym
1012	atomData[r][Mulcol] = Mult
1013	if atomData[r][colLabels.index('I/A')] == 'A':
1014	ui = colLabels.index('U11')
1015	CSI = G2spc.GetCSuinel(Sytsym)
1016	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
1017	for i in range(6):
1018	ci = i+ui
1019	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1020	if CSI[2][i]:
1021	Atoms.SetCellStyle(r,ci,WHITE,False)
1022	SetupGeneral()
1023	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1024	if atomData[r][c] == 'I':
1025	Uij = atomData[r][c+2:c+8]
1026	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1027	Atoms.SetCellStyle(r,c+1,WHITE,False)
1028	Atoms.SetCellTextColour(r,c+1,BLACK)
1029	for i in range(6):
1030	ci = i+colLabels.index('U11')
1031	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1032	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1033	atomData[r][ci] = 0.0
1034	else:
1035	value = atomData[r][c+1]
1036	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1037	atomData[r][c+1] = 0.0
1038	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1039	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1040	for i in range(6):
1041	ci = i+colLabels.index('U11')
1042	atomData[r][ci] = value*CSI[3][i]
1043	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1044	Atoms.SetCellTextColour(r,ci,BLACK)
1045	if CSI[2][i]:
1046	Atoms.SetCellStyle(r,ci,WHITE,False)
1047	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1048	value = atomData[r][c]
1049	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1050	iUij = CSI[0][c-colLabels.index('U11')]
1051	for i in range(6):
1052	if iUij == CSI[0][i]:
1053	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1054	elif Atoms.GetColLabelValue(c) == 'refine':
1055	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1056	if 'Atoms' in data['Drawing']:
1057	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1058	wx.CallAfter(Paint)
1059
1060	def AtomTypeSelect(event):
1061	r,c = event.GetRow(),event.GetCol()
1062	if Atoms.GetColLabelValue(c) == 'Type':
1063	PE = G2elemGUI.PickElement(G2frame)
1064	if PE.ShowModal() == wx.ID_OK:
1065	if PE.Elem != 'None':
1066	atomData[r][c] = PE.Elem.strip()
1067	name = atomData[r][c]
1068	if len(name) in [2,4]:
1069	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1070	else:
1071	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1072	PE.Destroy()
1073	SetupGeneral()
1074	wx.CallAfter(Paint)
1075	value = Atoms.GetCellValue(r,c)
1076	atomData[r][c] = value
1077	ID = atomData[r][-1]
1078	if 'Atoms' in data['Drawing']:
1079	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1080	SetupGeneral()
1081	else:
1082	event.Skip()
1083
1084	def RowSelect(event):
1085	r,c = event.GetRow(),event.GetCol()
1086	if not event.AltDown():
1087	Atoms.frm = -1
1088	G2frame.dataFrame.SetStatusText('')
1089	if r < 0 and c < 0:
1090	if Atoms.IsSelection():
1091	Atoms.ClearSelection()
1092	elif c < 0: #only row clicks
1093	if event.ControlDown():
1094	if r in Atoms.GetSelectedRows():
1095	Atoms.DeselectRow(r)
1096	else:
1097	Atoms.SelectRow(r,True)
1098	elif event.ShiftDown():
1099	indxs = Atoms.GetSelectedRows()
1100	Atoms.ClearSelection()
1101	ibeg = 0
1102	if indxs:
1103	ibeg = indxs[-1]
1104	for row in range(ibeg,r+1):
1105	Atoms.SelectRow(row,True)
1106	elif event.AltDown():
1107	if atomData[r][-1] in rbAtmDict:
1108	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1109	Atoms.frm = -1
1110	Atoms.ClearSelection()
1111	else:
1112	if Atoms.frm < 0: #pick atom to be moved
1113	Atoms.frm = r
1114	Atoms.SelectRow(r,True)
1115	n = colLabels.index('Name')
1116	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1117	else: #move it
1118	item = atomData.pop(Atoms.frm)
1119	atomData.insert(r,item)
1120	Atoms.frm = -1
1121	G2frame.dataFrame.SetStatusText('')
1122	wx.CallAfter(Paint)
1123	else:
1124	Atoms.ClearSelection()
1125	Atoms.SelectRow(r,True)
1126
1127	def ChangeSelection(event):
1128	r,c = event.GetRow(),event.GetCol()
1129	if r < 0 and c < 0:
1130	Atoms.ClearSelection()
1131	if c < 0:
1132	if r in Atoms.GetSelectedRows():
1133	Atoms.DeselectRow(r)
1134	else:
1135	Atoms.SelectRow(r,True)
1136	if r < 0:
1137	if c in Atoms.GetSelectedCols():
1138	Atoms.DeselectCol(c)
1139	else:
1140	Atoms.SelectCol(c,True)
1141
1142	def Paint():
1143
1144	table = []
1145	rowLabels = []
1146	for i,atom in enumerate(atomData):
1147	table.append(atom)
1148	rowLabels.append(str(i))
1149	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1150	Atoms.SetTable(atomTable, True)
1151	Atoms.frm = -1
1152	colType = colLabels.index('Type')
1153	colR = colLabels.index('refine')
1154	colSS = colLabels.index('site sym')
1155	colX = colLabels.index('x')
1156	colIA = colLabels.index('I/A')
1157	colU11 = colLabels.index('U11')
1158	colUiso = colLabels.index('Uiso')
1159	attr = wx.grid.GridCellAttr()
1160	attr.IncRef() #fix from Jim Hester
1161	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1162	for c in range(colX,colX+3):
1163	Atoms.SetColAttr(c, attr)
1164	for i in range(colU11-1,colU11+6):
1165	Atoms.SetColSize(i,50)
1166	for row in range(Atoms.GetNumberRows()):
1167	atId = atomData[row][-1]
1168	rbExcl = rbAtmDict.get(atId,'')
1169	Atoms.SetReadOnly(row,colSS,True) #site sym
1170	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1171	if Atoms.GetCellValue(row,colIA) == 'A':
1172	CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')])
1173	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1174	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1175	for i in range(6):
1176	ci = colU11+i
1177	Atoms.SetCellTextColour(row,ci,BLACK)
1178	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1179	if CSI[2][i] and 'U' not in rbExcl:
1180	Atoms.SetCellStyle(row,ci,WHITE,False)
1181	else:
1182	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1183	Atoms.SetCellTextColour(row,colUiso,BLACK)
1184	if 'U' in rbExcl:
1185	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1186	for i in range(6):
1187	ci = colU11+i
1188	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1189	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1190	if 'X' in rbExcl:
1191	for c in range(0,colX+3):
1192	if c != colR:
1193	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1194	Atoms.AutoSizeColumns(False)
1195
1196	# FillAtomsGrid executable code starts here
1197	generalData = data['General']
1198	atomData = data['Atoms']
1199	DData = data['Drawing']
1200	resRBData = data['RBModels'].get('Residue',[])
1201	vecRBData = data['RBModels'].get('Vector',[])
1202	rbAtmDict = {}
1203	for rbObj in resRBData+vecRBData:
1204	exclList = ['X' for i in range(len(rbObj['Ids']))]
1205	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1206	if rbObj['ThermalMotion'][0] != 'None':
1207	for id in rbObj['Ids']:
1208	rbAtmDict[id] += 'U'
1209	# exclList will be 'x' or 'xu' if TLS used in RB
1210	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1211	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1212	if atomData:
1213	for item in Items:
1214	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1215	else:
1216	for item in Items:
1217	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1218	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1219	if 'showABC' in data['Drawing']:
1220	for item in Items:
1221	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1222	else:
1223	for item in Items:
1224	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1225
1226	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1227	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1228	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1229	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1230	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1231	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1232	if generalData['Type'] == 'magnetic':
1233	colLabels += ['Mx','My','Mz']
1234	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1235	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1236	elif generalData['Type'] == 'macromolecular':
1237	colLabels = ['res no','residue','chain'] + colLabels
1238	Types = [wg.GRID_VALUE_STRING,
1239	wg.GRID_VALUE_CHOICE+AAchoice,
1240	wg.GRID_VALUE_STRING] + Types
1241	elif generalData['Type'] == 'modulated':
1242	Types += []
1243	colLabels += []
1244	SGData = data['General']['SGData']
1245	G2frame.dataFrame.SetStatusText('')
1246	if SGData['SGPolax']:
1247	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1248	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1249	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1250	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1251	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1252	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1253	Atoms.SetMargins(0,0)
1254
1255	G2frame.dataFrame.setSizePosLeft([700,300])
1256	Paint()
1257
1258	def OnAtomAdd(event):
1259	AtomAdd(0,0,0)
1260	FillAtomsGrid(Atoms)
1261	event.StopPropagation()
1262	if data['Drawing']:
1263	G2plt.PlotStructure(G2frame,data)
1264
1265	def OnAtomViewAdd(event):
1266	try:
1267	drawData = data['Drawing']
1268	x,y,z = drawData['viewPoint'][0]
1269	AtomAdd(x,y,z)
1270	except:
1271	AtomAdd(0,0,0)
1272	FillAtomsGrid(Atoms)
1273	event.StopPropagation()
1274	G2plt.PlotStructure(G2frame,data)
1275
1276	def AtomAdd(x,y,z,El='H',Name='UNK'):
1277	atomData = data['Atoms']
1278	generalData = data['General']
1279	Ncol = Atoms.GetNumberCols()
1280	atId = ran.randint(0,sys.maxint)
1281	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1282	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1283	if generalData['Type'] == 'macromolecular':
1284	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1285	elif generalData['Type'] == 'nuclear':
1286	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1287	elif generalData['Type'] == 'magnetic':
1288	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1289	SetupGeneral()
1290	if 'Atoms' in data['Drawing']:
1291	DrawAtomAdd(data['Drawing'],atomData[-1])
1292
1293	def OnAtomInsert(event):
1294	AtomInsert(0,0,0)
1295	FillAtomsGrid(Atoms)
1296	event.StopPropagation()
1297	G2plt.PlotStructure(G2frame,data)
1298
1299	def OnAtomViewInsert(event):
1300	if 'Drawing' in data:
1301	drawData = data['Drawing']
1302	x,y,z = drawData['viewPoint'][0]
1303	AtomAdd(x,y,z)
1304	FillAtomsGrid(Atoms)
1305	event.StopPropagation()
1306
1307	def OnAtomMove(event):
1308	drawData = data['Drawing']
1309	atomData = data['Atoms']
1310	x,y,z = drawData['viewPoint'][0]
1311	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1312	cx = colLabels.index('x')
1313	indx = Atoms.GetSelectedRows()
1314	if len(indx) != 1:
1315	print '** ERROR - only one atom can be moved **'
1316	elif atomData[indx[0]][-1] in rbAtmDict:
1317	print '** ERROR - Atoms in rigid bodies can not be moved **'
1318	else:
1319	atomData[indx[0]][cx:cx+3] = [x,y,z]
1320	SetupGeneral()
1321	FillAtomsGrid(Atoms)
1322	ID = atomData[indx[0]][-1]
1323	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1324	G2plt.PlotStructure(G2frame,data)
1325	event.StopPropagation()
1326
1327	def DrawAtomsReplaceByID(drawingData,atom,ID):
1328	IDs = [ID,]
1329	atomData = drawingData['Atoms']
1330	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1331	for ind in indx:
1332	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1333
1334	def MakeDrawAtom(atom,oldatom=None):
1335	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1336	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1337	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1338	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1339	generalData = data['General']
1340	SGData = generalData['SGData']
1341	if generalData['Type'] == 'nuclear':
1342	if oldatom:
1343	opr = oldatom[5]
1344	if atom[9] == 'A':
1345	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1346	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1347	else:
1348	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1349	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1350	else:
1351	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1352	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1353	ct,cs = [1,8] #type & color
1354	elif generalData['Type'] == 'macromolecular':
1355	try:
1356	oneLetter = AA3letter.index(atom[1])
1357	except ValueError:
1358	oneLetter = -1
1359	atomInfo = [[atom[1].strip()+atom[0],]+
1360	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1361	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1362	ct,cs = [4,11] #type & color
1363	elif generalData['Type'] == 'magnetic':
1364	if oldatom:
1365	atomInfo = [atom[:2]+oldatom[3:]][0]
1366	else:
1367	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1368	ct,cs = [1,8] #type & color
1369	# elif generalData['Type'] == 'modulated':
1370	# ????? for future
1371	atNum = generalData['AtomTypes'].index(atom[ct])
1372	atomInfo[cs] = list(generalData['Color'][atNum])
1373	return atomInfo
1374
1375	def AtomInsert(x,y,z):
1376	indx = Atoms.GetSelectedRows()
1377	if indx:
1378	indx = indx[0]
1379	atomData = data['Atoms']
1380	generalData = data['General']
1381	Ncol = Atoms.GetNumberCols()
1382	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1383	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1384	atId = ran.randint(0,sys.maxint)
1385	if generalData['Type'] == 'macromolecular':
1386	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1387	elif generalData['Type'] == 'nuclear':
1388	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1389	elif generalData['Type'] == 'magnetic':
1390	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])
1391	SetupGeneral()
1392
1393	def AtomDelete(event):
1394	indx = Atoms.GetSelectedRows()
1395	IDs = []
1396	if indx:
1397	atomData = data['Atoms']
1398	indx.reverse()
1399	for ind in indx:
1400	atom = atomData[ind]
1401	if atom[-1] in rbAtmDict:
1402	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1403	else:
1404	IDs.append(atom[-1])
1405	del atomData[ind]
1406	if 'Atoms' in data['Drawing']:
1407	DrawAtomsDeleteByIDs(IDs)
1408	wx.CallAfter(FillAtomsGrid,Atoms)
1409	G2plt.PlotStructure(G2frame,data)
1410	SetupGeneral()
1411	event.StopPropagation()
1412
1413	def AtomRefine(event):
1414	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1415	c = colLabels.index('refine')
1416	indx = Atoms.GetSelectedRows()
1417	if indx:
1418	atomData = data['Atoms']
1419	generalData = data['General']
1420	Type = generalData['Type']
1421	if Type in ['nuclear','macromolecular']:
1422	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1423	elif Type == 'magnetic':
1424	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1425	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1426	if dlg.ShowModal() == wx.ID_OK:
1427	sel = dlg.GetSelections()
1428	parms = ''
1429	for x in sel:
1430	parms += choice[x][0]
1431	for r in indx:
1432	if not Atoms.IsReadOnly(r,c):
1433	atomData[r][c] = parms
1434	Atoms.ForceRefresh()
1435	dlg.Destroy()
1436
1437	def AtomModify(event):
1438	indx = Atoms.GetSelectedRows()
1439	if indx:
1440	atomData = data['Atoms']
1441	generalData = data['General']
1442	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1443	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1444	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1445	parm = ''
1446	if dlg.ShowModal() == wx.ID_OK:
1447	sel = dlg.GetSelection()
1448	parm = choices[sel]
1449	cid = colLabels.index(parm)
1450	dlg.Destroy()
1451	if parm in ['Type']:
1452	dlg = G2elemGUI.PickElement(G2frame)
1453	if dlg.ShowModal() == wx.ID_OK:
1454	if dlg.Elem not in ['None']:
1455	El = dlg.Elem.strip()
1456	for r in indx:
1457	if not Atoms.IsReadOnly(r,cid):
1458	atomData[r][cid] = El
1459	if len(El) in [2,4]:
1460	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1461	else:
1462	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1463	SetupGeneral()
1464	if 'Atoms' in data['Drawing']:
1465	for r in indx:
1466	ID = atomData[r][-1]
1467	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1468	FillAtomsGrid(Atoms)
1469	dlg.Destroy()
1470	elif parm in ['Name',]:
1471	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1472	wx.YES_NO \| wx.ICON_QUESTION)
1473	try:
1474	result = dlg.ShowModal()
1475	if result == wx.ID_YES:
1476	for r in indx:
1477	if not Atoms.IsReadOnly(r,cid+1):
1478	El = atomData[r][cid+1]
1479	if len(El) in [2,4]:
1480	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1481	else:
1482	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1483	FillAtomsGrid(Atoms)
1484	finally:
1485	dlg.Destroy()
1486
1487	elif parm in ['I/A']:
1488	choices = ['Isotropic','Anisotropic']
1489	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1490	if dlg.ShowModal() == wx.ID_OK:
1491	sel = dlg.GetSelection()
1492	parm = choices[sel][0]
1493	for r in indx:
1494	if not Atoms.IsReadOnly(r,cid):
1495	atomData[r][cid] = parm
1496	FillAtomsGrid(Atoms)
1497	dlg.Destroy()
1498	elif parm in ['frac','Uiso']:
1499	limits = [0.,1.]
