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source: trunk/GSASIIphsGUI.py @ 1052

Last change on this file since 1052 was 1052, checked in by vondreele, 10 years ago
fix to 64bit version - needed a SetFocus?() after MC/SA run in case user changed focus commented out March-Dollase from MC/SA - not implemented yet
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 245.2 KB

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1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2013-09-07 19:30:29 +0000 (Sat, 07 Sep 2013) $
5	# $Author: vondreele $
6	# $Revision: 1052 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1052 2013-09-07 19:30:29Z 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: 1052 $")
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	MCSA = 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	MCSA['Data source'] = refList.GetValue()
658
659	def OnDmin(event):
660	try:
661	val = float(dmin.GetValue())
662	if 1.0 <= val < 5.0:
663	MCSA['dmin'] = val
664	except ValueError:
665	pass
666	dmin.SetValue("%.3f"%(MCSA['dmin'])) #reset in case of error
667
668	def OnCycles(event):
669	MCSA['Cycles'] = int(cycles.GetValue())
670
671	def OnAlist(event):
672	MCSA['Algorithm'] = Alist.GetValue()
673	wx.CallAfter(UpdateGeneral)
674
675	def OnSlope(event):
676	try:
677	val = float(slope.GetValue())
678	if .25 <= val < 1.0:
679	MCSA['log slope'] = val
680	except ValueError:
681	pass
682	slope.SetValue("%.3f"%(MCSA['log slope'])) #reset in case of error
683
684	def OnAjump(event):
685	Obj = event.GetEventObject()
686	name,ind = Indx[Obj.GetId()]
687	try:
688	val = float(Obj.GetValue())
689	if .0 <= val <= 1.0:
690	MCSA[name][ind] = val
691	except ValueError:
692	pass
693	Obj.SetValue("%.3f"%(MCSA[name][ind]))
694
695	def OnRanStart(event):
696	MCSA['ranStart'] = ranStart.GetValue()
697
698	def OnAnneal(event):
699	Obj = event.GetEventObject()
700	ind,fmt = Indx[Obj.GetId()]
701	if ind == 2: #No. trials
702	try:
703	val = int(Obj.GetValue())
704	if 1 <= val:
705	MCSA['Annealing'][ind] = val
706	except ValueError:
707	Obj.SetValue(fmt%(MCSA['Annealing'][ind]))
708	else:
709	try:
710	val = float(Obj.GetValue())
711	if .0 <= val:
712	MCSA['Annealing'][ind] = val
713	Obj.SetValue(fmt%(MCSA['Annealing'][ind]))
714	except ValueError:
715	MCSA['Annealing'][ind] = None
716	Obj.SetValue(str(MCSA['Annealing'][ind]))
717
718	refList = []
719	if len(data['Pawley ref']):
720	refList = ['Pawley reflections']
721	for item in data['Histograms'].keys():
722	if 'HKLF' in item or 'PWDR' in item:
723	refList.append(item)
724	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
725	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
726	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
727	refList = wx.ComboBox(General,-1,value=MCSA['Data source'],choices=refList,
728	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
729	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
730	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
731	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,wx.ALIGN_CENTER_VERTICAL)
732	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSA['dmin']),style=wx.TE_PROCESS_ENTER)
733	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
734	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
735	lineSizer.Add(dmin,0,wx.ALIGN_CENTER_VERTICAL)
736	mcsaSizer.Add(lineSizer)
737	mcsaSizer.Add((5,5),)
738	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
739	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,wx.ALIGN_CENTER_VERTICAL)
740	Cchoice = ['1','2','3','6','10','20','30','60','100']
741	cycles = wx.ComboBox(General,-1,value=str(MCSA.get('Cycles',1)),choices=Cchoice,
742	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
743	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
744	line2Sizer.Add(cycles,0,wx.ALIGN_CENTER_VERTICAL)
745	line2Sizer.Add((5,0),)
746	ranStart = wx.CheckBox(General,-1,label=' Random start? (ignored if Start temp = None)')
747	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
748	ranStart.SetValue(MCSA.get('ranStart',True))
749	line2Sizer.Add(ranStart,0,wx.ALIGN_CENTER_VERTICAL)
750	mcsaSizer.Add(line2Sizer)
751	mcsaSizer.Add((5,5),)
752	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
753	Achoice = ['log','fast'] #these work
754	# Achoice = ['log','fast','cauchy','boltzmann','Tremayne']
755	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
756	Alist = wx.ComboBox(General,-1,value=MCSA['Algorithm'],choices=Achoice,
757	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
758	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
759	line3Sizer.Add(Alist,0,wx.ALIGN_CENTER_VERTICAL)
760	if MCSA['Algorithm'] in ['Tremayne','fast','boltzmann','cauchy']:
761	Names = [' A-jump: ',' B-jump: ']
762	parms = 'Jump coeff'
763	if MCSA['Algorithm'] in ['boltzmann','cauchy']:
764	Names = [' A-jump: ']
765	elif 'fast' in MCSA['Algorithm']:
766	Names = [' quench: ',' m-factor: ',' n-factor: ']
767	parms = 'fast parms'
768	for i,name in enumerate(Names):
769	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
770	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSA[parms][i]),style=wx.TE_PROCESS_ENTER)
771	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
772	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
773	Indx[Ajump.GetId()] = [parms,i]
774	line3Sizer.Add(Ajump,0,wx.ALIGN_CENTER_VERTICAL)
775	elif 'log' in MCSA['Algorithm']:
776	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,wx.ALIGN_CENTER_VERTICAL)
777	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSA['log slope']),style=wx.TE_PROCESS_ENTER)
778	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
779	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
780	line3Sizer.Add(slope,0,wx.ALIGN_CENTER_VERTICAL)
781	mcsaSizer.Add(line3Sizer)
782	mcsaSizer.Add((5,5),)
783	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
784	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
785	names = [' Start temp: ',' Final temp: ',' No. trials: ']
786	fmts = ['%.1f','%.5f','%d']
787	for i,[name,fmt] in enumerate(zip(names,fmts)):
788	if MCSA['Annealing'][i]:
789	text = fmt%(MCSA['Annealing'][i])
790	else:
791	text = 'None'
792	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
793	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
794	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
795	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
796	Indx[anneal.GetId()] = [i,fmt]
797	line3Sizer.Add(anneal,0,wx.ALIGN_CENTER_VERTICAL)
798	mcsaSizer.Add(line3Sizer)
799	return mcsaSizer
800
801	# UpdateGeneral execution continues here
802	if General.GetSizer():
803	General.GetSizer().Clear(True)
804	mainSizer = wx.BoxSizer(wx.VERTICAL)
805	mainSizer.Add((5,5),0)
806	mainSizer.Add(NameSizer(),0)
807	mainSizer.Add((5,5),0)
808	mainSizer.Add(CellSizer(),0)
809	mainSizer.Add((5,5),0)
810
811	Indx = {}
812	denSizer = None
813	if len(generalData['AtomTypes']):
814	denSizer = DenSizer()
815	mainSizer.Add(denSizer[0])
816	mainSizer.Add((5,5),0)
817	mainSizer.Add(ElemSizer())
818	G2gd.HorizontalLine(mainSizer,General)
819
820	mainSizer.Add(PawleySizer())
821	G2gd.HorizontalLine(mainSizer,General)
822
823	mainSizer.Add(MapSizer())
824	G2gd.HorizontalLine(mainSizer,General)
825
826	mainSizer.Add(FlipSizer())
827	G2gd.HorizontalLine(mainSizer,General)
828
829	mainSizer.Add(MCSASizer())
830	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
831	G2frame.dataFrame.SetStatusText('')
832
833	################################################################################
834	##### Atom routines
835	################################################################################
836
837	def FillAtomsGrid(Atoms):
838	'''Display the contents of the Atoms tab
839	'''
840	def RefreshAtomGrid(event):
841
842	r,c = event.GetRow(),event.GetCol()
843	if r < 0 and c < 0:
844	for row in range(Atoms.GetNumberRows()):
845	Atoms.SelectRow(row,True)
846	if r < 0: #double click on col label! Change all atoms!
847	sel = -1
848	noSkip = True
849	if Atoms.GetColLabelValue(c) == 'refine':
850	Type = generalData['Type']
851	if Type in ['nuclear','macromolecular']:
852	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
853	elif Type in ['magnetic',]:
854	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
855	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
856	if dlg.ShowModal() == wx.ID_OK:
857	sel = dlg.GetSelections()
858	parms = ''
859	for x in sel:
860	parms += choice[x][0]
861	dlg.Destroy()
862	elif Atoms.GetColLabelValue(c) == 'I/A':
863	choice = ['Isotropic','Anisotropic']
864	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
865	if dlg.ShowModal() == wx.ID_OK:
866	sel = dlg.GetSelection()
867	parms = choice[sel][0]
868	dlg.Destroy()
869	elif Atoms.GetColLabelValue(c) == 'Type':
870	choice = generalData['AtomTypes']
871	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
872	if dlg.ShowModal() == wx.ID_OK:
873	sel = dlg.GetSelection()
874	parms = choice[sel]
875	noSkip = False
876	Atoms.ClearSelection()
877	for row in range(Atoms.GetNumberRows()):
878	if parms == atomData[row][c]:
879	Atoms.SelectRow(row,True)
880	dlg.Destroy()
881	SetupGeneral()
882	elif Atoms.GetColLabelValue(c) == 'residue':
883	choice = []
884	for r in range(Atoms.GetNumberRows()):
885	if str(atomData[r][c]) not in choice:
886	choice.append(str(atomData[r][c]))
887	choice.sort()
888	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
889	if dlg.ShowModal() == wx.ID_OK:
890	sel = dlg.GetSelection()
891	parms = choice[sel]
892	noSkip = False
893	Atoms.ClearSelection()
894	for row in range(Atoms.GetNumberRows()):
895	if parms == atomData[row][c]:
896	Atoms.SelectRow(row,True)
897	dlg.Destroy()
898	elif Atoms.GetColLabelValue(c) == 'res no':
899	choice = []
900	for r in range(Atoms.GetNumberRows()):
901	if str(atomData[r][c]) not in choice:
902	choice.append(str(atomData[r][c]))
903	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
904	if dlg.ShowModal() == wx.ID_OK:
905	sel = dlg.GetSelection()
906	parms = choice[sel]
907	noSkip = False
908	Atoms.ClearSelection()
909	for row in range(Atoms.GetNumberRows()):
910	if int(parms) == atomData[row][c]:
911	Atoms.SelectRow(row,True)
912	dlg.Destroy()
913	elif Atoms.GetColLabelValue(c) == 'chain':
914	choice = []
915	for r in range(Atoms.GetNumberRows()):
916	if atomData[r][c] not in choice:
917	choice.append(atomData[r][c])
918	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
919	if dlg.ShowModal() == wx.ID_OK:
920	sel = dlg.GetSelection()
921	parms = choice[sel]
922	noSkip = False
923	Atoms.ClearSelection()
924	for row in range(Atoms.GetNumberRows()):
925	if parms == atomData[row][c]:
926	Atoms.SelectRow(row,True)
927	dlg.Destroy()
928	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
929	pass #& then change all 'I' atoms
930	if sel >= 0 and noSkip:
931	ui = colLabels.index('U11')
932	us = colLabels.index('Uiso')
933	ss = colLabels.index('site sym')
934	for r in range(Atoms.GetNumberRows()):
935	ID = atomData[r][-1]
936	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
937	if parms == 'A': #'I' --> 'A'
938	Uiso = float(Atoms.GetCellValue(r,us))
939	sytsym = atomData[r][ss]
940	CSI = G2spc.GetCSuinel(sytsym)
941	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
942	atomData[r][us] = 0.0
943	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
944	for i in range(6):
945	ci = ui+i
946	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
947	if CSI[2][i]:
948	Atoms.SetCellStyle(r,ci,WHITE,False)
949	else: #'A' --> 'I'
950	Uij = atomData[r][ui:ui+6]
951	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
952	atomData[r][us] = Uiso
953	Atoms.SetCellStyle(r,us,WHITE,False)
954	for i in range(6):
955	ci = ui+i
956	atomData[r][ci] = 0.0
957	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
958	if not Atoms.IsReadOnly(r,c):
959	if Atoms.GetColLabelValue(c) == 'refine':
960	rbExcl = rbAtmDict.get(atomData[r][-1],'')
961	if rbExcl:
962	for excl in rbExcl:
963	atomData[r][c] = parms.replace(excl,'')
964	else:
965	atomData[r][c] = parms
966	else:
967	atomData[r][c] = parms
968	if 'Atoms' in data['Drawing']:
969	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
970	wx.CallAfter(Paint)
971
972	def ChangeAtomCell(event):
973
974	def chkUij(Uij,CSI): #needs to do something!!!
