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source: trunk/GSASIIphsGUI.py @ 1142

Last change on this file since 1142 was 1142, checked in by vondreele, 12 years ago
add 2*Fo-Fc omit to Fourier map collection
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1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2013-11-07 21:47:59 +0000 (Thu, 07 Nov 2013) $
5	# $Author: vondreele $
6	# $Revision: 1142 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1142 2013-11-07 21:47:59Z 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: 1142 $")
37	import GSASIIlattice as G2lat
38	import GSASIIspc as G2spc
39	import GSASIIElem as G2elem
40	import GSASIIElemGUI as G2elemGUI
41	import GSASIIddataGUI as G2ddG
42	import GSASIIplot as G2plt
43	import GSASIIgrid as G2gd
44	import GSASIIIO as G2IO
45	import GSASIIstrMain as G2stMn
46	import GSASIImath as G2mth
47	import GSASIIpwd as G2pwd
48	import numpy as np
49	import numpy.linalg as nl
50	import numpy.ma as ma
51
52	VERY_LIGHT_GREY = wx.Colour(235,235,235)
53	WHITE = wx.Colour(255,255,255)
54	BLACK = wx.Colour(0,0,0)
55	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
56	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
57	# trig functions in degrees
58	sind = lambda x: np.sin(x*np.pi/180.)
59	tand = lambda x: np.tan(x*np.pi/180.)
60	cosd = lambda x: np.cos(x*np.pi/180.)
61	asind = lambda x: 180.*np.arcsin(x)/np.pi
62	acosd = lambda x: 180.*np.arccos(x)/np.pi
63
64	def SetPhaseWindow(mainFrame,phasePage,mainSizer):
65	phasePage.SetSizer(mainSizer)
66	Size = mainSizer.GetMinSize()
67	Size[0] += 40
68	Size[1] = max(Size[1],430) + 35
69	phasePage.SetSize(Size)
70	phasePage.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
71	mainFrame.setSizePosLeft(Size)
72
73	def UpdatePhaseData(G2frame,Item,data,oldPage):
74	'''Create the data display window contents when a phase is clicked on
75	in the man (data tree) window.
76	Called only from :meth:`GSASIIgrid.MovePatternTreeToGrid`,
77	which in turn is called from :meth:`GSASII.GSASII.OnPatternTreeSelChanged`
78	when a tree item is selected.
79
80	:param wx.frame G2frame: the main GSAS-II frame object
81	:param wx.TreeItemId Item: the tree item that was selected
82	:param dict data: all the information on the phase in a dictionary
83	:param int oldPage: This sets a tab to select when moving
84	from one phase to another, in which case the same tab is selected
85	to display first. This is set only when the previous data tree
86	selection is a phase, if not the value is None. The default action
87	is to bring up the General tab.
88
89	'''
90
91	#patch
92	if 'RBModels' not in data:
93	data['RBModels'] = {}
94	if 'MCSA' not in data:
95	data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
96	if isinstance(data['MCSA']['Results'],dict):
97	data['MCSA']['Results'] = []
98	#end patch
99
100	global rbAtmDict
101	rbAtmDict = {}
102	if G2frame.dataDisplay:
103	G2frame.dataDisplay.Destroy()
104	PhaseName = G2frame.PatternTree.GetItemText(Item)
105	G2gd.SetDataMenuBar(G2frame)
106	G2frame.dataFrame.SetLabel('Phase Data for '+PhaseName)
107	G2frame.dataFrame.CreateStatusBar()
108	G2frame.dataDisplay = G2gd.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize())
109	G2frame.dataDisplay.gridList = [] # list of all grids in notebook
110
111	def SetupGeneral():
112	generalData = data['General']
113	atomData = data['Atoms']
114	generalData['AtomTypes'] = []
115	generalData['Isotopes'] = {}
116	# various patches
117	if 'Isotope' not in generalData:
118	generalData['Isotope'] = {}
119	if 'Data plot type' not in generalData:
120	generalData['Data plot type'] = 'Mustrain'
121	if 'POhkl' not in generalData:
122	generalData['POhkl'] = [0,0,1]
123	if 'Map' not in generalData:
124	generalData['Map'] = mapDefault
125	if 'Flip' not in generalData:
126	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
127	'k-factor':0.1,'k-Max':20.}
128	if 'doPawley' not in generalData:
129	generalData['doPawley'] = False
130	if 'Pawley dmin' not in generalData:
131	generalData['Pawley dmin'] = 1.0
132	if 'Pawley neg wt' not in generalData:
133	generalData['Pawley neg wt'] = 0.0
134	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
135	'MCSA controls' not in generalData:
136	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
137	'dmin':2.0,'Algorithm':'fast','Jump coeff':[0.95,0.5],'boltzmann':1.0,
138	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[]}
139	# end of patches
140	generalData['NoAtoms'] = {}
141	generalData['BondRadii'] = []
142	generalData['AngleRadii'] = []
143	generalData['vdWRadii'] = []
144	generalData['AtomMass'] = []
145	generalData['Color'] = []
146	generalData['Mydir'] = G2frame.dirname
147	cx,ct,cs,cia = [3,1,7,9]
148	if generalData['Type'] =='macromolecular':
149	cx,ct,cs,cia = [6,4,10,12]
150	generalData['AtomPtrs'] = [cx,ct,cs,cia]
151	for atom in atomData:
152	atom[ct] = atom[ct].lower().capitalize() #force to standard form
153	if generalData['AtomTypes'].count(atom[ct]):
154	generalData['NoAtoms'][atom[ct]] += atom[cs-1]*float(atom[cs+1])
155	elif atom[ct] != 'UNK':
156	Info = G2elem.GetAtomInfo(atom[ct])
157	generalData['AtomTypes'].append(atom[ct])
158	generalData['Z'] = Info['Z']
159	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
160	generalData['BondRadii'].append(Info['Drad'])
161	generalData['AngleRadii'].append(Info['Arad'])
162	generalData['vdWRadii'].append(Info['Vdrad'])
163	if atom[ct] in generalData['Isotope']:
164	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]][0])
165	else:
166	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
167	generalData['AtomMass'].append(Info['Mass'])
168	generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
169	generalData['Color'].append(Info['Color'])
170	F000X = 0.
171	F000N = 0.
172	for i,elem in enumerate(generalData['AtomTypes']):
173	F000X += generalData['NoAtoms'][elem]*generalData['Z']
174	isotope = generalData['Isotope'][elem]
175	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope][1]
176	generalData['F000X'] = F000X
177	generalData['F000N'] = F000N
178
179
180	################################################################################
181	##### General phase routines
182	################################################################################
183
184	def UpdateGeneral():
185	'''Draw the controls for the General phase data subpage
186	'''
187
188	""" This is the default dictionary structure for phase data
189	(taken from GSASII.py)
190	'General':{
191	'Name':PhaseName
192	'Type':'nuclear'
193	'SGData':SGData
194	'Cell':[False,10.,10.,10.,90.,90.,90,1000.]
195	'AtomPtrs':[]
196	'Histogram list':['',]
197	'Pawley dmin':1.0,
198	'Pawley neg wt':0.0}
199	'Atoms':[]
200	'Drawing':{}
201	"""
202	# UpdateGeneral execution starts here
203	phaseTypes = ['nuclear','modulated','magnetic','macromolecular']
204	SetupGeneral()
205	generalData = data['General']
206	Map = generalData['Map']
207	Flip = generalData['Flip']
208	MCSAdata = generalData['MCSA controls']
209	PWDR = any(['PWDR' in item for item in data['Histograms'].keys()])
210	# UpdateGeneral execution continues below
211
212	def NameSizer():
213	def OnPhaseName(event):
214	oldName = generalData['Name']
215	generalData['Name'] = NameTxt.GetValue()
216	G2frame.G2plotNB.Rename(oldName,generalData['Name'])
217	G2frame.dataFrame.SetLabel('Phase Data for '+generalData['Name'])
218	G2frame.PatternTree.SetItemText(Item,generalData['Name'])
219	#Hmm, need to change phase name key in Reflection Lists for each histogram
220
221	def OnPhaseType(event):
222	if not generalData['AtomTypes']: #can change only if no atoms!
223	generalData['Type'] = TypeTxt.GetValue()
224	wx.CallAfter(UpdateGeneral)
225	else:
226	TypeTxt.SetValue(generalData['Type'])
227
228	def OnSpaceGroup(event):
229	SpcGp = SGTxt.GetValue()
230	SGErr,SGData = G2spc.SpcGroup(SpcGp)
231	# try a lookup on the user-supplied name
232	if SGErr:
233	SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
234	if SpGrpNorm:
235	E,SGData = G2spc.SpcGroup(SpGrpNorm)
236	if not E: SGErr = False
237	if SGErr:
238	text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
239	SGTxt.SetValue(generalData['SGData']['SpGrp'])
240	msg = 'Space Group Error'
241	Style = wx.ICON_EXCLAMATION
242	else:
243	text = G2spc.SGPrint(SGData)
244	generalData['SGData'] = SGData
245	msg = 'Space Group Information'
246	Style = wx.ICON_INFORMATION
247	Text = ''
248	for line in text:
249	Text += line+'\n'
250	wx.MessageBox(Text,caption=msg,style=Style)
251	wx.CallAfter(UpdateGeneral)
252
253	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
254	nameSizer.Add(wx.StaticText(General,-1,' Phase name: '),0,wx.ALIGN_CENTER_VERTICAL)
255	NameTxt = wx.TextCtrl(General,-1,value=generalData['Name'],style=wx.TE_PROCESS_ENTER)
256	NameTxt.Bind(wx.EVT_TEXT_ENTER,OnPhaseName)
257	NameTxt.Bind(wx.EVT_KILL_FOCUS,OnPhaseName)
258	nameSizer.Add(NameTxt,0,wx.ALIGN_CENTER_VERTICAL)
259	nameSizer.Add(wx.StaticText(General,-1,' Phase type: '),0,wx.ALIGN_CENTER_VERTICAL)
260	TypeTxt = wx.ComboBox(General,-1,value=generalData['Type'],choices=phaseTypes,
261	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
262	TypeTxt.Bind(wx.EVT_COMBOBOX, OnPhaseType)
263	nameSizer.Add(TypeTxt,0,wx.ALIGN_CENTER_VERTICAL)
264	nameSizer.Add(wx.StaticText(General,-1,' Space group: '),0,wx.ALIGN_CENTER_VERTICAL)
265	SGTxt = wx.TextCtrl(General,-1,value=generalData['SGData']['SpGrp'],style=wx.TE_PROCESS_ENTER)
266	SGTxt.Bind(wx.EVT_TEXT_ENTER,OnSpaceGroup)
267	nameSizer.Add(SGTxt,0,wx.ALIGN_CENTER_VERTICAL)
268	return nameSizer
269
270	def CellSizer():
271
272	cellGUIlist = [[['m3','m3m'],4,zip([" Unit cell: a = "," Vol = "],["%.5f","%.3f"],[True,False],[0,0])],
273	[['3R','3mR'],6,zip([" a = "," alpha = "," Vol = "],["%.5f","%.3f","%.3f"],[True,True,False],[0,2,0])],
274	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],6,zip([" a = "," c = "," Vol = "],["%.5f","%.5f","%.3f"],[True,True,False],[0,2,0])],
275	[['mmm'],8,zip([" a = "," b = "," c = "," Vol = "],["%.5f","%.5f","%.5f","%.3f"],
276	[True,True,True,False],[0,1,2,0])],
277	[['2/m'+'a'],10,zip([" a = "," b = "," c = "," alpha = "," Vol = "],
278	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
279	[['2/m'+'b'],10,zip([" a = "," b = "," c = "," beta = "," Vol = "],
280	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
281	[['2/m'+'c'],10,zip([" a = "," b = "," c = "," gamma = "," Vol = "],
282	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
283	[['-1'],8,zip([" a = "," b = "," c = "," Vol = "," alpha = "," beta = "," gamma = "],
284	["%.5f","%.5f","%.5f","%.3f","%.3f","%.3f","%.3f"],
285	[True,True,True,False,True,True,True],[0,1,2,0,3,4,5])]]
286
287	def OnCellRef(event):
288	generalData['Cell'][0] = cellRef.GetValue()
289
290	def OnCellChange(event):
291	SGData = generalData['SGData']
292	laue = SGData['SGLaue']
293	if laue == '2/m':
294	laue += SGData['SGUniq']
295	cell = generalData['Cell']
296	Obj = event.GetEventObject()
297	ObjId = cellList.index(Obj.GetId())
298	try:
299	value = max(1.0,float(Obj.GetValue()))
300	except ValueError:
301	if ObjId < 3: #bad cell edge - reset
302	value = controls[6+ObjId]
303	else: #bad angle
304	value = 90.
305	if laue in ['m3','m3m']:
306	cell[1] = cell[2] = cell[3] = value
307	cell[4] = cell[5] = cell[6] = 90.0
308	Obj.SetValue("%.5f"%(cell[1]))
309	elif laue in ['3R','3mR']:
310	if ObjId == 0:
311	cell[1] = cell[2] = cell[3] = value
312	Obj.SetValue("%.5f"%(cell[1]))
313	else:
314	cell[4] = cell[5] = cell[6] = value
315	Obj.SetValue("%.5f"%(cell[4]))
316	elif laue in ['3','3m1','31m','6/m','6/mmm','4/m','4/mmm']:
317	cell[4] = cell[5] = 90.
318	cell[6] = 120.
319	if laue in ['4/m','4/mmm']:
320	cell[6] = 90.
321	if ObjId == 0:
322	cell[1] = cell[2] = value
323	Obj.SetValue("%.5f"%(cell[1]))
324	else:
325	cell[3] = value
326	Obj.SetValue("%.5f"%(cell[3]))
327	elif laue in ['mmm']:
328	cell[ObjId+1] = value
329	cell[4] = cell[5] = cell[6] = 90.
330	Obj.SetValue("%.5f"%(cell[ObjId+1]))
331	elif laue in ['2/m'+'a']:
332	cell[5] = cell[6] = 90.
333	if ObjId != 3:
334	cell[ObjId+1] = value
335	Obj.SetValue("%.5f"%(cell[ObjId+1]))
336	else:
337	cell[4] = value
338	Obj.SetValue("%.3f"%(cell[4]))
339	elif laue in ['2/m'+'b']:
340	cell[4] = cell[6] = 90.
341	if ObjId != 3:
342	cell[ObjId+1] = value
343	Obj.SetValue("%.5f"%(cell[ObjId+1]))
344	else:
345	cell[5] = value
346	Obj.SetValue("%.3f"%(cell[5]))
347	elif laue in ['2/m'+'c']:
348	cell[5] = cell[6] = 90.
349	if ObjId != 3:
350	cell[ObjId+1] = value
351	Obj.SetValue("%.5f"%(cell[ObjId+1]))
352	else:
353	cell[6] = value
354	Obj.SetValue("%.3f"%(cell[6]))
355	else:
356	cell[ObjId+1] = value
357	if ObjId < 3:
358	Obj.SetValue("%.5f"%(cell[1+ObjId]))
359	else:
360	Obj.SetValue("%.3f"%(cell[1+ObjId]))
361	cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
362	volVal.SetValue("%.3f"%(cell[7]))
363	density,mattCoeff = G2mth.getDensity(generalData)
364	if denSizer:
365	denSizer[1].SetValue('%.3f'%(density))
366	if denSizer[2]:
367	denSizer[2].SetValue('%.3f'%(mattCoeff))
368	generalData['Cell'] = cell
369
370	cell = generalData['Cell']
371	laue = generalData['SGData']['SGLaue']
372	if laue == '2/m':
373	laue += generalData['SGData']['SGUniq']
374	for cellGUI in cellGUIlist:
375	if laue in cellGUI[0]:
376	useGUI = cellGUI
377	cellSizer = wx.FlexGridSizer(2,useGUI[1]+1,5,5)
378	if PWDR:
379	cellRef = wx.CheckBox(General,-1,label='Refine unit cell:')
380	cellSizer.Add(cellRef,0,wx.ALIGN_CENTER_VERTICAL)
381	cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef)
382	cellRef.SetValue(cell[0])
383	cellList = []
384	for txt,fmt,ifEdit,Id in useGUI[2]:
385	cellSizer.Add(wx.StaticText(General,label=txt),0,wx.ALIGN_CENTER_VERTICAL)
386	if ifEdit: #a,b,c,etc.