1500	val = 1.0
1501	if parm in ['Uiso']:
1502	limits = [0.,0.25]
1503	val = 0.01
1504	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1505	if dlg.ShowModal() == wx.ID_OK:
1506	parm = dlg.GetValue()
1507	for r in indx:
1508	if not Atoms.IsReadOnly(r,cid):
1509	atomData[r][cid] = parm
1510	SetupGeneral()
1511	FillAtomsGrid(Atoms)
1512	dlg.Destroy()
1513	elif parm in ['x','y','z']:
1514	limits = [-1.,1.]
1515	val = 0.
1516	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1517	if dlg.ShowModal() == wx.ID_OK:
1518	parm = dlg.GetValue()
1519	for r in indx:
1520	if not Atoms.IsReadOnly(r,cid):
1521	atomData[r][cid] += parm
1522	SetupGeneral()
1523	FillAtomsGrid(Atoms)
1524	dlg.Destroy()
1525
1526	def AtomTransform(event):
1527	indx = Atoms.GetSelectedRows()
1528	if indx:
1529	generalData = data['General']
1530	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1531	cx = colLabels.index('x')
1532	cuia = colLabels.index('I/A')
1533	cuij = colLabels.index('U11')
1534	css = colLabels.index('site sym')
1535	atomData = data['Atoms']
1536	generalData = data['General']
1537	SGData = generalData['SGData']
1538	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1539	New = False
1540	try:
1541	if dlg.ShowModal() == wx.ID_OK:
1542	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1543	Cell = np.array(Cell)
1544	cent = SGData['SGCen'][Cent]
1545	M,T = SGData['SGOps'][Opr]
1546	for ind in indx:
1547	XYZ = np.array(atomData[ind][cx:cx+3])
1548	XYZ = np.inner(M,XYZ)+T
1549	if Inv:
1550	XYZ = -XYZ
1551	XYZ = XYZ+cent+Cell
1552	if Force:
1553	XYZ = G2spc.MoveToUnitCell(XYZ)
1554	if New:
1555	atom = copy.copy(atomData[ind])
1556	else:
1557	atom = atomData[ind]
1558	atom[cx:cx+3] = XYZ
1559	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1560	if atom[cuia] == 'A':
1561	Uij = atom[cuij:cuij+6]
1562	U = G2spc.Uij2U(Uij)
1563	U = np.inner(np.inner(M,U),M)
1564	Uij = G2spc.U2Uij(U)
1565	atom[cuij:cuij+6] = Uij
1566	if New:
1567	atomData.append(atom)
1568	finally:
1569	dlg.Destroy()
1570	Atoms.ClearSelection()
1571	if New:
1572	FillAtomsGrid(Atoms)
1573	else:
1574	Atoms.ForceRefresh()
1575
1576	def OnDistAnglePrt(event):
1577	fp = file(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile
1578	)[0]+'.disagl'),'w')
1579	OnDistAngle(event,fp=fp)
1580	fp.close()
1581
1582	def OnDistAngle(event,fp=None):
1583	indx = Atoms.GetSelectedRows()
1584	Oxyz = []
1585	xyz = []
1586	DisAglData = {}
1587	DisAglCtls = {}
1588	if indx:
1589	generalData = data['General']
1590	DisAglData['OrigIndx'] = indx
1591	if 'DisAglCtls' in generalData:
1592	DisAglCtls = generalData['DisAglCtls']
1593	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1594	if dlg.ShowModal() == wx.ID_OK:
1595	DisAglCtls = dlg.GetData()
1596	else:
1597	dlg.Destroy()
1598	return
1599	dlg.Destroy()
1600	generalData['DisAglCtls'] = DisAglCtls
1601	atomData = data['Atoms']
1602	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1603	cx = colLabels.index('x')
1604	cn = colLabels.index('Name')
1605	for i,atom in enumerate(atomData):
1606	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1607	if i in indx:
1608	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1609	DisAglData['OrigAtoms'] = Oxyz
1610	DisAglData['TargAtoms'] = xyz
1611	generalData = data['General']
1612	DisAglData['SGData'] = generalData['SGData']
1613	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1614	if 'pId' in data:
1615	DisAglData['pId'] = data['pId']
1616	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1617	try:
1618	if fp:
1619	G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
1620	else:
1621	G2stMn.PrintDistAngle(DisAglCtls,DisAglData)
1622	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1623	G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types')
1624	else:
1625	print "select one or more rows of atoms"
1626	G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
1627
1628	def OnReImport(event):
1629	print 'reimport atoms from file to be developed'
1630	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1631	rdlist = G2frame.OnImportGeneric(reqrdr,
1632	G2frame.ImportPhaseReaderlist,
1633	'phase')
1634	if len(rdlist) == 0: return
1635	# for now rdlist is only expected to have one element
1636	# for now always use the first phase for when multiple phases are ever implemented
1637	# but it would be better to loop until we find a phase that matches the one in data
1638	for rd in rdlist:
1639	# rd contains all info for a phase
1640	PhaseName = rd.Phase['General']['Name']
1641	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1642	print rd.Phase['Atoms']
1643	return
1644
1645	################################################################################
1646	#Structure drawing GUI stuff
1647	################################################################################
1648
1649	def SetupDrawingData():
1650	generalData = data['General']
1651	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1652	atomData = data['Atoms']
1653	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1654	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1655	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1656	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1657	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1658	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1659	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1660	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1661	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1662	'bondList':{},'viewDir':[1,0,0]}
1663	V0 = np.array([0,0,1])
1664	V = np.inner(Amat,V0)
1665	V /= np.sqrt(np.sum(V**2))
1666	A = np.arccos(np.sum(V*V0))
1667	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1668	try:
1669	drawingData = data['Drawing']
1670	except KeyError:
1671	data['Drawing'] = {}
1672	drawingData = data['Drawing']
1673	if not drawingData: #fill with defaults if empty
1674	drawingData.update(defaultDrawing)
1675	if 'Zstep' not in drawingData:
1676	drawingData['Zstep'] = 0.5
1677	if 'contourLevel' not in drawingData:
1678	drawingData['contourLevel'] = 1.
1679	if 'viewDir' not in drawingData:
1680	drawingData['viewDir'] = [0,0,1]
1681	if 'Quaternion' not in drawingData:
1682	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1683	if 'showRigidBodies' not in drawingData:
1684	drawingData['showRigidBodies'] = True
1685	cx,ct,cs,ci = [0,0,0,0]
1686	if generalData['Type'] == 'nuclear':
1687	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1688	elif generalData['Type'] == 'macromolecular':
1689	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1690	elif generalData['Type'] == 'magnetic':
1691	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1692	# elif generalData['Type'] == 'modulated':
1693	# ????? for future
1694	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1695	if not drawingData.get('Atoms'):
1696	for atom in atomData:
1697	DrawAtomAdd(drawingData,atom)
1698	data['Drawing'] = drawingData
1699
1700	def DrawAtomAdd(drawingData,atom):
1701	drawingData['Atoms'].append(MakeDrawAtom(atom))
1702
1703	def OnRestraint(event):
1704	indx = drawAtoms.GetSelectedRows()
1705	restData = G2frame.PatternTree.GetItemPyData(
1706	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1707	drawingData = data['Drawing']
1708	generalData = data['General']
1709	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1710	cx,ct,cs,ci = drawingData['atomPtrs']
1711	atomData = drawingData['Atoms']
1712	atNames = []
1713	atXYZ = []
1714	atSymOp = []
1715	atIndx = []
1716	for item in indx:
1717	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1718	atSymOp.append(atomData[item][cs-1])
1719	atIndx.append(atomData[item][ci])
1720	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1721	try:
1722	bondData = restData[PhaseName]['Bond']
1723	except KeyError:
1724	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1725	restData[PhaseName] = {}
1726	restData[PhaseName]['Bond'] = bondData
1727	dist = G2mth.getRestDist(atXYZ,Amat)
1728	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1729	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1730	try:
1731	angleData = restData[PhaseName]['Angle']
1732	except KeyError:
1733	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1734	restData[PhaseName] = {}
1735	restData[PhaseName]['Angle'] = angleData
1736	angle = G2mth.getRestAngle(atXYZ,Amat)
1737	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1738	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1739	try:
1740	planeData = restData[PhaseName]['Plane']
1741	except KeyError:
1742	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1743	restData[PhaseName] = {}
1744	restData[PhaseName]['Plane'] = planeData
1745	plane = G2mth.getRestPlane(atXYZ,Amat)
1746	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1747	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1748	try:
1749	chiralData = restData[PhaseName]['Chiral']
1750	except KeyError:
1751	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1752	restData[PhaseName] = {}
1753	restData[PhaseName]['Chiral'] = chiralData
1754	volume = G2mth.getRestChiral(atXYZ,Amat)
1755	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1756	else:
1757	print '**** ERROR wrong number of atoms selected for this restraint'
1758	return
1759	G2frame.PatternTree.SetItemPyData(
1760	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1761
1762	def OnDefineRB(event):
1763	indx = drawAtoms.GetSelectedRows()
1764	indx.sort()
1765	RBData = G2frame.PatternTree.GetItemPyData(
1766	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1767	drawingData = data['Drawing']
1768	generalData = data['General']
1769	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1770	cx,ct,cs,ci = drawingData['atomPtrs']
1771	atomData = drawingData['Atoms']
1772	rbXYZ = []
1773	rbType = []
1774	atNames = []
1775	AtInfo = RBData['Residue']['AtInfo']
1776	for i,item in enumerate(indx):
1777	rbtype = atomData[item][ct]
1778	atNames.append(rbtype+str(i))
1779	rbType.append(rbtype)
1780	if rbtype not in AtInfo:
1781	Info = G2elem.GetAtomInfo(rbtype)
1782	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1783	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1784	rbXYZ = np.array(rbXYZ)
1785	rbXYZ -= rbXYZ[0]
1786	rbId = ran.randint(0,sys.maxint)
1787	rbName = 'UNKRB'
1788	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1789	'Edit rigid body name',rbName ,style=wx.OK)
1790	if dlg.ShowModal() == wx.ID_OK:
1791	rbName = dlg.GetValue()
1792	dlg.Destroy()
1793	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1794	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1795	RBData['RBIds']['Residue'].append(rbId)
1796	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1797