975	return Uij
976
977	r,c = event.GetRow(),event.GetCol()
978	if r >= 0 and c >= 0:
979	ID = atomData[r][-1]
980	if Atoms.GetColLabelValue(c) in ['x','y','z']:
981	ci = colLabels.index('x')
982	XYZ = atomData[r][ci:ci+3]
983	if None in XYZ:
984	XYZ = [0,0,0]
985	SScol = colLabels.index('site sym')
986	Mulcol = colLabels.index('mult')
987	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
988	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
989	atomData[r][SScol] = Sytsym
990	atomData[r][Mulcol] = Mult
991	if atomData[r][colLabels.index('I/A')] == 'A':
992	ui = colLabels.index('U11')
993	CSI = G2spc.GetCSuinel(Sytsym)
994	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
995	for i in range(6):
996	ci = i+ui
997	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
998	if CSI[2][i]:
999	Atoms.SetCellStyle(r,ci,WHITE,False)
1000	SetupGeneral()
1001	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1002	if atomData[r][c] == 'I':
1003	Uij = atomData[r][c+2:c+8]
1004	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1005	Atoms.SetCellStyle(r,c+1,WHITE,False)
1006	Atoms.SetCellTextColour(r,c+1,BLACK)
1007	for i in range(6):
1008	ci = i+colLabels.index('U11')
1009	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1010	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1011	atomData[r][ci] = 0.0
1012	else:
1013	value = atomData[r][c+1]
1014	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1015	atomData[r][c+1] = 0.0
1016	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1017	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1018	for i in range(6):
1019	ci = i+colLabels.index('U11')
1020	atomData[r][ci] = value*CSI[3][i]
1021	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1022	Atoms.SetCellTextColour(r,ci,BLACK)
1023	if CSI[2][i]:
1024	Atoms.SetCellStyle(r,ci,WHITE,False)
1025	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1026	value = atomData[r][c]
1027	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1028	iUij = CSI[0][c-colLabels.index('U11')]
1029	for i in range(6):
1030	if iUij == CSI[0][i]:
1031	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1032	elif Atoms.GetColLabelValue(c) == 'refine':
1033	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1034	if 'Atoms' in data['Drawing']:
1035	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1036	wx.CallAfter(Paint)
1037
1038	def AtomTypeSelect(event):
1039	r,c = event.GetRow(),event.GetCol()
1040	if Atoms.GetColLabelValue(c) == 'Type':
1041	PE = G2elemGUI.PickElement(G2frame)
1042	if PE.ShowModal() == wx.ID_OK:
1043	if PE.Elem != 'None':
1044	atomData[r][c] = PE.Elem.strip()
1045	name = atomData[r][c]
1046	if len(name) in [2,4]:
1047	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1048	else:
1049	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1050	PE.Destroy()
1051	SetupGeneral()
1052	wx.CallAfter(Paint)
1053	value = Atoms.GetCellValue(r,c)
1054	atomData[r][c] = value
1055	ID = atomData[r][-1]
1056	if 'Atoms' in data['Drawing']:
1057	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1058	SetupGeneral()
1059	else:
1060	event.Skip()
1061
1062	def RowSelect(event):
1063	r,c = event.GetRow(),event.GetCol()
1064	if not event.AltDown():
1065	Atoms.frm = -1
1066	G2frame.dataFrame.SetStatusText('')
1067	if r < 0 and c < 0:
1068	if Atoms.IsSelection():
1069	Atoms.ClearSelection()
1070	elif c < 0: #only row clicks
1071	if event.ControlDown():
1072	if r in Atoms.GetSelectedRows():
1073	Atoms.DeselectRow(r)
1074	else:
1075	Atoms.SelectRow(r,True)
1076	elif event.ShiftDown():
1077	indxs = Atoms.GetSelectedRows()
1078	Atoms.ClearSelection()
1079	ibeg = 0
1080	if indxs:
1081	ibeg = indxs[-1]
1082	for row in range(ibeg,r+1):
1083	Atoms.SelectRow(row,True)
1084	elif event.AltDown():
1085	if atomData[r][-1] in rbAtmDict:
1086	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1087	Atoms.frm = -1
1088	Atoms.ClearSelection()
1089	else:
1090	if Atoms.frm < 0: #pick atom to be moved
1091	Atoms.frm = r
1092	Atoms.SelectRow(r,True)
1093	n = colLabels.index('Name')
1094	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1095	else: #move it
1096	item = atomData.pop(Atoms.frm)
1097	atomData.insert(r,item)
1098	Atoms.frm = -1
1099	G2frame.dataFrame.SetStatusText('')
1100	wx.CallAfter(Paint)
1101	else:
1102	Atoms.ClearSelection()
1103	Atoms.SelectRow(r,True)
1104
1105	def ChangeSelection(event):
1106	r,c = event.GetRow(),event.GetCol()
1107	if r < 0 and c < 0:
1108	Atoms.ClearSelection()
1109	if c < 0:
1110	if r in Atoms.GetSelectedRows():
1111	Atoms.DeselectRow(r)
1112	else:
1113	Atoms.SelectRow(r,True)
1114	if r < 0:
1115	if c in Atoms.GetSelectedCols():
1116	Atoms.DeselectCol(c)
1117	else:
1118	Atoms.SelectCol(c,True)
1119
1120	def Paint():
1121
1122	table = []
1123	rowLabels = []
1124	for i,atom in enumerate(atomData):
1125	table.append(atom)
1126	rowLabels.append(str(i))
1127	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1128	Atoms.SetTable(atomTable, True)
1129	Atoms.frm = -1
1130	colType = colLabels.index('Type')
1131	colR = colLabels.index('refine')
1132	colSS = colLabels.index('site sym')
1133	colX = colLabels.index('x')
1134	colIA = colLabels.index('I/A')
1135	colU11 = colLabels.index('U11')
1136	colUiso = colLabels.index('Uiso')
1137	attr = wx.grid.GridCellAttr()
1138	attr.IncRef() #fix from Jim Hester
1139	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1140	for c in range(colX,colX+3):
1141	Atoms.SetColAttr(c, attr)
1142	for i in range(colU11-1,colU11+6):
1143	Atoms.SetColSize(i,50)
1144	for row in range(Atoms.GetNumberRows()):
1145	atId = atomData[row][-1]
1146	rbExcl = rbAtmDict.get(atId,'')
1147	Atoms.SetReadOnly(row,colSS,True) #site sym
1148	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1149	if Atoms.GetCellValue(row,colIA) == 'A':
1150	CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')])
1151	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1152	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1153	for i in range(6):
1154	ci = colU11+i
1155	Atoms.SetCellTextColour(row,ci,BLACK)
1156	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1157	if CSI[2][i] and 'U' not in rbExcl:
1158	Atoms.SetCellStyle(row,ci,WHITE,False)
1159	else:
1160	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1161	Atoms.SetCellTextColour(row,colUiso,BLACK)
1162	if 'U' in rbExcl:
1163	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1164	for i in range(6):
1165	ci = colU11+i
1166	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1167	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1168	if 'X' in rbExcl:
1169	for c in range(0,colX+3):
1170	if c != colR:
1171	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1172	Atoms.AutoSizeColumns(False)
1173
1174	# FillAtomsGrid executable code starts here
1175	generalData = data['General']
1176	atomData = data['Atoms']
1177	DData = data['Drawing']
1178	resRBData = data['RBModels'].get('Residue',[])
1179	vecRBData = data['RBModels'].get('Vector',[])
1180	rbAtmDict = {}
1181	for rbObj in resRBData+vecRBData:
1182	exclList = ['X' for i in range(len(rbObj['Ids']))]
1183	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1184	if rbObj['ThermalMotion'][0] != 'None':
1185	for id in rbObj['Ids']:
1186	rbAtmDict[id] += 'U'
1187	# exclList will be 'x' or 'xu' if TLS used in RB
1188	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1189	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1190	if atomData:
1191	for item in Items:
1192	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1193	else:
1194	for item in Items:
1195	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1196	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1197	if 'showABC' in data['Drawing']:
1198	for item in Items:
1199	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1200	else:
1201	for item in Items:
1202	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1203
1204	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1205	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1206	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1207	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1208	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1209	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1210	if generalData['Type'] == 'magnetic':
1211	colLabels += ['Mx','My','Mz']
1212	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1213	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1214	elif generalData['Type'] == 'macromolecular':
1215	colLabels = ['res no','residue','chain'] + colLabels
1216	Types = [wg.GRID_VALUE_STRING,
1217	wg.GRID_VALUE_CHOICE+AAchoice,
1218	wg.GRID_VALUE_STRING] + Types
1219	elif generalData['Type'] == 'modulated':
1220	Types += []
1221	colLabels += []
1222	SGData = data['General']['SGData']
1223	G2frame.dataFrame.SetStatusText('')
1224	if SGData['SGPolax']:
1225	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1226	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1227	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1228	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1229	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1230	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1231	Atoms.SetMargins(0,0)
1232
1233	G2frame.dataFrame.setSizePosLeft([700,300])
1234	Paint()
1235
1236	def OnAtomAdd(event):
1237	AtomAdd(0,0,0)
1238	FillAtomsGrid(Atoms)
1239	event.StopPropagation()
1240	if data['Drawing']:
1241	G2plt.PlotStructure(G2frame,data)
1242
1243	def OnAtomViewAdd(event):
1244	try:
1245	drawData = data['Drawing']
1246	x,y,z = drawData['viewPoint'][0]
1247	AtomAdd(x,y,z)
1248	except:
1249	AtomAdd(0,0,0)
1250	FillAtomsGrid(Atoms)
1251	event.StopPropagation()
1252	G2plt.PlotStructure(G2frame,data)
1253
1254	def AtomAdd(x,y,z,El='H',Name='UNK'):
1255	atomData = data['Atoms']
1256	generalData = data['General']
1257	Ncol = Atoms.GetNumberCols()
1258	atId = ran.randint(0,sys.maxint)
1259	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1260	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1261	if generalData['Type'] == 'macromolecular':
1262	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1263	elif generalData['Type'] == 'nuclear':
1264	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1265	elif generalData['Type'] == 'magnetic':
1266	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1267	SetupGeneral()
1268	if 'Atoms' in data['Drawing']:
1269	DrawAtomAdd(data['Drawing'],atomData[-1])
1270
1271	def OnAtomInsert(event):
1272	AtomInsert(0,0,0)
1273	FillAtomsGrid(Atoms)
1274	event.StopPropagation()
1275	G2plt.PlotStructure(G2frame,data)
1276
1277	def OnAtomViewInsert(event):
1278	if 'Drawing' in data:
1279	drawData = data['Drawing']
1280	x,y,z = drawData['viewPoint'][0]
1281	AtomAdd(x,y,z)
1282	FillAtomsGrid(Atoms)
1283	event.StopPropagation()
1284
1285	def OnAtomMove(event):
1286	drawData = data['Drawing']
1287	atomData = data['Atoms']
1288	x,y,z = drawData['viewPoint'][0]
1289	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1290	cx = colLabels.index('x')
1291	indx = Atoms.GetSelectedRows()
1292	if len(indx) != 1:
1293	print '** ERROR - only one atom can be moved **'
1294	elif atomData[indx[0]][-1] in rbAtmDict:
1295	print '** ERROR - Atoms in rigid bodies can not be moved **'
1296	else:
1297	atomData[indx[0]][cx:cx+3] = [x,y,z]
1298	SetupGeneral()
1299	FillAtomsGrid(Atoms)
1300	ID = atomData[indx[0]][-1]
1301	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1302	G2plt.PlotStructure(G2frame,data)
1303	event.StopPropagation()
1304
1305	def DrawAtomsReplaceByID(drawingData,atom,ID):
1306	IDs = [ID,]
1307	atomData = drawingData['Atoms']
1308	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1309	for ind in indx:
1310	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1311
1312	def MakeDrawAtom(atom,oldatom=None):
1313	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1314	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1315	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1316	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1317	generalData = data['General']
1318	SGData = generalData['SGData']
1319	if generalData['Type'] == 'nuclear':
1320	if oldatom:
1321	opr = oldatom[5]
1322	if atom[9] == 'A':
1323	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1324	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1325	else:
1326	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1327	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1328	else:
1329	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1330	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1331	ct,cs = [1,8] #type & color
1332	elif generalData['Type'] == 'macromolecular':
1333	try:
1334	oneLetter = AA3letter.index(atom[1])
1335	except ValueError:
1336	oneLetter = -1
1337	atomInfo = [[atom[1].strip()+atom[0],]+
1338	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1339	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1340	ct,cs = [4,11] #type & color
1341	elif generalData['Type'] == 'magnetic':
1342	if oldatom:
1343	atomInfo = [atom[:2]+oldatom[3:]][0]
1344	else:
1345	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1346	ct,cs = [1,8] #type & color
1347	# elif generalData['Type'] == 'modulated':
1348	# ????? for future
1349	atNum = generalData['AtomTypes'].index(atom[ct])
1350	atomInfo[cs] = list(generalData['Color'][atNum])
1351	return atomInfo
1352
1353	def AtomInsert(x,y,z):
1354	indx = Atoms.GetSelectedRows()
1355	if indx:
1356	indx = indx[0]
1357	atomData = data['Atoms']
1358	generalData = data['General']
1359	Ncol = Atoms.GetNumberCols()
1360	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1361	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1362	atId = ran.randint(0,sys.maxint)
1363	if generalData['Type'] == 'macromolecular':
1364	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1365	elif generalData['Type'] == 'nuclear':
1366	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1367	elif generalData['Type'] == 'magnetic':
1368	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])
1369	SetupGeneral()
1370
1371	def AtomDelete(event):
1372	indx = Atoms.GetSelectedRows()
1373	IDs = []
1374	if indx:
1375	atomData = data['Atoms']
1376	indx.reverse()
1377	for ind in indx:
1378	atom = atomData[ind]
1379	if atom[-1] in rbAtmDict:
1380	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1381	else:
1382	IDs.append(atom[-1])
1383	del atomData[ind]
1384	if 'Atoms' in data['Drawing']:
1385	DrawAtomsDeleteByIDs(IDs)
1386	wx.CallAfter(FillAtomsGrid,Atoms)
1387	G2plt.PlotStructure(G2frame,data)
1388	SetupGeneral()
1389	event.StopPropagation()
1390
1391	def AtomRefine(event):
1392	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1393	c = colLabels.index('refine')
1394	indx = Atoms.GetSelectedRows()
1395	if indx:
1396	atomData = data['Atoms']
1397	generalData = data['General']
1398	Type = generalData['Type']
1399	if Type in ['nuclear','macromolecular']:
1400	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1401	elif Type == 'magnetic':
1402	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1403	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1404	if dlg.ShowModal() == wx.ID_OK:
1405	sel = dlg.GetSelections()
1406	parms = ''
1407	for x in sel:
1408	parms += choice[x][0]
1409	for r in indx:
1410	if not Atoms.IsReadOnly(r,c):
1411	atomData[r][c] = parms
1412	Atoms.ForceRefresh()
1413	dlg.Destroy()
1414
1415	def AtomModify(event):
1416	indx = Atoms.GetSelectedRows()
1417	if indx:
1418	atomData = data['Atoms']
1419	generalData = data['General']
1420	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1421	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1422	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1423	parm = ''
1424	if dlg.ShowModal() == wx.ID_OK:
1425	sel = dlg.GetSelection()
1426	parm = choices[sel]
1427	cid = colLabels.index(parm)
1428	dlg.Destroy()
1429	if parm in ['Type']:
1430	dlg = G2elemGUI.PickElement(G2frame)
1431	if dlg.ShowModal() == wx.ID_OK:
1432	if dlg.Elem not in ['None']:
1433	El = dlg.Elem.strip()
1434	for r in indx:
1435	if not Atoms.IsReadOnly(r,cid):
1436	atomData[r][cid] = El
1437	if len(El) in [2,4]:
1438	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1439	else:
1440	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1441	SetupGeneral()
1442	if 'Atoms' in data['Drawing']:
1443	for r in indx:
1444	ID = atomData[r][-1]
1445	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1446	FillAtomsGrid(Atoms)
1447	dlg.Destroy()
1448	elif parm in ['Name',]:
1449	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1450	wx.YES_NO \| wx.ICON_QUESTION)
1451	try:
1452	result = dlg.ShowModal()
1453	if result == wx.ID_YES:
1454	for r in indx:
1455	if not Atoms.IsReadOnly(r,cid+1):
1456	El = atomData[r][cid+1]
1457	if len(El) in [2,4]:
1458	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1459	else:
1460	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1461	FillAtomsGrid(Atoms)
1462	finally:
1463	dlg.Destroy()
1464
1465	elif parm in ['I/A']:
1466	choices = ['Isotropic','Anisotropic']
1467	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1468	if dlg.ShowModal() == wx.ID_OK:
1469	sel = dlg.GetSelection()
1470	parm = choices[sel][0]
1471	for r in indx:
1472	if not Atoms.IsReadOnly(r,cid):
1473	atomData[r][cid] = parm
1474	FillAtomsGrid(Atoms)
1475	dlg.Destroy()
1476	elif parm in ['frac','Uiso']:
1477	limits = [0.,1.]
1478	val = 1.0
1479	if parm in ['Uiso']:
1480	limits = [0.,0.25]
1481	val = 0.01
1482	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1483	if dlg.ShowModal() == wx.ID_OK:
1484	parm = dlg.GetValue()
1485	for r in indx:
1486	if not Atoms.IsReadOnly(r,cid):
1487	atomData[r][cid] = parm
1488	SetupGeneral()
1489	FillAtomsGrid(Atoms)
1490	dlg.Destroy()
1491	elif parm in ['x','y','z']:
1492	limits = [-1.,1.]
1493	val = 0.