387	cellVal = wx.TextCtrl(General,value=(fmt%(cell[Id+1])),
388	style=wx.TE_PROCESS_ENTER)
389	cellVal.Bind(wx.EVT_TEXT_ENTER,OnCellChange)
390	cellVal.Bind(wx.EVT_KILL_FOCUS,OnCellChange)
391	cellSizer.Add(cellVal,0,wx.ALIGN_CENTER_VERTICAL)
392	cellList.append(cellVal.GetId())
393	else: #volume
394	volVal = wx.TextCtrl(General,value=(fmt%(cell[7])),style=wx.TE_READONLY)
395	volVal.SetBackgroundColour(VERY_LIGHT_GREY)
396	cellSizer.Add(volVal,0,wx.ALIGN_CENTER_VERTICAL)
397	return cellSizer
398
399	def ElemSizer():
400
401	def OnIsotope(event):
402	Obj = event.GetEventObject()
403	item = Indx[Obj.GetId()]
404	isotope = Obj.GetValue()
405	generalData['Isotope'][item] = isotope
406	indx = generalData['AtomTypes'].index(item)
407	data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope][0]
408	density,mattCoeff = G2mth.getDensity(generalData)
409	denSizer[1].SetValue('%.3f'%(density))
410	if denSizer[2]:
411	denSizer[2].SetValue('%.3f'%(mattCoeff))
412
413	elemSizer = wx.FlexGridSizer(8,len(generalData['AtomTypes'])+1,1,1)
414	elemSizer.Add(wx.StaticText(General,label=' Elements'),0,wx.ALIGN_CENTER_VERTICAL)
415	for elem in generalData['AtomTypes']:
416	typTxt = wx.TextCtrl(General,value=elem,style=wx.TE_READONLY)
417	typTxt.SetBackgroundColour(VERY_LIGHT_GREY)
418	elemSizer.Add(typTxt,0,wx.ALIGN_CENTER_VERTICAL)
419	elemSizer.Add(wx.StaticText(General,label=' Isotope'),0,wx.ALIGN_CENTER_VERTICAL)
420	for elem in generalData['AtomTypes']:
421	choices = generalData['Isotopes'][elem].keys()
422	isoSel = wx.ComboBox(General,-1,value=generalData['Isotope'][elem],choices=choices,
423	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
424	isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope)
425	Indx[isoSel.GetId()] = elem
426	elemSizer.Add(isoSel,1,wx.ALIGN_CENTER_VERTICAL\|wx.EXPAND)
427	elemSizer.Add(wx.StaticText(General,label=' No. per cell'),0,wx.ALIGN_CENTER_VERTICAL)
428	for elem in generalData['AtomTypes']:
429	numbTxt = wx.TextCtrl(General,value='%.1f'%(generalData['NoAtoms'][elem]),
430	style=wx.TE_READONLY)
431	numbTxt.SetBackgroundColour(VERY_LIGHT_GREY)
432	elemSizer.Add(numbTxt,0,wx.ALIGN_CENTER_VERTICAL)
433	elemSizer.Add(wx.StaticText(General,label=' Atom weight'),0,wx.ALIGN_CENTER_VERTICAL)
434	for wt in generalData['AtomMass']:
435	wtTxt = wx.TextCtrl(General,value='%.3f'%(wt),style=wx.TE_READONLY)
436	wtTxt.SetBackgroundColour(VERY_LIGHT_GREY)
437	elemSizer.Add(wtTxt,0,wx.ALIGN_CENTER_VERTICAL)
438	elemSizer.Add(wx.StaticText(General,label=' Bond radii'),0,wx.ALIGN_CENTER_VERTICAL)
439	for rad in generalData['BondRadii']:
440	bondRadii = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
441	bondRadii.SetBackgroundColour(VERY_LIGHT_GREY)
442	elemSizer.Add(bondRadii,0,wx.ALIGN_CENTER_VERTICAL)
443	elemSizer.Add(wx.StaticText(General,label=' Angle radii'),0,wx.ALIGN_CENTER_VERTICAL)
444	for rad in generalData['AngleRadii']:
445	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
446	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
447	elemSizer.Add(elemTxt,0,wx.ALIGN_CENTER_VERTICAL)
448	elemSizer.Add(wx.StaticText(General,label=' van der Waals radii'),0,wx.ALIGN_CENTER_VERTICAL)
449	for rad in generalData['vdWRadii']:
450	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
451	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
452	elemSizer.Add(elemTxt,0,wx.ALIGN_CENTER_VERTICAL)
453	elemSizer.Add(wx.StaticText(General,label=' Default color'),0,wx.ALIGN_CENTER_VERTICAL)
454	for R,G,B in generalData['Color']:
455	colorTxt = wx.TextCtrl(General,value='',style=wx.TE_READONLY)
456	colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
457	elemSizer.Add(colorTxt,0,wx.ALIGN_CENTER_VERTICAL)
458	return elemSizer
459
460	def DenSizer():
461
462	mass = G2mth.getMass(generalData)
463	density,mattCoeff = G2mth.getDensity(generalData)
464	denSizer = wx.BoxSizer(wx.HORIZONTAL)
465	denSizer.Add(wx.StaticText(General,-1,' Density: '),0,wx.ALIGN_CENTER_VERTICAL)
466	denTxt = wx.TextCtrl(General,-1,'%.3f'%(density),style=wx.TE_READONLY)
467	denTxt.SetBackgroundColour(VERY_LIGHT_GREY)
468	denSizer.Add(denTxt,0,wx.ALIGN_CENTER_VERTICAL)
469	mattTxt = None
470	if generalData['Type'] == 'macromolecular' and mass > 0.0:
471	denSizer.Add(wx.StaticText(General,-1,' Matthews coeff.: '),
472	0,wx.ALIGN_CENTER_VERTICAL)
473	mattTxt = wx.TextCtrl(General,-1,'%.3f'%(mattCoeff),style=wx.TE_READONLY)
474	mattTxt.SetBackgroundColour(VERY_LIGHT_GREY)
475	denSizer.Add(mattTxt,0,wx.ALIGN_CENTER_VERTICAL)
476	return denSizer,denTxt,mattTxt
477
478	def PawleySizer():
479
480	def OnPawleyRef(event):
481	generalData['doPawley'] = pawlRef.GetValue()
482
483	def OnPawleyVal(event):
484	try:
485	dmin = float(pawlVal.GetValue())
486	if 0.25 <= dmin <= 20.:
487	generalData['Pawley dmin'] = dmin
488	except ValueError:
489	pass
490	pawlVal.SetValue("%.3f"%(generalData['Pawley dmin'])) #reset in case of error
491
492	def OnPawleyNegWt(event):
493	try:
494	wt = float(pawlNegWt.GetValue())
495	if 0. <= wt <= 1.:
496	generalData['Pawley neg wt'] = wt
497	except ValueError:
498	pass
499	pawlNegWt.SetValue("%.4f"%(generalData['Pawley neg wt'])) #reset in case of error
500
501	pawleySizer = wx.BoxSizer(wx.HORIZONTAL)
502	pawleySizer.Add(wx.StaticText(General,label=' Pawley controls: '),0,wx.ALIGN_CENTER_VERTICAL)
503	pawlRef = wx.CheckBox(General,-1,label=' Do Pawley refinement?')
504	pawlRef.SetValue(generalData['doPawley'])
505	pawlRef.Bind(wx.EVT_CHECKBOX,OnPawleyRef)
506	pawleySizer.Add(pawlRef,0,wx.ALIGN_CENTER_VERTICAL)
507	pawleySizer.Add(wx.StaticText(General,label=' Pawley dmin: '),0,wx.ALIGN_CENTER_VERTICAL)
508	pawlVal = wx.TextCtrl(General,value='%.3f'%(generalData['Pawley dmin']),style=wx.TE_PROCESS_ENTER)
509	pawlVal.Bind(wx.EVT_TEXT_ENTER,OnPawleyVal)
510	pawlVal.Bind(wx.EVT_KILL_FOCUS,OnPawleyVal)
511	pawleySizer.Add(pawlVal,0,wx.ALIGN_CENTER_VERTICAL)
512	pawleySizer.Add(wx.StaticText(General,label=' Pawley neg. wt.: '),0,wx.ALIGN_CENTER_VERTICAL)
513	pawlNegWt = wx.TextCtrl(General,value='%.4f'%(generalData['Pawley neg wt']),style=wx.TE_PROCESS_ENTER)
514	pawlNegWt.Bind(wx.EVT_TEXT_ENTER,OnPawleyNegWt)
515	pawlNegWt.Bind(wx.EVT_KILL_FOCUS,OnPawleyNegWt)
516	pawleySizer.Add(pawlNegWt,0,wx.ALIGN_CENTER_VERTICAL)
517	return pawleySizer
518
519	def MapSizer():
520
521	def OnMapType(event):
522	Map['MapType'] = mapType.GetValue()
523
524	def OnRefList(event):
525	Map['RefList'] = refList.GetValue()
526
527	def OnResVal(event):
528	try:
529	res = float(mapRes.GetValue())
530	if 0.25 <= res <= 20.:
531	Map['Resolution'] = res
532	except ValueError:
533	pass
534	mapRes.SetValue("%.2f"%(Map['Resolution'])) #reset in case of error
535
536	def OnCutOff(event):
537	try:
538	res = float(cutOff.GetValue())
539	if 10.0 <= res <= 100.:
540	Map['cutOff'] = res
541	except ValueError:
542	pass
543	cutOff.SetValue("%.1f"%(Map['cutOff'])) #reset in case of error
544
545	#patch
546	if 'cutOff' not in Map:
547	Map['cutOff'] = 100.0
548	mapTypes = ['Fobs','Fcalc','delt-F','2*Fo-Fc','Omit','2Fo-Fc Omit','Patterson']
549	refList = data['Histograms'].keys()
550	if not generalData['AtomTypes']:
551	mapTypes = ['Patterson',]
552	Map['MapType'] = 'Patterson'
553	mapSizer = wx.BoxSizer(wx.VERTICAL)
554	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
555	lineSizer.Add(wx.StaticText(General,label=' Fourier map controls: Map type: '),0,wx.ALIGN_CENTER_VERTICAL)
556	mapType = wx.ComboBox(General,-1,value=Map['MapType'],choices=mapTypes,
557	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
558	mapType.Bind(wx.EVT_COMBOBOX,OnMapType)
559	lineSizer.Add(mapType,0,wx.ALIGN_CENTER_VERTICAL)
560	lineSizer.Add(wx.StaticText(General,label=' Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
561	refList = wx.ComboBox(General,-1,value=Map['RefList'],choices=refList,
562	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
563	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
564	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
565	mapSizer.Add(lineSizer,0,wx.ALIGN_CENTER_VERTICAL)
566	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
567	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,wx.ALIGN_CENTER_VERTICAL)
568	mapRes = wx.TextCtrl(General,value='%.2f'%(Map['Resolution']),style=wx.TE_PROCESS_ENTER)
569	mapRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
570	mapRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
571	line2Sizer.Add(mapRes,0,wx.ALIGN_CENTER_VERTICAL)
572	line2Sizer.Add(wx.StaticText(General,label=' Peak cutoff %: '),0,wx.ALIGN_CENTER_VERTICAL)
573	cutOff = wx.TextCtrl(General,value='%.1f'%(Map['cutOff']),style=wx.TE_PROCESS_ENTER)
574	cutOff.Bind(wx.EVT_TEXT_ENTER,OnCutOff)
575	cutOff.Bind(wx.EVT_KILL_FOCUS,OnCutOff)
576	line2Sizer.Add(cutOff,0,wx.ALIGN_CENTER_VERTICAL)
577	mapSizer.Add(line2Sizer,0,wx.ALIGN_CENTER_VERTICAL)
578	return mapSizer
579
580	def FlipSizer():
581	if 'k-Max' not in Flip: Flip['k-Max'] = 20.
582
583	def OnRefList(event):
584	Flip['RefList'] = refList.GetValue()
585
586	def OnNormElem(event):
587	PE = G2elemGUI.PickElement(G2frame,ifNone=True)
588	if PE.ShowModal() == wx.ID_OK:
589	Flip['Norm element'] = PE.Elem.strip()
590	normElem.SetLabel(Flip['Norm element'])
591	PE.Destroy()
592
593	def OnResVal(event):
594	try:
595	res = float(flipRes.GetValue())
596	if 0.25 <= res <= 20.:
597	Flip['Resolution'] = res
598	except ValueError:
599	pass
600	flipRes.SetValue("%.2f"%(Flip['Resolution'])) #reset in case of error
601
602	def OnkFactor(event):
603	try:
604	res = float(kFactor.GetValue())
605	if 0.1 <= res <= 1.2:
606	Flip['k-factor'] = res
607	except ValueError:
608	pass
609	kFactor.SetValue("%.3f"%(Flip['k-factor'])) #reset in case of error
610
611	def OnkMax(event):
612	try:
613	res = float(kMax.GetValue())
614	if res >= 10.:
615	Flip['k-Max'] = res
616	except ValueError:
617	pass
618	kMax.SetValue("%.1f"%(Flip['k-Max'])) #reset in case of error
619
620	refList = data['Histograms'].keys()
621	flipSizer = wx.BoxSizer(wx.VERTICAL)
622	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
623	lineSizer.Add(wx.StaticText(General,label=' Charge flip controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
624	refList = wx.ComboBox(General,-1,value=Flip['RefList'],choices=refList,
625	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
626	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
627	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
628	lineSizer.Add(wx.StaticText(General,label=' Normalizing element: '),0,wx.ALIGN_CENTER_VERTICAL)
629	normElem = wx.Button(General,label=Flip['Norm element'],style=wx.TE_READONLY)
630	normElem.Bind(wx.EVT_BUTTON,OnNormElem)
631	lineSizer.Add(normElem,0,wx.ALIGN_CENTER_VERTICAL)
632	flipSizer.Add(lineSizer,0,wx.ALIGN_CENTER_VERTICAL)
633	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
634	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,wx.ALIGN_CENTER_VERTICAL)
635	flipRes = wx.TextCtrl(General,value='%.2f'%(Flip['Resolution']),style=wx.TE_PROCESS_ENTER)
636	flipRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
637	flipRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
638	line2Sizer.Add(flipRes,0,wx.ALIGN_CENTER_VERTICAL)
639	line2Sizer.Add(wx.StaticText(General,label=' k-Factor (0.1-1.2): '),0,wx.ALIGN_CENTER_VERTICAL)
640	kFactor = wx.TextCtrl(General,value='%.3f'%(Flip['k-factor']),style=wx.TE_PROCESS_ENTER)
641	kFactor.Bind(wx.EVT_TEXT_ENTER,OnkFactor)
642	kFactor.Bind(wx.EVT_KILL_FOCUS,OnkFactor)
643	line2Sizer.Add(kFactor,0,wx.ALIGN_CENTER_VERTICAL)
644	line2Sizer.Add(wx.StaticText(General,label=' k-Max (>=10.0): '),0,wx.ALIGN_CENTER_VERTICAL)
645	kMax = wx.TextCtrl(General,value='%.1f'%(Flip['k-Max']),style=wx.TE_PROCESS_ENTER)
646	kMax.Bind(wx.EVT_TEXT_ENTER,OnkMax)
647	kMax.Bind(wx.EVT_KILL_FOCUS,OnkMax)
648	line2Sizer.Add(kMax,0,wx.ALIGN_CENTER_VERTICAL)
649	flipSizer.Add(line2Sizer,0,wx.ALIGN_CENTER_VERTICAL)
650	return flipSizer
651
652	def MCSASizer():
653	Ind = {}
654
655	def OnRefList(event):
656	MCSAdata['Data source'] = refList.GetValue()
657
658	def OnDmin(event):
659	try:
660	val = float(dmin.GetValue())
661	if 1.0 <= val < 5.0:
662	MCSAdata['dmin'] = val
663	except ValueError:
664	pass
665	dmin.SetValue("%.3f"%(MCSAdata['dmin'])) #reset in case of error
666	MCSAdata['newDmin'] = True
667
668	def OnCycles(event):
669	MCSAdata['Cycles'] = int(cycles.GetValue())
670
671	def OnAlist(event):
672	MCSAdata['Algorithm'] = Alist.GetValue()
673	wx.CallAfter(UpdateGeneral)
674
675	def OnSlope(event):
676	try:
677	val = float(slope.GetValue())
678	if .25 <= val < 1.0:
679	MCSAdata['log slope'] = val
680	except ValueError:
681	pass
682	slope.SetValue("%.3f"%(MCSAdata['log slope'])) #reset in case of error
683
684	def OnAjump(event):
685	Obj = event.GetEventObject()
686	name,ind = Indx[Obj.GetId()]
687	try:
688	val = float(Obj.GetValue())
689	if .0 <= val <= 1.0:
690	MCSAdata[name][ind] = val
691	except ValueError:
692	pass
693	Obj.SetValue("%.3f"%(MCSAdata[name][ind]))
694
695	def OnRanStart(event):
696	MCSAdata['ranStart'] = ranStart.GetValue()
697
698	def OnAutoRan(event):
699	MCSAdata['autoRan'] = autoRan.GetValue()
700
701	def OnRanRange(event):
702	try:
703	val = float(ranRange.GetValue())/100
704	if 0.01 <= val <= 0.99:
705	MCSAdata['ranRange'] = val
706	except ValueError:
707	pass
708	ranRange.SetValue('%.1f'%(MCSAdata['ranRange']*100.))