1798	################################################################################
1799	##### Atom draw routines
1800	################################################################################
1801
1802	def UpdateDrawAtoms(atomStyle=''):
1803	def RefreshAtomGrid(event):
1804	def SetChoice(name,c,n=0):
1805	choice = []
1806	for r in range(len(atomData)):
1807	if n:
1808	srchStr = str(atomData[r][c][:n])
1809	else:
1810	srchStr = str(atomData[r][c])
1811	if srchStr not in choice:
1812	if n:
1813	choice.append(str(atomData[r][c][:n]))
1814	else:
1815	choice.append(str(atomData[r][c]))
1816	choice.sort()
1817
1818	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
1819	if dlg.ShowModal() == wx.ID_OK:
1820	sel = dlg.GetSelections()
1821	parms = []
1822	for x in sel:
1823	parms.append(choice[x])
1824	noSkip = False
1825	drawAtoms.ClearSelection()
1826	drawingData['selectedAtoms'] = []
1827	for row in range(len(atomData)):
1828	test = atomData[row][c]
1829	if n:
1830	test = test[:n]
1831	if test in parms:
1832	drawAtoms.SelectRow(row,True)
1833	drawingData['selectedAtoms'].append(row)
1834	G2plt.PlotStructure(G2frame,data)
1835	dlg.Destroy()
1836
1837	r,c = event.GetRow(),event.GetCol()
1838	if r < 0 and c < 0:
1839	for row in range(drawAtoms.GetNumberRows()):
1840	drawingData['selectedAtoms'].append(row)
1841	drawAtoms.SelectRow(row,True)
1842	elif r < 0: #dclick on col label
1843	sel = -1
1844	Parms = False
1845	noSkip = True
1846	if drawAtoms.GetColLabelValue(c) == 'Style':
1847	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1848	if dlg.ShowModal() == wx.ID_OK:
1849	sel = dlg.GetSelection()
1850	parms = styleChoice[sel]
1851	for r in range(len(atomData)):
1852	atomData[r][c] = parms
1853	drawAtoms.SetCellValue(r,c,parms)
1854	FindBondsDraw()
1855	G2plt.PlotStructure(G2frame,data)
1856	dlg.Destroy()
1857	elif drawAtoms.GetColLabelValue(c) == 'Label':
1858	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
1859	if dlg.ShowModal() == wx.ID_OK:
1860	sel = dlg.GetSelection()
1861	parms = labelChoice[sel]
1862	for r in range(len(atomData)):
1863	atomData[r][c] = parms
1864	drawAtoms.SetCellValue(r,c,parms)
1865	dlg.Destroy()
1866	elif drawAtoms.GetColLabelValue(c) == 'Color':
1867	dlg = wx.ColourDialog(G2frame)
1868	if dlg.ShowModal() == wx.ID_OK:
1869	color = dlg.GetColourData().GetColour()
1870	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1871	attr.SetReadOnly(True)
1872	attr.SetBackgroundColour(color)
1873	for r in range(len(atomData)):
1874	atomData[r][c] = color
1875	drawingData['Atoms'][r][c] = color
1876	drawAtoms.SetAttr(r,c,attr)
1877	UpdateDrawAtoms()
1878	dlg.Destroy()
1879	elif drawAtoms.GetColLabelValue(c) == 'Residue':
1880	SetChoice('Residue',c,3)
1881	elif drawAtoms.GetColLabelValue(c) == '1-letter':
1882	SetChoice('1-letter',c,1)
1883	elif drawAtoms.GetColLabelValue(c) == 'Chain':
1884	SetChoice('Chain',c)
1885	elif drawAtoms.GetColLabelValue(c) == 'Name':
1886	SetChoice('Name',c)
1887	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
1888	SetChoice('Name',c)
1889	elif drawAtoms.GetColLabelValue(c) == 'Type':
1890	SetChoice('Type',c)
1891	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
1892	drawAtoms.ClearSelection()
1893	else:
1894	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
1895	atomData[r][c] = drawAtoms.GetCellValue(r,c)
1896	FindBondsDraw()
1897	elif drawAtoms.GetColLabelValue(c) == 'Color':
1898	dlg = wx.ColourDialog(G2frame)
1899	if dlg.ShowModal() == wx.ID_OK:
1900	color = dlg.GetColourData().GetColour()
1901	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1902	attr.SetReadOnly(True)
1903	attr.SetBackgroundColour(color)
1904	atomData[r][c] = color
1905	drawingData['Atoms'][r][c] = color
1906	drawAtoms.SetAttr(i,cs+2,attr)
1907	dlg.Destroy()
1908	UpdateDrawAtoms()
1909	G2plt.PlotStructure(G2frame,data)
1910
1911	def RowSelect(event):
1912	r,c = event.GetRow(),event.GetCol()
1913	if r < 0 and c < 0:
1914	if drawAtoms.IsSelection():
1915	drawAtoms.ClearSelection()
1916	elif c < 0: #only row clicks
1917	if event.ControlDown():
1918	if r in drawAtoms.GetSelectedRows():
1919	drawAtoms.DeselectRow(r)
1920	else:
1921	drawAtoms.SelectRow(r,True)
1922	elif event.ShiftDown():
1923	indxs = drawAtoms.GetSelectedRows()
1924	drawAtoms.ClearSelection()
1925	ibeg = 0
1926	if indxs:
1927	ibeg = indxs[-1]
1928	for row in range(ibeg,r+1):
1929	drawAtoms.SelectRow(row,True)
1930	else:
1931	drawAtoms.ClearSelection()
1932	drawAtoms.SelectRow(r,True)
1933	drawingData['selectedAtoms'] = []
1934	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
1935	G2plt.PlotStructure(G2frame,data)
1936
1937	# UpdateDrawAtoms executable code starts here
1938	G2frame.dataFrame.SetStatusText('')
1939	generalData = data['General']
1940	SetupDrawingData()
1941	drawingData = data['Drawing']
1942	cx,ct,cs,ci = drawingData['atomPtrs']
1943	atomData = drawingData['Atoms']
1944	if atomStyle:
1945	for atom in atomData:
1946	atom[cs] = atomStyle
1947	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
1948	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
1949	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
1950	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1951	labelChoice = [' ','type','name','number']
1952	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
1953	if generalData['Type'] == 'macromolecular':
1954	colLabels = ['Residue','1-letter','Chain'] + colLabels
1955	Types = 3*[wg.GRID_VALUE_STRING,]+Types
1956	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
1957	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
1958	labelChoice = [' ','type','name','number','residue','1-letter','chain']
1959	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
1960	# elif generalData['Type'] == 'modulated':
1961	# Types += []
1962	# colLabels += []
1963	table = []
1964	rowLabels = []
1965	for i,atom in enumerate(drawingData['Atoms']):
1966	table.append(atom[:colLabels.index('I/A')+1])
1967	rowLabels.append(str(i))
1968
1969	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1970	drawAtoms.SetTable(atomTable, True)
1971	drawAtoms.SetMargins(0,0)
1972	drawAtoms.AutoSizeColumns(True)
1973	drawAtoms.SetColSize(colLabels.index('Style'),80)
1974	drawAtoms.SetColSize(colLabels.index('Color'),50)
1975	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
1976	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1977	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
1978	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1979	for i,atom in enumerate(drawingData['Atoms']):
1980	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1981	attr.SetReadOnly(True)
1982	attr.SetBackgroundColour(atom[cs+2])
1983	drawAtoms.SetAttr(i,cs+2,attr)
1984	drawAtoms.SetCellValue(i,cs+2,'')
1985	indx = drawingData['selectedAtoms']
1986	if indx:
1987	for r in range(len(atomData)):
1988	if r in indx:
1989	drawAtoms.SelectRow(r)
1990	for c in range(len(colLabels)):
1991	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1992	attr.SetReadOnly(True)
1993	attr.SetBackgroundColour(VERY_LIGHT_GREY)
1994	if colLabels[c] not in ['Style','Label','Color']:
1995	drawAtoms.SetColAttr(c,attr)
1996	G2frame.dataFrame.setSizePosLeft([600,300])
1997
1998	FindBondsDraw()
1999	drawAtoms.ClearSelection()
2000	# G2plt.PlotStructure(G2frame,data)
2001
2002	def DrawAtomStyle(event):
2003	indx = drawAtoms.GetSelectedRows()
2004	if indx:
2005	generalData = data['General']
2006	atomData = data['Drawing']['Atoms']
2007	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2008	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2009	if generalData['Type'] == 'macromolecular':
2010	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
2011	'backbone','ribbons','schematic']
2012	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2013	if dlg.ShowModal() == wx.ID_OK:
2014	sel = dlg.GetSelection()
2015	parms = styleChoice[sel]
2016	for r in indx:
2017	atomData[r][cs] = parms
2018	drawAtoms.SetCellValue(r,cs,parms)
2019	dlg.Destroy()
2020	FindBondsDraw()
2021	drawAtoms.ClearSelection()
2022	G2plt.PlotStructure(G2frame,data)
2023
2024	def DrawAtomLabel(event):
2025	indx = drawAtoms.GetSelectedRows()
2026	if indx:
2027	generalData = data['General']
2028	atomData = data['Drawing']['Atoms']
2029	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2030	styleChoice = [' ','type','name','number']
2031	if generalData['Type'] == 'macromolecular':
2032	styleChoice = [' ','type','name','number','residue','1-letter','chain']
2033	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
2034	if dlg.ShowModal() == wx.ID_OK:
2035	sel = dlg.GetSelection()
2036	parms = styleChoice[sel]
2037	for r in indx:
2038	atomData[r][cs+1] = parms
2039	drawAtoms.SetCellValue(r,cs+1,parms)
2040	dlg.Destroy()
2041	drawAtoms.ClearSelection()
2042	G2plt.PlotStructure(G2frame,data)
2043
2044	def DrawAtomColor(event):
2045
2046	indx = drawAtoms.GetSelectedRows()
2047	if indx:
2048	if len(indx) > 1:
2049	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2050	else:
2051	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2052	generalData = data['General']
2053	atomData = data['Drawing']['Atoms']
2054	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2055	atmColors = []
2056	atmTypes = []
2057	for r in indx:
2058	if atomData[r][cs+2] not in atmColors:
2059	atmColors.append(atomData[r][cs+2])
2060	atmTypes.append(atomData[r][ct])
2061	if len(atmColors) > 16:
2062	break
2063	colors = wx.ColourData()
2064	colors.SetChooseFull(True)
2065	dlg = wx.ColourDialog(G2frame)
2066	if dlg.ShowModal() == wx.ID_OK:
2067	for i in range(len(atmColors)):
2068	atmColors[i] = dlg.GetColourData().GetColour()
2069	colorDict = dict(zip(atmTypes,atmColors))
2070	for r in indx:
2071	color = colorDict[atomData[r][ct]]
2072	atomData[r][cs+2] = color
2073	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2074	attr.SetBackgroundColour(color)
2075	drawAtoms.SetAttr(r,cs+2,attr)
2076	data['Drawing']['Atoms'][r][cs+2] = color
2077	drawAtoms.ClearSelection()
2078	dlg.Destroy()
2079	G2frame.dataFrame.SetStatusText('')
2080	G2plt.PlotStructure(G2frame,data)
2081
2082	def ResetAtomColors(event):
2083	generalData = data['General']
2084	atomData = data['Drawing']['Atoms']
2085	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2086	for atom in atomData:
2087	atNum = generalData['AtomTypes'].index(atom[ct])
2088	atom[cs+2] = list(generalData['Color'][atNum])
2089	UpdateDrawAtoms()
2090	drawAtoms.ClearSelection()
2091	G2plt.PlotStructure(G2frame,data)
2092
2093	def SetViewPoint(event):
2094	indx = drawAtoms.GetSelectedRows()
2095	if indx:
2096	atomData = data['Drawing']['Atoms']
2097	cx = data['Drawing']['atomPtrs'][0]
2098	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2099	drawAtoms.ClearSelection() #do I really want to do this?