1494	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1495	if dlg.ShowModal() == wx.ID_OK:
1496	parm = dlg.GetValue()
1497	for r in indx:
1498	if not Atoms.IsReadOnly(r,cid):
1499	atomData[r][cid] += parm
1500	SetupGeneral()
1501	FillAtomsGrid(Atoms)
1502	dlg.Destroy()
1503
1504	def AtomTransform(event):
1505	indx = Atoms.GetSelectedRows()
1506	if indx:
1507	generalData = data['General']
1508	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1509	cx = colLabels.index('x')
1510	cuia = colLabels.index('I/A')
1511	cuij = colLabels.index('U11')
1512	css = colLabels.index('site sym')
1513	atomData = data['Atoms']
1514	generalData = data['General']
1515	SGData = generalData['SGData']
1516	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1517	New = False
1518	try:
1519	if dlg.ShowModal() == wx.ID_OK:
1520	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1521	Cell = np.array(Cell)
1522	cent = SGData['SGCen'][Cent]
1523	M,T = SGData['SGOps'][Opr]
1524	for ind in indx:
1525	XYZ = np.array(atomData[ind][cx:cx+3])
1526	XYZ = np.inner(M,XYZ)+T
1527	if Inv:
1528	XYZ = -XYZ
1529	XYZ = XYZ+cent+Cell
1530	if Force:
1531	XYZ = G2spc.MoveToUnitCell(XYZ)
1532	if New:
1533	atom = copy.copy(atomData[ind])
1534	else:
1535	atom = atomData[ind]
1536	atom[cx:cx+3] = XYZ
1537	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1538	if atom[cuia] == 'A':
1539	Uij = atom[cuij:cuij+6]
1540	U = G2spc.Uij2U(Uij)
1541	U = np.inner(np.inner(M,U),M)
1542	Uij = G2spc.U2Uij(U)
1543	atom[cuij:cuij+6] = Uij
1544	if New:
1545	atomData.append(atom)
1546	finally:
1547	dlg.Destroy()
1548	Atoms.ClearSelection()
1549	if New:
1550	FillAtomsGrid(Atoms)
1551	else:
1552	Atoms.ForceRefresh()
1553
1554	def OnDistAnglePrt(event):
1555	fp = file(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile
1556	)[0]+'.disagl'),'w')
1557	OnDistAngle(event,fp=fp)
1558	fp.close()
1559
1560	def OnDistAngle(event,fp=None):
1561	indx = Atoms.GetSelectedRows()
1562	Oxyz = []
1563	xyz = []
1564	DisAglData = {}
1565	DisAglCtls = {}
1566	if indx:
1567	generalData = data['General']
1568	DisAglData['OrigIndx'] = indx
1569	if 'DisAglCtls' in generalData:
1570	DisAglCtls = generalData['DisAglCtls']
1571	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1572	if dlg.ShowModal() == wx.ID_OK:
1573	DisAglCtls = dlg.GetData()
1574	else:
1575	dlg.Destroy()
1576	return
1577	dlg.Destroy()
1578	generalData['DisAglCtls'] = DisAglCtls
1579	atomData = data['Atoms']
1580	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1581	cx = colLabels.index('x')
1582	cn = colLabels.index('Name')
1583	for i,atom in enumerate(atomData):
1584	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1585	if i in indx:
1586	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1587	DisAglData['OrigAtoms'] = Oxyz
1588	DisAglData['TargAtoms'] = xyz
1589	generalData = data['General']
1590	DisAglData['SGData'] = generalData['SGData']
1591	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1592	if 'pId' in data:
1593	DisAglData['pId'] = data['pId']
1594	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1595	try:
1596	if fp:
1597	G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
1598	else:
1599	G2stMn.PrintDistAngle(DisAglCtls,DisAglData)
1600	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1601	G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types')
1602	else:
1603	print "select one or more rows of atoms"
1604	G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
1605
1606	def OnReImport(event):
1607	print 'reimport atoms from file to be developed'
1608	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1609	rdlist = G2frame.OnImportGeneric(reqrdr,
1610	G2frame.ImportPhaseReaderlist,
1611	'phase')
1612	if len(rdlist) == 0: return
1613	# for now rdlist is only expected to have one element
1614	# for now always use the first phase for when multiple phases are ever implemented
1615	# but it would be better to loop until we find a phase that matches the one in data
1616	for rd in rdlist:
1617	# rd contains all info for a phase
1618	PhaseName = rd.Phase['General']['Name']
1619	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1620	print rd.Phase['Atoms']
1621	return
1622
1623	################################################################################
1624	#Structure drawing GUI stuff
1625	################################################################################
1626
1627	def SetupDrawingData():
1628	generalData = data['General']
1629	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1630	atomData = data['Atoms']
1631	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1632	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1633	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1634	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1635	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1636	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1637	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1638	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1639	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1640	'bondList':{},'viewDir':[1,0,0]}
1641	V0 = np.array([0,0,1])
1642	V = np.inner(Amat,V0)
1643	V /= np.sqrt(np.sum(V**2))
1644	A = np.arccos(np.sum(V*V0))
1645	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1646	try:
1647	drawingData = data['Drawing']
1648	except KeyError:
1649	data['Drawing'] = {}
1650	drawingData = data['Drawing']
1651	if not drawingData: #fill with defaults if empty
1652	drawingData.update(defaultDrawing)
1653	if 'Zstep' not in drawingData:
1654	drawingData['Zstep'] = 0.5
1655	if 'contourLevel' not in drawingData:
1656	drawingData['contourLevel'] = 1.
1657	if 'viewDir' not in drawingData:
1658	drawingData['viewDir'] = [0,0,1]
1659	if 'Quaternion' not in drawingData:
1660	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1661	if 'showRigidBodies' not in drawingData:
1662	drawingData['showRigidBodies'] = True
1663	cx,ct,cs,ci = [0,0,0,0]
1664	if generalData['Type'] == 'nuclear':
1665	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1666	elif generalData['Type'] == 'macromolecular':
1667	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1668	elif generalData['Type'] == 'magnetic':
1669	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1670	# elif generalData['Type'] == 'modulated':
1671	# ????? for future
1672	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1673	if not drawingData.get('Atoms'):
1674	for atom in atomData:
1675	DrawAtomAdd(drawingData,atom)
1676	data['Drawing'] = drawingData
1677
1678	def DrawAtomAdd(drawingData,atom):
1679	drawingData['Atoms'].append(MakeDrawAtom(atom))
1680
1681	def OnRestraint(event):
1682	indx = drawAtoms.GetSelectedRows()
1683	restData = G2frame.PatternTree.GetItemPyData(
1684	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1685	drawingData = data['Drawing']
1686	generalData = data['General']
1687	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1688	cx,ct,cs,ci = drawingData['atomPtrs']
1689	atomData = drawingData['Atoms']
1690	atNames = []
1691	atXYZ = []
1692	atSymOp = []
1693	atIndx = []
1694	for item in indx:
1695	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1696	atSymOp.append(atomData[item][cs-1])
1697	atIndx.append(atomData[item][ci])
1698	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1699	try:
1700	bondData = restData[PhaseName]['Bond']
1701	except KeyError:
1702	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1703	restData[PhaseName] = {}
1704	restData[PhaseName]['Bond'] = bondData
1705	dist = G2mth.getRestDist(atXYZ,Amat)
1706	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1707	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1708	try:
1709	angleData = restData[PhaseName]['Angle']
1710	except KeyError:
1711	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1712	restData[PhaseName] = {}
1713	restData[PhaseName]['Angle'] = angleData
1714	angle = G2mth.getRestAngle(atXYZ,Amat)
1715	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1716	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1717	try:
1718	planeData = restData[PhaseName]['Plane']
1719	except KeyError:
1720	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1721	restData[PhaseName] = {}
1722	restData[PhaseName]['Plane'] = planeData
1723	plane = G2mth.getRestPlane(atXYZ,Amat)
1724	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1725	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1726	try:
1727	chiralData = restData[PhaseName]['Chiral']
1728	except KeyError:
1729	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1730	restData[PhaseName] = {}
1731	restData[PhaseName]['Chiral'] = chiralData
1732	volume = G2mth.getRestChiral(atXYZ,Amat)
1733	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1734	else:
1735	print '**** ERROR wrong number of atoms selected for this restraint'
1736	return
1737	G2frame.PatternTree.SetItemPyData(
1738	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1739
1740	def OnDefineRB(event):
1741	indx = drawAtoms.GetSelectedRows()
1742	indx.sort()
1743	RBData = G2frame.PatternTree.GetItemPyData(
1744	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1745	drawingData = data['Drawing']
1746	generalData = data['General']
1747	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1748	cx,ct,cs,ci = drawingData['atomPtrs']
1749	atomData = drawingData['Atoms']
1750	rbXYZ = []
1751	rbType = []
1752	atNames = []
1753	AtInfo = RBData['Residue']['AtInfo']
1754	for i,item in enumerate(indx):
1755	rbtype = atomData[item][ct]
1756	atNames.append(rbtype+str(i))
1757	rbType.append(rbtype)
1758	if rbtype not in AtInfo:
1759	Info = G2elem.GetAtomInfo(rbtype)
1760	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1761	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1762	rbXYZ = np.array(rbXYZ)
1763	rbXYZ -= rbXYZ[0]
1764	rbId = ran.randint(0,sys.maxint)
1765	rbName = 'UNKRB'
1766	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1767	'Edit rigid body name',rbName ,style=wx.OK)
1768	if dlg.ShowModal() == wx.ID_OK:
1769	rbName = dlg.GetValue()
1770	dlg.Destroy()
1771	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1772	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1773	RBData['RBIds']['Residue'].append(rbId)
1774	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1775
1776	################################################################################
1777	##### Atom draw routines
1778	################################################################################
1779
1780	def UpdateDrawAtoms(atomStyle=''):
1781	def RefreshAtomGrid(event):
1782	def SetChoice(name,c,n=0):
1783	choice = []
1784	for r in range(len(atomData)):
1785	if n:
1786	srchStr = str(atomData[r][c][:n])
1787	else:
1788	srchStr = str(atomData[r][c])
1789	if srchStr not in choice:
1790	if n:
1791	choice.append(str(atomData[r][c][:n]))
1792	else:
1793	choice.append(str(atomData[r][c]))
1794	choice.sort()
1795
1796	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
1797	if dlg.ShowModal() == wx.ID_OK:
1798	sel = dlg.GetSelections()
1799	parms = []
1800	for x in sel:
1801	parms.append(choice[x])
1802	noSkip = False
1803	drawAtoms.ClearSelection()
1804	drawingData['selectedAtoms'] = []
1805	for row in range(len(atomData)):
1806	test = atomData[row][c]
1807	if n:
1808	test = test[:n]
1809	if test in parms:
1810	drawAtoms.SelectRow(row,True)
1811	drawingData['selectedAtoms'].append(row)
1812	G2plt.PlotStructure(G2frame,data)
1813	dlg.Destroy()
1814
1815	r,c = event.GetRow(),event.GetCol()
1816	if r < 0 and c < 0:
1817	for row in range(drawAtoms.GetNumberRows()):
1818	drawingData['selectedAtoms'].append(row)
1819	drawAtoms.SelectRow(row,True)
1820	elif r < 0: #dclick on col label
1821	sel = -1
1822	Parms = False
1823	noSkip = True
1824	if drawAtoms.GetColLabelValue(c) == 'Style':
1825	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1826	if dlg.ShowModal() == wx.ID_OK:
1827	sel = dlg.GetSelection()
1828	parms = styleChoice[sel]
1829	for r in range(len(atomData)):
1830	atomData[r][c] = parms
1831	drawAtoms.SetCellValue(r,c,parms)
1832	FindBondsDraw()
1833	G2plt.PlotStructure(G2frame,data)
1834	dlg.Destroy()
1835	elif drawAtoms.GetColLabelValue(c) == 'Label':
1836	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
1837	if dlg.ShowModal() == wx.ID_OK:
1838	sel = dlg.GetSelection()
1839	parms = labelChoice[sel]
1840	for r in range(len(atomData)):
1841	atomData[r][c] = parms
1842	drawAtoms.SetCellValue(r,c,parms)
1843	dlg.Destroy()
1844	elif drawAtoms.GetColLabelValue(c) == 'Color':
1845	dlg = wx.ColourDialog(G2frame)
1846	if dlg.ShowModal() == wx.ID_OK:
1847	color = dlg.GetColourData().GetColour()
1848	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1849	attr.SetReadOnly(True)
1850	attr.SetBackgroundColour(color)
1851	for r in range(len(atomData)):
1852	atomData[r][c] = color
1853	drawingData['Atoms'][r][c] = color
1854	drawAtoms.SetAttr(r,c,attr)
1855	UpdateDrawAtoms()
1856	dlg.Destroy()
1857	elif drawAtoms.GetColLabelValue(c) == 'Residue':
1858	SetChoice('Residue',c,3)
1859	elif drawAtoms.GetColLabelValue(c) == '1-letter':
1860	SetChoice('1-letter',c,1)
1861	elif drawAtoms.GetColLabelValue(c) == 'Chain':
1862	SetChoice('Chain',c)
1863	elif drawAtoms.GetColLabelValue(c) == 'Name':
1864	SetChoice('Name',c)
1865	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
1866	SetChoice('Name',c)
1867	elif drawAtoms.GetColLabelValue(c) == 'Type':
1868	SetChoice('Type',c)
1869	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
1870	drawAtoms.ClearSelection()
1871	else:
1872	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
1873	atomData[r][c] = drawAtoms.GetCellValue(r,c)
1874	FindBondsDraw()
1875	elif drawAtoms.GetColLabelValue(c) == 'Color':
1876	dlg = wx.ColourDialog(G2frame)
1877	if dlg.ShowModal() == wx.ID_OK:
1878	color = dlg.GetColourData().GetColour()
1879	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1880	attr.SetReadOnly(True)
1881	attr.SetBackgroundColour(color)
1882	atomData[r][c] = color
1883	drawingData['Atoms'][r][c] = color
1884	drawAtoms.SetAttr(i,cs+2,attr)
1885	dlg.Destroy()
1886	UpdateDrawAtoms()
1887	G2plt.PlotStructure(G2frame,data)
1888
1889	def RowSelect(event):
1890	r,c = event.GetRow(),event.GetCol()
1891	if r < 0 and c < 0:
1892	if drawAtoms.IsSelection():
1893	drawAtoms.ClearSelection()
1894	elif c < 0: #only row clicks
1895	if event.ControlDown():
1896	if r in drawAtoms.GetSelectedRows():
1897	drawAtoms.DeselectRow(r)
1898	else:
1899	drawAtoms.SelectRow(r,True)
1900	elif event.ShiftDown():
1901	indxs = drawAtoms.GetSelectedRows()
1902	drawAtoms.ClearSelection()
1903	ibeg = 0
1904	if indxs:
1905	ibeg = indxs[-1]
1906	for row in range(ibeg,r+1):
1907	drawAtoms.SelectRow(row,True)
1908	else:
1909	drawAtoms.ClearSelection()
1910	drawAtoms.SelectRow(r,True)
1911	drawingData['selectedAtoms'] = []
1912	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
1913	G2plt.PlotStructure(G2frame,data)
1914
1915	# UpdateDrawAtoms executable code starts here
1916	G2frame.dataFrame.SetStatusText('')
1917	generalData = data['General']
1918	SetupDrawingData()
1919	drawingData = data['Drawing']
1920	cx,ct,cs,ci = drawingData['atomPtrs']
1921	atomData = drawingData['Atoms']
1922	if atomStyle:
1923	for atom in atomData:
1924	atom[cs] = atomStyle
1925	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
1926	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
1927	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
1928	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1929	labelChoice = [' ','type','name','number']
1930	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
1931	if generalData['Type'] == 'macromolecular':
1932	colLabels = ['Residue','1-letter','Chain'] + colLabels
1933	Types = 3*[wg.GRID_VALUE_STRING,]+Types
1934	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
1935	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
1936	labelChoice = [' ','type','name','number','residue','1-letter','chain']
1937	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
1938	# elif generalData['Type'] == 'modulated':
1939	# Types += []
1940	# colLabels += []
1941	table = []
1942	rowLabels = []
1943	for i,atom in enumerate(drawingData['Atoms']):
1944	table.append(atom[:colLabels.index('I/A')+1])
1945	rowLabels.append(str(i))
1946
1947	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1948	drawAtoms.SetTable(atomTable, True)
1949	drawAtoms.SetMargins(0,0)
1950	drawAtoms.AutoSizeColumns(True)
1951	drawAtoms.SetColSize(colLabels.index('Style'),80)
1952	drawAtoms.SetColSize(colLabels.index('Color'),50)
1953	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
1954	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1955	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
1956	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1957	for i,atom in enumerate(drawingData['Atoms']):
1958	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1959	attr.SetReadOnly(True)
1960	attr.SetBackgroundColour(atom[cs+2])
1961	drawAtoms.SetAttr(i,cs+2,attr)
1962	drawAtoms.SetCellValue(i,cs+2,'')
1963	indx = drawingData['selectedAtoms']
1964	if indx:
1965	for r in range(len(atomData)):
1966	if r in indx:
1967	drawAtoms.SelectRow(r)
1968	for c in range(len(colLabels)):
1969	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1970	attr.SetReadOnly(True)
1971	attr.SetBackgroundColour(VERY_LIGHT_GREY)
1972	if colLabels[c] not in ['Style','Label','Color']:
1973	drawAtoms.SetColAttr(c,attr)
1974	G2frame.dataFrame.setSizePosLeft([600,300])
1975
1976	FindBondsDraw()
1977	drawAtoms.ClearSelection()
1978	# G2plt.PlotStructure(G2frame,data)
1979
1980	def DrawAtomStyle(event):
1981	indx = drawAtoms.GetSelectedRows()
1982	if indx:
1983	generalData = data['General']
1984	atomData = data['Drawing']['Atoms']
1985	cx,ct,cs,ci = data['Drawing']['atomPtrs']
1986	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1987	if generalData['Type'] == 'macromolecular':
1988	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
1989	'backbone','ribbons','schematic']
1990	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1991	if dlg.ShowModal() == wx.ID_OK:
1992	sel = dlg.GetSelection()
1993	parms = styleChoice[sel]
1994	for r in indx:
1995	atomData[r][cs] = parms
1996	drawAtoms.SetCellValue(r,cs,parms)
1997	dlg.Destroy()
1998	FindBondsDraw()
1999	drawAtoms.ClearSelection()
2000	G2plt.PlotStructure(G2frame,data)
2001
2002	def DrawAtomLabel(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 = [' ','type','name','number']
2009	if generalData['Type'] == 'macromolecular':
2010	styleChoice = [' ','type','name','number','residue','1-letter','chain']
2011	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
2012	if dlg.ShowModal() == wx.ID_OK:
2013	sel = dlg.GetSelection()
2014	parms = styleChoice[sel]
2015	for r in indx:
2016	atomData[r][cs+1] = parms
2017	drawAtoms.SetCellValue(r,cs+1,parms)
2018	dlg.Destroy()
2019	drawAtoms.ClearSelection()
2020	G2plt.PlotStructure(G2frame,data)
2021
2022	def DrawAtomColor(event):
2023
2024	indx = drawAtoms.GetSelectedRows()
2025	if indx:
2026	if len(indx) > 1:
2027	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2028	else:
2029	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2030	generalData = data['General']
2031	atomData = data['Drawing']['Atoms']
2032	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2033	atmColors = []
2034	atmTypes = []
2035	for r in indx:
2036	if atomData[r][cs+2] not in atmColors:
2037	atmColors.append(atomData[r][cs+2])
2038	atmTypes.append(atomData[r][ct])
2039	if len(atmColors) > 16:
2040	break
2041	colors = wx.ColourData()
2042	colors.SetChooseFull(True)
2043	dlg = wx.ColourDialog(G2frame)
2044	if dlg.ShowModal() == wx.ID_OK:
2045	for i in range(len(atmColors)):
2046	atmColors[i] = dlg.GetColourData().GetColour()
2047	colorDict = dict(zip(atmTypes,atmColors))
2048	for r in indx:
2049	color = colorDict[atomData[r][ct]]
2050	atomData[r][cs+2] = color
2051	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2052	attr.SetBackgroundColour(color)
2053	drawAtoms.SetAttr(r,cs+2,attr)
2054	data['Drawing']['Atoms'][r][cs+2] = color
2055	drawAtoms.ClearSelection()
2056	dlg.Destroy()
2057	G2frame.dataFrame.SetStatusText('')
2058	G2plt.PlotStructure(G2frame,data)
2059
2060	def ResetAtomColors(event):
2061	generalData = data['General']
2062	atomData = data['Drawing']['Atoms']
2063	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2064	for atom in atomData:
2065	atNum = generalData['AtomTypes'].index(atom[ct])
2066	atom[cs+2] = list(generalData['Color'][atNum])
2067	UpdateDrawAtoms()
2068	drawAtoms.ClearSelection()
2069	G2plt.PlotStructure(G2frame,data)
2070
2071	def SetViewPoint(event):
2072	indx = drawAtoms.GetSelectedRows()
2073	if indx:
2074	atomData = data['Drawing']['Atoms']
2075	cx = data['Drawing']['atomPtrs'][0]
2076	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2077	drawAtoms.ClearSelection() #do I really want to do this?