709
710	def OnAnneal(event):
711	Obj = event.GetEventObject()
712	ind,fmt = Indx[Obj.GetId()]
713	if ind == 2: #No. trials
714	try:
715	val = int(Obj.GetValue())
716	if 1 <= val:
717	MCSAdata['Annealing'][ind] = val
718	except ValueError:
719	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
720	else:
721	try:
722	val = float(Obj.GetValue())
723	if .0 <= val:
724	MCSAdata['Annealing'][ind] = val
725	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
726	except ValueError:
727	MCSAdata['Annealing'][ind] = None
728	Obj.SetValue(str(MCSAdata['Annealing'][ind]))
729
730	refList = []
731	if len(data['Pawley ref']):
732	refList = ['Pawley reflections']
733	for item in data['Histograms'].keys():
734	if 'HKLF' in item or 'PWDR' in item:
735	refList.append(item)
736	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
737	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
738	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
739	refList = wx.ComboBox(General,-1,value=MCSAdata['Data source'],choices=refList,
740	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
741	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
742	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
743	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,wx.ALIGN_CENTER_VERTICAL)
744	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['dmin']),style=wx.TE_PROCESS_ENTER)
745	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
746	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
747	lineSizer.Add(dmin,0,wx.ALIGN_CENTER_VERTICAL)
748	mcsaSizer.Add(lineSizer)
749	mcsaSizer.Add((5,5),)
750	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
751	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,wx.ALIGN_CENTER_VERTICAL)
752	Cchoice = ['1','2','3','6','10','20','30','60','100']
753	cycles = wx.ComboBox(General,-1,value=str(MCSAdata.get('Cycles',1)),choices=Cchoice,
754	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
755	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
756	line2Sizer.Add(cycles,0,wx.ALIGN_CENTER_VERTICAL)
757	line2Sizer.Add((5,0),)
758	ranStart = wx.CheckBox(General,-1,label=' MC/SA Refine at ')
759	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
760	ranStart.SetValue(MCSAdata.get('ranStart',False))
761	line2Sizer.Add(ranStart,0,wx.ALIGN_CENTER_VERTICAL)
762	ranRange = wx.TextCtrl(General,-1,value='%.1f'%(MCSAdata.get('ranRange',0.10)*100),style=wx.TE_PROCESS_ENTER)
763	ranRange.Bind(wx.EVT_TEXT_ENTER,OnRanRange)
764	ranRange.Bind(wx.EVT_KILL_FOCUS,OnRanRange)
765	line2Sizer.Add(ranRange,0,wx.ALIGN_CENTER_VERTICAL)
766	line2Sizer.Add(wx.StaticText(General,label='% of ranges. '),0,wx.ALIGN_CENTER_VERTICAL)
767	# autoRan = wx.CheckBox(General,-1,label=' Do auto range reduction? ')
768	# autoRan.Bind(wx.EVT_CHECKBOX, OnAutoRan)
769	# autoRan.SetValue(MCSAdata.get('autoRan',False))
770	# line2Sizer.Add(autoRan,0,wx.ALIGN_CENTER_VERTICAL)
771	mcsaSizer.Add(line2Sizer)
772	mcsaSizer.Add((5,5),)
773	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
774	Achoice = ['log','fast'] #these work
775	# Achoice = ['log','fast','cauchy','boltzmann']
776	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
777	Alist = wx.ComboBox(General,-1,value=MCSAdata['Algorithm'],choices=Achoice,
778	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
779	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
780	line3Sizer.Add(Alist,0,wx.ALIGN_CENTER_VERTICAL)
781	if MCSAdata['Algorithm'] in ['fast','boltzmann','cauchy']:
782	Names = [' A-jump: ',' B-jump: ']
783	parms = 'Jump coeff'
784	if MCSAdata['Algorithm'] in ['boltzmann','cauchy']:
785	Names = [' A-jump: ']
786	elif 'fast' in MCSAdata['Algorithm']:
787	Names = [' quench: ',' m-factor: ',' n-factor: ']
788	parms = 'fast parms'
789	for i,name in enumerate(Names):
790	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
791	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata[parms][i]),style=wx.TE_PROCESS_ENTER)
792	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
793	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
794	Indx[Ajump.GetId()] = [parms,i]
795	line3Sizer.Add(Ajump,0,wx.ALIGN_CENTER_VERTICAL)
796	elif 'log' in MCSAdata['Algorithm']:
797	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,wx.ALIGN_CENTER_VERTICAL)
798	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['log slope']),style=wx.TE_PROCESS_ENTER)
799	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
800	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
801	line3Sizer.Add(slope,0,wx.ALIGN_CENTER_VERTICAL)
802	mcsaSizer.Add(line3Sizer)
803	mcsaSizer.Add((5,5),)
804	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
805	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
806	names = [' Start temp: ',' Final temp: ',' No. trials: ']
807	fmts = ['%.1f','%.5f','%d']
808	for i,[name,fmt] in enumerate(zip(names,fmts)):
809	if MCSAdata['Annealing'][i]:
810	text = fmt%(MCSAdata['Annealing'][i])
811	else:
812	text = 'None'
813	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
814	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
815	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
816	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
817	Indx[anneal.GetId()] = [i,fmt]
818	line3Sizer.Add(anneal,0,wx.ALIGN_CENTER_VERTICAL)
819	mcsaSizer.Add(line3Sizer)
820	return mcsaSizer
821
822	# UpdateGeneral execution continues here
823	if General.GetSizer():
824	General.GetSizer().Clear(True)
825	mainSizer = wx.BoxSizer(wx.VERTICAL)
826	mainSizer.Add((5,5),0)
827	mainSizer.Add(NameSizer(),0)
828	mainSizer.Add((5,5),0)
829	mainSizer.Add(CellSizer(),0)
830	mainSizer.Add((5,5),0)
831
832	Indx = {}
833	denSizer = None
834	if len(generalData['AtomTypes']):
835	denSizer = DenSizer()
836	mainSizer.Add(denSizer[0])
837	mainSizer.Add((5,5),0)
838	mainSizer.Add(ElemSizer())
839	G2gd.HorizontalLine(mainSizer,General)
840
841	mainSizer.Add(PawleySizer())
842	G2gd.HorizontalLine(mainSizer,General)
843
844	mainSizer.Add(MapSizer())
845	G2gd.HorizontalLine(mainSizer,General)
846
847	mainSizer.Add(FlipSizer())
848	G2gd.HorizontalLine(mainSizer,General)
849
850	mainSizer.Add(MCSASizer())
851	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
852	G2frame.dataFrame.SetStatusText('')
853
854	################################################################################
855	##### Atom routines
856	################################################################################
857
858	def FillAtomsGrid(Atoms):
859	'''Display the contents of the Atoms tab
860	'''
861	def RefreshAtomGrid(event):
862
863	r,c = event.GetRow(),event.GetCol()
864	if r < 0 and c < 0:
865	for row in range(Atoms.GetNumberRows()):
866	Atoms.SelectRow(row,True)
867	if r < 0: #double click on col label! Change all atoms!
868	sel = -1
869	noSkip = True
870	if Atoms.GetColLabelValue(c) == 'refine':
871	Type = generalData['Type']
872	if Type in ['nuclear','macromolecular']:
873	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
874	elif Type in ['magnetic',]:
875	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
876	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
877	if dlg.ShowModal() == wx.ID_OK:
878	sel = dlg.GetSelections()
879	parms = ''
880	for x in sel:
881	parms += choice[x][0]
882	dlg.Destroy()
883	elif Atoms.GetColLabelValue(c) == 'I/A':
884	choice = ['Isotropic','Anisotropic']
885	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
886	if dlg.ShowModal() == wx.ID_OK:
887	sel = dlg.GetSelection()
888	parms = choice[sel][0]
889	dlg.Destroy()
890	elif Atoms.GetColLabelValue(c) == 'Type':
891	choice = generalData['AtomTypes']
892	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
893	if dlg.ShowModal() == wx.ID_OK:
894	sel = dlg.GetSelection()
895	parms = choice[sel]
896	noSkip = False
897	Atoms.ClearSelection()
898	for row in range(Atoms.GetNumberRows()):
899	if parms == atomData[row][c]:
900	Atoms.SelectRow(row,True)
901	dlg.Destroy()
902	SetupGeneral()
903	elif Atoms.GetColLabelValue(c) == 'residue':
904	choice = []
905	for r in range(Atoms.GetNumberRows()):
906	if str(atomData[r][c]) not in choice:
907	choice.append(str(atomData[r][c]))
908	choice.sort()
909	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
910	if dlg.ShowModal() == wx.ID_OK:
911	sel = dlg.GetSelection()
912	parms = choice[sel]
913	noSkip = False
914	Atoms.ClearSelection()
915	for row in range(Atoms.GetNumberRows()):
916	if parms == atomData[row][c]:
917	Atoms.SelectRow(row,True)
918	dlg.Destroy()
919	elif Atoms.GetColLabelValue(c) == 'res no':
920	choice = []
921	for r in range(Atoms.GetNumberRows()):
922	if str(atomData[r][c]) not in choice:
923	choice.append(str(atomData[r][c]))
924	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
925	if dlg.ShowModal() == wx.ID_OK:
926	sel = dlg.GetSelection()
927	parms = choice[sel]
928	noSkip = False
929	Atoms.ClearSelection()
930	for row in range(Atoms.GetNumberRows()):
931	if int(parms) == atomData[row][c]:
932	Atoms.SelectRow(row,True)
933	dlg.Destroy()
934	elif Atoms.GetColLabelValue(c) == 'chain':
935	choice = []
936	for r in range(Atoms.GetNumberRows()):
937	if atomData[r][c] not in choice:
938	choice.append(atomData[r][c])
939	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
940	if dlg.ShowModal() == wx.ID_OK:
941	sel = dlg.GetSelection()
942	parms = choice[sel]
943	noSkip = False
944	Atoms.ClearSelection()
945	for row in range(Atoms.GetNumberRows()):
946	if parms == atomData[row][c]:
947	Atoms.SelectRow(row,True)
948	dlg.Destroy()
949	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
950	pass #& then change all 'I' atoms
951	if sel >= 0 and noSkip:
952	ui = colLabels.index('U11')
953	us = colLabels.index('Uiso')
954	ss = colLabels.index('site sym')
955	for r in range(Atoms.GetNumberRows()):
956	ID = atomData[r][-1]
957	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
958	if parms == 'A': #'I' --> 'A'
959	Uiso = float(Atoms.GetCellValue(r,us))
960	sytsym = atomData[r][ss]
961	CSI = G2spc.GetCSuinel(sytsym)
962	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
963	atomData[r][us] = 0.0
964	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
965	for i in range(6):
966	ci = ui+i
967	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
968	if CSI[2][i]:
969	Atoms.SetCellStyle(r,ci,WHITE,False)
970	else: #'A' --> 'I'
971	Uij = atomData[r][ui:ui+6]
972	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
973	atomData[r][us] = Uiso
974	Atoms.SetCellStyle(r,us,WHITE,False)
975	for i in range(6):
976	ci = ui+i
977	atomData[r][ci] = 0.0
978	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
979	if not Atoms.IsReadOnly(r,c):
980	if Atoms.GetColLabelValue(c) == 'refine':
981	rbExcl = rbAtmDict.get(atomData[r][-1],'')
982	if rbExcl:
983	for excl in rbExcl:
984	atomData[r][c] = parms.replace(excl,'')
985	else:
986	atomData[r][c] = parms
987	else:
988	atomData[r][c] = parms
989	if 'Atoms' in data['Drawing']:
990	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
991	wx.CallAfter(Paint)
992
993	def ChangeAtomCell(event):
994
995	def chkUij(Uij,CSI): #needs to do something!!!