2100	G2plt.PlotStructure(G2frame,data)
2101
2102	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2103	cx = data['Drawing']['atomPtrs'][0]
2104	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2105	return False
2106	else:
2107	return True
2108
2109	def AddSymEquiv(event):
2110	indx = drawAtoms.GetSelectedRows()
2111	indx.sort()
2112	if indx:
2113	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2114	cx = colLabels.index('x')
2115	cuia = colLabels.index('I/A')
2116	cuij = cuia+2
2117	atomData = data['Drawing']['Atoms']
2118	generalData = data['General']
2119	SGData = generalData['SGData']
2120	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2121	try:
2122	if dlg.ShowModal() == wx.ID_OK:
2123	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2124	Cell = np.array(Cell)
2125	cent = SGData['SGCen'][Cent]
2126	M,T = SGData['SGOps'][Opr]
2127	for ind in indx:
2128	XYZ = np.array(atomData[ind][cx:cx+3])
2129	XYZ = np.inner(M,XYZ)+T
2130	if Inv:
2131	XYZ = -XYZ
2132	XYZ = XYZ+cent+Cell
2133	if Force:
2134	XYZ = G2spc.MoveToUnitCell(XYZ)
2135	if noDuplicate(XYZ,atomData):
2136	atom = copy.copy(atomData[ind])
2137	atom[cx:cx+3] = XYZ
2138	atomOp = atom[cx+3]
2139	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2140	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2141	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2142	if atom[cuia] == 'A':
2143	Uij = atom[cuij:cuij+6]
2144	U = G2spc.Uij2U(Uij)
2145	U = np.inner(np.inner(M,U),M)
2146	Uij = G2spc.U2Uij(U)
2147	atom[cuij:cuij+6] = Uij
2148	atomData.append(atom)
2149	finally:
2150	dlg.Destroy()
2151	UpdateDrawAtoms()
2152	drawAtoms.ClearSelection()
2153	G2plt.PlotStructure(G2frame,data)
2154
2155	def TransformSymEquiv(event):
2156	indx = drawAtoms.GetSelectedRows()
2157	indx.sort()
2158	if indx:
2159	atomData = data['Drawing']['Atoms']
2160	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2161	cx = colLabels.index('x')
2162	cuia = colLabels.index('I/A')
2163	cuij = cuia+2
2164	atomData = data['Drawing']['Atoms']
2165	generalData = data['General']
2166	SGData = generalData['SGData']
2167	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2168	try:
2169	if dlg.ShowModal() == wx.ID_OK:
2170	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2171	Cell = np.array(Cell)
2172	cent = SGData['SGCen'][Cent]
2173	M,T = SGData['SGOps'][Opr]
2174	for ind in indx:
2175	XYZ = np.array(atomData[ind][cx:cx+3])
2176	XYZ = np.inner(M,XYZ)+T
2177	if Inv:
2178	XYZ = -XYZ
2179	XYZ = XYZ+cent+Cell
2180	if Force:
2181	XYZ = G2spc.MoveToUnitCell(XYZ)
2182	atom = atomData[ind]
2183	atom[cx:cx+3] = XYZ
2184	atomOp = atom[cx+3]
2185	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2186	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2187	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2188	if atom[cuia] == 'A':
2189	Uij = atom[cuij:cuij+6]
2190	U = G2spc.Uij2U(Uij)
2191	U = np.inner(np.inner(M,U),M)
2192	Uij = G2spc.U2Uij(U)
2193	atom[cuij:cuij+6] = Uij
2194	data['Drawing']['Atoms'] = atomData
2195	finally:
2196	dlg.Destroy()
2197	UpdateDrawAtoms()
2198	drawAtoms.ClearSelection()
2199	G2plt.PlotStructure(G2frame,data)
2200
2201	def FillCoordSphere(event):
2202	generalData = data['General']
2203	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2204	radii = generalData['BondRadii']
2205	atomTypes = generalData['AtomTypes']
2206	try:
2207	indH = atomTypes.index('H')
2208	radii[indH] = 0.5
2209	except:
2210	pass
2211	indx = drawAtoms.GetSelectedRows()
2212	if indx:
2213	indx.sort()
2214	atomData = data['Drawing']['Atoms']
2215	numAtoms = len(atomData)
2216	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2217	generalData = data['General']
2218	SGData = generalData['SGData']
2219	cellArray = G2lat.CellBlock(1)
2220	wx.BeginBusyCursor()
2221	try:
2222	for ind in indx:
2223	atomA = atomData[ind]
2224	xyzA = np.array(atomA[cx:cx+3])
2225	indA = atomTypes.index(atomA[ct])
2226	for atomB in atomData[:numAtoms]:
2227	indB = atomTypes.index(atomB[ct])
2228	sumR = radii[indA]+radii[indB]
2229	xyzB = np.array(atomB[cx:cx+3])
2230	for xyz in cellArray+xyzB:
2231	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2232	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2233	if noDuplicate(xyz,atomData):
2234	oprB = atomB[cx+3]
2235	C = xyz-xyzB
2236	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2237	newAtom = atomB[:]
2238	newAtom[cx:cx+3] = xyz
2239	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2240	atomData.append(newAtom)
2241	finally:
2242	wx.EndBusyCursor()
2243	data['Drawing']['Atoms'] = atomData
2244	UpdateDrawAtoms()
2245	drawAtoms.ClearSelection()
2246	G2plt.PlotStructure(G2frame,data)
2247
2248	def FillUnitCell(event):
2249	indx = drawAtoms.GetSelectedRows()
2250	indx.sort()
2251	if indx:
2252	atomData = data['Drawing']['Atoms']
2253	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2254	cx = colLabels.index('x')
2255	cuia = colLabels.index('I/A')
2256	cuij = cuia+2
2257	generalData = data['General']
2258	SGData = generalData['SGData']
2259	wx.BeginBusyCursor()
2260	try:
2261	for ind in indx:
2262	atom = atomData[ind]
2263	XYZ = np.array(atom[cx:cx+3])
2264	if atom[cuia] == 'A':
2265	Uij = atom[cuij:cuij+6]
2266	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2267	for item in result:
2268	atom = copy.copy(atomData[ind])
2269	atom[cx:cx+3] = item[0]
2270	atom[cx+3] = str(item[2])+'+' \
2271	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2272	atom[cuij:cuij+6] = item[1]
2273	Opp = G2spc.Opposite(item[0])
2274	for xyz in Opp:
2275	if noDuplicate(xyz,atomData):
2276	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2277	cell = '1'+'+'+ \
2278	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2279	atom[cx:cx+3] = xyz
2280	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2281	atomData.append(atom[:])
2282	else:
2283	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2284	for item in result:
2285	atom = copy.copy(atomData[ind])
2286	atom[cx:cx+3] = item[0]
2287	atom[cx+3] = str(item[1])+'+' \
2288	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2289	Opp = G2spc.Opposite(item[0])
2290	for xyz in Opp:
2291	if noDuplicate(xyz,atomData):
2292	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2293	cell = '1'+'+'+ \
2294	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2295	atom[cx:cx+3] = xyz
2296	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2297	atomData.append(atom[:])
2298	data['Drawing']['Atoms'] = atomData
2299	finally:
2300	wx.EndBusyCursor()
2301	UpdateDrawAtoms()
2302	drawAtoms.ClearSelection()
2303	G2plt.PlotStructure(G2frame,data)
2304
2305	def FindBondsToo(): #works but slow for large structures - keep as reference
2306	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2307	atomData = data['Drawing']['Atoms']
2308	generalData = data['General']
2309	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2310	radii = generalData['BondRadii']
2311	atomTypes = generalData['AtomTypes']
2312	try:
2313	indH = atomTypes.index('H')
2314	radii[indH] = 0.5
2315	except:
2316	pass
2317	for atom in atomData:
2318	atom[-1] = []
2319	Atoms = []
2320	for i,atom in enumerate(atomData):
2321	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2322	for atomA in Atoms:
2323	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2324	for atomB in Atoms:
2325	Dx = atomB[1]-atomA[1]
2326	DX = np.inner(Amat,Dx)
2327	dist = np.sqrt(np.sum(DX**2))
2328	sumR = atomA[3]+atomB[3]
2329	if 0.5 < dist <= 0.85*sumR:
2330	i = atomA[0]
2331	if atomA[2] == 'polyhedra':
2332	atomData[i][-1].append(DX)
2333	elif atomB[1] != 'polyhedra':
2334	j = atomB[0]
2335	atomData[i][-1].append(Dx*atomA[3]/sumR)
2336	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2337
2338	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2339	import numpy.ma as ma
2340	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2341	hydro = data['Drawing']['showHydrogen']
2342	atomData = data['Drawing']['Atoms']
2343	generalData = data['General']
2344	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2345	radii = generalData['BondRadii']
2346	atomTypes = generalData['AtomTypes']
2347	try:
2348	indH = atomTypes.index('H')
2349	radii[indH] = 0.5
2350	except:
2351	pass
2352	for atom in atomData:
2353	atom[-2] = [] #clear out old bonds/polyhedra
2354	atom[-1] = []
2355	Indx = range(len(atomData))
2356	Atoms = []
2357	Styles = []
2358	Radii = []
2359	for atom in atomData:
2360	Atoms.append(np.array(atom[cx:cx+3]))
2361	Styles.append(atom[cs])
2362	try:
2363	if not hydro and atom[ct] == 'H':
2364	Radii.append(0.0)
2365	else:
2366	Radii.append(radii[atomTypes.index(atom[ct])])
2367	except ValueError: #changed atom type!
2368	Radii.append(0.20)
2369	Atoms = np.array(Atoms)
2370	Radii = np.array(Radii)
2371	IASR = zip(Indx,Atoms,Styles,Radii)
2372	for atomA in IASR:
2373	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2374	Dx = Atoms-atomA[1]
2375	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
2376	sumR = atomA[3]+Radii
2377	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2378	i = atomA[0]
2379	for j in IndB[0]:
2380	if Styles[i] == 'polyhedra':
2381	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2382	elif Styles[j] != 'polyhedra' and j > i:
2383	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2384	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2385	if Styles[i] == 'polyhedra':
2386	Bonds = atomData[i][-2]
2387	Faces = []
2388	if len(Bonds) > 2:
2389	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2390	for face in FaceGen:
2391	vol = nl.det(face)
2392	if abs(vol) > 1. or len(Bonds) == 3:
2393	if vol < 0.:
2394	face = [face[0],face[2],face[1]]
2395	face = np.array(face)
2396	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2397	norm = np.cross(face[1]-face[0],face[2]-face[0])
2398	norm /= np.sqrt(np.sum(norm**2))
2399	Faces.append([face,norm])
2400	atomData[i][-1] = Faces
2401
2402	def DrawAtomsDelete(event):
2403	indx = drawAtoms.GetSelectedRows()
2404	indx.sort()
2405	if indx:
2406	atomData = data['Drawing']['Atoms']
2407	indx.reverse()
2408	for ind in indx:
2409	del atomData[ind]
2410	UpdateDrawAtoms()
2411	drawAtoms.ClearSelection()
2412	G2plt.PlotStructure(G2frame,data)
2413	event.StopPropagation()
2414
2415	def OnReloadDrawAtoms(event):
2416	data['Drawing']['Atoms'] = []
2417	UpdateDrawAtoms()
2418	drawAtoms.ClearSelection()
2419	G2plt.PlotStructure(G2frame,data)
2420	event.StopPropagation()
2421
2422	def DrawAtomsDeleteByIDs(IDs):
2423	atomData = data['Drawing']['Atoms']
2424	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2425	indx.reverse()
2426	for ind in indx:
2427	del atomData[ind]
2428
2429	def ChangeDrawAtomsByIDs(colName,IDs,value):
2430	atomData = data['Drawing']['Atoms']
2431	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2432	if colName == 'Name':
2433	col = ct-1
2434	elif colName == 'Type':
2435	col = ct
2436	elif colName == 'I/A':
2437	col = cs
2438	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2439	for ind in indx:
2440	atomData[ind][col] = value
2441
2442	def OnDrawPlane(event):
2443	indx = drawAtoms.GetSelectedRows()
2444	if len(indx) < 4:
2445	print '**** ERROR - need 4+ atoms for plane calculation'
2446	return
2447	PlaneData = {}
2448	drawingData = data['Drawing']
2449	atomData = drawingData['Atoms']
2450	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2451	cx = colLabels.index('x')
2452	cn = colLabels.index('Name')
2453	xyz = []
2454	for i,atom in enumerate(atomData):
2455	if i in indx:
2456	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2457	generalData = data['General']
2458	PlaneData['Name'] = generalData['Name']
2459	PlaneData['Atoms'] = xyz
2460	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2461	G2stMn.BestPlane(PlaneData)
2462
2463	def OnDrawDistVP(event):
2464	# distance to view point
2465	indx = drawAtoms.GetSelectedRows()
2466	if not indx:
2467	print '***** ERROR - no atoms selected'
2468	return
2469	generalData = data['General']
2470	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2471	drawingData = data['Drawing']
2472	viewPt = np.array(drawingData['viewPoint'][0])
2473	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2474	atomDData = drawingData['Atoms']
2475	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2476	cx = colLabels.index('x')
2477	cn = colLabels.index('Name')
2478	for i in indx:
2479	atom = atomDData[i]
2480	Dx = np.array(atom[cx:cx+3])-viewPt
2481	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2482	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2483
2484	def OnDrawDAT(event):
2485	#distance, angle, torsion
2486	indx = drawAtoms.GetSelectedRows()
2487	if len(indx) not in [2,3,4]:
2488	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2489	return
2490	DATData = {}
2491	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2492	drawingData = data['Drawing']
2493	atomData = data['Atoms']
2494	atomDData = drawingData['Atoms']
2495	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2496	cx = colLabels.index('x')
2497	cn = colLabels.index('Name')
2498	cid = colLabels.index('I/A')+8
2499	xyz = []
2500	Oxyz = []
2501	DATData['Natoms'] = len(indx)
2502	for i in indx:
2503	atom = atomDData[i]
2504	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2505	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2506	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2507	DATData['Datoms'] = xyz
2508	DATData['Oatoms'] = Oxyz
2509	generalData = data['General']
2510	DATData['Name'] = generalData['Name']
2511	DATData['SGData'] = generalData['SGData']
2512	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2513	if 'pId' in data:
2514	DATData['pId'] = data['pId']
2515	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2516	G2stMn.DisAglTor(DATData)
2517
2518	################################################################################
2519	#### Draw Options page
2520	################################################################################
2521
2522	def UpdateDrawOptions():
2523	import copy
2524	import wx.lib.colourselect as wcs
2525	def SlopSizer():
2526	def OnCameraPos(event):
2527	drawingData['cameraPos'] = cameraPos.GetValue()
2528	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2529	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2530	G2plt.PlotStructure(G2frame,data)
2531
2532	def OnZclip(event):
2533	drawingData['Zclip'] = Zclip.GetValue()
2534	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2535	G2plt.PlotStructure(G2frame,data)
2536
2537	def OnZstep(event):
2538	try:
2539	step = float(Zstep.GetValue())
2540	if not (0.01 <= step <= 1.0):
2541	raise ValueError
2542	except ValueError:
2543	step = drawingData['Zstep']
2544	drawingData['Zstep'] = step
2545	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2546
2547	def OnMoveZ(event):
2548	move = MoveZ.GetValue()*drawingData['Zstep']
2549	MoveZ.SetValue(0)
2550	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2551	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2552	VD /= np.sqrt(np.sum(VD**2))
2553	VP += move*VD
2554	VP = np.inner(Bmat,VP)
2555	drawingData['viewPoint'][0] = VP
2556	panel = drawOptions.GetChildren()
2557	names = [child.GetName() for child in panel]
2558	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2559	G2plt.PlotStructure(G2frame,data)
2560
2561	def OnVdWScale(event):
2562	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2563	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2564	G2plt.PlotStructure(G2frame,data)
2565
2566	def OnEllipseProb(event):
2567	drawingData['ellipseProb'] = ellipseProb.GetValue()
2568	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2569	G2plt.PlotStructure(G2frame,data)
2570
2571	def OnBallScale(event):
2572	drawingData['ballScale'] = ballScale.GetValue()/100.
2573	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2574	G2plt.PlotStructure(G2frame,data)
2575
2576	def OnBondRadius(event):
2577	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2578	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2579	G2plt.PlotStructure(G2frame,data)
2580
2581	def OnContourLevel(event):
2582	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2583	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2584	G2plt.PlotStructure(G2frame,data)
2585
2586	def OnMapSize(event):
2587	drawingData['mapSize'] = mapSize.GetValue()/10.