2078	G2plt.PlotStructure(G2frame,data)
2079
2080	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2081	cx = data['Drawing']['atomPtrs'][0]
2082	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2083	return False
2084	else:
2085	return True
2086
2087	def AddSymEquiv(event):
2088	indx = drawAtoms.GetSelectedRows()
2089	indx.sort()
2090	if indx:
2091	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2092	cx = colLabels.index('x')
2093	cuia = colLabels.index('I/A')
2094	cuij = cuia+2
2095	atomData = data['Drawing']['Atoms']
2096	generalData = data['General']
2097	SGData = generalData['SGData']
2098	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2099	try:
2100	if dlg.ShowModal() == wx.ID_OK:
2101	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2102	Cell = np.array(Cell)
2103	cent = SGData['SGCen'][Cent]
2104	M,T = SGData['SGOps'][Opr]
2105	for ind in indx:
2106	XYZ = np.array(atomData[ind][cx:cx+3])
2107	XYZ = np.inner(M,XYZ)+T
2108	if Inv:
2109	XYZ = -XYZ
2110	XYZ = XYZ+cent+Cell
2111	if Force:
2112	XYZ = G2spc.MoveToUnitCell(XYZ)
2113	if noDuplicate(XYZ,atomData):
2114	atom = copy.copy(atomData[ind])
2115	atom[cx:cx+3] = XYZ
2116	atomOp = atom[cx+3]
2117	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2118	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2119	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2120	if atom[cuia] == 'A':
2121	Uij = atom[cuij:cuij+6]
2122	U = G2spc.Uij2U(Uij)
2123	U = np.inner(np.inner(M,U),M)
2124	Uij = G2spc.U2Uij(U)
2125	atom[cuij:cuij+6] = Uij
2126	atomData.append(atom)
2127	finally:
2128	dlg.Destroy()
2129	UpdateDrawAtoms()
2130	drawAtoms.ClearSelection()
2131	G2plt.PlotStructure(G2frame,data)
2132
2133	def TransformSymEquiv(event):
2134	indx = drawAtoms.GetSelectedRows()
2135	indx.sort()
2136	if indx:
2137	atomData = data['Drawing']['Atoms']
2138	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2139	cx = colLabels.index('x')
2140	cuia = colLabels.index('I/A')
2141	cuij = cuia+2
2142	atomData = data['Drawing']['Atoms']
2143	generalData = data['General']
2144	SGData = generalData['SGData']
2145	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2146	try:
2147	if dlg.ShowModal() == wx.ID_OK:
2148	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2149	Cell = np.array(Cell)
2150	cent = SGData['SGCen'][Cent]
2151	M,T = SGData['SGOps'][Opr]
2152	for ind in indx:
2153	XYZ = np.array(atomData[ind][cx:cx+3])
2154	XYZ = np.inner(M,XYZ)+T
2155	if Inv:
2156	XYZ = -XYZ
2157	XYZ = XYZ+cent+Cell
2158	if Force:
2159	XYZ = G2spc.MoveToUnitCell(XYZ)
2160	atom = atomData[ind]
2161	atom[cx:cx+3] = XYZ
2162	atomOp = atom[cx+3]
2163	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2164	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2165	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2166	if atom[cuia] == 'A':
2167	Uij = atom[cuij:cuij+6]
2168	U = G2spc.Uij2U(Uij)
2169	U = np.inner(np.inner(M,U),M)
2170	Uij = G2spc.U2Uij(U)
2171	atom[cuij:cuij+6] = Uij
2172	data['Drawing']['Atoms'] = atomData
2173	finally:
2174	dlg.Destroy()
2175	UpdateDrawAtoms()
2176	drawAtoms.ClearSelection()
2177	G2plt.PlotStructure(G2frame,data)
2178
2179	def FillCoordSphere(event):
2180	generalData = data['General']
2181	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2182	radii = generalData['BondRadii']
2183	atomTypes = generalData['AtomTypes']
2184	try:
2185	indH = atomTypes.index('H')
2186	radii[indH] = 0.5
2187	except:
2188	pass
2189	indx = drawAtoms.GetSelectedRows()
2190	if indx:
2191	indx.sort()
2192	atomData = data['Drawing']['Atoms']
2193	numAtoms = len(atomData)
2194	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2195	generalData = data['General']
2196	SGData = generalData['SGData']
2197	cellArray = G2lat.CellBlock(1)
2198	wx.BeginBusyCursor()
2199	try:
2200	for ind in indx:
2201	atomA = atomData[ind]
2202	xyzA = np.array(atomA[cx:cx+3])
2203	indA = atomTypes.index(atomA[ct])
2204	for atomB in atomData[:numAtoms]:
2205	indB = atomTypes.index(atomB[ct])
2206	sumR = radii[indA]+radii[indB]
2207	xyzB = np.array(atomB[cx:cx+3])
2208	for xyz in cellArray+xyzB:
2209	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2210	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2211	if noDuplicate(xyz,atomData):
2212	oprB = atomB[cx+3]
2213	C = xyz-xyzB
2214	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2215	newAtom = atomB[:]
2216	newAtom[cx:cx+3] = xyz
2217	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2218	atomData.append(newAtom)
2219	finally:
2220	wx.EndBusyCursor()
2221	data['Drawing']['Atoms'] = atomData
2222	UpdateDrawAtoms()
2223	drawAtoms.ClearSelection()
2224	G2plt.PlotStructure(G2frame,data)
2225
2226	def FillUnitCell(event):
2227	indx = drawAtoms.GetSelectedRows()
2228	indx.sort()
2229	if indx:
2230	atomData = data['Drawing']['Atoms']
2231	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2232	cx = colLabels.index('x')
2233	cuia = colLabels.index('I/A')
2234	cuij = cuia+2
2235	generalData = data['General']
2236	SGData = generalData['SGData']
2237	wx.BeginBusyCursor()
2238	try:
2239	for ind in indx:
2240	atom = atomData[ind]
2241	XYZ = np.array(atom[cx:cx+3])
2242	if atom[cuia] == 'A':
2243	Uij = atom[cuij:cuij+6]
2244	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2245	for item in result:
2246	atom = copy.copy(atomData[ind])
2247	atom[cx:cx+3] = item[0]
2248	atom[cx+3] = str(item[2])+'+' \
2249	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2250	atom[cuij:cuij+6] = item[1]
2251	Opp = G2spc.Opposite(item[0])
2252	for xyz in Opp:
2253	if noDuplicate(xyz,atomData):
2254	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2255	cell = '1'+'+'+ \
2256	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2257	atom[cx:cx+3] = xyz
2258	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2259	atomData.append(atom[:])
2260	else:
2261	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2262	for item in result:
2263	atom = copy.copy(atomData[ind])
2264	atom[cx:cx+3] = item[0]
2265	atom[cx+3] = str(item[1])+'+' \
2266	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2267	Opp = G2spc.Opposite(item[0])
2268	for xyz in Opp:
2269	if noDuplicate(xyz,atomData):
2270	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2271	cell = '1'+'+'+ \
2272	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2273	atom[cx:cx+3] = xyz
2274	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2275	atomData.append(atom[:])
2276	data['Drawing']['Atoms'] = atomData
2277	finally:
2278	wx.EndBusyCursor()
2279	UpdateDrawAtoms()
2280	drawAtoms.ClearSelection()
2281	G2plt.PlotStructure(G2frame,data)
2282
2283	def FindBondsToo(): #works but slow for large structures - keep as reference
2284	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2285	atomData = data['Drawing']['Atoms']
2286	generalData = data['General']
2287	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2288	radii = generalData['BondRadii']
2289	atomTypes = generalData['AtomTypes']
2290	try:
2291	indH = atomTypes.index('H')
2292	radii[indH] = 0.5
2293	except:
2294	pass
2295	for atom in atomData:
2296	atom[-1] = []
2297	Atoms = []
2298	for i,atom in enumerate(atomData):
2299	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2300	for atomA in Atoms:
2301	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2302	for atomB in Atoms:
2303	Dx = atomB[1]-atomA[1]
2304	DX = np.inner(Amat,Dx)
2305	dist = np.sqrt(np.sum(DX**2))
2306	sumR = atomA[3]+atomB[3]
2307	if 0.5 < dist <= 0.85*sumR:
2308	i = atomA[0]
2309	if atomA[2] == 'polyhedra':
2310	atomData[i][-1].append(DX)
2311	elif atomB[1] != 'polyhedra':
2312	j = atomB[0]
2313	atomData[i][-1].append(Dx*atomA[3]/sumR)
2314	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2315
2316	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2317	import numpy.ma as ma
2318	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2319	hydro = data['Drawing']['showHydrogen']
2320	atomData = data['Drawing']['Atoms']
2321	generalData = data['General']
2322	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2323	radii = generalData['BondRadii']
2324	atomTypes = generalData['AtomTypes']
2325	try:
2326	indH = atomTypes.index('H')
2327	radii[indH] = 0.5
2328	except:
2329	pass
2330	for atom in atomData:
2331	atom[-2] = [] #clear out old bonds/polyhedra
2332	atom[-1] = []
2333	Indx = range(len(atomData))
2334	Atoms = []
2335	Styles = []
2336	Radii = []
2337	for atom in atomData:
2338	Atoms.append(np.array(atom[cx:cx+3]))
2339	Styles.append(atom[cs])
2340	try:
2341	if not hydro and atom[ct] == 'H':
2342	Radii.append(0.0)
2343	else:
2344	Radii.append(radii[atomTypes.index(atom[ct])])
2345	except ValueError: #changed atom type!