996	return Uij
997
998	r,c = event.GetRow(),event.GetCol()
999	if r >= 0 and c >= 0:
1000	ID = atomData[r][-1]
1001	if Atoms.GetColLabelValue(c) in ['x','y','z']:
1002	ci = colLabels.index('x')
1003	XYZ = atomData[r][ci:ci+3]
1004	if None in XYZ:
1005	XYZ = [0,0,0]
1006	SScol = colLabels.index('site sym')
1007	Mulcol = colLabels.index('mult')
1008	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1009	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
1010	atomData[r][SScol] = Sytsym
1011	atomData[r][Mulcol] = Mult
1012	if atomData[r][colLabels.index('I/A')] == 'A':
1013	ui = colLabels.index('U11')
1014	CSI = G2spc.GetCSuinel(Sytsym)
1015	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
1016	for i in range(6):
1017	ci = i+ui
1018	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1019	if CSI[2][i]:
1020	Atoms.SetCellStyle(r,ci,WHITE,False)
1021	SetupGeneral()
1022	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1023	if atomData[r][c] == 'I':
1024	Uij = atomData[r][c+2:c+8]
1025	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1026	Atoms.SetCellStyle(r,c+1,WHITE,False)
1027	Atoms.SetCellTextColour(r,c+1,BLACK)
1028	for i in range(6):
1029	ci = i+colLabels.index('U11')
1030	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1031	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1032	atomData[r][ci] = 0.0
1033	else:
1034	value = atomData[r][c+1]
1035	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1036	atomData[r][c+1] = 0.0
1037	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1038	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1039	for i in range(6):
1040	ci = i+colLabels.index('U11')
1041	atomData[r][ci] = value*CSI[3][i]
1042	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1043	Atoms.SetCellTextColour(r,ci,BLACK)
1044	if CSI[2][i]:
1045	Atoms.SetCellStyle(r,ci,WHITE,False)
1046	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1047	value = atomData[r][c]
1048	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1049	iUij = CSI[0][c-colLabels.index('U11')]
1050	for i in range(6):
1051	if iUij == CSI[0][i]:
1052	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1053	elif Atoms.GetColLabelValue(c) == 'refine':
1054	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1055	if 'Atoms' in data['Drawing']:
1056	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1057	wx.CallAfter(Paint)
1058
1059	def AtomTypeSelect(event):
1060	r,c = event.GetRow(),event.GetCol()
1061	if Atoms.GetColLabelValue(c) == 'Type':
1062	PE = G2elemGUI.PickElement(G2frame)
1063	if PE.ShowModal() == wx.ID_OK:
1064	if PE.Elem != 'None':
1065	atomData[r][c] = PE.Elem.strip()
1066	name = atomData[r][c]
1067	if len(name) in [2,4]:
1068	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1069	else:
1070	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1071	PE.Destroy()
1072	SetupGeneral()
1073	wx.CallAfter(Paint)
1074	value = Atoms.GetCellValue(r,c)
1075	atomData[r][c] = value
1076	ID = atomData[r][-1]
1077	if 'Atoms' in data['Drawing']:
1078	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1079	SetupGeneral()
1080	else:
1081	event.Skip()
1082
1083	def RowSelect(event):
1084	r,c = event.GetRow(),event.GetCol()
1085	if not event.AltDown():
1086	Atoms.frm = -1
1087	G2frame.dataFrame.SetStatusText('')
1088	if r < 0 and c < 0:
1089	if Atoms.IsSelection():
1090	Atoms.ClearSelection()
1091	elif c < 0: #only row clicks
1092	if event.ControlDown():
1093	if r in Atoms.GetSelectedRows():
1094	Atoms.DeselectRow(r)
1095	else:
1096	Atoms.SelectRow(r,True)
1097	elif event.ShiftDown():
1098	indxs = Atoms.GetSelectedRows()
1099	Atoms.ClearSelection()
1100	ibeg = 0
1101	if indxs:
1102	ibeg = indxs[-1]
1103	for row in range(ibeg,r+1):
1104	Atoms.SelectRow(row,True)
1105	elif event.AltDown():
1106	if atomData[r][-1] in rbAtmDict:
1107	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1108	Atoms.frm = -1
1109	Atoms.ClearSelection()
1110	else:
1111	if Atoms.frm < 0: #pick atom to be moved
1112	Atoms.frm = r
1113	Atoms.SelectRow(r,True)
1114	n = colLabels.index('Name')
1115	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1116	else: #move it
1117	item = atomData.pop(Atoms.frm)
1118	atomData.insert(r,item)
1119	Atoms.frm = -1
1120	G2frame.dataFrame.SetStatusText('')
1121	wx.CallAfter(Paint)
1122	else:
1123	Atoms.ClearSelection()
1124	Atoms.SelectRow(r,True)
1125
1126	def ChangeSelection(event):
1127	r,c = event.GetRow(),event.GetCol()
1128	if r < 0 and c < 0:
1129	Atoms.ClearSelection()
1130	if c < 0:
1131	if r in Atoms.GetSelectedRows():
1132	Atoms.DeselectRow(r)
1133	else:
1134	Atoms.SelectRow(r,True)
1135	if r < 0:
1136	if c in Atoms.GetSelectedCols():
1137	Atoms.DeselectCol(c)
1138	else:
1139	Atoms.SelectCol(c,True)
1140
1141	def Paint():
1142
1143	table = []
1144	rowLabels = []
1145	for i,atom in enumerate(atomData):
1146	table.append(atom)
1147	rowLabels.append(str(i))
1148	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1149	Atoms.SetTable(atomTable, True)
1150	Atoms.frm = -1
1151	colType = colLabels.index('Type')
1152	colR = colLabels.index('refine')
1153	colSS = colLabels.index('site sym')
1154	colX = colLabels.index('x')
1155	colIA = colLabels.index('I/A')
1156	colU11 = colLabels.index('U11')
1157	colUiso = colLabels.index('Uiso')
1158	attr = wx.grid.GridCellAttr()
1159	attr.IncRef() #fix from Jim Hester
1160	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1161	for c in range(colX,colX+3):
1162	Atoms.SetColAttr(c, attr)
1163	for i in range(colU11-1,colU11+6):
1164	Atoms.SetColSize(i,50)
1165	for row in range(Atoms.GetNumberRows()):
1166	atId = atomData[row][-1]
1167	rbExcl = rbAtmDict.get(atId,'')
1168	Atoms.SetReadOnly(row,colSS,True) #site sym
1169	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1170	if Atoms.GetCellValue(row,colIA) == 'A':
1171	CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')])
1172	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1173	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1174	for i in range(6):
1175	ci = colU11+i
1176	Atoms.SetCellTextColour(row,ci,BLACK)
1177	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1178	if CSI[2][i] and 'U' not in rbExcl:
1179	Atoms.SetCellStyle(row,ci,WHITE,False)
1180	else:
1181	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1182	Atoms.SetCellTextColour(row,colUiso,BLACK)
1183	if 'U' in rbExcl:
1184	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1185	for i in range(6):
1186	ci = colU11+i
1187	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1188	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1189	if 'X' in rbExcl:
1190	for c in range(0,colX+3):
1191	if c != colR:
1192	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1193	Atoms.AutoSizeColumns(False)
1194
1195	# FillAtomsGrid executable code starts here
1196	generalData = data['General']
1197	atomData = data['Atoms']
1198	DData = data['Drawing']
1199	resRBData = data['RBModels'].get('Residue',[])
1200	vecRBData = data['RBModels'].get('Vector',[])
1201	rbAtmDict = {}
1202	for rbObj in resRBData+vecRBData:
1203	exclList = ['X' for i in range(len(rbObj['Ids']))]
1204	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1205	if rbObj['ThermalMotion'][0] != 'None':
1206	for id in rbObj['Ids']:
1207	rbAtmDict[id] += 'U'
1208	# exclList will be 'x' or 'xu' if TLS used in RB
1209	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1210	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1211	if atomData:
1212	for item in Items:
1213	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1214	else:
1215	for item in Items:
1216	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1217	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1218	if 'showABC' in data['Drawing']:
1219	for item in Items:
1220	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1221	else:
1222	for item in Items:
1223	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1224
1225	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1226	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1227	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1228	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1229	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1230	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1231	if generalData['Type'] == 'magnetic':
1232	colLabels += ['Mx','My','Mz']
1233	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1234	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1235	elif generalData['Type'] == 'macromolecular':
1236	colLabels = ['res no','residue','chain'] + colLabels
1237	Types = [wg.GRID_VALUE_STRING,
1238	wg.GRID_VALUE_CHOICE+AAchoice,
1239	wg.GRID_VALUE_STRING] + Types
1240	elif generalData['Type'] == 'modulated':
1241	Types += []
1242	colLabels += []
1243	SGData = data['General']['SGData']
1244	G2frame.dataFrame.SetStatusText('')
1245	if SGData['SGPolax']:
1246	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1247	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1248	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1249	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1250	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1251	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1252	Atoms.SetMargins(0,0)
1253
1254	G2frame.dataFrame.setSizePosLeft([700,300])
1255	Paint()
1256
1257	def OnAtomAdd(event):
1258	AtomAdd(0,0,0)
1259	FillAtomsGrid(Atoms)
1260	event.StopPropagation()
1261	if data['Drawing']:
1262	G2plt.PlotStructure(G2frame,data)
1263
1264	def OnAtomViewAdd(event):
1265	try:
1266	drawData = data['Drawing']
1267	x,y,z = drawData['viewPoint'][0]
1268	AtomAdd(x,y,z)
1269	except:
1270	AtomAdd(0,0,0)
1271	FillAtomsGrid(Atoms)
1272	event.StopPropagation()
1273	G2plt.PlotStructure(G2frame,data)
1274
1275	def AtomAdd(x,y,z,El='H',Name='UNK'):
1276	atomData = data['Atoms']
1277	generalData = data['General']
1278	Ncol = Atoms.GetNumberCols()
1279	atId = ran.randint(0,sys.maxint)
1280	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1281	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1282	if generalData['Type'] == 'macromolecular':
1283	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1284	elif generalData['Type'] == 'nuclear':
1285	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1286	elif generalData['Type'] == 'magnetic':
1287	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1288	SetupGeneral()
1289	if 'Atoms' in data['Drawing']:
1290	DrawAtomAdd(data['Drawing'],atomData[-1])
1291
1292	def OnAtomInsert(event):
1293	AtomInsert(0,0,0)
1294	FillAtomsGrid(Atoms)
1295	event.StopPropagation()
1296	G2plt.PlotStructure(G2frame,data)
1297
1298	def OnAtomViewInsert(event):
1299	if 'Drawing' in data:
1300	drawData = data['Drawing']
1301	x,y,z = drawData['viewPoint'][0]
1302	AtomAdd(x,y,z)
1303	FillAtomsGrid(Atoms)
1304	event.StopPropagation()
1305
1306	def OnAtomMove(event):
1307	drawData = data['Drawing']
1308	atomData = data['Atoms']
1309	x,y,z = drawData['viewPoint'][0]
1310	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1311	cx = colLabels.index('x')
1312	indx = Atoms.GetSelectedRows()
1313	if len(indx) != 1:
1314	print '** ERROR - only one atom can be moved **'
1315	elif atomData[indx[0]][-1] in rbAtmDict:
1316	print '** ERROR - Atoms in rigid bodies can not be moved **'
1317	else:
1318	atomData[indx[0]][cx:cx+3] = [x,y,z]
1319	SetupGeneral()
1320	FillAtomsGrid(Atoms)
1321	ID = atomData[indx[0]][-1]
1322	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1323	G2plt.PlotStructure(G2frame,data)
1324	event.StopPropagation()
1325
1326	def DrawAtomsReplaceByID(drawingData,atom,ID):
1327	IDs = [ID,]
1328	atomData = drawingData['Atoms']
1329	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1330	for ind in indx:
1331	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1332
1333	def MakeDrawAtom(atom,oldatom=None):
1334	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1335	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1336	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1337	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1338	generalData = data['General']
1339	SGData = generalData['SGData']
1340	if generalData['Type'] == 'nuclear':
1341	if oldatom:
1342	opr = oldatom[5]
1343	if atom[9] == 'A':
1344	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1345	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1346	else:
1347	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1348	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1349	else:
1350	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1351	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1352	ct,cs = [1,8] #type & color
1353	elif generalData['Type'] == 'macromolecular':
1354	try:
1355	oneLetter = AA3letter.index(atom[1])
1356	except ValueError:
1357	oneLetter = -1
1358	atomInfo = [[atom[1].strip()+atom[0],]+
1359	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1360	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1361	ct,cs = [4,11] #type & color
1362	elif generalData['Type'] == 'magnetic':
1363	if oldatom:
1364	atomInfo = [atom[:2]+oldatom[3:]][0]
1365	else:
1366	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1367	ct,cs = [1,8] #type & color
1368	# elif generalData['Type'] == 'modulated':
1369	# ????? for future
1370	atNum = generalData['AtomTypes'].index(atom[ct])
1371	atomInfo[cs] = list(generalData['Color'][atNum])
1372	return atomInfo
1373
1374	def AtomInsert(x,y,z):
1375	indx = Atoms.GetSelectedRows()
1376	if indx:
1377	indx = indx[0]
1378	atomData = data['Atoms']
1379	generalData = data['General']
1380	Ncol = Atoms.GetNumberCols()
1381	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1382	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1383	atId = ran.randint(0,sys.maxint)
1384	if generalData['Type'] == 'macromolecular':
1385	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1386	elif generalData['Type'] == 'nuclear':
1387	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1388	elif generalData['Type'] == 'magnetic':
1389	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1390	SetupGeneral()
1391
1392	def AtomDelete(event):
1393	indx = Atoms.GetSelectedRows()
1394	IDs = []
1395	if indx:
1396	atomData = data['Atoms']
1397	indx.reverse()
1398	for ind in indx:
1399	atom = atomData[ind]
1400	if atom[-1] in rbAtmDict:
1401	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1402	else:
1403	IDs.append(atom[-1])
1404	del atomData[ind]
1405	if 'Atoms' in data['Drawing']:
1406	DrawAtomsDeleteByIDs(IDs)
1407	wx.CallAfter(FillAtomsGrid,Atoms)
1408	G2plt.PlotStructure(G2frame,data)
1409	SetupGeneral()
1410	event.StopPropagation()
1411
1412	def AtomRefine(event):
1413	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1414	c = colLabels.index('refine')
1415	indx = Atoms.GetSelectedRows()
1416	if indx:
1417	atomData = data['Atoms']
1418	generalData = data['General']
1419	Type = generalData['Type']
1420	if Type in ['nuclear','macromolecular']:
1421	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1422	elif Type == 'magnetic':
1423	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1424	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1425	if dlg.ShowModal() == wx.ID_OK:
1426	sel = dlg.GetSelections()
1427	parms = ''
1428	for x in sel:
1429	parms += choice[x][0]
1430	for r in indx:
1431	if not Atoms.IsReadOnly(r,c):
1432	atomData[r][c] = parms
1433	Atoms.ForceRefresh()
1434	dlg.Destroy()
1435
1436	def AtomModify(event):
1437	indx = Atoms.GetSelectedRows()
1438	if indx:
1439	atomData = data['Atoms']
1440	generalData = data['General']
1441	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1442	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1443	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1444	parm = ''
1445	if dlg.ShowModal() == wx.ID_OK:
1446	sel = dlg.GetSelection()
1447	parm = choices[sel]
1448	cid = colLabels.index(parm)
1449	dlg.Destroy()
1450	if parm in ['Type']:
1451	dlg = G2elemGUI.PickElement(G2frame)
1452	if dlg.ShowModal() == wx.ID_OK:
1453	if dlg.Elem not in ['None']:
1454	El = dlg.Elem.strip()
1455	for r in indx:
1456	if not Atoms.IsReadOnly(r,cid):
1457	atomData[r][cid] = El
1458	if len(El) in [2,4]:
1459	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1460	else:
1461	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1462	SetupGeneral()
1463	if 'Atoms' in data['Drawing']:
1464	for r in indx:
1465	ID = atomData[r][-1]
1466	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1467	FillAtomsGrid(Atoms)
1468	dlg.Destroy()
1469	elif parm in ['Name',]:
1470	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1471	wx.YES_NO \| wx.ICON_QUESTION)
1472	try:
1473	result = dlg.ShowModal()
1474	if result == wx.ID_YES:
1475	for r in indx:
1476	if not Atoms.IsReadOnly(r,cid+1):
1477	El = atomData[r][cid+1]
1478	if len(El) in [2,4]:
1479	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1480	else:
1481	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1482	FillAtomsGrid(Atoms)
1483	finally:
1484	dlg.Destroy()
1485
1486	elif parm in ['I/A']:
1487	choices = ['Isotropic','Anisotropic']
1488	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1489	if dlg.ShowModal() == wx.ID_OK:
1490	sel = dlg.GetSelection()
1491	parm = choices[sel][0]
1492	for r in indx:
1493	if not Atoms.IsReadOnly(r,cid):
1494	atomData[r][cid] = parm
1495	FillAtomsGrid(Atoms)
1496	dlg.Destroy()
1497	elif parm in ['frac','Uiso']:
1498	limits = [0.,1.]