2588	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2589	G2plt.PlotStructure(G2frame,data)
2590
2591
2592	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2593	slideSizer = wx.FlexGridSizer(7,2)
2594	slideSizer.AddGrowableCol(1,1)
2595
2596	cameraPosTxt = wx.StaticText(drawOptions,-1,
2597	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2598	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2599	slideSizer.Add(cameraPosTxt,0,wx.ALIGN_CENTER_VERTICAL)
2600	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2601	cameraPos.SetRange(10,500)
2602	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2603	G2frame.dataDisplay.cameraSlider = cameraPos
2604	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2605
2606	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2607	slideSizer.Add(ZclipTxt,0,wx.ALIGN_CENTER_VERTICAL)
2608	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2609	Zclip.SetRange(1,99)
2610	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2611	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2612
2613	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2614	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,wx.ALIGN_CENTER_VERTICAL)
2615	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2616	style=wx.TE_PROCESS_ENTER)
2617	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2618	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2619	ZstepSizer.Add(Zstep,0,wx.ALIGN_CENTER_VERTICAL)
2620	slideSizer.Add(ZstepSizer)
2621	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2622	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,wx.ALIGN_CENTER_VERTICAL)
2623	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2624	MoveZ.SetValue(0)
2625	MoveZ.SetRange(-1,1)
2626	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2627	MoveSizer.Add(MoveZ)
2628	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2629
2630	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2631	slideSizer.Add(vdwScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2632	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2633	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2634	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2635
2636	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2637	slideSizer.Add(ellipseProbTxt,0,wx.ALIGN_CENTER_VERTICAL)
2638	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2639	ellipseProb.SetRange(1,99)
2640	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2641	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2642
2643	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2644	slideSizer.Add(ballScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2645	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2646	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2647	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2648
2649	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2650	slideSizer.Add(bondRadiusTxt,0,wx.ALIGN_CENTER_VERTICAL)
2651	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2652	bondRadius.SetRange(1,25)
2653	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2654	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2655
2656	if generalData['Map']['rhoMax']:
2657	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2658	slideSizer.Add(contourLevelTxt,0,wx.ALIGN_CENTER_VERTICAL)
2659	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2660	contourLevel.SetRange(1,100)
2661	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2662	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2663	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2664	slideSizer.Add(mapSizeTxt,0,wx.ALIGN_CENTER_VERTICAL)
2665	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2666	mapSize.SetRange(1,100)
2667	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2668	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2669
2670	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2671	slopSizer.Add((10,5),0)
2672	slopSizer.SetMinSize(wx.Size(350,10))
2673	return slopSizer
2674
2675	def ShowSizer():
2676
2677	def OnBackColor(event):
2678	drawingData['backColor'] = event.GetValue()
2679	G2plt.PlotStructure(G2frame,data)
2680
2681	def OnShowABC(event):
2682	drawingData['showABC'] = showABC.GetValue()
2683	G2plt.PlotStructure(G2frame,data)
2684
2685	def OnShowUnitCell(event):
2686	drawingData['unitCellBox'] = unitCellBox.GetValue()
2687	G2plt.PlotStructure(G2frame,data)
2688
2689	def OnShowHyd(event):
2690	drawingData['showHydrogen'] = showHydrogen.GetValue()
2691	FindBondsDraw()
2692	G2plt.PlotStructure(G2frame,data)
2693
2694	def OnShowRB(event):
2695	drawingData['showRigidBodies'] = showRB.GetValue()
2696	FindBondsDraw()
2697	G2plt.PlotStructure(G2frame,data)
2698
2699	def OnViewPoint(event):
2700	Obj = event.GetEventObject()
2701	viewPt = Obj.GetValue().split()
2702	try:
2703	VP = [float(viewPt[i]) for i in range(3)]
2704	except (ValueError,IndexError):
2705	VP = drawingData['viewPoint'][0]
2706	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2707	drawingData['viewPoint'][0] = VP
2708	G2plt.PlotStructure(G2frame,data)
2709
2710	def OnViewDir(event):
2711	Obj = event.GetEventObject()
2712	viewDir = Obj.GetValue().split()
2713	try:
2714	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2715	VD = np.array([float(viewDir[i]) for i in range(3)])
2716	VC = np.inner(Amat,VD)
2717	VC /= np.sqrt(np.sum(VC**2))
2718	V = np.array(drawingData['viewDir'])
2719	VB = np.inner(Amat,V)
2720	VB /= np.sqrt(np.sum(VB**2))
2721	VX = np.cross(VC,VB)
2722	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2723	QV = G2mth.AVdeg2Q(A,VX)
2724	Q = drawingData['Quaternion']
2725	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2726	except (ValueError,IndexError):
2727	VD = drawingData['viewDir']
2728	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2729	drawingData['viewDir'] = VD
2730	G2plt.PlotStructure(G2frame,data)
2731
2732	showSizer = wx.BoxSizer(wx.VERTICAL)
2733	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2734	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,wx.ALIGN_CENTER_VERTICAL)
2735	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2736	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2737	lineSizer.Add(backColor,0,wx.ALIGN_CENTER_VERTICAL)
2738	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,wx.ALIGN_CENTER_VERTICAL)
2739	VD = drawingData['viewDir']
2740	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2741	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2742	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2743	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2744	G2frame.dataDisplay.viewDir = viewDir
2745	lineSizer.Add(viewDir,0,wx.ALIGN_CENTER_VERTICAL)
2746	showSizer.Add(lineSizer)
2747	showSizer.Add((0,5),0)
2748
2749	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2750	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2751	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2752	showABC.SetValue(drawingData['showABC'])
2753	lineSizer.Add(showABC,0,wx.ALIGN_CENTER_VERTICAL)
2754	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,wx.ALIGN_CENTER_VERTICAL)
2755	VP = drawingData['viewPoint'][0]
2756	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2757	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2758	G2frame.dataDisplay.viewPoint = viewPoint
2759	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2760	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2761	lineSizer.Add(viewPoint,0,wx.ALIGN_CENTER_VERTICAL)
2762	showSizer.Add(lineSizer)
2763	showSizer.Add((0,5),0)
2764
2765	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2766
2767	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2768	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2769	unitCellBox.SetValue(drawingData['unitCellBox'])
2770	line2Sizer.Add(unitCellBox,0,wx.ALIGN_CENTER_VERTICAL)
2771
2772	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2773	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2774	showHydrogen.SetValue(drawingData['showHydrogen'])
2775	line2Sizer.Add(showHydrogen,0,wx.ALIGN_CENTER_VERTICAL)
2776
2777	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2778	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2779	showRB.SetValue(drawingData['showRigidBodies'])
2780	line2Sizer.Add(showRB,0,wx.ALIGN_CENTER_VERTICAL)
2781
2782	showSizer.Add(line2Sizer)
2783	return showSizer
2784
2785	def RadSizer():
2786
2787	def OnSizeHatoms(event):
2788	try:
2789	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2790	except ValueError:
2791	value = 0.5
2792	drawingData['sizeH'] = value
2793	sizeH.SetValue("%.2f"%(value))
2794	G2plt.PlotStructure(G2frame,data)
2795
2796	def OnRadFactor(event):
2797	try:
2798	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2799	except ValueError:
2800	value = 0.85
2801	drawingData['radiusFactor'] = value
2802	radFactor.SetValue("%.2f"%(value))
2803	FindBondsDraw()
2804	G2plt.PlotStructure(G2frame,data)
2805
2806	radSizer = wx.BoxSizer(wx.HORIZONTAL)
2807	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,wx.ALIGN_CENTER_VERTICAL)
2808	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2809	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
2810	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
2811	radSizer.Add(sizeH,0,wx.ALIGN_CENTER_VERTICAL)
2812
2813	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,wx.ALIGN_CENTER_VERTICAL)
2814	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2815	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
2816	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
2817	radSizer.Add(radFactor,0,wx.ALIGN_CENTER_VERTICAL)
2818	return radSizer
2819
2820	# UpdateDrawOptions exectable code starts here
2821	generalData = data['General']
2822	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2823	SetupDrawingData()
2824	drawingData = data['Drawing']
2825	if generalData['Type'] == 'nuclear':
2826	pickChoice = ['Atoms','Bonds','Torsions','Planes']
2827	elif generalData['Type'] == 'macromolecular':
2828	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
2829
2830	G2frame.dataFrame.SetStatusText('')
2831	if drawOptions.GetSizer():
2832	drawOptions.GetSizer().Clear(True)
2833	mainSizer = wx.BoxSizer(wx.VERTICAL)
2834	mainSizer.Add((5,5),0)
2835	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,wx.ALIGN_CENTER_VERTICAL)
2836	mainSizer.Add((5,5),0)
2837	mainSizer.Add(SlopSizer(),0)
2838	mainSizer.Add((5,5),0)
2839	mainSizer.Add(ShowSizer(),0,)
2840	mainSizer.Add((5,5),0)
2841	mainSizer.Add(RadSizer(),0,)
2842	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
2843
2844	################################################################################
2845	#### Texture routines
2846	################################################################################
2847
2848	def UpdateTexture():
2849	def SetSHCoef():
2850	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
2851	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
2852	SHCoeff = textureData['SH Coeff'][1]
2853	for cofName in SHCoeff:
2854	if cofName in cofNames:
2855	newSHCoef[cofName] = SHCoeff[cofName]
2856	return newSHCoef
2857
2858	def OnShOrder(event):
2859	Obj = event.GetEventObject()
2860	textureData['Order'] = int(Obj.GetValue())
2861	textureData['SH Coeff'][1] = SetSHCoef()
2862	wx.CallAfter(UpdateTexture)
2863	G2plt.PlotTexture(G2frame,data)
2864
2865	def OnShModel(event):
2866	Obj = event.GetEventObject()
2867	textureData['Model'] = Obj.GetValue()
2868	textureData['SH Coeff'][1] = SetSHCoef()
2869	wx.CallAfter(UpdateTexture)
2870	G2plt.PlotTexture(G2frame,data)
2871
2872	def OnSHRefine(event):
2873	Obj = event.GetEventObject()
2874	textureData['SH Coeff'][0] = Obj.GetValue()
2875
2876	def OnSHShow(event):
2877	Obj = event.GetEventObject()
2878	textureData['SHShow'] = Obj.GetValue()
2879	wx.CallAfter(UpdateTexture)
2880
2881	def OnProjSel(event):
2882	Obj = event.GetEventObject()
2883	G2frame.Projection = Obj.GetValue()
2884	G2plt.PlotTexture(G2frame,data)
2885
2886	def OnColorSel(event):
2887	Obj = event.GetEventObject()
2888	G2frame.ContourColor = Obj.GetValue()
2889	G2plt.PlotTexture(G2frame,data)
2890
2891	def OnAngRef(event):
2892	Obj = event.GetEventObject()
2893	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
2894
2895	def OnAngValue(event):
2896	Obj = event.GetEventObject()
2897	try:
2898	value = float(Obj.GetValue())
2899	except ValueError:
2900	value = textureData[valIndx[Obj.GetId()]][1]
2901	Obj.SetValue('%8.2f'%(value))
2902	textureData[valIndx[Obj.GetId()]][1] = value
2903
2904	def OnODFValue(event):
2905	Obj = event.GetEventObject()
2906	try:
2907	value = float(Obj.GetValue())
2908	except ValueError:
2909	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
2910	Obj.SetValue('%8.3f'%(value))
2911	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
2912	G2plt.PlotTexture(G2frame,data)
2913
2914	def OnPfType(event):
2915	Obj = event.GetEventObject()
2916	textureData['PlotType'] = Obj.GetValue()
2917	wx.CallAfter(UpdateTexture)
2918	G2plt.PlotTexture(G2frame,data)
2919
2920	def OnPFValue(event):
2921	Obj = event.GetEventObject()
2922	Saxis = Obj.GetValue().split()
2923	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2924	try:
2925	hkl = [int(Saxis[i]) for i in range(3)]
2926	except (ValueError,IndexError):
2927	hkl = textureData['PFhkl']
2928	if not np.any(np.array(hkl)): #can't be all zeros!
2929	hkl = textureData['PFhkl']
2930	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
2931	textureData['PFhkl'] = hkl
2932	else:
2933	try:
2934	xyz = [float(Saxis[i]) for i in range(3)]
2935	except (ValueError,IndexError):
2936	xyz = textureData['PFxyz']
2937	if not np.any(np.array(xyz)): #can't be all zeros!
2938	xyz = textureData['PFxyz']
2939	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
2940	textureData['PFxyz'] = xyz
2941	G2plt.PlotTexture(G2frame,data)
2942
2943	# UpdateTexture executable starts here
2944	G2frame.dataFrame.SetStatusText('')
2945	generalData = data['General']
2946	SGData = generalData['SGData']
2947	try:
2948	textureData = generalData['SH Texture']
2949	except KeyError: #fix old files!
2950	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
2951	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
2952	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
2953	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
2954	if 'SHShow' not in textureData: #another fix
2955	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2956	try: #another fix!