2346	Radii.append(0.20)
2347	Atoms = np.array(Atoms)
2348	Radii = np.array(Radii)
2349	IASR = zip(Indx,Atoms,Styles,Radii)
2350	for atomA in IASR:
2351	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2352	Dx = Atoms-atomA[1]
2353	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
2354	sumR = atomA[3]+Radii
2355	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2356	i = atomA[0]
2357	for j in IndB[0]:
2358	if Styles[i] == 'polyhedra':
2359	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2360	elif Styles[j] != 'polyhedra' and j > i:
2361	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2362	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2363	if Styles[i] == 'polyhedra':
2364	Bonds = atomData[i][-2]
2365	Faces = []
2366	if len(Bonds) > 2:
2367	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2368	for face in FaceGen:
2369	vol = nl.det(face)
2370	if abs(vol) > 1. or len(Bonds) == 3:
2371	if vol < 0.:
2372	face = [face[0],face[2],face[1]]
2373	face = np.array(face)
2374	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2375	norm = np.cross(face[1]-face[0],face[2]-face[0])
2376	norm /= np.sqrt(np.sum(norm**2))
2377	Faces.append([face,norm])
2378	atomData[i][-1] = Faces
2379
2380	def DrawAtomsDelete(event):
2381	indx = drawAtoms.GetSelectedRows()
2382	indx.sort()
2383	if indx:
2384	atomData = data['Drawing']['Atoms']
2385	indx.reverse()
2386	for ind in indx:
2387	del atomData[ind]
2388	UpdateDrawAtoms()
2389	drawAtoms.ClearSelection()
2390	G2plt.PlotStructure(G2frame,data)
2391	event.StopPropagation()
2392
2393	def OnReloadDrawAtoms(event):
2394	data['Drawing']['Atoms'] = []
2395	UpdateDrawAtoms()
2396	drawAtoms.ClearSelection()
2397	G2plt.PlotStructure(G2frame,data)
2398	event.StopPropagation()
2399
2400	def DrawAtomsDeleteByIDs(IDs):
2401	atomData = data['Drawing']['Atoms']
2402	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2403	indx.reverse()
2404	for ind in indx:
2405	del atomData[ind]
2406
2407	def ChangeDrawAtomsByIDs(colName,IDs,value):
2408	atomData = data['Drawing']['Atoms']
2409	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2410	if colName == 'Name':
2411	col = ct-1
2412	elif colName == 'Type':
2413	col = ct
2414	elif colName == 'I/A':
2415	col = cs
2416	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2417	for ind in indx:
2418	atomData[ind][col] = value
2419
2420	def OnDrawPlane(event):
2421	indx = drawAtoms.GetSelectedRows()
2422	if len(indx) < 4:
2423	print '**** ERROR - need 4+ atoms for plane calculation'
2424	return
2425	PlaneData = {}
2426	drawingData = data['Drawing']
2427	atomData = drawingData['Atoms']
2428	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2429	cx = colLabels.index('x')
2430	cn = colLabels.index('Name')
2431	xyz = []
2432	for i,atom in enumerate(atomData):
2433	if i in indx:
2434	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2435	generalData = data['General']
2436	PlaneData['Name'] = generalData['Name']
2437	PlaneData['Atoms'] = xyz
2438	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2439	G2stMn.BestPlane(PlaneData)
2440
2441	def OnDrawDistVP(event):
2442	# distance to view point
2443	indx = drawAtoms.GetSelectedRows()
2444	if not indx:
2445	print '***** ERROR - no atoms selected'
2446	return
2447	generalData = data['General']
2448	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2449	drawingData = data['Drawing']
2450	viewPt = np.array(drawingData['viewPoint'][0])
2451	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2452	atomDData = drawingData['Atoms']
2453	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2454	cx = colLabels.index('x')
2455	cn = colLabels.index('Name')
2456	for i in indx:
2457	atom = atomDData[i]
2458	Dx = np.array(atom[cx:cx+3])-viewPt
2459	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2460	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2461
2462	def OnDrawDAT(event):
2463	#distance, angle, torsion
2464	indx = drawAtoms.GetSelectedRows()
2465	if len(indx) not in [2,3,4]:
2466	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2467	return
2468	DATData = {}
2469	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2470	drawingData = data['Drawing']
2471	atomData = data['Atoms']
2472	atomDData = drawingData['Atoms']
2473	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2474	cx = colLabels.index('x')
2475	cn = colLabels.index('Name')
2476	cid = colLabels.index('I/A')+8
2477	xyz = []
2478	Oxyz = []
2479	DATData['Natoms'] = len(indx)
2480	for i in indx:
2481	atom = atomDData[i]
2482	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2483	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2484	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2485	DATData['Datoms'] = xyz
2486	DATData['Oatoms'] = Oxyz
2487	generalData = data['General']
2488	DATData['Name'] = generalData['Name']
2489	DATData['SGData'] = generalData['SGData']
2490	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2491	if 'pId' in data:
2492	DATData['pId'] = data['pId']
2493	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2494	G2stMn.DisAglTor(DATData)
2495
2496	################################################################################
2497	#### Draw Options page
2498	################################################################################
2499
2500	def UpdateDrawOptions():
2501	import copy
2502	import wx.lib.colourselect as wcs
2503	def SlopSizer():
2504	def OnCameraPos(event):
2505	drawingData['cameraPos'] = cameraPos.GetValue()
2506	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2507	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2508	G2plt.PlotStructure(G2frame,data)
2509
2510	def OnZclip(event):
2511	drawingData['Zclip'] = Zclip.GetValue()
2512	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2513	G2plt.PlotStructure(G2frame,data)
2514
2515	def OnZstep(event):
2516	try:
2517	step = float(Zstep.GetValue())
2518	if not (0.01 <= step <= 1.0):
2519	raise ValueError
2520	except ValueError:
2521	step = drawingData['Zstep']
2522	drawingData['Zstep'] = step
2523	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2524
2525	def OnMoveZ(event):
2526	move = MoveZ.GetValue()*drawingData['Zstep']
2527	MoveZ.SetValue(0)
2528	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2529	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2530	VD /= np.sqrt(np.sum(VD**2))
2531	VP += move*VD
2532	VP = np.inner(Bmat,VP)
2533	drawingData['viewPoint'][0] = VP
2534	panel = drawOptions.GetChildren()
2535	names = [child.GetName() for child in panel]
2536	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2537	G2plt.PlotStructure(G2frame,data)
2538
2539	def OnVdWScale(event):
2540	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2541	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2542	G2plt.PlotStructure(G2frame,data)
2543
2544	def OnEllipseProb(event):
2545	drawingData['ellipseProb'] = ellipseProb.GetValue()
2546	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2547	G2plt.PlotStructure(G2frame,data)
2548
2549	def OnBallScale(event):
2550	drawingData['ballScale'] = ballScale.GetValue()/100.
2551	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2552	G2plt.PlotStructure(G2frame,data)
2553
2554	def OnBondRadius(event):
2555	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2556	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2557	G2plt.PlotStructure(G2frame,data)
2558
2559	def OnContourLevel(event):
2560	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2561	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2562	G2plt.PlotStructure(G2frame,data)
2563
2564	def OnMapSize(event):
2565	drawingData['mapSize'] = mapSize.GetValue()/10.
2566	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2567	G2plt.PlotStructure(G2frame,data)
2568
2569
2570	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2571	slideSizer = wx.FlexGridSizer(7,2)
2572	slideSizer.AddGrowableCol(1,1)
2573
2574	cameraPosTxt = wx.StaticText(drawOptions,-1,
2575	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2576	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2577	slideSizer.Add(cameraPosTxt,0,wx.ALIGN_CENTER_VERTICAL)
2578	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2579	cameraPos.SetRange(10,500)
2580	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2581	G2frame.dataDisplay.cameraSlider = cameraPos
2582	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2583
2584	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2585	slideSizer.Add(ZclipTxt,0,wx.ALIGN_CENTER_VERTICAL)
2586	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2587	Zclip.SetRange(1,99)
2588	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2589	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2590
2591	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2592	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,wx.ALIGN_CENTER_VERTICAL)
2593	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2594	style=wx.TE_PROCESS_ENTER)
2595	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2596	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2597	ZstepSizer.Add(Zstep,0,wx.ALIGN_CENTER_VERTICAL)
2598	slideSizer.Add(ZstepSizer)
2599	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2600	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,wx.ALIGN_CENTER_VERTICAL)
2601	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2602	MoveZ.SetValue(0)
2603	MoveZ.SetRange(-1,1)
2604	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2605	MoveSizer.Add(MoveZ)
2606	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2607
2608	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2609	slideSizer.Add(vdwScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2610	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2611	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2612	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2613
2614	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2615	slideSizer.Add(ellipseProbTxt,0,wx.ALIGN_CENTER_VERTICAL)
2616	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2617	ellipseProb.SetRange(1,99)
2618	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2619	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2620
2621	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2622	slideSizer.Add(ballScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2623	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2624	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2625	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2626
2627	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2628	slideSizer.Add(bondRadiusTxt,0,wx.ALIGN_CENTER_VERTICAL)
2629	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2630	bondRadius.SetRange(1,25)
2631	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2632	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2633
2634	if generalData['Map']['rhoMax']:
2635	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2636	slideSizer.Add(contourLevelTxt,0,wx.ALIGN_CENTER_VERTICAL)
2637	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2638	contourLevel.SetRange(1,100)
2639	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2640	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2641	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2642	slideSizer.Add(mapSizeTxt,0,wx.ALIGN_CENTER_VERTICAL)
2643	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2644	mapSize.SetRange(1,100)
2645	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2646	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2647
2648	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2649	slopSizer.Add((10,5),0)
2650	slopSizer.SetMinSize(wx.Size(350,10))
2651	return slopSizer
2652
2653	def ShowSizer():
2654
2655	def OnBackColor(event):
2656	drawingData['backColor'] = event.GetValue()
2657	G2plt.PlotStructure(G2frame,data)
2658
2659	def OnShowABC(event):
2660	drawingData['showABC'] = showABC.GetValue()
2661	G2plt.PlotStructure(G2frame,data)
2662
2663	def OnShowUnitCell(event):
2664	drawingData['unitCellBox'] = unitCellBox.GetValue()
2665	G2plt.PlotStructure(G2frame,data)
2666
2667	def OnShowHyd(event):
2668	drawingData['showHydrogen'] = showHydrogen.GetValue()
2669	FindBondsDraw()
2670	G2plt.PlotStructure(G2frame,data)
2671
2672	def OnShowRB(event):
2673	drawingData['showRigidBodies'] = showRB.GetValue()
2674	FindBondsDraw()
2675	G2plt.PlotStructure(G2frame,data)
2676
2677	def OnViewPoint(event):
2678	Obj = event.GetEventObject()
2679	viewPt = Obj.GetValue().split()
2680	try:
2681	VP = [float(viewPt[i]) for i in range(3)]
2682	except (ValueError,IndexError):
2683	VP = drawingData['viewPoint'][0]
2684	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2685	drawingData['viewPoint'][0] = VP
2686	G2plt.PlotStructure(G2frame,data)
2687
2688	def OnViewDir(event):
2689	Obj = event.GetEventObject()
2690	viewDir = Obj.GetValue().split()
2691	try:
2692	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2693	VD = np.array([float(viewDir[i]) for i in range(3)])
2694	VC = np.inner(Amat,VD)
2695	VC /= np.sqrt(np.sum(VC**2))
2696	V = np.array(drawingData['viewDir'])
2697	VB = np.inner(Amat,V)
2698	VB /= np.sqrt(np.sum(VB**2))
2699	VX = np.cross(VC,VB)
2700	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2701	QV = G2mth.AVdeg2Q(A,VX)
2702	Q = drawingData['Quaternion']
2703	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2704	except (ValueError,IndexError):
2705	VD = drawingData['viewDir']
2706	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2707	drawingData['viewDir'] = VD
2708	G2plt.PlotStructure(G2frame,data)
2709
2710	showSizer = wx.BoxSizer(wx.VERTICAL)
2711	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2712	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,wx.ALIGN_CENTER_VERTICAL)
2713	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2714	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2715	lineSizer.Add(backColor,0,wx.ALIGN_CENTER_VERTICAL)
2716	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,wx.ALIGN_CENTER_VERTICAL)
2717	VD = drawingData['viewDir']
2718	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2719	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2720	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2721	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2722	G2frame.dataDisplay.viewDir = viewDir
2723	lineSizer.Add(viewDir,0,wx.ALIGN_CENTER_VERTICAL)
2724	showSizer.Add(lineSizer)
2725	showSizer.Add((0,5),0)
2726
2727	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2728	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2729	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2730	showABC.SetValue(drawingData['showABC'])
2731	lineSizer.Add(showABC,0,wx.ALIGN_CENTER_VERTICAL)
2732	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,wx.ALIGN_CENTER_VERTICAL)
2733	VP = drawingData['viewPoint'][0]
2734	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2735	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2736	G2frame.dataDisplay.viewPoint = viewPoint
2737	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2738	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2739	lineSizer.Add(viewPoint,0,wx.ALIGN_CENTER_VERTICAL)
2740	showSizer.Add(lineSizer)
2741	showSizer.Add((0,5),0)
2742
2743	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2744
2745	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2746	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2747	unitCellBox.SetValue(drawingData['unitCellBox'])
2748	line2Sizer.Add(unitCellBox,0,wx.ALIGN_CENTER_VERTICAL)
2749
2750	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2751	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2752	showHydrogen.SetValue(drawingData['showHydrogen'])
2753	line2Sizer.Add(showHydrogen,0,wx.ALIGN_CENTER_VERTICAL)
2754
2755	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2756	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2757	showRB.SetValue(drawingData['showRigidBodies'])
2758	line2Sizer.Add(showRB,0,wx.ALIGN_CENTER_VERTICAL)
2759
2760	showSizer.Add(line2Sizer)
2761	return showSizer
2762
2763	def RadSizer():
2764
2765	def OnSizeHatoms(event):
2766	try:
2767	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2768	except ValueError:
2769	value = 0.5
2770	drawingData['sizeH'] = value
2771	sizeH.SetValue("%.2f"%(value))
2772	G2plt.PlotStructure(G2frame,data)
2773
2774	def OnRadFactor(event):
2775	try:
2776	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2777	except ValueError:
2778	value = 0.85
2779	drawingData['radiusFactor'] = value
2780	radFactor.SetValue("%.2f"%(value))
2781	FindBondsDraw()
2782	G2plt.PlotStructure(G2frame,data)
2783
2784	radSizer = wx.BoxSizer(wx.HORIZONTAL)
2785	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,wx.ALIGN_CENTER_VERTICAL)
2786	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2787	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
2788	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
2789	radSizer.Add(sizeH,0,wx.ALIGN_CENTER_VERTICAL)
2790
2791	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,wx.ALIGN_CENTER_VERTICAL)
2792	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2793	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
2794	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
2795	radSizer.Add(radFactor,0,wx.ALIGN_CENTER_VERTICAL)
2796	return radSizer
2797
2798	# UpdateDrawOptions exectable code starts here
2799	generalData = data['General']
2800	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2801	SetupDrawingData()
2802	drawingData = data['Drawing']
2803	if generalData['Type'] == 'nuclear':
2804	pickChoice = ['Atoms','Bonds','Torsions','Planes']
2805	elif generalData['Type'] == 'macromolecular':
2806	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
2807
2808	G2frame.dataFrame.SetStatusText('')
2809	if drawOptions.GetSizer():
2810	drawOptions.GetSizer().Clear(True)
2811	mainSizer = wx.BoxSizer(wx.VERTICAL)
2812	mainSizer.Add((5,5),0)
2813	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,wx.ALIGN_CENTER_VERTICAL)
2814	mainSizer.Add((5,5),0)
2815	mainSizer.Add(SlopSizer(),0)
2816	mainSizer.Add((5,5),0)
2817	mainSizer.Add(ShowSizer(),0,)
2818	mainSizer.Add((5,5),0)
2819	mainSizer.Add(RadSizer(),0,)
2820	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
2821
2822	################################################################################
2823	#### Texture routines
2824	################################################################################
2825
2826	def UpdateTexture():
2827	def SetSHCoef():
2828	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
2829	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
2830	SHCoeff = textureData['SH Coeff'][1]
2831	for cofName in SHCoeff:
2832	if cofName in cofNames:
2833	newSHCoef[cofName] = SHCoeff[cofName]
2834	return newSHCoef
2835
2836	def OnShOrder(event):
2837	Obj = event.GetEventObject()
2838	textureData['Order'] = int(Obj.GetValue())
2839	textureData['SH Coeff'][1] = SetSHCoef()
2840	wx.CallAfter(UpdateTexture)
2841	G2plt.PlotTexture(G2frame,data)
2842
2843	def OnShModel(event):
2844	Obj = event.GetEventObject()
2845	textureData['Model'] = Obj.GetValue()
2846	textureData['SH Coeff'][1] = SetSHCoef()
2847	wx.CallAfter(UpdateTexture)
2848	G2plt.PlotTexture(G2frame,data)
2849
2850	def OnSHRefine(event):
2851	Obj = event.GetEventObject()
2852	textureData['SH Coeff'][0] = Obj.GetValue()
2853
2854	def OnSHShow(event):
2855	Obj = event.GetEventObject()
2856	textureData['SHShow'] = Obj.GetValue()
2857	wx.CallAfter(UpdateTexture)
2858
2859	def OnProjSel(event):
2860	Obj = event.GetEventObject()
2861	G2frame.Projection = Obj.GetValue()
2862	G2plt.PlotTexture(G2frame,data)
2863
2864	def OnColorSel(event):
2865	Obj = event.GetEventObject()
2866	G2frame.ContourColor = Obj.GetValue()
2867	G2plt.PlotTexture(G2frame,data)
2868
2869	def OnAngRef(event):
2870	Obj = event.GetEventObject()
2871	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
2872
2873	def OnAngValue(event):
2874	Obj = event.GetEventObject()
2875	try:
2876	value = float(Obj.GetValue())
2877	except ValueError:
2878	value = textureData[valIndx[Obj.GetId()]][1]
2879	Obj.SetValue('%8.2f'%(value))
2880	textureData[valIndx[Obj.GetId()]][1] = value
2881
2882	def OnODFValue(event):
2883	Obj = event.GetEventObject()
2884	try:
2885	value = float(Obj.GetValue())
2886	except ValueError:
2887	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
2888	Obj.SetValue('%8.3f'%(value))
2889	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
2890	G2plt.PlotTexture(G2frame,data)
2891
2892	def OnPfType(event):
2893	Obj = event.GetEventObject()
2894	textureData['PlotType'] = Obj.GetValue()
2895	wx.CallAfter(UpdateTexture)
2896	G2plt.PlotTexture(G2frame,data)
2897
2898	def OnPFValue(event):
2899	Obj = event.GetEventObject()
2900	Saxis = Obj.GetValue().split()
2901	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2902	try:
2903	hkl = [int(Saxis[i]) for i in range(3)]
2904	except (ValueError,IndexError):
2905	hkl = textureData['PFhkl']
2906	if not np.any(np.array(hkl)): #can't be all zeros!