1499	val = 1.0
1500	if parm in ['Uiso']:
1501	limits = [0.,0.25]
1502	val = 0.01
1503	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1504	if dlg.ShowModal() == wx.ID_OK:
1505	parm = dlg.GetValue()
1506	for r in indx:
1507	if not Atoms.IsReadOnly(r,cid):
1508	atomData[r][cid] = parm
1509	SetupGeneral()
1510	FillAtomsGrid(Atoms)
1511	dlg.Destroy()
1512	elif parm in ['x','y','z']:
1513	limits = [-1.,1.]
1514	val = 0.
1515	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1516	if dlg.ShowModal() == wx.ID_OK:
1517	parm = dlg.GetValue()
1518	for r in indx:
1519	if not Atoms.IsReadOnly(r,cid):
1520	atomData[r][cid] += parm
1521	SetupGeneral()
1522	FillAtomsGrid(Atoms)
1523	dlg.Destroy()
1524
1525	def AtomTransform(event):
1526	indx = Atoms.GetSelectedRows()
1527	if indx:
1528	generalData = data['General']
1529	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1530	cx = colLabels.index('x')
1531	cuia = colLabels.index('I/A')
1532	cuij = colLabels.index('U11')
1533	css = colLabels.index('site sym')
1534	atomData = data['Atoms']
1535	generalData = data['General']
1536	SGData = generalData['SGData']
1537	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1538	New = False
1539	try:
1540	if dlg.ShowModal() == wx.ID_OK:
1541	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1542	Cell = np.array(Cell)
1543	cent = SGData['SGCen'][Cent]
1544	M,T = SGData['SGOps'][Opr]
1545	for ind in indx:
1546	XYZ = np.array(atomData[ind][cx:cx+3])
1547	XYZ = np.inner(M,XYZ)+T
1548	if Inv:
1549	XYZ = -XYZ
1550	XYZ = XYZ+cent+Cell
1551	if Force:
1552	XYZ = G2spc.MoveToUnitCell(XYZ)
1553	if New:
1554	atom = copy.copy(atomData[ind])
1555	else:
1556	atom = atomData[ind]
1557	atom[cx:cx+3] = XYZ
1558	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1559	if atom[cuia] == 'A':
1560	Uij = atom[cuij:cuij+6]
1561	U = G2spc.Uij2U(Uij)
1562	U = np.inner(np.inner(M,U),M)
1563	Uij = G2spc.U2Uij(U)
1564	atom[cuij:cuij+6] = Uij
1565	if New:
1566	atomData.append(atom)
1567	finally:
1568	dlg.Destroy()
1569	Atoms.ClearSelection()
1570	if New:
1571	FillAtomsGrid(Atoms)
1572	else:
1573	Atoms.ForceRefresh()
1574
1575	def OnDistAnglePrt(event):
1576	fp = file(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile
1577	)[0]+'.disagl'),'w')
1578	OnDistAngle(event,fp=fp)
1579	fp.close()
1580
1581	def OnDistAngle(event,fp=None):
1582	indx = Atoms.GetSelectedRows()
1583	Oxyz = []
1584	xyz = []
1585	DisAglData = {}
1586	DisAglCtls = {}
1587	if indx:
1588	generalData = data['General']
1589	DisAglData['OrigIndx'] = indx
1590	if 'DisAglCtls' in generalData:
1591	DisAglCtls = generalData['DisAglCtls']
1592	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1593	if dlg.ShowModal() == wx.ID_OK:
1594	DisAglCtls = dlg.GetData()
1595	else:
1596	dlg.Destroy()
1597	return
1598	dlg.Destroy()
1599	generalData['DisAglCtls'] = DisAglCtls
1600	atomData = data['Atoms']
1601	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1602	cx = colLabels.index('x')
1603	cn = colLabels.index('Name')
1604	for i,atom in enumerate(atomData):
1605	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1606	if i in indx:
1607	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1608	DisAglData['OrigAtoms'] = Oxyz
1609	DisAglData['TargAtoms'] = xyz
1610	generalData = data['General']
1611	DisAglData['SGData'] = generalData['SGData']
1612	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1613	if 'pId' in data:
1614	DisAglData['pId'] = data['pId']
1615	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1616	try:
1617	if fp:
1618	G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
1619	else:
1620	G2stMn.PrintDistAngle(DisAglCtls,DisAglData)
1621	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1622	G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types')
1623	else:
1624	print "select one or more rows of atoms"
1625	G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
1626
1627	def OnReImport(event):
1628	generalData = data['General']
1629	cx,ct,cs,cia = generalData['AtomPtrs']
1630	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1631	rdlist = G2frame.OnImportGeneric(reqrdr,
1632	G2frame.ImportPhaseReaderlist,'phase')
1633	if len(rdlist) == 0: return
1634	# rdlist is only expected to have one element
1635	rd = rdlist[0]
1636	G2frame.OnFileSave(event)
1637	# rd contains all info for a phase
1638	PhaseName = rd.Phase['General']['Name']
1639	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1640	atomData = data['Atoms']
1641	atomNames = []
1642	for atom in atomData:
1643	atomNames.append(atom[:ct+1])
1644	for atom in rd.Phase['Atoms']:
1645	try:
1646	idx = atomNames.index(atom[:ct+1])
1647	atomData[idx][:-1] = atom[:-1]
1648	except ValueError:
1649	print atom[:ct+1], 'not in Atom array; not updated'
1650	wx.CallAfter(FillAtomsGrid,Atoms)
1651
1652
1653	################################################################################
1654	#Structure drawing GUI stuff
1655	################################################################################
1656
1657	def SetupDrawingData():
1658	generalData = data['General']
1659	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1660	atomData = data['Atoms']
1661	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1662	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1663	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1664	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1665	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1666	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1667	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1668	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1669	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1670	'bondList':{},'viewDir':[1,0,0]}
1671	V0 = np.array([0,0,1])
1672	V = np.inner(Amat,V0)
1673	V /= np.sqrt(np.sum(V**2))
1674	A = np.arccos(np.sum(V*V0))
1675	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1676	try:
1677	drawingData = data['Drawing']
1678	except KeyError:
1679	data['Drawing'] = {}
1680	drawingData = data['Drawing']
1681	if not drawingData: #fill with defaults if empty
1682	drawingData.update(defaultDrawing)
1683	if 'Zstep' not in drawingData:
1684	drawingData['Zstep'] = 0.5
1685	if 'contourLevel' not in drawingData:
1686	drawingData['contourLevel'] = 1.
1687	if 'viewDir' not in drawingData:
1688	drawingData['viewDir'] = [0,0,1]
1689	if 'Quaternion' not in drawingData:
1690	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1691	if 'showRigidBodies' not in drawingData:
1692	drawingData['showRigidBodies'] = True
1693	cx,ct,cs,ci = [0,0,0,0]
1694	if generalData['Type'] == 'nuclear':
1695	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1696	elif generalData['Type'] == 'macromolecular':
1697	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1698	elif generalData['Type'] == 'magnetic':
1699	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1700	# elif generalData['Type'] == 'modulated':
1701	# ????? for future
1702	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1703	if not drawingData.get('Atoms'):
1704	for atom in atomData:
1705	DrawAtomAdd(drawingData,atom)
1706	data['Drawing'] = drawingData
1707
1708	def DrawAtomAdd(drawingData,atom):
1709	drawingData['Atoms'].append(MakeDrawAtom(atom))
1710
1711	def OnRestraint(event):
1712	indx = drawAtoms.GetSelectedRows()
1713	restData = G2frame.PatternTree.GetItemPyData(
1714	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1715	drawingData = data['Drawing']
1716	generalData = data['General']
1717	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1718	cx,ct,cs,ci = drawingData['atomPtrs']
1719	atomData = drawingData['Atoms']
1720	atNames = []
1721	atXYZ = []
1722	atSymOp = []
1723	atIndx = []
1724	for item in indx:
1725	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1726	atSymOp.append(atomData[item][cs-1])
1727	atIndx.append(atomData[item][ci])
1728	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1729	try:
1730	bondData = restData[PhaseName]['Bond']
1731	except KeyError:
1732	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1733	restData[PhaseName] = {}
1734	restData[PhaseName]['Bond'] = bondData
1735	dist = G2mth.getRestDist(atXYZ,Amat)
1736	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1737	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1738	try:
1739	angleData = restData[PhaseName]['Angle']
1740	except KeyError:
1741	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1742	restData[PhaseName] = {}
1743	restData[PhaseName]['Angle'] = angleData
1744	angle = G2mth.getRestAngle(atXYZ,Amat)
1745	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1746	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1747	try:
1748	planeData = restData[PhaseName]['Plane']
1749	except KeyError:
1750	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1751	restData[PhaseName] = {}
1752	restData[PhaseName]['Plane'] = planeData
1753	plane = G2mth.getRestPlane(atXYZ,Amat)
1754	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1755	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1756	try:
1757	chiralData = restData[PhaseName]['Chiral']
1758	except KeyError:
1759	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1760	restData[PhaseName] = {}
1761	restData[PhaseName]['Chiral'] = chiralData
1762	volume = G2mth.getRestChiral(atXYZ,Amat)
1763	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1764	else:
1765	print '**** ERROR wrong number of atoms selected for this restraint'
1766	return
1767	G2frame.PatternTree.SetItemPyData(
1768	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1769
1770	def OnDefineRB(event):
1771	indx = drawAtoms.GetSelectedRows()
1772	indx.sort()
1773	RBData = G2frame.PatternTree.GetItemPyData(
1774	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1775	drawingData = data['Drawing']
1776	generalData = data['General']
1777	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1778	cx,ct,cs,ci = drawingData['atomPtrs']
1779	atomData = drawingData['Atoms']
1780	rbXYZ = []
1781	rbType = []
1782	atNames = []
1783	AtInfo = RBData['Residue']['AtInfo']
1784	for i,item in enumerate(indx):
1785	rbtype = atomData[item][ct]
1786	atNames.append(rbtype+str(i))
1787	rbType.append(rbtype)
1788	if rbtype not in AtInfo:
1789	Info = G2elem.GetAtomInfo(rbtype)
1790	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1791	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1792	rbXYZ = np.array(rbXYZ)
1793	rbXYZ -= rbXYZ[0]
1794	rbId = ran.randint(0,sys.maxint)
1795	rbName = 'UNKRB'
1796	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1797	'Edit rigid body name',rbName ,style=wx.OK)
1798	if dlg.ShowModal() == wx.ID_OK:
1799	rbName = dlg.GetValue()
1800	dlg.Destroy()
1801	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1802	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1803	RBData['RBIds']['Residue'].append(rbId)
1804	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1805
1806	################################################################################
1807	##### Atom draw routines
1808	################################################################################
1809
1810	def UpdateDrawAtoms(atomStyle=''):
1811	def RefreshAtomGrid(event):
1812	def SetChoice(name,c,n=0):
1813	choice = []
1814	for r in range(len(atomData)):
1815	if n:
1816	srchStr = str(atomData[r][c][:n])
1817	else:
1818	srchStr = str(atomData[r][c])
1819	if srchStr not in choice:
1820	if n:
1821	choice.append(str(atomData[r][c][:n]))
1822	else:
1823	choice.append(str(atomData[r][c]))
1824	choice.sort()
1825
1826	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
1827	if dlg.ShowModal() == wx.ID_OK:
1828	sel = dlg.GetSelections()
1829	parms = []
1830	for x in sel:
1831	parms.append(choice[x])
1832	noSkip = False
1833	drawAtoms.ClearSelection()
1834	drawingData['selectedAtoms'] = []
1835	for row in range(len(atomData)):
1836	test = atomData[row][c]
1837	if n:
1838	test = test[:n]
1839	if test in parms:
1840	drawAtoms.SelectRow(row,True)
1841	drawingData['selectedAtoms'].append(row)
1842	G2plt.PlotStructure(G2frame,data)
1843	dlg.Destroy()
1844
1845	r,c = event.GetRow(),event.GetCol()
1846	if r < 0 and c < 0:
1847	for row in range(drawAtoms.GetNumberRows()):
1848	drawingData['selectedAtoms'].append(row)
1849	drawAtoms.SelectRow(row,True)
1850	elif r < 0: #dclick on col label
1851	sel = -1
1852	Parms = False
1853	noSkip = True
1854	if drawAtoms.GetColLabelValue(c) == 'Style':
1855	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1856	if dlg.ShowModal() == wx.ID_OK:
1857	sel = dlg.GetSelection()
1858	parms = styleChoice[sel]
1859	for r in range(len(atomData)):
1860	atomData[r][c] = parms
1861	drawAtoms.SetCellValue(r,c,parms)
1862	FindBondsDraw()
1863	G2plt.PlotStructure(G2frame,data)
1864	dlg.Destroy()
1865	elif drawAtoms.GetColLabelValue(c) == 'Label':
1866	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
1867	if dlg.ShowModal() == wx.ID_OK:
1868	sel = dlg.GetSelection()
1869	parms = labelChoice[sel]
1870	for r in range(len(atomData)):
1871	atomData[r][c] = parms
1872	drawAtoms.SetCellValue(r,c,parms)
1873	dlg.Destroy()
1874	elif drawAtoms.GetColLabelValue(c) == 'Color':
1875	dlg = wx.ColourDialog(G2frame)
1876	if dlg.ShowModal() == wx.ID_OK:
1877	color = dlg.GetColourData().GetColour()
1878	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1879	attr.SetReadOnly(True)
1880	attr.SetBackgroundColour(color)
1881	for r in range(len(atomData)):
1882	atomData[r][c] = color
1883	drawingData['Atoms'][r][c] = color
1884	drawAtoms.SetAttr(r,c,attr)
1885	UpdateDrawAtoms()
1886	dlg.Destroy()
1887	elif drawAtoms.GetColLabelValue(c) == 'Residue':
1888	SetChoice('Residue',c,3)
1889	elif drawAtoms.GetColLabelValue(c) == '1-letter':
1890	SetChoice('1-letter',c,1)
1891	elif drawAtoms.GetColLabelValue(c) == 'Chain':
1892	SetChoice('Chain',c)
1893	elif drawAtoms.GetColLabelValue(c) == 'Name':
1894	SetChoice('Name',c)
1895	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
1896	SetChoice('Name',c)
1897	elif drawAtoms.GetColLabelValue(c) == 'Type':
1898	SetChoice('Type',c)
1899	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
1900	drawAtoms.ClearSelection()
1901	else:
1902	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
1903	atomData[r][c] = drawAtoms.GetCellValue(r,c)
1904	FindBondsDraw()
1905	elif drawAtoms.GetColLabelValue(c) == 'Color':
1906	dlg = wx.ColourDialog(G2frame)
1907	if dlg.ShowModal() == wx.ID_OK:
1908	color = dlg.GetColourData().GetColour()
1909	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1910	attr.SetReadOnly(True)
1911	attr.SetBackgroundColour(color)
1912	atomData[r][c] = color
1913	drawingData['Atoms'][r][c] = color
1914	drawAtoms.SetAttr(i,cs+2,attr)
1915	dlg.Destroy()
1916	UpdateDrawAtoms()
1917	G2plt.PlotStructure(G2frame,data)
1918
1919	def RowSelect(event):
1920	r,c = event.GetRow(),event.GetCol()
1921	if r < 0 and c < 0:
1922	if drawAtoms.IsSelection():
1923	drawAtoms.ClearSelection()
1924	elif c < 0: #only row clicks
1925	if event.ControlDown():
1926	if r in drawAtoms.GetSelectedRows():
1927	drawAtoms.DeselectRow(r)
1928	else:
1929	drawAtoms.SelectRow(r,True)
1930	elif event.ShiftDown():
1931	indxs = drawAtoms.GetSelectedRows()
1932	drawAtoms.ClearSelection()