2957	x = textureData['PlotType']
2958	except KeyError:
2959	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2960	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
2961	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
2962	if generalData['doPawley'] and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Sequental results'):
2963	G2frame.dataFrame.RefineTexture.Enable(True)
2964	shAngles = ['omega','chi','phi']
2965	if Texture.GetSizer():
2966	Texture.GetSizer().Clear(True)
2967	mainSizer = wx.BoxSizer(wx.VERTICAL)
2968	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
2969	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,wx.ALIGN_CENTER_VERTICAL)
2970	titleSizer.Add(wx.StaticText(Texture,-1,
2971	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
2972	0,wx.ALIGN_CENTER_VERTICAL)
2973	mainSizer.Add(titleSizer,0)
2974	mainSizer.Add((0,5),0)
2975	shSizer = wx.FlexGridSizer(1,6,5,5)
2976	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,wx.ALIGN_CENTER_VERTICAL)
2977	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
2978	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2979	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
2980	shSizer.Add(shModel,0,wx.ALIGN_CENTER_VERTICAL)
2981	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,wx.ALIGN_CENTER_VERTICAL)
2982	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
2983	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2984	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
2985	shSizer.Add(shOrder,0,wx.ALIGN_CENTER_VERTICAL)
2986	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
2987	shRef.SetValue(textureData['SH Coeff'][0])
2988	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
2989	shSizer.Add(shRef,0,wx.ALIGN_CENTER_VERTICAL)
2990	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
2991	shShow.SetValue(textureData['SHShow'])
2992	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
2993	shSizer.Add(shShow,0,wx.ALIGN_CENTER_VERTICAL)
2994	mainSizer.Add(shSizer,0,0)
2995	mainSizer.Add((0,5),0)
2996	PTSizer = wx.FlexGridSizer(2,4,5,5)
2997	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,wx.ALIGN_CENTER_VERTICAL)
2998	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
2999	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
3000	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3001	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
3002	PTSizer.Add(pfType,0,wx.ALIGN_CENTER_VERTICAL)
3003	if 'Axial' not in textureData['PlotType']:
3004	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,wx.ALIGN_CENTER_VERTICAL)
3005	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
3006	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3007	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
3008	PTSizer.Add(projSel,0,wx.ALIGN_CENTER_VERTICAL)
3009	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3010	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,wx.ALIGN_CENTER_VERTICAL)
3011	PH = textureData['PFhkl']
3012	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
3013	else:
3014	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,wx.ALIGN_CENTER_VERTICAL)
3015	PX = textureData['PFxyz']
3016	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
3017	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
3018	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
3019	PTSizer.Add(pfVal,0,wx.ALIGN_CENTER_VERTICAL)
3020	if 'Axial' not in textureData['PlotType']:
3021	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,wx.ALIGN_CENTER_VERTICAL)
3022	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3023	choice.sort()
3024	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
3025	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3026	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
3027	PTSizer.Add(colorSel,0,wx.ALIGN_CENTER_VERTICAL)
3028	mainSizer.Add(PTSizer,0,wx.ALIGN_CENTER_VERTICAL)
3029	mainSizer.Add((0,5),0)
3030	if textureData['SHShow']:
3031	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,wx.ALIGN_CENTER_VERTICAL)
3032	mainSizer.Add((0,5),0)
3033	ODFSizer = wx.FlexGridSizer(2,8,2,2)
3034	ODFIndx = {}
3035	ODFkeys = textureData['SH Coeff'][1].keys()
3036	ODFkeys.sort()
3037	for item in ODFkeys:
3038	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,wx.ALIGN_CENTER_VERTICAL)
3039	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3040	ODFIndx[ODFval.GetId()] = item
3041	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3042	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3043	ODFSizer.Add(ODFval,0,wx.ALIGN_CENTER_VERTICAL)
3044	mainSizer.Add(ODFSizer,0,wx.ALIGN_CENTER_VERTICAL)
3045	mainSizer.Add((0,5),0)
3046	mainSizer.Add((0,5),0)
3047	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,wx.ALIGN_CENTER_VERTICAL)
3048	mainSizer.Add((0,5),0)
3049	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3050	angIndx = {}
3051	valIndx = {}
3052	for item in ['Sample omega','Sample chi','Sample phi']:
3053	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3054	angRef.SetValue(textureData[item][0])
3055	angIndx[angRef.GetId()] = item
3056	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3057	angSizer.Add(angRef,0,wx.ALIGN_CENTER_VERTICAL)
3058	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3059	valIndx[angVal.GetId()] = item
3060	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3061	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3062	angSizer.Add(angVal,0,wx.ALIGN_CENTER_VERTICAL)
3063	angSizer.Add((5,0),0)
3064	mainSizer.Add(angSizer,0,wx.ALIGN_CENTER_VERTICAL)
3065	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3066
3067	################################################################################
3068	##### DData routines - GUI stuff in GSASIIddataGUI.py
3069	################################################################################
3070
3071	def OnHklfAdd(event):
3072	UseList = data['Histograms']
3073	keyList = UseList.keys()
3074	TextList = []
3075	if G2frame.PatternTree.GetCount():
3076	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3077	while item:
3078	name = G2frame.PatternTree.GetItemText(item)
3079	if name not in keyList and 'HKLF' in name:
3080	TextList.append(name)
3081	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3082	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3083	try:
3084	if dlg.ShowModal() == wx.ID_OK:
3085	result = dlg.GetSelections()
3086	for i in result:
3087	histoName = TextList[i]
3088	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3089	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3090	'Extinction':['Lorentzian','None',
3091	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3092	wx.BeginBusyCursor()
3093	UpdateHKLFdata(histoName)
3094	wx.EndBusyCursor()
3095	data['Histograms'] = UseList
3096	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3097	finally:
3098	dlg.Destroy()
3099
3100	def UpdateHKLFdata(histoName):
3101	generalData = data['General']
3102	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3103	refDict,reflData = G2frame.PatternTree.GetItemPyData(Id)
3104	SGData = generalData['SGData']
3105	Cell = generalData['Cell'][1:7]
3106	G,g = G2lat.cell2Gmat(Cell)
3107	for ref in reflData:
3108	H = ref[:3]
3109	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3110	iabsnt,ref[3],ref[11],ref[12] = G2spc.GenHKLf(H,SGData)
3111	G2frame.PatternTree.SetItemPyData(Id,[refDict,reflData])
3112
3113	def OnPwdrAdd(event):
3114	generalData = data['General']
3115	SGData = generalData['SGData']
3116	UseList = data['Histograms']
3117	newList = []
3118	NShkl = len(G2spc.MustrainNames(SGData))
3119	NDij = len(G2spc.HStrainNames(SGData))
3120	keyList = UseList.keys()
3121	TextList = ['All PWDR']
3122	if G2frame.PatternTree.GetCount():
3123	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3124	while item:
3125	name = G2frame.PatternTree.GetItemText(item)
3126	if name not in keyList and 'PWDR' in name:
3127	TextList.append(name)
3128	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3129	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3130	try:
3131	if dlg.ShowModal() == wx.ID_OK:
3132	result = dlg.GetSelections()
3133	for i in result: newList.append(TextList[i])
3134	if 'All PWDR' in newList:
3135	newList = TextList[1:]
3136	for histoName in newList:
3137	pId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3138	UseList[histoName] = {'Histogram':histoName,'Show':False,
3139	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3140	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3141	[1.,1.,1.,0.,0.,0.],6*[False,]],
3142	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3143	NShkl[0.01,],NShkl[False,]],
3144	'HStrain':[NDij[0.0,],NDij[False,]],
3145	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3146	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,pId,'Reflection Lists'))
3147	refList[generalData['Name']] = []
3148	data['Histograms'] = UseList
3149	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3150	finally:
3151	dlg.Destroy()
3152
3153	def OnDataDelete(event):
3154	UseList = data['Histograms']
3155	keyList = ['All',]+UseList.keys()
3156	keyList.sort()
3157	DelList = []
3158	if UseList:
3159	DelList = []
3160	dlg = wx.MultiChoiceDialog(G2frame,
3161	'Which histogram to delete from this phase?', 'Delete histogram',
3162	keyList, wx.CHOICEDLG_STYLE)
3163	try:
3164	if dlg.ShowModal() == wx.ID_OK:
3165	result = dlg.GetSelections()
3166	for i in result:
3167	DelList.append(keyList[i])
3168	if 'All' in DelList:
3169	DelList = keyList[1:]
3170	for i in DelList:
3171	del UseList[i]
3172	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3173	finally:
3174	dlg.Destroy()
3175
3176	################################################################################
3177	##### Rigid bodies
3178	################################################################################
3179
3180	def FillRigidBodyGrid(refresh=True):
3181	'''Fill the Rigid Body Phase information tab page.
3182	Note that the page is a ScrolledWindow, not a Grid
3183	'''
3184	def OnThermSel(event): #needs to be seen by VecRbSizer!
3185	Obj = event.GetEventObject()
3186	RBObj = Indx[Obj.GetId()]
3187	val = Obj.GetValue()
3188	Ttype = 'A'
3189	if val == 'Uiso':
3190	Ttype = 'I'
3191	RBObj['ThermalMotion'][0] = 'Uiso'
3192	elif val == 'T':
3193	RBObj['ThermalMotion'][0] = 'T'
3194	elif val == 'TL':
3195	RBObj['ThermalMotion'][0] = 'TL'
3196	elif val == 'TLS':
3197	RBObj['ThermalMotion'][0] = 'TLS'
3198	wx.CallAfter(FillRigidBodyGrid,True)
3199	if val != 'None':
3200	cia = data['General']['AtomPtrs'][3]
3201	for i,id in enumerate(RBObj['Ids']):
3202	data['Atoms'][AtLookUp[id]][cia] = Ttype
3203	G2plt.PlotStructure(G2frame,data)
3204
3205	def ThermDataSizer(RBObj,rbType):
3206
3207	def OnThermval(event):
3208	Obj = event.GetEventObject()
3209	item = Indx[Obj.GetId()]
3210	try:
3211	val = float(Obj.GetValue())
3212	RBObj['ThermalMotion'][1][item] = val
3213	except ValueError:
3214	pass
3215	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3216	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3217	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3218	cia = data['General']['AtomPtrs'][3]
3219	for i,id in enumerate(RBObj['Ids']):
3220	if Uout[i][0] == 'I':
3221	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3222	else:
3223	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3224	G2plt.PlotStructure(G2frame,data)
3225
3226	def OnTLSRef(event):
3227	Obj = event.GetEventObject()
3228	item = Indx[Obj.GetId()]
3229	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3230
3231	thermSizer = wx.FlexGridSizer(1,9,5,5)
3232	model = RBObj['ThermalMotion']
3233	if model[0] == 'Uiso':
3234	names = ['Uiso',]
3235	elif 'T' in model[0]:
3236	names = ['T11','T22','T33','T12','T13','T23']
3237	if 'L' in model[0]:
3238	names += ['L11','L22','L33','L12','L13','L23']
3239	if 'S' in model[0]:
3240	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3241	for i,name in enumerate(names):
3242	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,wx.ALIGN_CENTER_VERTICAL)
3243	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3244	style=wx.TE_PROCESS_ENTER)
3245	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3246	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3247	Indx[thermVal.GetId()] = i
3248	thermSizer.Add(thermVal)
3249	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3250	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3251	Tcheck.SetValue(model[2][i])
3252	Indx[Tcheck.GetId()] = i
3253	thermSizer.Add(Tcheck,0,wx.ALIGN_CENTER_VERTICAL)
3254	return thermSizer
3255
3256	def LocationSizer(RBObj,rbType):
3257
3258	def OnOrigRef(event):
3259	RBObj['Orig'][1] = Ocheck.GetValue()
3260
3261	def OnOrienRef(event):
3262	RBObj['Orient'][1] = Qcheck.GetValue()
3263
3264	def OnOrigX(event):
3265	Obj = event.GetEventObject()
3266	item = Indx[Obj.GetId()]
3267	try:
3268	val = float(Obj.GetValue())
3269	RBObj['Orig'][0][item] = val
3270	Obj.SetValue('%8.5f'%(val))
3271	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3272	for i,id in enumerate(RBObj['Ids']):
3273	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3274	data['Drawing']['Atoms'] = []
3275	UpdateDrawAtoms(atomStyle)
3276	G2plt.PlotStructure(G2frame,data)
3277	except ValueError:
3278	pass
3279
3280	def OnOrien(event):
3281	Obj = event.GetEventObject()
3282	item = Indx[Obj.GetId()]
3283	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3284	V = np.inner(Bmat,V)
3285	try:
3286	val = float(Obj.GetValue())
3287	if item:
3288	V[item-1] = val
3289	else:
3290	A = val
3291	Obj.SetValue('%8.5f'%(val))
3292	V = np.inner(Amat,V)
3293	Q = G2mth.AVdeg2Q(A,V)
3294	if not any(Q):
3295	raise ValueError
3296	RBObj['Orient'][0] = Q
3297	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3298	for i,id in enumerate(RBObj['Ids']):
3299	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3300	data['Drawing']['Atoms'] = []
3301	UpdateDrawAtoms(atomStyle)
3302	G2plt.PlotStructure(G2frame,data)
3303	except ValueError:
3304	pass
3305
3306	topSizer = wx.FlexGridSizer(2,6,5,5)
3307	Orig = RBObj['Orig'][0]
3308	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3309	Orien = [Orien,]
3310	Orien.extend(OrienV/nl.norm(OrienV))
3311	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,wx.ALIGN_CENTER_VERTICAL)
3312	for ix,x in enumerate(Orig):
3313	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3314	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3315	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3316	Indx[origX.GetId()] = ix
3317	topSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3318	topSizer.Add((5,0),)
3319	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3320	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3321	Ocheck.SetValue(RBObj['Orig'][1])
3322	topSizer.Add(Ocheck,0,wx.ALIGN_CENTER_VERTICAL)
3323	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,wx.ALIGN_CENTER_VERTICAL)
3324	for ix,x in enumerate(Orien):
3325	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3326	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3327	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3328	Indx[orien.GetId()] = ix
3329	topSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3330	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3331	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3332	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3333	Qcheck.SetValue(RBObj['Orient'][1])
3334	topSizer.Add(Qcheck)
3335	return topSizer
3336
3337	def ResrbSizer(RBObj):
3338	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3339
3340	def OnTorsionRef(event):
3341	Obj = event.GetEventObject()
3342	item = Indx[Obj.GetId()]
3343	RBObj['Torsions'][item][1] = Obj.GetValue()
3344
3345	def OnTorsion(event):
3346	Obj = event.GetEventObject()
3347	item = Indx[Obj.GetId()]
3348	try:
3349	val = float(Obj.GetValue())
3350	RBObj['Torsions'][item][0] = val
3351	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3352	for i,id in enumerate(RBObj['Ids']):
3353	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3354	except ValueError:
3355	pass