2907	hkl = textureData['PFhkl']
2908	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
2909	textureData['PFhkl'] = hkl
2910	else:
2911	try:
2912	xyz = [float(Saxis[i]) for i in range(3)]
2913	except (ValueError,IndexError):
2914	xyz = textureData['PFxyz']
2915	if not np.any(np.array(xyz)): #can't be all zeros!
2916	xyz = textureData['PFxyz']
2917	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
2918	textureData['PFxyz'] = xyz
2919	G2plt.PlotTexture(G2frame,data)
2920
2921	# UpdateTexture executable starts here
2922	G2frame.dataFrame.SetStatusText('')
2923	generalData = data['General']
2924	SGData = generalData['SGData']
2925	try:
2926	textureData = generalData['SH Texture']
2927	except KeyError: #fix old files!
2928	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
2929	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
2930	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
2931	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
2932	if 'SHShow' not in textureData: #another fix
2933	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2934	try: #another fix!
2935	x = textureData['PlotType']
2936	except KeyError:
2937	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2938	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
2939	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
2940	if generalData['doPawley'] and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Sequental results'):
2941	G2frame.dataFrame.RefineTexture.Enable(True)
2942	shAngles = ['omega','chi','phi']
2943	if Texture.GetSizer():
2944	Texture.GetSizer().Clear(True)
2945	mainSizer = wx.BoxSizer(wx.VERTICAL)
2946	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
2947	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,wx.ALIGN_CENTER_VERTICAL)
2948	titleSizer.Add(wx.StaticText(Texture,-1,
2949	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
2950	0,wx.ALIGN_CENTER_VERTICAL)
2951	mainSizer.Add(titleSizer,0)
2952	mainSizer.Add((0,5),0)
2953	shSizer = wx.FlexGridSizer(1,6,5,5)
2954	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,wx.ALIGN_CENTER_VERTICAL)
2955	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
2956	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2957	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
2958	shSizer.Add(shModel,0,wx.ALIGN_CENTER_VERTICAL)
2959	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,wx.ALIGN_CENTER_VERTICAL)
2960	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
2961	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2962	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
2963	shSizer.Add(shOrder,0,wx.ALIGN_CENTER_VERTICAL)
2964	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
2965	shRef.SetValue(textureData['SH Coeff'][0])
2966	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
2967	shSizer.Add(shRef,0,wx.ALIGN_CENTER_VERTICAL)
2968	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
2969	shShow.SetValue(textureData['SHShow'])
2970	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
2971	shSizer.Add(shShow,0,wx.ALIGN_CENTER_VERTICAL)
2972	mainSizer.Add(shSizer,0,0)
2973	mainSizer.Add((0,5),0)
2974	PTSizer = wx.FlexGridSizer(2,4,5,5)
2975	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,wx.ALIGN_CENTER_VERTICAL)
2976	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
2977	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
2978	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2979	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
2980	PTSizer.Add(pfType,0,wx.ALIGN_CENTER_VERTICAL)
2981	if 'Axial' not in textureData['PlotType']:
2982	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,wx.ALIGN_CENTER_VERTICAL)
2983	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
2984	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2985	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
2986	PTSizer.Add(projSel,0,wx.ALIGN_CENTER_VERTICAL)
2987	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2988	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,wx.ALIGN_CENTER_VERTICAL)
2989	PH = textureData['PFhkl']
2990	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
2991	else:
2992	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,wx.ALIGN_CENTER_VERTICAL)
2993	PX = textureData['PFxyz']
2994	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
2995	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
2996	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
2997	PTSizer.Add(pfVal,0,wx.ALIGN_CENTER_VERTICAL)
2998	if 'Axial' not in textureData['PlotType']:
2999	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,wx.ALIGN_CENTER_VERTICAL)
3000	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3001	choice.sort()
3002	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
3003	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3004	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
3005	PTSizer.Add(colorSel,0,wx.ALIGN_CENTER_VERTICAL)
3006	mainSizer.Add(PTSizer,0,wx.ALIGN_CENTER_VERTICAL)
3007	mainSizer.Add((0,5),0)
3008	if textureData['SHShow']:
3009	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,wx.ALIGN_CENTER_VERTICAL)
3010	mainSizer.Add((0,5),0)
3011	ODFSizer = wx.FlexGridSizer(2,8,2,2)
3012	ODFIndx = {}
3013	ODFkeys = textureData['SH Coeff'][1].keys()
3014	ODFkeys.sort()
3015	for item in ODFkeys:
3016	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,wx.ALIGN_CENTER_VERTICAL)
3017	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3018	ODFIndx[ODFval.GetId()] = item
3019	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3020	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3021	ODFSizer.Add(ODFval,0,wx.ALIGN_CENTER_VERTICAL)
3022	mainSizer.Add(ODFSizer,0,wx.ALIGN_CENTER_VERTICAL)
3023	mainSizer.Add((0,5),0)
3024	mainSizer.Add((0,5),0)
3025	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,wx.ALIGN_CENTER_VERTICAL)
3026	mainSizer.Add((0,5),0)
3027	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3028	angIndx = {}
3029	valIndx = {}
3030	for item in ['Sample omega','Sample chi','Sample phi']:
3031	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3032	angRef.SetValue(textureData[item][0])
3033	angIndx[angRef.GetId()] = item
3034	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3035	angSizer.Add(angRef,0,wx.ALIGN_CENTER_VERTICAL)
3036	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3037	valIndx[angVal.GetId()] = item
3038	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3039	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3040	angSizer.Add(angVal,0,wx.ALIGN_CENTER_VERTICAL)
3041	angSizer.Add((5,0),0)
3042	mainSizer.Add(angSizer,0,wx.ALIGN_CENTER_VERTICAL)
3043	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3044
3045	################################################################################
3046	##### DData routines - GUI stuff in GSASIIddataGUI.py
3047	################################################################################
3048
3049	def OnHklfAdd(event):
3050	UseList = data['Histograms']
3051	keyList = UseList.keys()
3052	TextList = []
3053	if G2frame.PatternTree.GetCount():
3054	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3055	while item:
3056	name = G2frame.PatternTree.GetItemText(item)
3057	if name not in keyList and 'HKLF' in name:
3058	TextList.append(name)
3059	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3060	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3061	try:
3062	if dlg.ShowModal() == wx.ID_OK:
3063	result = dlg.GetSelections()
3064	for i in result:
3065	histoName = TextList[i]
3066	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3067	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3068	'Extinction':['Lorentzian','None',
3069	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3070	wx.BeginBusyCursor()
3071	UpdateHKLFdata(histoName)
3072	wx.EndBusyCursor()
3073	data['Histograms'] = UseList
3074	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3075	finally:
3076	dlg.Destroy()
3077
3078	def UpdateHKLFdata(histoName):
3079	generalData = data['General']
3080	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3081	refDict,reflData = G2frame.PatternTree.GetItemPyData(Id)
3082	SGData = generalData['SGData']
3083	Cell = generalData['Cell'][1:7]
3084	G,g = G2lat.cell2Gmat(Cell)
3085	for ref in reflData:
3086	H = ref[:3]
3087	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3088	iabsnt,ref[3],ref[11],ref[12] = G2spc.GenHKLf(H,SGData)
3089	G2frame.PatternTree.SetItemPyData(Id,[refDict,reflData])
3090
3091	def OnPwdrAdd(event):
3092	generalData = data['General']
3093	SGData = generalData['SGData']
3094	UseList = data['Histograms']
3095	newList = []
3096	NShkl = len(G2spc.MustrainNames(SGData))
3097	NDij = len(G2spc.HStrainNames(SGData))
3098	keyList = UseList.keys()
3099	TextList = ['All PWDR']
3100	if G2frame.PatternTree.GetCount():
3101	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3102	while item:
3103	name = G2frame.PatternTree.GetItemText(item)
3104	if name not in keyList and 'PWDR' in name:
3105	TextList.append(name)
3106	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3107	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3108	try:
3109	if dlg.ShowModal() == wx.ID_OK:
3110	result = dlg.GetSelections()
3111	for i in result: newList.append(TextList[i])
3112	if 'All PWDR' in newList:
3113	newList = TextList[1:]
3114	for histoName in newList:
3115	pId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3116	UseList[histoName] = {'Histogram':histoName,'Show':False,
3117	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3118	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3119	[1.,1.,1.,0.,0.,0.],6*[False,]],
3120	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3121	NShkl[0.01,],NShkl[False,]],
3122	'HStrain':[NDij[0.0,],NDij[False,]],
3123	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3124	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,pId,'Reflection Lists'))
3125	refList[generalData['Name']] = []
3126	data['Histograms'] = UseList
3127	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3128	finally:
3129	dlg.Destroy()
3130
3131	def OnDataDelete(event):
3132	UseList = data['Histograms']
3133	keyList = ['All',]+UseList.keys()
3134	keyList.sort()
3135	DelList = []
3136	if UseList:
3137	DelList = []
3138	dlg = wx.MultiChoiceDialog(G2frame,
3139	'Which histogram to delete from this phase?', 'Delete histogram',
3140	keyList, wx.CHOICEDLG_STYLE)
3141	try:
3142	if dlg.ShowModal() == wx.ID_OK:
3143	result = dlg.GetSelections()
3144	for i in result:
3145	DelList.append(keyList[i])
3146	if 'All' in DelList:
3147	DelList = keyList[1:]
3148	for i in DelList:
3149	del UseList[i]
3150	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3151	finally:
3152	dlg.Destroy()
3153
3154	################################################################################
3155	##### Rigid bodies
3156	################################################################################
3157
3158	def FillRigidBodyGrid(refresh=True):
3159	'''Fill the Rigid Body Phase information tab page.
3160	Note that the page is a ScrolledWindow, not a Grid
3161	'''
3162	def OnThermSel(event): #needs to be seen by VecRbSizer!