1933	ibeg = 0
1934	if indxs:
1935	ibeg = indxs[-1]
1936	for row in range(ibeg,r+1):
1937	drawAtoms.SelectRow(row,True)
1938	else:
1939	drawAtoms.ClearSelection()
1940	drawAtoms.SelectRow(r,True)
1941	drawingData['selectedAtoms'] = []
1942	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
1943	G2plt.PlotStructure(G2frame,data)
1944
1945	# UpdateDrawAtoms executable code starts here
1946	G2frame.dataFrame.SetStatusText('')
1947	generalData = data['General']
1948	SetupDrawingData()
1949	drawingData = data['Drawing']
1950	cx,ct,cs,ci = drawingData['atomPtrs']
1951	atomData = drawingData['Atoms']
1952	if atomStyle:
1953	for atom in atomData:
1954	atom[cs] = atomStyle
1955	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
1956	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
1957	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
1958	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1959	labelChoice = [' ','type','name','number']
1960	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
1961	if generalData['Type'] == 'macromolecular':
1962	colLabels = ['Residue','1-letter','Chain'] + colLabels
1963	Types = 3*[wg.GRID_VALUE_STRING,]+Types
1964	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
1965	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
1966	labelChoice = [' ','type','name','number','residue','1-letter','chain']
1967	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
1968	# elif generalData['Type'] == 'modulated':
1969	# Types += []
1970	# colLabels += []
1971	table = []
1972	rowLabels = []
1973	for i,atom in enumerate(drawingData['Atoms']):
1974	table.append(atom[:colLabels.index('I/A')+1])
1975	rowLabels.append(str(i))
1976
1977	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1978	drawAtoms.SetTable(atomTable, True)
1979	drawAtoms.SetMargins(0,0)
1980	drawAtoms.AutoSizeColumns(True)
1981	drawAtoms.SetColSize(colLabels.index('Style'),80)
1982	drawAtoms.SetColSize(colLabels.index('Color'),50)
1983	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
1984	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1985	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
1986	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1987	for i,atom in enumerate(drawingData['Atoms']):
1988	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1989	attr.SetReadOnly(True)
1990	attr.SetBackgroundColour(atom[cs+2])
1991	drawAtoms.SetAttr(i,cs+2,attr)
1992	drawAtoms.SetCellValue(i,cs+2,'')
1993	indx = drawingData['selectedAtoms']
1994	if indx:
1995	for r in range(len(atomData)):
1996	if r in indx:
1997	drawAtoms.SelectRow(r)
1998	for c in range(len(colLabels)):
1999	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2000	attr.SetReadOnly(True)
2001	attr.SetBackgroundColour(VERY_LIGHT_GREY)
2002	if colLabels[c] not in ['Style','Label','Color']:
2003	drawAtoms.SetColAttr(c,attr)
2004	G2frame.dataFrame.setSizePosLeft([600,300])
2005
2006	FindBondsDraw()
2007	drawAtoms.ClearSelection()
2008	# G2plt.PlotStructure(G2frame,data)
2009
2010	def DrawAtomStyle(event):
2011	indx = drawAtoms.GetSelectedRows()
2012	if indx:
2013	generalData = data['General']
2014	atomData = data['Drawing']['Atoms']
2015	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2016	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2017	if generalData['Type'] == 'macromolecular':
2018	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
2019	'backbone','ribbons','schematic']
2020	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2021	if dlg.ShowModal() == wx.ID_OK:
2022	sel = dlg.GetSelection()
2023	parms = styleChoice[sel]
2024	for r in indx:
2025	atomData[r][cs] = parms
2026	drawAtoms.SetCellValue(r,cs,parms)
2027	dlg.Destroy()
2028	FindBondsDraw()
2029	drawAtoms.ClearSelection()
2030	G2plt.PlotStructure(G2frame,data)
2031
2032	def DrawAtomLabel(event):
2033	indx = drawAtoms.GetSelectedRows()
2034	if indx:
2035	generalData = data['General']
2036	atomData = data['Drawing']['Atoms']
2037	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2038	styleChoice = [' ','type','name','number']
2039	if generalData['Type'] == 'macromolecular':
2040	styleChoice = [' ','type','name','number','residue','1-letter','chain']
2041	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
2042	if dlg.ShowModal() == wx.ID_OK:
2043	sel = dlg.GetSelection()
2044	parms = styleChoice[sel]
2045	for r in indx:
2046	atomData[r][cs+1] = parms
2047	drawAtoms.SetCellValue(r,cs+1,parms)
2048	dlg.Destroy()
2049	drawAtoms.ClearSelection()
2050	G2plt.PlotStructure(G2frame,data)
2051
2052	def DrawAtomColor(event):
2053
2054	indx = drawAtoms.GetSelectedRows()
2055	if indx:
2056	if len(indx) > 1:
2057	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2058	else:
2059	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2060	generalData = data['General']
2061	atomData = data['Drawing']['Atoms']
2062	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2063	atmColors = []
2064	atmTypes = []
2065	for r in indx:
2066	if atomData[r][cs+2] not in atmColors:
2067	atmColors.append(atomData[r][cs+2])
2068	atmTypes.append(atomData[r][ct])
2069	if len(atmColors) > 16:
2070	break
2071	colors = wx.ColourData()
2072	colors.SetChooseFull(True)
2073	dlg = wx.ColourDialog(G2frame)
2074	if dlg.ShowModal() == wx.ID_OK:
2075	for i in range(len(atmColors)):
2076	atmColors[i] = dlg.GetColourData().GetColour()
2077	colorDict = dict(zip(atmTypes,atmColors))
2078	for r in indx:
2079	color = colorDict[atomData[r][ct]]
2080	atomData[r][cs+2] = color
2081	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2082	attr.SetBackgroundColour(color)
2083	drawAtoms.SetAttr(r,cs+2,attr)
2084	data['Drawing']['Atoms'][r][cs+2] = color
2085	drawAtoms.ClearSelection()
2086	dlg.Destroy()
2087	G2frame.dataFrame.SetStatusText('')
2088	G2plt.PlotStructure(G2frame,data)
2089
2090	def ResetAtomColors(event):
2091	generalData = data['General']
2092	atomData = data['Drawing']['Atoms']
2093	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2094	for atom in atomData:
2095	atNum = generalData['AtomTypes'].index(atom[ct])
2096	atom[cs+2] = list(generalData['Color'][atNum])
2097	UpdateDrawAtoms()
2098	drawAtoms.ClearSelection()
2099	G2plt.PlotStructure(G2frame,data)
2100
2101	def SetViewPoint(event):
2102	indx = drawAtoms.GetSelectedRows()
2103	if indx:
2104	atomData = data['Drawing']['Atoms']
2105	cx = data['Drawing']['atomPtrs'][0]
2106	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2107	drawAtoms.ClearSelection() #do I really want to do this?
2108	G2plt.PlotStructure(G2frame,data)
2109
2110	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2111	cx = data['Drawing']['atomPtrs'][0]
2112	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2113	return False
2114	else:
2115	return True
2116
2117	def AddSymEquiv(event):
2118	indx = drawAtoms.GetSelectedRows()
2119	indx.sort()
2120	if indx:
2121	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2122	cx = colLabels.index('x')
2123	cuia = colLabels.index('I/A')
2124	cuij = cuia+2
2125	atomData = data['Drawing']['Atoms']
2126	generalData = data['General']
2127	SGData = generalData['SGData']
2128	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2129	try:
2130	if dlg.ShowModal() == wx.ID_OK:
2131	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2132	Cell = np.array(Cell)
2133	cent = SGData['SGCen'][Cent]
2134	M,T = SGData['SGOps'][Opr]
2135	for ind in indx:
2136	XYZ = np.array(atomData[ind][cx:cx+3])
2137	XYZ = np.inner(M,XYZ)+T
2138	if Inv:
2139	XYZ = -XYZ
2140	XYZ = XYZ+cent+Cell
2141	if Force:
2142	XYZ = G2spc.MoveToUnitCell(XYZ)
2143	if noDuplicate(XYZ,atomData):
2144	atom = copy.copy(atomData[ind])
2145	atom[cx:cx+3] = XYZ
2146	atomOp = atom[cx+3]
2147	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2148	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2149	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2150	if atom[cuia] == 'A':
2151	Uij = atom[cuij:cuij+6]
2152	U = G2spc.Uij2U(Uij)
2153	U = np.inner(np.inner(M,U),M)
2154	Uij = G2spc.U2Uij(U)
2155	atom[cuij:cuij+6] = Uij
2156	atomData.append(atom)
2157	finally:
2158	dlg.Destroy()
2159	UpdateDrawAtoms()
2160	drawAtoms.ClearSelection()
2161	G2plt.PlotStructure(G2frame,data)
2162
2163	def TransformSymEquiv(event):
2164	indx = drawAtoms.GetSelectedRows()
2165	indx.sort()
2166	if indx:
2167	atomData = data['Drawing']['Atoms']
2168	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2169	cx = colLabels.index('x')
2170	cuia = colLabels.index('I/A')
2171	cuij = cuia+2
2172	atomData = data['Drawing']['Atoms']
2173	generalData = data['General']
2174	SGData = generalData['SGData']
2175	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2176	try:
2177	if dlg.ShowModal() == wx.ID_OK:
2178	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2179	Cell = np.array(Cell)
2180	cent = SGData['SGCen'][Cent]
2181	M,T = SGData['SGOps'][Opr]
2182	for ind in indx:
2183	XYZ = np.array(atomData[ind][cx:cx+3])
2184	XYZ = np.inner(M,XYZ)+T
2185	if Inv:
2186	XYZ = -XYZ
2187	XYZ = XYZ+cent+Cell
2188	if Force:
2189	XYZ = G2spc.MoveToUnitCell(XYZ)
2190	atom = atomData[ind]
2191	atom[cx:cx+3] = XYZ
2192	atomOp = atom[cx+3]
2193	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2194	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2195	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2196	if atom[cuia] == 'A':
2197	Uij = atom[cuij:cuij+6]
2198	U = G2spc.Uij2U(Uij)
2199	U = np.inner(np.inner(M,U),M)
2200	Uij = G2spc.U2Uij(U)
2201	atom[cuij:cuij+6] = Uij
2202	data['Drawing']['Atoms'] = atomData
2203	finally:
2204	dlg.Destroy()
2205	UpdateDrawAtoms()
2206	drawAtoms.ClearSelection()
2207	G2plt.PlotStructure(G2frame,data)
2208
2209	def FillCoordSphere(event):
2210	generalData = data['General']
2211	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2212	radii = generalData['BondRadii']
2213	atomTypes = generalData['AtomTypes']
2214	try:
2215	indH = atomTypes.index('H')
2216	radii[indH] = 0.5
2217	except:
2218	pass
2219	indx = drawAtoms.GetSelectedRows()
2220	if indx:
2221	indx.sort()
2222	atomData = data['Drawing']['Atoms']
2223	numAtoms = len(atomData)
2224	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2225	generalData = data['General']
2226	SGData = generalData['SGData']
2227	cellArray = G2lat.CellBlock(1)
2228	wx.BeginBusyCursor()
2229	try:
2230	for ind in indx:
2231	atomA = atomData[ind]
2232	xyzA = np.array(atomA[cx:cx+3])
2233	indA = atomTypes.index(atomA[ct])
2234	for atomB in atomData[:numAtoms]:
2235	indB = atomTypes.index(atomB[ct])
2236	sumR = radii[indA]+radii[indB]
2237	xyzB = np.array(atomB[cx:cx+3])
2238	for xyz in cellArray+xyzB:
2239	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2240	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2241	if noDuplicate(xyz,atomData):
2242	oprB = atomB[cx+3]
2243	C = xyz-xyzB
2244	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2245	newAtom = atomB[:]
2246	newAtom[cx:cx+3] = xyz
2247	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2248	atomData.append(newAtom)
2249	finally:
2250	wx.EndBusyCursor()
2251	data['Drawing']['Atoms'] = atomData
2252	UpdateDrawAtoms()
2253	drawAtoms.ClearSelection()
2254	G2plt.PlotStructure(G2frame,data)
2255
2256	def FillUnitCell(event):
2257	indx = drawAtoms.GetSelectedRows()
2258	indx.sort()
2259	if indx:
2260	atomData = data['Drawing']['Atoms']
2261	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2262	cx = colLabels.index('x')
2263	cuia = colLabels.index('I/A')
2264	cuij = cuia+2
2265	generalData = data['General']
2266	SGData = generalData['SGData']
2267	wx.BeginBusyCursor()
2268	try:
2269	for ind in indx:
2270	atom = atomData[ind]
2271	XYZ = np.array(atom[cx:cx+3])
2272	if atom[cuia] == 'A':
2273	Uij = atom[cuij:cuij+6]
2274	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2275	for item in result:
2276	atom = copy.copy(atomData[ind])
2277	atom[cx:cx+3] = item[0]
2278	atom[cx+3] = str(item[2])+'+' \
2279	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2280	atom[cuij:cuij+6] = item[1]
2281	Opp = G2spc.Opposite(item[0])
2282	for xyz in Opp:
2283	if noDuplicate(xyz,atomData):
2284	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2285	cell = '1'+'+'+ \
2286	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2287	atom[cx:cx+3] = xyz
2288	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2289	atomData.append(atom[:])
2290	else:
2291	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2292	for item in result:
2293	atom = copy.copy(atomData[ind])
2294	atom[cx:cx+3] = item[0]
2295	atom[cx+3] = str(item[1])+'+' \
2296	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2297	Opp = G2spc.Opposite(item[0])
2298	for xyz in Opp:
2299	if noDuplicate(xyz,atomData):
2300	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2301	cell = '1'+'+'+ \
2302	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2303	atom[cx:cx+3] = xyz
2304	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2305	atomData.append(atom[:])
2306	data['Drawing']['Atoms'] = atomData
2307	finally:
2308	wx.EndBusyCursor()
2309	UpdateDrawAtoms()
2310	drawAtoms.ClearSelection()
2311	G2plt.PlotStructure(G2frame,data)
2312
2313	def FindBondsToo(): #works but slow for large structures - keep as reference
2314	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2315	atomData = data['Drawing']['Atoms']
2316	generalData = data['General']
2317	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2318	radii = generalData['BondRadii']
2319	atomTypes = generalData['AtomTypes']
2320	try:
2321	indH = atomTypes.index('H')
2322	radii[indH] = 0.5
2323	except:
2324	pass
2325	for atom in atomData:
2326	atom[-1] = []
2327	Atoms = []
2328	for i,atom in enumerate(atomData):
2329	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2330	for atomA in Atoms:
2331	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2332	for atomB in Atoms:
2333	Dx = atomB[1]-atomA[1]
2334	DX = np.inner(Amat,Dx)
2335	dist = np.sqrt(np.sum(DX**2))
2336	sumR = atomA[3]+atomB[3]
2337	if 0.5 < dist <= 0.85*sumR:
2338	i = atomA[0]
2339	if atomA[2] == 'polyhedra':
2340	atomData[i][-1].append(DX)
2341	elif atomB[1] != 'polyhedra':
2342	j = atomB[0]
2343	atomData[i][-1].append(Dx*atomA[3]/sumR)
2344	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2345
2346	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2347	import numpy.ma as ma
2348	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2349	hydro = data['Drawing']['showHydrogen']
2350	atomData = data['Drawing']['Atoms']
2351	generalData = data['General']
2352	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2353	radii = generalData['BondRadii']
2354	atomTypes = generalData['AtomTypes']
2355	try:
2356	indH = atomTypes.index('H')
2357	radii[indH] = 0.5
2358	except:
2359	pass
2360	for atom in atomData:
2361	atom[-2] = [] #clear out old bonds/polyhedra
2362	atom[-1] = []
2363	Indx = range(len(atomData))
2364	Atoms = []
2365	Styles = []
2366	Radii = []
2367	for atom in atomData:
2368	Atoms.append(np.array(atom[cx:cx+3]))
2369	Styles.append(atom[cs])
2370	try:
2371	if not hydro and atom[ct] == 'H':
2372	Radii.append(0.0)
2373	else:
2374	Radii.append(radii[atomTypes.index(atom[ct])])
2375	except ValueError: #changed atom type!