3356	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3357	data['Drawing']['Atoms'] = []
3358	UpdateDrawAtoms(atomStyle)
3359	drawAtoms.ClearSelection()
3360	G2plt.PlotStructure(G2frame,data)
3361
3362	def OnDelResRB(event):
3363	Obj = event.GetEventObject()
3364	RBId = Indx[Obj.GetId()]
3365	RBData['Residue'][RBId]['useCount'] -= 1
3366	RBObjs = data['RBModels']['Residue']
3367	for rbObj in RBObjs:
3368	if RBId == rbObj['RBId']:
3369	data['RBModels']['Residue'].remove(rbObj)
3370	G2plt.PlotStructure(G2frame,data)
3371	wx.CallAfter(FillRigidBodyGrid,True)
3372
3373	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3374	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3375	topLine = wx.BoxSizer(wx.HORIZONTAL)
3376	topLine.Add(wx.StaticText(RigidBodies,-1,
3377	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3378	rbId = RBObj['RBId']
3379	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3380	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3381	Indx[delRB.GetId()] = rbId
3382	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3383	resrbSizer.Add(topLine)
3384	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3385	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,wx.ALIGN_CENTER_VERTICAL)
3386	torSizer = wx.FlexGridSizer(1,6,5,5)
3387	for itors,tors in enumerate(RBObj['Torsions']):
3388	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,wx.ALIGN_CENTER_VERTICAL)
3389	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3390	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3391	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3392	Indx[torsTxt.GetId()] = itors
3393	torSizer.Add(torsTxt)
3394	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3395	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3396	torCheck.SetValue(tors[1])
3397	Indx[torCheck.GetId()] = itors
3398	torSizer.Add(torCheck,0,wx.ALIGN_CENTER_VERTICAL)
3399	resrbSizer.Add(torSizer)
3400	tchoice = ['None','Uiso','T','TL','TLS']
3401	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3402	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3403	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3404	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3405	Indx[thermSel.GetId()] = RBObj
3406	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3407	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3408	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3409	resrbSizer.Add(thermSizer)
3410	if RBObj['ThermalMotion'][0] != 'None':
3411	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3412	return resrbSizer
3413
3414	def VecrbSizer(RBObj):
3415	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3416
3417	def OnDelVecRB(event):
3418	Obj = event.GetEventObject()
3419	RBId = Indx[Obj.GetId()]
3420	RBData['Vector'][RBId]['useCount'] -= 1
3421	RBObjs = data['RBModels']['Vector']
3422	for rbObj in RBObjs:
3423	if RBId == rbObj['RBId']:
3424	data['RBModels']['Vector'].remove(rbObj)
3425	G2plt.PlotStructure(G2frame,data)
3426	wx.CallAfter(FillRigidBodyGrid,True)
3427
3428	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3429	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3430	topLine = wx.BoxSizer(wx.HORIZONTAL)
3431	topLine.Add(wx.StaticText(RigidBodies,-1,
3432	'Name: '+RBObj['RBname']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3433	rbId = RBObj['RBId']
3434	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3435	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3436	Indx[delRB.GetId()] = rbId
3437	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3438	vecrbSizer.Add(topLine)
3439	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3440	tchoice = ['None','Uiso','T','TL','TLS']
3441	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3442	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3443	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3444	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3445	Indx[thermSel.GetId()] = RBObj
3446	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3447	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3448	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3449	vecrbSizer.Add(thermSizer)
3450	if RBObj['ThermalMotion'][0] != 'None':
3451	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3452	return vecrbSizer
3453
3454	# FillRigidBodyGrid executable code starts here
3455	if refresh:
3456	RigidBodies.DestroyChildren()
3457	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3458	general = data['General']
3459	cx = general['AtomPtrs'][0]
3460	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3461	RBData = G2frame.PatternTree.GetItemPyData(
3462	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3463	Indx = {}
3464	atomStyle = 'balls & sticks'
3465	if 'macro' in general['Type']:
3466	atomStyle = 'sticks'
3467	G2frame.dataFrame.SetStatusText('')
3468	mainSizer = wx.BoxSizer(wx.VERTICAL)
3469	if not data['RBModels']:
3470	mainSizer.Add((5,5),0)
3471	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,wx.ALIGN_CENTER_VERTICAL)
3472	mainSizer.Add((5,5),0)
3473	if 'Residue' in data['RBModels']:
3474	mainSizer.Add((5,5),0)
3475	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3476	mainSizer.Add((5,5),0)
3477	for RBObj in data['RBModels']['Residue']:
3478	mainSizer.Add(ResrbSizer(RBObj))
3479	if 'Vector' in data['RBModels']:
3480	mainSizer.Add((5,5),0)
3481	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3482	mainSizer.Add((5,5),0)
3483	for RBObj in data['RBModels']['Vector']:
3484	mainSizer.Add(VecrbSizer(RBObj))
3485
3486	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3487
3488	def OnRBCopyParms(event):
3489	RBObjs = []
3490	for rbType in ['Vector','Residue']:
3491	RBObjs += data['RBModels'].get(rbType,[])
3492	if not len(RBObjs):
3493	print '** ERROR - no rigid bodies defined **'
3494	return
3495	if len(RBObjs) == 1:
3496	print '** INFO - only one rigid body defined; nothing to copy to **'
3497	return
3498	Source = []
3499	sourceRB = {}
3500	for RBObj in RBObjs:
3501	Source.append(RBObj['RBname'])
3502	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3503	if dlg.ShowModal() == wx.ID_OK:
3504	sel = dlg.GetSelection()
3505	name = Source[sel]
3506	for item in ['Orig','Orient','ThermalMotion']:
3507	sourceRB.update({item:RBObjs[sel][item],})
3508	dlg.Destroy()
3509	if not sourceRB:
3510	return
3511	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3512	if dlg.ShowModal() == wx.ID_OK:
3513	sel = dlg.GetSelections()
3514	for x in sel:
3515	RBObjs[x].update(copy.copy(sourceRB))
3516	G2plt.PlotStructure(G2frame,data)
3517	wx.CallAfter(FillRigidBodyGrid(True))
3518
3519	def OnRBAssign(event):
3520
3521	G2frame.dataFrame.SetStatusText('')
3522	RBData = G2frame.PatternTree.GetItemPyData(
3523	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3524	rbNames = {}
3525	for rbVec in RBData['Vector']:
3526	if rbVec != 'AtInfo':
3527	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3528	for rbRes in RBData['Residue']:
3529	if rbRes != 'AtInfo':
3530	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3531	if not rbNames:
3532	print '** ERROR - no rigid bodies defined **'
3533	return
3534	general = data['General']
3535	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3536	cx,ct = general['AtomPtrs'][:2]
3537	atomData = data['Atoms']
3538	Indx = {}
3539	atInd = [-1,-1,-1]
3540	data['testRBObj'] = {}
3541
3542	def Draw():
3543
3544	def OnOk(event):
3545	rbType = data['testRBObj']['rbType']
3546	RBObjs = data['RBModels'].get(rbType,[])
3547	rbObj = data['testRBObj']['rbObj']
3548	rbId = rbObj['RBId']
3549	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3550	Ids = []
3551	dmax = 0.0
3552	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3553	for xyz in newXYZ:
3554	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3555	dmax = max(dmax,np.min(dist))
3556	id = np.argmin(dist)
3557	Ids.append(atomData[id][-1])
3558	atomData[id][cx:cx+3] = xyz
3559	if dmax > 1.0:
3560	print '** WARNING - some atoms not found or misidentified **'
3561	print '** check torsion angles & try again **'
3562	OkBtn.SetLabel('Not Ready')
3563	OkBtn.Enable(False)
3564	return
3565	rbObj['Ids'] = Ids
3566	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3567	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3568	RBObjs.append(rbObj)
3569	data['RBModels'][rbType] = RBObjs
3570	RBData[rbType][rbId]['useCount'] += 1
3571	del data['testRBObj']
3572	G2plt.PlotStructure(G2frame,data)
3573	FillRigidBodyGrid(True)
3574
3575	def OnCancel(event):
3576	del data['testRBObj']
3577	FillRigidBodyGrid(True)
3578
3579	def OnRBSel(event):
3580	selection = rbSel.GetValue()
3581	rbType,rbId = rbNames[selection]
3582	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3583	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3584	data['testRBObj']['rbType'] = rbType
3585	data['testRBObj']['rbData'] = RBData
3586	data['testRBObj']['Sizers'] = {}
3587	rbRef = RBData[rbType][rbId]['rbRef']
3588	data['testRBObj']['rbRef'] = rbRef
3589	refType = []
3590	refName = []
3591	for ref in rbRef[:3]:
3592	reftype = data['testRBObj']['rbAtTypes'][ref]
3593	refType.append(reftype)
3594	refName.append(reftype+' '+str(rbRef[0]))
3595	atNames,AtNames = fillAtNames(refType,atomData,ct)
3596	data['testRBObj']['atNames'] = atNames
3597	data['testRBObj']['AtNames'] = AtNames
3598	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3599	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3600	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3601	data['testRBObj']['torAtms'] = []
3602	for item in RBData[rbType][rbId].get('rbSeq',[]):
3603	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3604	data['testRBObj']['torAtms'].append([-1,-1,-1])
3605	Draw()
3606
3607	def fillAtNames(refType,atomData,ct):
3608	atNames = [{},{},{}]
3609	AtNames = {}
3610	for iatm,atom in enumerate(atomData):
3611	AtNames[atom[ct-1]] = iatm
3612	for i,reftype in enumerate(refType):
3613	if atom[ct] == reftype:
3614	atNames[i][atom[ct-1]] = iatm
3615	return atNames,AtNames
3616
3617	def OnAtOrigPick(event):
3618	Obj = event.GetEventObject()
3619	item = Indx[Obj.GetId()]
3620	atName = Obj.GetValue()
3621	rbType = data['testRBObj']['rbType']
3622	atInd[0] = atNames[item][atName]
3623	if 'Vector' in rbType:
3624	rbObj = data['testRBObj']['rbObj']
3625	rbId = rbObj['RBId']
3626	rbRef = data['testRBObj']['rbRef']
3627	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3628	nref = atNames[item][atName]
3629	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3630	Nxyz = np.array(atomData[nref][cx:cx+3])
3631	Orig = Nxyz-Oxyz
3632	data['testRBObj']['rbObj']['Orig'][0] = Orig
3633	else:
3634	Orig = atomData[atNames[item][atName]][cx:cx+3]
3635	data['testRBObj']['rbObj']['Orig'][0] = Orig
3636	for x,item in zip(Orig,Xsizers):
3637	item.SetLabel('%10.5f'%(x))
3638	G2plt.PlotStructure(G2frame,data)
3639
3640	def OnAtQPick(event):
3641	Obj = event.GetEventObject()
3642	item = Indx[Obj.GetId()]
3643	atName = Obj.GetValue()
3644	atInd[item] = atNames[item][atName]
3645	if any([x<0 for x in atInd]):
3646	return
3647	OkBtn.SetLabel('OK')
3648	OkBtn.Enable(True)
3649	rbType = data['testRBObj']['rbType']
3650	rbObj = data['testRBObj']['rbObj']
3651	rbId = rbObj['RBId']
3652	rbRef = data['testRBObj']['rbRef']
3653	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3654	rbOrig = rbXYZ[rbRef[0]]
3655	VAR = rbXYZ[rbRef[1]]-rbOrig
3656	VBR = rbXYZ[rbRef[2]]-rbOrig
3657	if rbType == 'Vector':
3658	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3659	else:
3660	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3661	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3662	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3663	VCC = np.cross(VAR,VAC)
3664	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3665	VAR = G2mth.prodQVQ(QuatA,VAR)
3666	VBR = G2mth.prodQVQ(QuatA,VBR)
3667	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3668	QuatC = G2mth.prodQQ(QuatB,QuatA)
3669	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3670	for x,item in zip(QuatC,Osizers):
3671	item.SetLabel('%10.4f'%(x))
3672	if rbType == 'Vector':
3673	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3674	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3675	Orig = Nxyz-Oxyz
3676	data['testRBObj']['rbObj']['Orig'][0] = Orig
3677	for x,item in zip(Orig,Xsizers):
3678	item.SetLabel('%10.5f'%(x))
3679	G2plt.PlotStructure(G2frame,data)
3680
3681	def OnTorAngle(event):
3682	OkBtn.SetLabel('OK')
3683	OkBtn.Enable(True)
3684	Obj = event.GetEventObject()
3685	[tor,torSlide] = Indx[Obj.GetId()]
3686	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3687	try:
3688	value = float(Obj.GetValue())
3689	except ValueError:
3690	value = Tors[0]
3691	Tors[0] = value
3692	Obj.SetValue('%8.3f'%(value))
3693	torSlide.SetValue(int(value*10))
3694	G2plt.PlotStructure(G2frame,data)
3695
3696	def OnTorSlide(event):
3697	OkBtn.SetLabel('OK')
3698	OkBtn.Enable(True)
3699	Obj = event.GetEventObject()
3700	tor,ang = Indx[Obj.GetId()]
3701	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3702	val = float(Obj.GetValue())/10.
3703	Tors[0] = val
3704	ang.SetValue('%8.3f'%(val))
3705	G2plt.PlotStructure(G2frame,data)
3706
3707	if len(data['testRBObj']):
3708	G2plt.PlotStructure(G2frame,data)
3709
3710	RigidBodies.DestroyChildren()
3711	mainSizer = wx.BoxSizer(wx.VERTICAL)
3712	mainSizer.Add((5,5),0)
3713	if data['testRBObj']:
3714	Xsizers = []
3715	Osizers = []
3716	rbObj = data['testRBObj']['rbObj']
3717	rbName = rbObj['RBname']
3718	rbId = rbObj['RBId']
3719	Orig = rbObj['Orig'][0]
3720	Orien = rbObj['Orient'][0]
3721	rbRef = data['testRBObj']['rbRef']
3722	Torsions = rbObj['Torsions']
3723	refName = []
3724	for ref in rbRef:
3725	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3726	atNames = data['testRBObj']['atNames']
3727	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3728	0,wx.ALIGN_CENTER_VERTICAL)
3729	mainSizer.Add((5,5),0)
3730	OriSizer = wx.FlexGridSizer(1,5,5,5)
3731	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,wx.ALIGN_CENTER_VERTICAL)
3732	for ix,x in enumerate(Orig):
3733	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3734	OriSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3735	Xsizers.append(origX)
3736	OriSizer.Add((5,0),)
3737	if len(atomData):
3738	choice = atNames[0].keys()
3739	choice.sort()
3740	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3741	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,wx.ALIGN_CENTER_VERTICAL)
3742	for ix,x in enumerate(Orien):
3743	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3744	OriSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3745	Osizers.append(orien)
3746	data['testRBObj']['Sizers']['Osizers'] = Osizers
3747	mainSizer.Add(OriSizer)
3748	mainSizer.Add((5,5),0)
3749	RefSizer = wx.FlexGridSizer(1,7,5,5)
3750	if len(atomData):
3751	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,wx.ALIGN_CENTER_VERTICAL)
3752	for i in [0,1,2]:
3753	choice = ['',]+atNames[i].keys()
3754	choice.sort()
3755	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,wx.ALIGN_CENTER_VERTICAL)
3756	atPick = wx.ComboBox(RigidBodies,-1,value='',
3757	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3758	if i:
3759	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3760	else:
3761	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3762	Indx[atPick.GetId()] = i
3763	RefSizer.Add(atPick,0,wx.ALIGN_CENTER_VERTICAL)
3764	mainSizer.Add(RefSizer)
3765	mainSizer.Add((5,5),0)
3766	if Torsions:
3767	AtNames = data['testRBObj']['AtNames']
3768	rbAtTypes = data['testRBObj']['rbAtTypes']
3769	rbSeq = RBData['Residue'][rbId]['rbSeq']
3770	TorSizer = wx.FlexGridSizer(1,4)
3771	TorSizer.AddGrowableCol(1,1)
3772	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3773	torName = ''
3774	for item in [seq[0],seq[1],seq[3][0]]:
3775	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3776	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,wx.ALIGN_CENTER_VERTICAL)
3777	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3778	torSlide.SetRange(0,3600)
3779	torSlide.SetValue(int(torsion[0]*10.))