3163	Obj = event.GetEventObject()
3164	RBObj = Indx[Obj.GetId()]
3165	val = Obj.GetValue()
3166	Ttype = 'A'
3167	if val == 'Uiso':
3168	Ttype = 'I'
3169	RBObj['ThermalMotion'][0] = 'Uiso'
3170	elif val == 'T':
3171	RBObj['ThermalMotion'][0] = 'T'
3172	elif val == 'TL':
3173	RBObj['ThermalMotion'][0] = 'TL'
3174	elif val == 'TLS':
3175	RBObj['ThermalMotion'][0] = 'TLS'
3176	wx.CallAfter(FillRigidBodyGrid,True)
3177	if val != 'None':
3178	cia = data['General']['AtomPtrs'][3]
3179	for i,id in enumerate(RBObj['Ids']):
3180	data['Atoms'][AtLookUp[id]][cia] = Ttype
3181	G2plt.PlotStructure(G2frame,data)
3182
3183	def ThermDataSizer(RBObj,rbType):
3184
3185	def OnThermval(event):
3186	Obj = event.GetEventObject()
3187	item = Indx[Obj.GetId()]
3188	try:
3189	val = float(Obj.GetValue())
3190	RBObj['ThermalMotion'][1][item] = val
3191	except ValueError:
3192	pass
3193	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3194	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3195	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3196	cia = data['General']['AtomPtrs'][3]
3197	for i,id in enumerate(RBObj['Ids']):
3198	if Uout[i][0] == 'I':
3199	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3200	else:
3201	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3202	G2plt.PlotStructure(G2frame,data)
3203
3204	def OnTLSRef(event):
3205	Obj = event.GetEventObject()
3206	item = Indx[Obj.GetId()]
3207	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3208
3209	thermSizer = wx.FlexGridSizer(1,9,5,5)
3210	model = RBObj['ThermalMotion']
3211	if model[0] == 'Uiso':
3212	names = ['Uiso',]
3213	elif 'T' in model[0]:
3214	names = ['T11','T22','T33','T12','T13','T23']
3215	if 'L' in model[0]:
3216	names += ['L11','L22','L33','L12','L13','L23']
3217	if 'S' in model[0]:
3218	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3219	for i,name in enumerate(names):
3220	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,wx.ALIGN_CENTER_VERTICAL)
3221	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3222	style=wx.TE_PROCESS_ENTER)
3223	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3224	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3225	Indx[thermVal.GetId()] = i
3226	thermSizer.Add(thermVal)
3227	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3228	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3229	Tcheck.SetValue(model[2][i])
3230	Indx[Tcheck.GetId()] = i
3231	thermSizer.Add(Tcheck,0,wx.ALIGN_CENTER_VERTICAL)
3232	return thermSizer
3233
3234	def LocationSizer(RBObj,rbType):
3235
3236	def OnOrigRef(event):
3237	RBObj['Orig'][1] = Ocheck.GetValue()
3238
3239	def OnOrienRef(event):
3240	RBObj['Orient'][1] = Qcheck.GetValue()
3241
3242	def OnOrigX(event):
3243	Obj = event.GetEventObject()
3244	item = Indx[Obj.GetId()]
3245	try:
3246	val = float(Obj.GetValue())
3247	RBObj['Orig'][0][item] = val
3248	Obj.SetValue('%8.5f'%(val))
3249	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3250	for i,id in enumerate(RBObj['Ids']):
3251	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3252	data['Drawing']['Atoms'] = []
3253	UpdateDrawAtoms(atomStyle)
3254	G2plt.PlotStructure(G2frame,data)
3255	except ValueError:
3256	pass
3257
3258	def OnOrien(event):
3259	Obj = event.GetEventObject()
3260	item = Indx[Obj.GetId()]
3261	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3262	V = np.inner(Bmat,V)
3263	try:
3264	val = float(Obj.GetValue())
3265	if item:
3266	V[item-1] = val
3267	else:
3268	A = val
3269	Obj.SetValue('%8.5f'%(val))
3270	V = np.inner(Amat,V)
3271	Q = G2mth.AVdeg2Q(A,V)
3272	if not any(Q):
3273	raise ValueError
3274	RBObj['Orient'][0] = Q
3275	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3276	for i,id in enumerate(RBObj['Ids']):
3277	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3278	data['Drawing']['Atoms'] = []
3279	UpdateDrawAtoms(atomStyle)
3280	G2plt.PlotStructure(G2frame,data)
3281	except ValueError:
3282	pass
3283
3284	topSizer = wx.FlexGridSizer(2,6,5,5)
3285	Orig = RBObj['Orig'][0]
3286	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3287	Orien = [Orien,]
3288	Orien.extend(OrienV/nl.norm(OrienV))
3289	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,wx.ALIGN_CENTER_VERTICAL)
3290	for ix,x in enumerate(Orig):
3291	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3292	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3293	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3294	Indx[origX.GetId()] = ix
3295	topSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3296	topSizer.Add((5,0),)
3297	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3298	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3299	Ocheck.SetValue(RBObj['Orig'][1])
3300	topSizer.Add(Ocheck,0,wx.ALIGN_CENTER_VERTICAL)
3301	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,wx.ALIGN_CENTER_VERTICAL)
3302	for ix,x in enumerate(Orien):
3303	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3304	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3305	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3306	Indx[orien.GetId()] = ix
3307	topSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3308	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3309	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3310	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3311	Qcheck.SetValue(RBObj['Orient'][1])
3312	topSizer.Add(Qcheck)
3313	return topSizer
3314
3315	def ResrbSizer(RBObj):
3316	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3317
3318	def OnTorsionRef(event):
3319	Obj = event.GetEventObject()
3320	item = Indx[Obj.GetId()]
3321	RBObj['Torsions'][item][1] = Obj.GetValue()
3322
3323	def OnTorsion(event):
3324	Obj = event.GetEventObject()
3325	item = Indx[Obj.GetId()]
3326	try:
3327	val = float(Obj.GetValue())
3328	RBObj['Torsions'][item][0] = val
3329	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3330	for i,id in enumerate(RBObj['Ids']):
3331	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3332	except ValueError:
3333	pass
3334	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3335	data['Drawing']['Atoms'] = []
3336	UpdateDrawAtoms(atomStyle)
3337	drawAtoms.ClearSelection()
3338	G2plt.PlotStructure(G2frame,data)
3339
3340	def OnDelResRB(event):
3341	Obj = event.GetEventObject()
3342	RBId = Indx[Obj.GetId()]
3343	RBData['Residue'][RBId]['useCount'] -= 1
3344	RBObjs = data['RBModels']['Residue']
3345	for rbObj in RBObjs:
3346	if RBId == rbObj['RBId']:
3347	data['RBModels']['Residue'].remove(rbObj)
3348	G2plt.PlotStructure(G2frame,data)
3349	wx.CallAfter(FillRigidBodyGrid,True)
3350
3351	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3352	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3353	topLine = wx.BoxSizer(wx.HORIZONTAL)
3354	topLine.Add(wx.StaticText(RigidBodies,-1,
3355	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3356	rbId = RBObj['RBId']
3357	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3358	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3359	Indx[delRB.GetId()] = rbId
3360	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3361	resrbSizer.Add(topLine)
3362	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3363	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,wx.ALIGN_CENTER_VERTICAL)
3364	torSizer = wx.FlexGridSizer(1,6,5,5)
3365	for itors,tors in enumerate(RBObj['Torsions']):
3366	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,wx.ALIGN_CENTER_VERTICAL)
3367	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3368	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3369	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3370	Indx[torsTxt.GetId()] = itors
3371	torSizer.Add(torsTxt)
3372	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3373	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3374	torCheck.SetValue(tors[1])
3375	Indx[torCheck.GetId()] = itors
3376	torSizer.Add(torCheck,0,wx.ALIGN_CENTER_VERTICAL)
3377	resrbSizer.Add(torSizer)
3378	tchoice = ['None','Uiso','T','TL','TLS']
3379	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3380	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3381	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3382	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3383	Indx[thermSel.GetId()] = RBObj
3384	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3385	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3386	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3387	resrbSizer.Add(thermSizer)
3388	if RBObj['ThermalMotion'][0] != 'None':
3389	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3390	return resrbSizer
3391
3392	def VecrbSizer(RBObj):
3393	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3394
3395	def OnDelVecRB(event):
3396	Obj = event.GetEventObject()
3397	RBId = Indx[Obj.GetId()]
3398	RBData['Vector'][RBId]['useCount'] -= 1
3399	RBObjs = data['RBModels']['Vector']
3400	for rbObj in RBObjs:
3401	if RBId == rbObj['RBId']:
3402	data['RBModels']['Vector'].remove(rbObj)
3403	G2plt.PlotStructure(G2frame,data)
3404	wx.CallAfter(FillRigidBodyGrid,True)
3405
3406	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3407	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3408	topLine = wx.BoxSizer(wx.HORIZONTAL)
3409	topLine.Add(wx.StaticText(RigidBodies,-1,
3410	'Name: '+RBObj['RBname']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3411	rbId = RBObj['RBId']
3412	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3413	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3414	Indx[delRB.GetId()] = rbId
3415	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3416	vecrbSizer.Add(topLine)
3417	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3418	tchoice = ['None','Uiso','T','TL','TLS']
3419	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3420	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3421	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3422	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3423	Indx[thermSel.GetId()] = RBObj
3424	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3425	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3426	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3427	vecrbSizer.Add(thermSizer)
3428	if RBObj['ThermalMotion'][0] != 'None':
3429	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3430	return vecrbSizer
3431
3432	# FillRigidBodyGrid executable code starts here
3433	if refresh:
3434	RigidBodies.DestroyChildren()
3435	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3436	general = data['General']
3437	cx = general['AtomPtrs'][0]
3438	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3439	RBData = G2frame.PatternTree.GetItemPyData(
3440	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3441	Indx = {}
3442	atomStyle = 'balls & sticks'
3443	if 'macro' in general['Type']:
3444	atomStyle = 'sticks'
3445	G2frame.dataFrame.SetStatusText('')
3446	mainSizer = wx.BoxSizer(wx.VERTICAL)
3447	if not data['RBModels']:
3448	mainSizer.Add((5,5),0)
3449	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,wx.ALIGN_CENTER_VERTICAL)
3450	mainSizer.Add((5,5),0)
3451	if 'Residue' in data['RBModels']:
3452	mainSizer.Add((5,5),0)
3453	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3454	mainSizer.Add((5,5),0)
3455	for RBObj in data['RBModels']['Residue']:
3456	mainSizer.Add(ResrbSizer(RBObj))
3457	if 'Vector' in data['RBModels']:
3458	mainSizer.Add((5,5),0)
3459	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3460	mainSizer.Add((5,5),0)
3461	for RBObj in data['RBModels']['Vector']:
3462	mainSizer.Add(VecrbSizer(RBObj))
3463
3464	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3465
3466	def OnRBCopyParms(event):
3467	RBObjs = []
3468	for rbType in ['Vector','Residue']:
3469	RBObjs += data['RBModels'].get(rbType,[])
3470	if not len(RBObjs):
3471	print '** ERROR - no rigid bodies defined **'
3472	return
3473	if len(RBObjs) == 1:
3474	print '** INFO - only one rigid body defined; nothing to copy to **'
3475	return
3476	Source = []
3477	sourceRB = {}
3478	for RBObj in RBObjs:
3479	Source.append(RBObj['RBname'])
3480	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3481	if dlg.ShowModal() == wx.ID_OK:
3482	sel = dlg.GetSelection()
3483	name = Source[sel]
3484	for item in ['Orig','Orient','ThermalMotion']:
3485	sourceRB.update({item:RBObjs[sel][item],})
3486	dlg.Destroy()
3487	if not sourceRB:
3488	return
3489	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3490	if dlg.ShowModal() == wx.ID_OK:
3491	sel = dlg.GetSelections()
3492	for x in sel:
3493	RBObjs[x].update(copy.copy(sourceRB))
3494	G2plt.PlotStructure(G2frame,data)
3495	wx.CallAfter(FillRigidBodyGrid(True))
3496
3497	def OnRBAssign(event):
3498
3499	G2frame.dataFrame.SetStatusText('')
3500	RBData = G2frame.PatternTree.GetItemPyData(
3501	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3502	rbNames = {}
3503	for rbVec in RBData['Vector']:
3504	if rbVec != 'AtInfo':
3505	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3506	for rbRes in RBData['Residue']:
3507	if rbRes != 'AtInfo':
3508	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3509	if not rbNames:
3510	print '** ERROR - no rigid bodies defined **'
3511	return
3512	general = data['General']
3513	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3514	cx,ct = general['AtomPtrs'][:2]
3515	atomData = data['Atoms']
3516	Indx = {}
3517	atInd = [-1,-1,-1]
3518	data['testRBObj'] = {}
3519
3520	def Draw():
3521
3522	def OnOk(event):
3523	rbType = data['testRBObj']['rbType']
3524	RBObjs = data['RBModels'].get(rbType,[])
3525	rbObj = data['testRBObj']['rbObj']
3526	rbId = rbObj['RBId']
3527	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3528	Ids = []
3529	dmax = 0.0
3530	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3531	for xyz in newXYZ:
3532	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3533	dmax = max(dmax,np.min(dist))
3534	id = np.argmin(dist)
3535	Ids.append(atomData[id][-1])
3536	atomData[id][cx:cx+3] = xyz
3537	if dmax > 0.5:
3538	print '** WARNING - some atoms not found or misidentified **'
3539	print '** check torsion angles & try again **'
3540	OkBtn.SetLabel('Not Ready')
3541	OkBtn.Enable(False)
3542	return
3543	rbObj['Ids'] = Ids
3544	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3545	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3546	RBObjs.append(rbObj)
3547	data['RBModels'][rbType] = RBObjs
3548	RBData[rbType][rbId]['useCount'] += 1
3549	del data['testRBObj']
3550	G2plt.PlotStructure(G2frame,data)
3551	FillRigidBodyGrid(True)
3552
3553	def OnCancel(event):
3554	del data['testRBObj']
3555	FillRigidBodyGrid(True)
3556
3557	def OnRBSel(event):
3558	selection = rbSel.GetValue()
3559	rbType,rbId = rbNames[selection]
3560	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3561	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3562	data['testRBObj']['rbType'] = rbType
3563	data['testRBObj']['rbData'] = RBData
3564	data['testRBObj']['Sizers'] = {}
3565	rbRef = RBData[rbType][rbId]['rbRef']
3566	data['testRBObj']['rbRef'] = rbRef
3567	refType = []
3568	refName = []
3569	for ref in rbRef[:3]:
3570	reftype = data['testRBObj']['rbAtTypes'][ref]
3571	refType.append(reftype)
3572	refName.append(reftype+' '+str(rbRef[0]))
3573	atNames,AtNames = fillAtNames(refType,atomData,ct)
3574	data['testRBObj']['atNames'] = atNames
3575	data['testRBObj']['AtNames'] = AtNames
3576	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3577	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3578	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3579	data['testRBObj']['torAtms'] = []
3580	for item in RBData[rbType][rbId].get('rbSeq',[]):
3581	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3582	data['testRBObj']['torAtms'].append([-1,-1,-1])
3583	Draw()
3584
3585	def fillAtNames(refType,atomData,ct):
3586	atNames = [{},{},{}]
3587	AtNames = {}
3588	for iatm,atom in enumerate(atomData):
3589	AtNames[atom[ct-1]] = iatm
3590	for i,reftype in enumerate(refType):
3591	if atom[ct] == reftype:
3592	atNames[i][atom[ct-1]] = iatm
3593	return atNames,AtNames
3594
3595	def OnAtOrigPick(event):
3596	Obj = event.GetEventObject()
3597	item = Indx[Obj.GetId()]
3598	atName = Obj.GetValue()
3599	rbType = data['testRBObj']['rbType']
3600	atInd[0] = atNames[item][atName]
3601	if 'Vector' in rbType:
3602	rbObj = data['testRBObj']['rbObj']
3603	rbId = rbObj['RBId']
3604	rbRef = data['testRBObj']['rbRef']
3605	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3606	nref = atNames[item][atName]
3607	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3608	Nxyz = np.array(atomData[nref][cx:cx+3])
3609	Orig = Nxyz-Oxyz
3610	data['testRBObj']['rbObj']['Orig'][0] = Orig
3611	else:
3612	Orig = atomData[atNames[item][atName]][cx:cx+3]
3613	data['testRBObj']['rbObj']['Orig'][0] = Orig
3614	for x,item in zip(Orig,Xsizers):
3615	item.SetLabel('%10.5f'%(x))
3616	G2plt.PlotStructure(G2frame,data)
3617
3618	def OnAtQPick(event):
3619	Obj = event.GetEventObject()
3620	item = Indx[Obj.GetId()]
3621	atName = Obj.GetValue()
3622	atInd[item] = atNames[item][atName]
3623	if any([x<0 for x in atInd]):
3624	return
3625	OkBtn.SetLabel('OK')
3626	OkBtn.Enable(True)
3627	rbType = data['testRBObj']['rbType']
3628	rbObj = data['testRBObj']['rbObj']
3629	rbId = rbObj['RBId']
3630	rbRef = data['testRBObj']['rbRef']
3631	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3632	rbOrig = rbXYZ[rbRef[0]]
3633	VAR = rbXYZ[rbRef[1]]-rbOrig
3634	VBR = rbXYZ[rbRef[2]]-rbOrig
3635	if rbType == 'Vector':
3636	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3637	else:
3638	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3639	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3640	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3641	VCC = np.cross(VAR,VAC)
3642	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3643	VAR = G2mth.prodQVQ(QuatA,VAR)
3644	VBR = G2mth.prodQVQ(QuatA,VBR)
3645	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3646	QuatC = G2mth.prodQQ(QuatB,QuatA)
3647	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3648	for x,item in zip(QuatC,Osizers):
3649	item.SetLabel('%10.4f'%(x))
3650	if rbType == 'Vector':
3651	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3652	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3653	Orig = Nxyz-Oxyz
3654	data['testRBObj']['rbObj']['Orig'][0] = Orig
3655	for x,item in zip(Orig,Xsizers):
3656	item.SetLabel('%10.5f'%(x))
3657	G2plt.PlotStructure(G2frame,data)
3658
3659	def OnTorAngle(event):
3660	OkBtn.SetLabel('OK')
3661	OkBtn.Enable(True)
3662	Obj = event.GetEventObject()
3663	[tor,torSlide] = Indx[Obj.GetId()]
3664	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3665	try:
3666	value = float(Obj.GetValue())
3667	except ValueError:
3668	value = Tors[0]
3669	Tors[0] = value
3670	Obj.SetValue('%8.3f'%(value))
3671	torSlide.SetValue(int(value*10))
3672	G2plt.PlotStructure(G2frame,data)
3673
3674	def OnTorSlide(event):
3675	OkBtn.SetLabel('OK')
3676	OkBtn.Enable(True)
3677	Obj = event.GetEventObject()
3678	tor,ang = Indx[Obj.GetId()]
3679	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3680	val = float(Obj.GetValue())/10.