2376	Radii.append(0.20)
2377	Atoms = np.array(Atoms)
2378	Radii = np.array(Radii)
2379	IASR = zip(Indx,Atoms,Styles,Radii)
2380	for atomA in IASR:
2381	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2382	Dx = Atoms-atomA[1]
2383	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
2384	sumR = atomA[3]+Radii
2385	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2386	i = atomA[0]
2387	for j in IndB[0]:
2388	if Styles[i] == 'polyhedra':
2389	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2390	elif Styles[j] != 'polyhedra' and j > i:
2391	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2392	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2393	if Styles[i] == 'polyhedra':
2394	Bonds = atomData[i][-2]
2395	Faces = []
2396	if len(Bonds) > 2:
2397	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2398	for face in FaceGen:
2399	vol = nl.det(face)
2400	if abs(vol) > 1. or len(Bonds) == 3:
2401	if vol < 0.:
2402	face = [face[0],face[2],face[1]]
2403	face = np.array(face)
2404	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2405	norm = np.cross(face[1]-face[0],face[2]-face[0])
2406	norm /= np.sqrt(np.sum(norm**2))
2407	Faces.append([face,norm])
2408	atomData[i][-1] = Faces
2409
2410	def DrawAtomsDelete(event):
2411	indx = drawAtoms.GetSelectedRows()
2412	indx.sort()
2413	if indx:
2414	atomData = data['Drawing']['Atoms']
2415	indx.reverse()
2416	for ind in indx:
2417	del atomData[ind]
2418	UpdateDrawAtoms()
2419	drawAtoms.ClearSelection()
2420	G2plt.PlotStructure(G2frame,data)
2421	event.StopPropagation()
2422
2423	def OnReloadDrawAtoms(event):
2424	data['Drawing']['Atoms'] = []
2425	UpdateDrawAtoms()
2426	drawAtoms.ClearSelection()
2427	G2plt.PlotStructure(G2frame,data)
2428	event.StopPropagation()
2429
2430	def DrawAtomsDeleteByIDs(IDs):
2431	atomData = data['Drawing']['Atoms']
2432	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2433	indx.reverse()
2434	for ind in indx:
2435	del atomData[ind]
2436
2437	def ChangeDrawAtomsByIDs(colName,IDs,value):
2438	atomData = data['Drawing']['Atoms']
2439	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2440	if colName == 'Name':
2441	col = ct-1
2442	elif colName == 'Type':
2443	col = ct
2444	elif colName == 'I/A':
2445	col = cs
2446	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2447	for ind in indx:
2448	atomData[ind][col] = value
2449
2450	def OnDrawPlane(event):
2451	indx = drawAtoms.GetSelectedRows()
2452	if len(indx) < 4:
2453	print '**** ERROR - need 4+ atoms for plane calculation'
2454	return
2455	PlaneData = {}
2456	drawingData = data['Drawing']
2457	atomData = drawingData['Atoms']
2458	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2459	cx = colLabels.index('x')
2460	cn = colLabels.index('Name')
2461	xyz = []
2462	for i,atom in enumerate(atomData):
2463	if i in indx:
2464	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2465	generalData = data['General']
2466	PlaneData['Name'] = generalData['Name']
2467	PlaneData['Atoms'] = xyz
2468	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2469	G2stMn.BestPlane(PlaneData)
2470
2471	def OnDrawDistVP(event):
2472	# distance to view point
2473	indx = drawAtoms.GetSelectedRows()
2474	if not indx:
2475	print '***** ERROR - no atoms selected'
2476	return
2477	generalData = data['General']
2478	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2479	drawingData = data['Drawing']
2480	viewPt = np.array(drawingData['viewPoint'][0])
2481	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2482	atomDData = drawingData['Atoms']
2483	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2484	cx = colLabels.index('x')
2485	cn = colLabels.index('Name')
2486	for i in indx:
2487	atom = atomDData[i]
2488	Dx = np.array(atom[cx:cx+3])-viewPt
2489	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2490	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2491
2492	def OnDrawDAT(event):
2493	#distance, angle, torsion
2494	indx = drawAtoms.GetSelectedRows()
2495	if len(indx) not in [2,3,4]:
2496	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2497	return
2498	DATData = {}
2499	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2500	drawingData = data['Drawing']
2501	atomData = data['Atoms']
2502	atomDData = drawingData['Atoms']
2503	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2504	cx = colLabels.index('x')
2505	cn = colLabels.index('Name')
2506	cid = colLabels.index('I/A')+8
2507	xyz = []
2508	Oxyz = []
2509	DATData['Natoms'] = len(indx)
2510	for i in indx:
2511	atom = atomDData[i]
2512	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2513	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2514	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2515	DATData['Datoms'] = xyz
2516	DATData['Oatoms'] = Oxyz
2517	generalData = data['General']
2518	DATData['Name'] = generalData['Name']
2519	DATData['SGData'] = generalData['SGData']
2520	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2521	if 'pId' in data:
2522	DATData['pId'] = data['pId']
2523	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2524	G2stMn.DisAglTor(DATData)
2525
2526	################################################################################
2527	#### Draw Options page
2528	################################################################################
2529
2530	def UpdateDrawOptions():
2531	import copy
2532	import wx.lib.colourselect as wcs
2533	def SlopSizer():
2534	def OnCameraPos(event):
2535	drawingData['cameraPos'] = cameraPos.GetValue()
2536	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2537	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2538	G2plt.PlotStructure(G2frame,data)
2539
2540	def OnZclip(event):
2541	drawingData['Zclip'] = Zclip.GetValue()
2542	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2543	G2plt.PlotStructure(G2frame,data)
2544
2545	def OnZstep(event):
2546	try:
2547	step = float(Zstep.GetValue())
2548	if not (0.01 <= step <= 1.0):
2549	raise ValueError
2550	except ValueError:
2551	step = drawingData['Zstep']
2552	drawingData['Zstep'] = step
2553	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2554
2555	def OnMoveZ(event):
2556	move = MoveZ.GetValue()*drawingData['Zstep']
2557	MoveZ.SetValue(0)
2558	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2559	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2560	VD /= np.sqrt(np.sum(VD**2))
2561	VP += move*VD
2562	VP = np.inner(Bmat,VP)
2563	drawingData['viewPoint'][0] = VP
2564	panel = drawOptions.GetChildren()
2565	names = [child.GetName() for child in panel]
2566	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2567	G2plt.PlotStructure(G2frame,data)
2568
2569	def OnVdWScale(event):
2570	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2571	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2572	G2plt.PlotStructure(G2frame,data)
2573
2574	def OnEllipseProb(event):
2575	drawingData['ellipseProb'] = ellipseProb.GetValue()
2576	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2577	G2plt.PlotStructure(G2frame,data)
2578
2579	def OnBallScale(event):
2580	drawingData['ballScale'] = ballScale.GetValue()/100.
2581	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2582	G2plt.PlotStructure(G2frame,data)
2583
2584	def OnBondRadius(event):
2585	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2586	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2587	G2plt.PlotStructure(G2frame,data)
2588
2589	def OnContourLevel(event):
2590	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2591	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2592	G2plt.PlotStructure(G2frame,data)
2593
2594	def OnMapSize(event):
2595	drawingData['mapSize'] = mapSize.GetValue()/10.
2596	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2597	G2plt.PlotStructure(G2frame,data)
2598
2599
2600	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2601	slideSizer = wx.FlexGridSizer(7,2)
2602	slideSizer.AddGrowableCol(1,1)
2603
2604	cameraPosTxt = wx.StaticText(drawOptions,-1,
2605	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2606	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2607	slideSizer.Add(cameraPosTxt,0,wx.ALIGN_CENTER_VERTICAL)
2608	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2609	cameraPos.SetRange(10,500)
2610	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2611	G2frame.dataDisplay.cameraSlider = cameraPos
2612	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2613
2614	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2615	slideSizer.Add(ZclipTxt,0,wx.ALIGN_CENTER_VERTICAL)
2616	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2617	Zclip.SetRange(1,99)
2618	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2619	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2620
2621	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2622	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,wx.ALIGN_CENTER_VERTICAL)
2623	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2624	style=wx.TE_PROCESS_ENTER)
2625	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2626	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2627	ZstepSizer.Add(Zstep,0,wx.ALIGN_CENTER_VERTICAL)
2628	slideSizer.Add(ZstepSizer)
2629	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2630	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,wx.ALIGN_CENTER_VERTICAL)
2631	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2632	MoveZ.SetValue(0)
2633	MoveZ.SetRange(-1,1)
2634	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2635	MoveSizer.Add(MoveZ)
2636	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2637
2638	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2639	slideSizer.Add(vdwScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2640	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2641	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2642	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2643
2644	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2645	slideSizer.Add(ellipseProbTxt,0,wx.ALIGN_CENTER_VERTICAL)
2646	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2647	ellipseProb.SetRange(1,99)
2648	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2649	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2650
2651	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2652	slideSizer.Add(ballScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2653	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2654	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2655	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2656
2657	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2658	slideSizer.Add(bondRadiusTxt,0,wx.ALIGN_CENTER_VERTICAL)
2659	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2660	bondRadius.SetRange(1,25)
2661	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2662	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2663
2664	if generalData['Map']['rhoMax']:
2665	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2666	slideSizer.Add(contourLevelTxt,0,wx.ALIGN_CENTER_VERTICAL)
2667	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2668	contourLevel.SetRange(1,100)
2669	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2670	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2671	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2672	slideSizer.Add(mapSizeTxt,0,wx.ALIGN_CENTER_VERTICAL)
2673	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2674	mapSize.SetRange(1,100)
2675	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2676	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2677
2678	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2679	slopSizer.Add((10,5),0)
2680	slopSizer.SetMinSize(wx.Size(350,10))
2681	return slopSizer
2682
2683	def ShowSizer():
2684
2685	def OnBackColor(event):
2686	drawingData['backColor'] = event.GetValue()
2687	G2plt.PlotStructure(G2frame,data)
2688
2689	def OnShowABC(event):
2690	drawingData['showABC'] = showABC.GetValue()
2691	G2plt.PlotStructure(G2frame,data)
2692
2693	def OnShowUnitCell(event):
2694	drawingData['unitCellBox'] = unitCellBox.GetValue()
2695	G2plt.PlotStructure(G2frame,data)
2696
2697	def OnShowHyd(event):
2698	drawingData['showHydrogen'] = showHydrogen.GetValue()
2699	FindBondsDraw()
2700	G2plt.PlotStructure(G2frame,data)
2701
2702	def OnShowRB(event):
2703	drawingData['showRigidBodies'] = showRB.GetValue()
2704	FindBondsDraw()
2705	G2plt.PlotStructure(G2frame,data)
2706
2707	def OnViewPoint(event):
2708	Obj = event.GetEventObject()
2709	viewPt = Obj.GetValue().split()
2710	try:
2711	VP = [float(viewPt[i]) for i in range(3)]
2712	except (ValueError,IndexError):
2713	VP = drawingData['viewPoint'][0]
2714	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2715	drawingData['viewPoint'][0] = VP
2716	G2plt.PlotStructure(G2frame,data)
2717
2718	def OnViewDir(event):
2719	Obj = event.GetEventObject()
2720	viewDir = Obj.GetValue().split()
2721	try:
2722	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2723	VD = np.array([float(viewDir[i]) for i in range(3)])
2724	VC = np.inner(Amat,VD)
2725	VC /= np.sqrt(np.sum(VC**2))
2726	V = np.array(drawingData['viewDir'])
2727	VB = np.inner(Amat,V)
2728	VB /= np.sqrt(np.sum(VB**2))
2729	VX = np.cross(VC,VB)
2730	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2731	QV = G2mth.AVdeg2Q(A,VX)
2732	Q = drawingData['Quaternion']
2733	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2734	except (ValueError,IndexError):
2735	VD = drawingData['viewDir']
2736	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2737	drawingData['viewDir'] = VD
2738	G2plt.PlotStructure(G2frame,data)
2739
2740	showSizer = wx.BoxSizer(wx.VERTICAL)
2741	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2742	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,wx.ALIGN_CENTER_VERTICAL)
2743	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2744	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2745	lineSizer.Add(backColor,0,wx.ALIGN_CENTER_VERTICAL)
2746	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,wx.ALIGN_CENTER_VERTICAL)
2747	VD = drawingData['viewDir']
2748	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2749	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2750	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2751	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2752	G2frame.dataDisplay.viewDir = viewDir
2753	lineSizer.Add(viewDir,0,wx.ALIGN_CENTER_VERTICAL)
2754	showSizer.Add(lineSizer)
2755	showSizer.Add((0,5),0)
2756
2757	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2758	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2759	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2760	showABC.SetValue(drawingData['showABC'])
2761	lineSizer.Add(showABC,0,wx.ALIGN_CENTER_VERTICAL)
2762	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,wx.ALIGN_CENTER_VERTICAL)
2763	VP = drawingData['viewPoint'][0]
2764	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2765	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2766	G2frame.dataDisplay.viewPoint = viewPoint
2767	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2768	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2769	lineSizer.Add(viewPoint,0,wx.ALIGN_CENTER_VERTICAL)
2770	showSizer.Add(lineSizer)
2771	showSizer.Add((0,5),0)
2772
2773	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2774
2775	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2776	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2777	unitCellBox.SetValue(drawingData['unitCellBox'])
2778	line2Sizer.Add(unitCellBox,0,wx.ALIGN_CENTER_VERTICAL)
2779
2780	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2781	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2782	showHydrogen.SetValue(drawingData['showHydrogen'])
2783	line2Sizer.Add(showHydrogen,0,wx.ALIGN_CENTER_VERTICAL)
2784
2785	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2786	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2787	showRB.SetValue(drawingData['showRigidBodies'])
2788	line2Sizer.Add(showRB,0,wx.ALIGN_CENTER_VERTICAL)
2789
2790	showSizer.Add(line2Sizer)
2791	return showSizer
2792
2793	def RadSizer():
2794
2795	def OnSizeHatoms(event):
2796	try:
2797	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2798	except ValueError:
2799	value = 0.5
2800	drawingData['sizeH'] = value
2801	sizeH.SetValue("%.2f"%(value))
2802	G2plt.PlotStructure(G2frame,data)
2803
2804	def OnRadFactor(event):
2805	try:
2806	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2807	except ValueError:
2808	value = 0.85
2809	drawingData['radiusFactor'] = value
2810	radFactor.SetValue("%.2f"%(value))
2811	FindBondsDraw()
2812	G2plt.PlotStructure(G2frame,data)
2813
2814	radSizer = wx.BoxSizer(wx.HORIZONTAL)
2815	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,wx.ALIGN_CENTER_VERTICAL)
2816	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2817	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
2818	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
2819	radSizer.Add(sizeH,0,wx.ALIGN_CENTER_VERTICAL)
2820
2821	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,wx.ALIGN_CENTER_VERTICAL)
2822	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2823	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
2824	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
2825	radSizer.Add(radFactor,0,wx.ALIGN_CENTER_VERTICAL)
2826	return radSizer
2827
2828	# UpdateDrawOptions exectable code starts here
2829	generalData = data['General']
2830	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2831	SetupDrawingData()
2832	drawingData = data['Drawing']
2833	if generalData['Type'] == 'nuclear':
2834	pickChoice = ['Atoms','Bonds','Torsions','Planes']
2835	elif generalData['Type'] == 'macromolecular':
2836	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
2837
2838	G2frame.dataFrame.SetStatusText('')
2839	if drawOptions.GetSizer():
2840	drawOptions.GetSizer().Clear(True)
2841	mainSizer = wx.BoxSizer(wx.VERTICAL)
2842	mainSizer.Add((5,5),0)
2843	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,wx.ALIGN_CENTER_VERTICAL)
2844	mainSizer.Add((5,5),0)
2845	mainSizer.Add(SlopSizer(),0)
2846	mainSizer.Add((5,5),0)
2847	mainSizer.Add(ShowSizer(),0,)
2848	mainSizer.Add((5,5),0)
2849	mainSizer.Add(RadSizer(),0,)
2850	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
2851
2852	################################################################################
2853	#### Texture routines
2854	################################################################################
2855
2856	def UpdateTexture():
2857	def SetSHCoef():
2858	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
2859	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
2860	SHCoeff = textureData['SH Coeff'][1]
2861	for cofName in SHCoeff:
2862	if cofName in cofNames:
2863	newSHCoef[cofName] = SHCoeff[cofName]
2864	return newSHCoef
2865
2866	def OnShOrder(event):
2867	Obj = event.GetEventObject()
2868	textureData['Order'] = int(Obj.GetValue())
2869	textureData['SH Coeff'][1] = SetSHCoef()
2870	wx.CallAfter(UpdateTexture)
2871	G2plt.PlotTexture(G2frame,data)
2872
2873	def OnShModel(event):
2874	Obj = event.GetEventObject()
2875	textureData['Model'] = Obj.GetValue()
2876	textureData['SH Coeff'][1] = SetSHCoef()
2877	wx.CallAfter(UpdateTexture)
2878	G2plt.PlotTexture(G2frame,data)
2879
2880	def OnSHRefine(event):
2881	Obj = event.GetEventObject()
2882	textureData['SH Coeff'][0] = Obj.GetValue()
2883
2884	def OnSHShow(event):
2885	Obj = event.GetEventObject()
2886	textureData['SHShow'] = Obj.GetValue()
2887	wx.CallAfter(UpdateTexture)
2888
2889	def OnProjSel(event):
2890	Obj = event.GetEventObject()
2891	G2frame.Projection = Obj.GetValue()
2892	G2plt.PlotTexture(G2frame,data)
2893
2894	def OnColorSel(event):
2895	Obj = event.GetEventObject()
2896	G2frame.ContourColor = Obj.GetValue()
2897	G2plt.PlotTexture(G2frame,data)
2898
2899	def OnAngRef(event):
2900	Obj = event.GetEventObject()
2901	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
2902
2903	def OnAngValue(event):
2904	Obj = event.GetEventObject()
2905	try:
2906	value = float(Obj.GetValue())
2907	except ValueError:
2908	value = textureData[valIndx[Obj.GetId()]][1]
2909	Obj.SetValue('%8.2f'%(value))
2910	textureData[valIndx[Obj.GetId()]][1] = value
2911
2912	def OnODFValue(event):
2913	Obj = event.GetEventObject()
2914	try:
2915	value = float(Obj.GetValue())
2916	except ValueError:
2917	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
2918	Obj.SetValue('%8.3f'%(value))
2919	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
2920	G2plt.PlotTexture(G2frame,data)
2921
2922	def OnPfType(event):
2923	Obj = event.GetEventObject()
2924	textureData['PlotType'] = Obj.GetValue()
2925	wx.CallAfter(UpdateTexture)
2926	G2plt.PlotTexture(G2frame,data)
2927
2928	def OnPFValue(event):
2929	Obj = event.GetEventObject()
2930	Saxis = Obj.GetValue().split()
2931	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2932	try:
2933	hkl = [int(Saxis[i]) for i in range(3)]
2934	except (ValueError,IndexError):
2935	hkl = textureData['PFhkl']
2936	if not np.any(np.array(hkl)): #can't be all zeros!