3780	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3781	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3782	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,wx.ALIGN_CENTER_VERTICAL)
3783	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
3784	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
3785	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
3786	Indx[torSlide.GetId()] = [t,ang]
3787	Indx[ang.GetId()] = [t,torSlide]
3788	TorSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
3789	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
3790	else:
3791	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,wx.ALIGN_CENTER_VERTICAL)
3792	else:
3793	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,wx.ALIGN_CENTER_VERTICAL)
3794	mainSizer.Add((5,5),0)
3795	topSizer = wx.BoxSizer(wx.HORIZONTAL)
3796	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,wx.ALIGN_CENTER_VERTICAL)
3797	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
3798	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3799	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
3800	topSizer.Add((5,5),0)
3801	topSizer.Add(rbSel,0,wx.ALIGN_CENTER_VERTICAL)
3802	mainSizer.Add(topSizer)
3803
3804	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
3805	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
3806	OkBtn.Enable(False)
3807	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
3808	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
3809	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
3810	btnSizer.Add((20,20),1)
3811	btnSizer.Add(OkBtn)
3812	btnSizer.Add(CancelBtn)
3813	btnSizer.Add((20,20),1)
3814	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
3815	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3816	Draw()
3817
3818	def OnAutoFindResRB(event):
3819	RBData = G2frame.PatternTree.GetItemPyData(
3820	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3821	rbKeys = RBData['Residue'].keys()
3822	rbKeys.remove('AtInfo')
3823	if not len(rbKeys):
3824	print '** ERROR - no residue rigid bodies are defined **'
3825	return
3826	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
3827	RBIds = dict(zip(RBNames,rbKeys))
3828	general = data['General']
3829	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3830	Atoms = data['Atoms']
3831	AtLookUp = G2mth.FillAtomLookUp(Atoms)
3832	if 'macro' not in general['Type']:
3833	print '** ERROR - this phase is not a macromolecule **'
3834	return
3835	if not len(Atoms):
3836	print '** ERROR - this phase has no atoms **'
3837	return
3838	RBObjs = []
3839	cx,ct = general['AtomPtrs'][:2]
3840	iatm = 0
3841	wx.BeginBusyCursor()
3842	try:
3843	while iatm < len(Atoms):
3844	atom = Atoms[iatm]
3845	res = atom[1].strip()
3846	numChain = ' %s %s'%(atom[0],atom[2])
3847	if res not in RBIds or atom[ct-1] == 'OXT':
3848	iatm += 1
3849	continue #skip for OXT, water molecules, etc.
3850	rbRes = RBData['Residue'][RBIds[res]]
3851	rbRef = rbRes['rbRef']
3852	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
3853	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
3854	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
3855	rbAtoms = []
3856	rbIds = []
3857	for iratm in range(len(rbRes['atNames'])):
3858	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
3859	rbIds.append(Atoms[iatm][20])
3860	iatm += 1 #puts this at beginning of next residue?
3861	Orig = rbAtoms[rbRef[0]]
3862	rbObj['RBId'] = RBIds[res]
3863	rbObj['Ids'] = rbIds
3864	rbObj['Orig'] = [Orig,False]
3865	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
3866	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
3867	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
3868	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
3869	VCC = np.cross(VAR,VAC)
3870	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3871	VAR = G2mth.prodQVQ(QuatA,VAR)
3872	VBR = G2mth.prodQVQ(QuatA,VBR)
3873	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3874	QuatC = G2mth.prodQQ(QuatB,QuatA)
3875	rbObj['Orient'] = [QuatC,' ']
3876	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3877	SXYZ = []
3878	TXYZ = []
3879	rbObj['Torsions'] = []
3880	for i,xyz in enumerate(rbRes['rbXYZ']):
3881	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
3882	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
3883	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
3884	VBR = SXYZ[Oatm]-SXYZ[Patm]
3885	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
3886	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
3887	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
3888	ang = 180.*D/np.pi
3889	rbObj['Torsions'].append([ang,False])
3890	for ride in Riders:
3891	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
3892	rbRes['useCount'] += 1
3893	RBObjs.append(rbObj)
3894	data['RBModels']['Residue'] = RBObjs
3895	for RBObj in RBObjs:
3896	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3897	for i,id in enumerate(RBObj['Ids']):
3898	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3899	finally:
3900	wx.EndBusyCursor()
3901	wx.CallAfter(FillRigidBodyGrid,True)
3902
3903	def OnRBRemoveAll(event):
3904	data['RBModels']['Residue'] = []
3905	data['RBModels']['Vector'] = []
3906	RBData = G2frame.PatternTree.GetItemPyData(
3907	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3908	for RBType in ['Vector','Residue']:
3909	for rbId in RBData[RBType]:
3910	RBData[RBType][rbId]['useCount'] = 0
3911	FillRigidBodyGrid(True)
3912
3913	def OnGlobalResRBTherm(event):
3914	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3915	RBObjs = data['RBModels']['Residue']
3916	names = ['None','Uiso','T','TL','TLS']
3917	cia = data['General']['AtomPtrs'][3]
3918	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
3919	if dlg.ShowModal() == wx.ID_OK:
3920	sel = dlg.GetSelection()
3921	parm = names[sel]
3922	Ttype = 'A'
3923	if parm == 'Uiso':
3924	Ttype = 'I'
3925	for rbObj in RBObjs:
3926	rbObj['ThermalMotion'][0] = parm
3927	if parm != 'None':
3928	for i,id in enumerate(rbObj['Ids']):
3929	data['Atoms'][AtLookUp[id]][cia] = Ttype
3930	dlg.Destroy()
3931	wx.CallAfter(FillRigidBodyGrid,True)
3932
3933	def OnGlobalResRBRef(event):
3934	RBObjs = data['RBModels']['Residue']
3935	names = ['Origin','Orient. angle','Full Orient.']
3936	nTor = 0
3937	for rbObj in RBObjs:
3938	nTor = max(nTor,len(rbObj['Torsions']))
3939	names += ['Torsion '+str(i) for i in range(nTor)]
3940	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
3941	names += ['Uiso',]
3942	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
3943	names += ['Tii','Tij','Lii','Lij','Sij']
3944	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
3945	names += ['Tii','Tij','Lii','Lij']
3946	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
3947	names += ['Tii','Tij']
3948
3949	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
3950	if dlg.ShowModal() == wx.ID_OK:
3951	sel = dlg.GetSelections()
3952	parms = []
3953	for x in sel:
3954	parms.append(names[x])
3955	wx.BeginBusyCursor()
3956	try:
3957	for rbObj in RBObjs:
3958	if 'Origin' in parms:
3959	rbObj['Orig'][1] = True
3960	else:
3961	rbObj['Orig'][1] = False
3962	if 'Full Orient.' in parms:
3963	rbObj['Orient'][1] = 'AV'
3964	elif 'Orient. angle' in parms:
3965	rbObj['Orient'][1] = 'A'
3966	else:
3967	rbObj['Orient'][1] = ' '
3968	for i in range(len(rbObj['Torsions'])):
3969	if 'Torsion '+str(i) in parms:
3970	rbObj['Torsions'][i][1] = True
3971	else:
3972	rbObj['Torsions'][i][1] = False
3973	if rbObj['ThermalMotion'][0] == 'Uiso':
3974	if 'Uiso' in parms:
3975	rbObj['ThermalMotion'][2][0] = True
3976	else:
3977	rbObj['ThermalMotion'][2][0] = False
3978	elif 'T' in rbObj['ThermalMotion'][0]:
3979	if 'Tii' in parms:
3980	rbObj['ThermalMotion'][2][0:2] = [True,True,True]
3981	else:
3982	rbObj['ThermalMotion'][2][0:2] = [False,False,False]
3983	if 'Tij' in parms:
3984	rbObj['ThermalMotion'][2][3:6] = [True,True,True]
3985	else:
3986	rbObj['ThermalMotion'][2][3:6] = [False,False,False]
3987	elif 'L' in rbObj['ThermalMotion'][0]:
3988	if 'Lii' in parms:
3989	rbObj['ThermalMotion'][2][6:9] = [True,True,True]
3990	else:
3991	rbObj['ThermalMotion'][2][6:9] = [False,False,False]
3992	if 'Lij' in parms:
3993	rbObj['ThermalMotion'][2][9:12] = [True,True,True]
3994	else:
3995	rbObj['ThermalMotion'][2][9:12] = [False,False,False]
3996	elif 'S' in rbObj['ThermalMotion'][0]:
3997	if 'Sij' in parms:
3998	rbObj['ThermalMotion'][2][12:20] = [True,True,True,True,True,True,True,True]
3999	else:
4000	rbObj['ThermalMotion'][2][12:20] = [False,False,False,False,False,False,False,False]
4001	finally:
4002	wx.EndBusyCursor()
4003	FillRigidBodyGrid()
4004
4005	################################################################################
4006	##### MC/SA routines
4007	################################################################################
4008
4009	def UpdateMCSA(Scroll=0):
4010	Indx = {}
4011
4012	def OnPosRef(event):
4013	Obj = event.GetEventObject()
4014	model,item,ix = Indx[Obj.GetId()]
4015	model[item][1][ix] = Obj.GetValue()
4016
4017	def OnPosVal(event):
4018	Obj = event.GetEventObject()
4019	model,item,ix = Indx[Obj.GetId()]
4020	try:
4021	model[item][0][ix] = float(Obj.GetValue())
4022	except ValueError:
4023	pass
4024	Obj.SetValue("%.4f"%(model[item][0][ix]))
4025	G2plt.PlotStructure(G2frame,data)
4026
4027	def OnPosRange(event):
4028	Obj = event.GetEventObject()
4029	model,item,ix = Indx[Obj.GetId()]
4030	Range = Obj.GetValue().split()
4031	try:
4032	rmin,rmax = [float(Range[i]) for i in range(2)]
4033	if rmin >= rmax:
4034	raise ValueError
4035	except (ValueError,IndexError):
4036	rmin,rmax = model[item][2][ix]
4037	model[item][2][ix] = [rmin,rmax]
4038	Obj.SetValue('%.3f %.3f'%(rmin,rmax))
4039
4040	def atomSizer(model):
4041
4042	atomsizer = wx.FlexGridSizer(1,7,5,5)
4043	atomsizer.Add(wx.StaticText(MCSA,-1,' Atom: '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4044	for ix,item in enumerate(['x','y','z']):
4045	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4046	posRef.SetValue(model['Pos'][1][ix])
4047	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4048	Indx[posRef.GetId()] = [model,'Pos',ix]
4049	atomsizer.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4050	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4051	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4052	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4053	Indx[posVal.GetId()] = [model,'Pos',ix]
4054	atomsizer.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4055	atomsizer.Add((5,5),0)
4056	for ix,item in enumerate(['x','y','z']):
4057	atomsizer.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4058	rmin,rmax = model['Pos'][2][ix]
4059	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4060	Indx[posRange.GetId()] = [model,'Pos',ix]
4061	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4062	posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4063	atomsizer.Add(posRange,0,wx.ALIGN_CENTER_VERTICAL)
4064	return atomsizer
4065
4066	def rbSizer(model):
4067
4068	def OnOrVar(event):
4069	Obj = event.GetEventObject()
4070	model = Indx[Obj.GetId()]
4071	model['Ovar'] = Obj.GetValue()
4072
4073	def OnOriVal(event):
4074	Obj = event.GetEventObject()
4075	model,ix,ObjA,ObjV = Indx[Obj.GetId()]
4076	A = model['Ori'][0][0]
4077	V = model['Ori'][0][1:]
4078	if ix:
4079	Anew = A
4080	Vec = ObjV.GetValue().split()
4081	try:
4082	Vnew = [float(Vec[i]) for i in range(3)]
4083	except ValueError:
4084	Vnew = V
4085	else:
4086	Vnew = V
4087	try:
4088	Anew = float(ObjA.GetValue())
4089	if not Anew: #==0.0!
4090	Anew = 360.
4091	except ValueError:
4092	Anew = A
4093	Q = G2mth.AVdeg2Q(Anew,Vnew)
4094	A,V = G2mth.Q2AVdeg(Q)
4095	model['Ori'][0][0] = A
4096	model['Ori'][0][1:] = V
4097	if ix:
4098	ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2]))
4099	else:
4100	ObjA.SetValue('%.5f'%(A))
4101	ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2]))
4102	G2plt.PlotStructure(G2frame,data)
4103	# UpdateMCSA()
4104
4105	def OnMolCent(event):
4106	Obj = event.GetEventObject()
4107	model = Indx[Obj.GetId()]
4108	model['MolCent'][1] = Obj.GetValue()
4109	if model['MolCent'][1]:
4110	G2mth.SetMolCent(model,RBData)
4111	G2plt.PlotStructure(G2frame,data)
4112
4113	rbsizer = wx.BoxSizer(wx.VERTICAL)
4114	rbsizer1 = wx.FlexGridSizer(