3681	Tors[0] = val
3682	ang.SetValue('%8.3f'%(val))
3683	G2plt.PlotStructure(G2frame,data)
3684
3685	if len(data['testRBObj']):
3686	G2plt.PlotStructure(G2frame,data)
3687
3688	RigidBodies.DestroyChildren()
3689	mainSizer = wx.BoxSizer(wx.VERTICAL)
3690	mainSizer.Add((5,5),0)
3691	if data['testRBObj']:
3692	Xsizers = []
3693	Osizers = []
3694	rbObj = data['testRBObj']['rbObj']
3695	rbName = rbObj['RBname']
3696	rbId = rbObj['RBId']
3697	Orig = rbObj['Orig'][0]
3698	Orien = rbObj['Orient'][0]
3699	rbRef = data['testRBObj']['rbRef']
3700	Torsions = rbObj['Torsions']
3701	refName = []
3702	for ref in rbRef:
3703	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3704	atNames = data['testRBObj']['atNames']
3705	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3706	0,wx.ALIGN_CENTER_VERTICAL)
3707	mainSizer.Add((5,5),0)
3708	OriSizer = wx.FlexGridSizer(1,5,5,5)
3709	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,wx.ALIGN_CENTER_VERTICAL)
3710	for ix,x in enumerate(Orig):
3711	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3712	OriSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3713	Xsizers.append(origX)
3714	OriSizer.Add((5,0),)
3715	if len(atomData):
3716	choice = atNames[0].keys()
3717	choice.sort()
3718	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3719	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,wx.ALIGN_CENTER_VERTICAL)
3720	for ix,x in enumerate(Orien):
3721	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3722	OriSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3723	Osizers.append(orien)
3724	data['testRBObj']['Sizers']['Osizers'] = Osizers
3725	mainSizer.Add(OriSizer)
3726	mainSizer.Add((5,5),0)
3727	RefSizer = wx.FlexGridSizer(1,7,5,5)
3728	if len(atomData):
3729	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,wx.ALIGN_CENTER_VERTICAL)
3730	for i in [0,1,2]:
3731	choice = ['',]+atNames[i].keys()
3732	choice.sort()
3733	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,wx.ALIGN_CENTER_VERTICAL)
3734	atPick = wx.ComboBox(RigidBodies,-1,value='',
3735	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3736	if i:
3737	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3738	else:
3739	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3740	Indx[atPick.GetId()] = i
3741	RefSizer.Add(atPick,0,wx.ALIGN_CENTER_VERTICAL)
3742	mainSizer.Add(RefSizer)
3743	mainSizer.Add((5,5),0)
3744	if Torsions:
3745	AtNames = data['testRBObj']['AtNames']
3746	rbAtTypes = data['testRBObj']['rbAtTypes']
3747	rbSeq = RBData['Residue'][rbId]['rbSeq']
3748	TorSizer = wx.FlexGridSizer(1,4)
3749	TorSizer.AddGrowableCol(1,1)
3750	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3751	torName = ''
3752	for item in [seq[0],seq[1],seq[3][0]]:
3753	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3754	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,wx.ALIGN_CENTER_VERTICAL)
3755	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3756	torSlide.SetRange(0,3600)
3757	torSlide.SetValue(int(torsion[0]*10.))
3758	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3759	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3760	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,wx.ALIGN_CENTER_VERTICAL)
3761	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
3762	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
3763	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
3764	Indx[torSlide.GetId()] = [t,ang]
3765	Indx[ang.GetId()] = [t,torSlide]
3766	TorSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
3767	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
3768	else:
3769	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,wx.ALIGN_CENTER_VERTICAL)
3770	else:
3771	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,wx.ALIGN_CENTER_VERTICAL)
3772	mainSizer.Add((5,5),0)
3773	topSizer = wx.BoxSizer(wx.HORIZONTAL)
3774	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,wx.ALIGN_CENTER_VERTICAL)
3775	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
3776	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3777	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
3778	topSizer.Add((5,5),0)
3779	topSizer.Add(rbSel,0,wx.ALIGN_CENTER_VERTICAL)
3780	mainSizer.Add(topSizer)
3781
3782	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
3783	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
3784	OkBtn.Enable(False)
3785	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
3786	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
3787	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
3788	btnSizer.Add((20,20),1)
3789	btnSizer.Add(OkBtn)
3790	btnSizer.Add(CancelBtn)
3791	btnSizer.Add((20,20),1)
3792	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
3793	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3794	Draw()
3795
3796	def OnAutoFindResRB(event):
3797	RBData = G2frame.PatternTree.GetItemPyData(
3798	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3799	rbKeys = RBData['Residue'].keys()
3800	rbKeys.remove('AtInfo')
3801	if not len(rbKeys):
3802	print '** ERROR - no residue rigid bodies are defined **'
3803	return
3804	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
3805	RBIds = dict(zip(RBNames,rbKeys))
3806	general = data['General']
3807	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3808	Atoms = data['Atoms']
3809	AtLookUp = G2mth.FillAtomLookUp(Atoms)
3810	if 'macro' not in general['Type']:
3811	print '** ERROR - this phase is not a macromolecule **'
3812	return
3813	if not len(Atoms):
3814	print '** ERROR - this phase has no atoms **'
3815	return
3816	RBObjs = []
3817	cx,ct = general['AtomPtrs'][:2]
3818	iatm = 0
3819	wx.BeginBusyCursor()
3820	try:
3821	while iatm < len(Atoms):
3822	atom = Atoms[iatm]
3823	res = atom[1].strip()
3824	numChain = ' %s %s'%(atom[0],atom[2])
3825	if res not in RBIds or atom[ct-1] == 'OXT':
3826	iatm += 1
3827	continue #skip for OXT, water molecules, etc.
3828	rbRes = RBData['Residue'][RBIds[res]]
3829	rbRef = rbRes['rbRef']
3830	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
3831	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
3832	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
3833	rbAtoms = []
3834	rbIds = []
3835	for iratm in range(len(rbRes['atNames'])):
3836	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
3837	rbIds.append(Atoms[iatm][20])
3838	iatm += 1 #puts this at beginning of next residue?
3839	Orig = rbAtoms[rbRef[0]]
3840	rbObj['RBId'] = RBIds[res]
3841	rbObj['Ids'] = rbIds
3842	rbObj['Orig'] = [Orig,False]
3843	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
3844	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
3845	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
3846	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
3847	VCC = np.cross(VAR,VAC)
3848	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3849	VAR = G2mth.prodQVQ(QuatA,VAR)
3850	VBR = G2mth.prodQVQ(QuatA,VBR)
3851	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3852	QuatC = G2mth.prodQQ(QuatB,QuatA)
3853	rbObj['Orient'] = [QuatC,' ']
3854	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3855	SXYZ = []
3856	TXYZ = []
3857	rbObj['Torsions'] = []
3858	for i,xyz in enumerate(rbRes['rbXYZ']):
3859	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
3860	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
3861	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
3862	VBR = SXYZ[Oatm]-SXYZ[Patm]
3863	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
3864	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
3865	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
3866	ang = 180.*D/np.pi
3867	rbObj['Torsions'].append([ang,False])
3868	for ride in Riders:
3869	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
3870	rbRes['useCount'] += 1
3871	RBObjs.append(rbObj)
3872	data['RBModels']['Residue'] = RBObjs
3873	for RBObj in RBObjs:
3874	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3875	for i,id in enumerate(RBObj['Ids']):
3876	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3877	finally:
3878	wx.EndBusyCursor()
3879	wx.CallAfter(FillRigidBodyGrid,True)
3880
3881	def OnRBRemoveAll(event):
3882	data['RBModels']['Residue'] = []
3883	data['RBModels']['Vector'] = []
3884	RBData = G2frame.PatternTree.GetItemPyData(
3885	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3886	for RBType in ['Vector','Residue']:
3887	for rbId in RBData[RBType]:
3888	RBData[RBType][rbId]['useCount'] = 0
3889	FillRigidBodyGrid(True)
3890
3891	def OnGlobalResRBTherm(event):
3892	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3893	RBObjs = data['RBModels']['Residue']
3894	names = ['None','Uiso','T','TL','TLS']
3895	cia = data['General']['AtomPtrs'][3]
3896	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
3897	if dlg.ShowModal() == wx.ID_OK:
3898	sel = dlg.GetSelection()
3899	parm = names[sel]
3900	Ttype = 'A'
3901	if parm == 'Uiso':
3902	Ttype = 'I'
3903	for rbObj in RBObjs:
3904	rbObj['ThermalMotion'][0] = parm
3905	if parm != 'None':
3906	for i,id in enumerate(rbObj['Ids']):
3907	data['Atoms'][AtLookUp[id]][cia] = Ttype
3908	dlg.Destroy()
3909	wx.CallAfter(FillRigidBodyGrid,True)
3910
3911	def OnGlobalResRBRef(event):
3912	RBObjs = data['RBModels']['Residue']
3913	names = ['Origin','Orient. angle','Full Orient.']
3914	nTor = 0
3915	for rbObj in RBObjs:
3916	nTor = max(nTor,len(rbObj['Torsions']))
3917	names += ['Torsion '+str(i) for i in range(nTor)]
3918	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
3919	names += ['Uiso',]
3920	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
3921	names += ['Tii','Tij','Lii','Lij','Sij']
3922	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
3923	names += ['Tii','Tij','Lii','Lij']
3924	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
3925	names += ['Tii','Tij']
3926
3927	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
3928	if dlg.ShowModal() == wx.ID_OK:
3929	sel = dlg.GetSelections()
3930	parms = []
3931	for x in sel:
3932	parms.append(names[x])
3933	wx.BeginBusyCursor()
3934	try:
3935	for rbObj in RBObjs:
3936	if 'Origin' in parms:
3937	rbObj['Orig'][1] = True
3938	else:
3939	rbObj['Orig'][1] = False
3940	if 'Full Orient.' in parms:
3941	rbObj['Orient'][1] = 'AV'
3942	elif 'Orient. angle' in parms:
3943	rbObj['Orient'][1] = 'A'
3944	else:
3945	rbObj['Orient'][1] = ' '
3946	for i in range(len(rbObj['Torsions'])):
3947	if 'Torsion '+str(i) in parms:
3948	rbObj['Torsions'][i][1] = True
3949	else:
3950	rbObj['Torsions'][i][1] = False
3951	if rbObj['ThermalMotion'][0] == 'Uiso':
3952	if 'Uiso' in parms:
3953	rbObj['ThermalMotion'][2][0] = True
3954	else:
3955	rbObj['ThermalMotion'][2][0] = False
3956	elif 'T' in rbObj['ThermalMotion'][0]:
3957	if 'Tii' in parms:
3958	rbObj['ThermalMotion'][2][0:2] = [True,True,True]
3959	else:
3960	rbObj['ThermalMotion'][2][0:2] = [False,False,False]
3961	if 'Tij' in parms:
3962	rbObj['ThermalMotion'][2][3:6] = [True,True,True]
3963	else:
3964	rbObj['ThermalMotion'][2][3:6] = [False,False,False]
3965	elif 'L' in rbObj['ThermalMotion'][0]:
3966	if 'Lii' in parms:
3967	rbObj['ThermalMotion'][2][6:9] = [True,True,True]
3968	else:
3969	rbObj['ThermalMotion'][2][6:9] = [False,False,False]
3970	if 'Lij' in parms:
3971	rbObj['ThermalMotion'][2][9:12] = [True,True,True]
3972	else:
3973	rbObj['ThermalMotion'][2][9:12] = [False,False,False]
3974	elif 'S' in rbObj['ThermalMotion'][0]:
3975	if 'Sij' in parms:
3976	rbObj['ThermalMotion'][2][12:20] = [True,True,True,True,True,True,True,True]
3977	else:
3978	rbObj['ThermalMotion'][2][12:20] = [False,False,False,False,False,False,False,False]
3979	finally:
3980	wx.EndBusyCursor()
3981	FillRigidBodyGrid()
3982
3983	################################################################################
3984	##### MC/SA routines
3985	################################################################################
3986
3987	def UpdateMCSA(Scroll=0):
3988	Indx = {}
3989
3990	def OnPosRef(event):
3991	Obj = event.GetEventObject()
3992	model,item,ix = Indx[Obj.GetId()]
3993	model[item][1][ix] = Obj.GetValue()
3994
3995	def OnPosVal(event):
3996	Obj = event.GetEventObject()
3997	model,item,ix = Indx[Obj.GetId()]
3998	try:
3999	model[item][0][ix] = float(Obj.GetValue())
4000	except ValueError:
4001	pass
4002	Obj.SetValue("%.4f"%(model[item][0][ix]))
4003	G2plt.PlotStructure(G2frame,data)
4004
4005	def OnPosRange(event):
4006	Obj = event.GetEventObject()
4007	model,item,ix = Indx[Obj.GetId()]
4008	Range = Obj.GetValue().split()
4009	try:
4010	rmin,rmax = [float(Range[i]) for i in range(2)]
4011	if rmin >= rmax:
4012	raise ValueError
4013	except (ValueError,IndexError):
4014	rmin,rmax = model[item][2][ix]
4015	model[item][2][ix] = [rmin,rmax]
4016	Obj.SetValue('%.3f %.3f'%(rmin,rmax))
4017
4018	def atomSizer(model):
4019
4020	atomsizer = wx.FlexGridSizer(1,7,5,5)
4021	atomsizer.Add(wx.StaticText(MCSA,-1,' Atom: '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4022	for ix,item in enumerate(['x','y','z']):
4023	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4024	posRef.SetValue(model['Pos'][1][ix])
4025	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4026	Indx[posRef.GetId()] = [model,'Pos',ix]
4027	atomsizer.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4028	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4029	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4030	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4031	Indx[posVal.GetId()] = [model,'Pos',ix]
4032	atomsizer.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4033	atomsizer.Add((5,5),0)
4034	for ix,item in enumerate(['x','y','z']):
4035	atomsizer.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4036	rmin,rmax = model['Pos'][2][ix]
4037	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4038	Indx[posRange.GetId()] = [model,'Pos',ix]
4039	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4040	posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4041	atomsizer.Add(posRange,0,wx.ALIGN_CENTER_VERTICAL)
4042	return atomsizer
4043
4044	def rbSizer(model):
4045
4046	def OnOrVar(event):
4047	Obj = event.GetEventObject()
4048	model = Indx[Obj.GetId()]
4049	model['Ovar'] = Obj.GetValue()
4050
4051	def OnOriVal(event):
4052	Obj = event.GetEventObject()
4053	model,ix = Indx[Obj.GetId()]
4054	A,V = G2mth.Q2AVdeg(model['Ori'][0])
4055	if ix:
4056	Anew = A
4057	Vec = Obj.GetValue().split()
4058	try:
4059	Vnew = [float(Vec[i]) for i in range(3)]
4060	except ValueError:
4061	Vnew = V
4062	else:
4063	Vnew = V
4064	try:
4065	Anew = float(Obj.GetValue())
4066	except ValueError:
4067	Anew = A
4068	model['Ori'][0] = G2mth.AVdeg2Q(Anew,Vnew)
4069	G2plt.PlotStructure(G2frame,data)
4070	UpdateMCSA()
4071
4072	def OnMolCent(event):
4073	Obj = event.GetEventObject()
4074	model = Indx[Obj.GetId()]
4075	model['MolCent'][1] = Obj.GetValue()
4076	if model['MolCent'][1]:
4077	G2mth.SetMolCent(model,RBData)
4078	G2plt.PlotStructure(G2frame,data)
4079
4080	rbsizer = wx.BoxSizer(wx.VERTICAL)
4081	rbsizer1 = wx.FlexGridSizer(1,7,5,5)
4082	rbsizer1.Add(wx.StaticText(MCSA,-1,model['Type']+': '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4083	for ix,item in enumerate(['x','y','z']):
4084	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4085	posRef.SetValue(model['Pos'][1][ix])
4086	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4087	Indx[posRef.GetId()] = [model,'Pos',ix]
4088	rbsizer1.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4089	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4090	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4091	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4092	Indx[posVal.GetId()] = [model,'Pos',ix]
4093	rbsizer1.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4094	molcent = wx.CheckBox(MCSA,-1,label=' Use mol. center? ')
4095	molcent.SetValue(model['MolCent'][1])
4096	molcent.Bind(wx.EVT_CHECKBOX,OnMolCent)
4097	Indx[molcent.GetId()] = model
4098	rbsizer1.Add(molcent,0,wx.ALIGN_CENTER_VERTICAL)
4099	for ix,item in enumerate(['x','y','z']):
4100	rbsizer1.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4101	rmin,rmax = model['Pos'][2][ix]
4102	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4103	Indx[posRange.GetId()] = [model,'Pos',ix]
4104	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4105