2937	hkl = textureData['PFhkl']
2938	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
2939	textureData['PFhkl'] = hkl
2940	else:
2941	try:
2942	xyz = [float(Saxis[i]) for i in range(3)]
2943	except (ValueError,IndexError):
2944	xyz = textureData['PFxyz']
2945	if not np.any(np.array(xyz)): #can't be all zeros!
2946	xyz = textureData['PFxyz']
2947	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
2948	textureData['PFxyz'] = xyz
2949	G2plt.PlotTexture(G2frame,data)
2950
2951	# UpdateTexture executable starts here
2952	G2frame.dataFrame.SetStatusText('')
2953	generalData = data['General']
2954	SGData = generalData['SGData']
2955	try:
2956	textureData = generalData['SH Texture']
2957	except KeyError: #fix old files!
2958	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
2959	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
2960	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
2961	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
2962	if 'SHShow' not in textureData: #another fix
2963	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2964	try: #another fix!
2965	x = textureData['PlotType']
2966	except KeyError:
2967	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2968	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
2969	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
2970	if generalData['doPawley'] and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Sequental results'):
2971	G2frame.dataFrame.RefineTexture.Enable(True)
2972	shAngles = ['omega','chi','phi']
2973	if Texture.GetSizer():
2974	Texture.GetSizer().Clear(True)
2975	mainSizer = wx.BoxSizer(wx.VERTICAL)
2976	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
2977	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,wx.ALIGN_CENTER_VERTICAL)
2978	titleSizer.Add(wx.StaticText(Texture,-1,
2979	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
2980	0,wx.ALIGN_CENTER_VERTICAL)
2981	mainSizer.Add(titleSizer,0)
2982	mainSizer.Add((0,5),0)
2983	shSizer = wx.FlexGridSizer(1,6,5,5)
2984	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,wx.ALIGN_CENTER_VERTICAL)
2985	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
2986	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2987	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
2988	shSizer.Add(shModel,0,wx.ALIGN_CENTER_VERTICAL)
2989	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,wx.ALIGN_CENTER_VERTICAL)
2990	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
2991	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2992	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
2993	shSizer.Add(shOrder,0,wx.ALIGN_CENTER_VERTICAL)
2994	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
2995	shRef.SetValue(textureData['SH Coeff'][0])
2996	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
2997	shSizer.Add(shRef,0,wx.ALIGN_CENTER_VERTICAL)
2998	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
2999	shShow.SetValue(textureData['SHShow'])
3000	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
3001	shSizer.Add(shShow,0,wx.ALIGN_CENTER_VERTICAL)
3002	mainSizer.Add(shSizer,0,0)
3003	mainSizer.Add((0,5),0)
3004	PTSizer = wx.FlexGridSizer(2,4,5,5)
3005	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,wx.ALIGN_CENTER_VERTICAL)
3006	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
3007	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
3008	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3009	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
3010	PTSizer.Add(pfType,0,wx.ALIGN_CENTER_VERTICAL)
3011	if 'Axial' not in textureData['PlotType']:
3012	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,wx.ALIGN_CENTER_VERTICAL)
3013	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
3014	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3015	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
3016	PTSizer.Add(projSel,0,wx.ALIGN_CENTER_VERTICAL)
3017	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3018	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,wx.ALIGN_CENTER_VERTICAL)
3019	PH = textureData['PFhkl']
3020	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
3021	else:
3022	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,wx.ALIGN_CENTER_VERTICAL)
3023	PX = textureData['PFxyz']
3024	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
3025	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
3026	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
3027	PTSizer.Add(pfVal,0,wx.ALIGN_CENTER_VERTICAL)
3028	if 'Axial' not in textureData['PlotType']:
3029	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,wx.ALIGN_CENTER_VERTICAL)
3030	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3031	choice.sort()
3032	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
3033	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3034	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
3035	PTSizer.Add(colorSel,0,wx.ALIGN_CENTER_VERTICAL)
3036	mainSizer.Add(PTSizer,0,wx.ALIGN_CENTER_VERTICAL)
3037	mainSizer.Add((0,5),0)
3038	if textureData['SHShow']:
3039	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,wx.ALIGN_CENTER_VERTICAL)
3040	mainSizer.Add((0,5),0)
3041	ODFSizer = wx.FlexGridSizer(2,8,2,2)
3042	ODFIndx = {}
3043	ODFkeys = textureData['SH Coeff'][1].keys()
3044	ODFkeys.sort()
3045	for item in ODFkeys:
3046	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,wx.ALIGN_CENTER_VERTICAL)
3047	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3048	ODFIndx[ODFval.GetId()] = item
3049	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3050	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3051	ODFSizer.Add(ODFval,0,wx.ALIGN_CENTER_VERTICAL)
3052	mainSizer.Add(ODFSizer,0,wx.ALIGN_CENTER_VERTICAL)
3053	mainSizer.Add((0,5),0)
3054	mainSizer.Add((0,5),0)
3055	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,wx.ALIGN_CENTER_VERTICAL)
3056	mainSizer.Add((0,5),0)
3057	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3058	angIndx = {}
3059	valIndx = {}
3060	for item in ['Sample omega','Sample chi','Sample phi']:
3061	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3062	angRef.SetValue(textureData[item][0])
3063	angIndx[angRef.GetId()] = item
3064	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3065	angSizer.Add(angRef,0,wx.ALIGN_CENTER_VERTICAL)
3066	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3067	valIndx[angVal.GetId()] = item
3068	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3069	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3070	angSizer.Add(angVal,0,wx.ALIGN_CENTER_VERTICAL)
3071	angSizer.Add((5,0),0)
3072	mainSizer.Add(angSizer,0,wx.ALIGN_CENTER_VERTICAL)
3073	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3074
3075	################################################################################
3076	##### DData routines - GUI stuff in GSASIIddataGUI.py
3077	################################################################################
3078
3079	def OnHklfAdd(event):
3080	UseList = data['Histograms']
3081	keyList = UseList.keys()
3082	TextList = []
3083	if G2frame.PatternTree.GetCount():
3084	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3085	while item:
3086	name = G2frame.PatternTree.GetItemText(item)
3087	if name not in keyList and 'HKLF' in name:
3088	TextList.append(name)
3089	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3090	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3091	try:
3092	if dlg.ShowModal() == wx.ID_OK:
3093	result = dlg.GetSelections()
3094	for i in result:
3095	histoName = TextList[i]
3096	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3097	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3098	'Extinction':['Lorentzian','None',
3099	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3100	wx.BeginBusyCursor()
3101	UpdateHKLFdata(histoName)
3102	wx.EndBusyCursor()
3103	data['Histograms'] = UseList
3104	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3105	finally:
3106	dlg.Destroy()
3107
3108	def UpdateHKLFdata(histoName):
3109	generalData = data['General']
3110	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3111	refDict,reflData = G2frame.PatternTree.GetItemPyData(Id)
3112	SGData = generalData['SGData']
3113	Cell = generalData['Cell'][1:7]
3114	G,g = G2lat.cell2Gmat(Cell)
3115	for iref,ref in enumerate(reflData['RefList']):
3116	H = list(ref[:3])
3117	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3118	iabsnt,ref[3],Uniq,phi = G2spc.GenHKLf(H,SGData)
3119	G2frame.PatternTree.SetItemPyData(Id,[refDict,reflData])
3120
3121	def OnPwdrAdd(event):
3122	generalData = data['General']
3123	SGData = generalData['SGData']
3124	UseList = data['Histograms']
3125	newList = []
3126	NShkl = len(G2spc.MustrainNames(SGData))
3127	NDij = len(G2spc.HStrainNames(SGData))
3128	keyList = UseList.keys()
3129	TextList = ['All PWDR']
3130	if G2frame.PatternTree.GetCount():
3131	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3132	while item:
3133	name = G2frame.PatternTree.GetItemText(item)
3134	if name not in keyList and 'PWDR' in name:
3135	TextList.append(name)
3136	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3137	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3138	try:
3139	if dlg.ShowModal() == wx.ID_OK:
3140	result = dlg.GetSelections()
3141	for i in result: newList.append(TextList[i])
3142	if 'All PWDR' in newList:
3143	newList = TextList[1:]
3144	for histoName in newList:
3145	pId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3146	UseList[histoName] = {'Histogram':histoName,'Show':False,
3147	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3148	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3149	[1.,1.,1.,0.,0.,0.],6*[False,]],
3150	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3151	NShkl[0.01,],NShkl[False,]],
3152	'HStrain':[NDij[0.0,],NDij[False,]],
3153	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3154	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,pId,'Reflection Lists'))
3155	refList[generalData['Name']] = []
3156	data['Histograms'] = UseList
3157	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3158	finally:
3159	dlg.Destroy()
3160
3161	def OnDataDelete(event):
3162	UseList = data['Histograms']
3163	keyList = ['All',]+UseList.keys()
3164	keyList.sort()
3165	DelList = []
3166	if UseList:
3167	DelList = []
3168	dlg = wx.MultiChoiceDialog(G2frame,
3169	'Which histogram to delete from this phase?', 'Delete histogram',
3170	keyList, wx.CHOICEDLG_STYLE)
3171	try:
3172	if dlg.ShowModal() == wx.ID_OK:
3173	result = dlg.GetSelections()
3174	for i in result:
3175	DelList.append(keyList[i])
3176	if 'All' in DelList:
3177	DelList = keyList[1:]
3178	for i in DelList:
3179	del UseList[i]
3180	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3181	finally:
3182	dlg.Destroy()
3183
3184	################################################################################
3185	##### Rigid bodies
3186	################################################################################
3187
3188	def FillRigidBodyGrid(refresh=True):
3189	'''Fill the Rigid Body Phase information tab page.
3190	Note that the page is a ScrolledWindow, not a Grid
3191	'''
3192	def OnThermSel(event): #needs to be seen by VecRbSizer!
3193	Obj = event.GetEventObject()
3194	RBObj = Indx[Obj.GetId()]
3195	val = Obj.GetValue()
3196	Ttype = 'A'
3197	if val == 'Uiso':
3198	Ttype = 'I'
3199	RBObj['ThermalMotion'][0] = 'Uiso'
3200	elif val == 'T':
3201	RBObj['ThermalMotion'][0] = 'T'
3202	elif val == 'TL':
3203	RBObj['ThermalMotion'][0] = 'TL'
3204	elif val == 'TLS':
3205	RBObj['ThermalMotion'][0] = 'TLS'
3206	wx.CallAfter(FillRigidBodyGrid,True)
3207	if val != 'None':
3208	cia = data['General']['AtomPtrs'][3]
3209	for i,id in enumerate(RBObj['Ids']):
3210	data['Atoms'][AtLookUp[id]][cia] = Ttype
3211	G2plt.PlotStructure(G2frame,data)
3212
3213	def ThermDataSizer(RBObj,rbType):
3214
3215	def OnThermval(event):
3216	Obj = event.GetEventObject()
3217	item = Indx[Obj.GetId()]
3218	try:
3219	val = float(Obj.GetValue())
3220	RBObj['ThermalMotion'][1][item] = val
3221	except ValueError:
3222	pass
3223	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3224	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3225	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3226	cia = data['General']['AtomPtrs'][3]
3227	for i,id in enumerate(RBObj['Ids']):
3228	if Uout[i][0] == 'I':
3229	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3230	else:
3231	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3232	G2plt.PlotStructure(G2frame,data)
3233
3234	def OnTLSRef(event):
3235	Obj = event.GetEventObject()
3236	item = Indx[Obj.GetId()]
3237	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3238
3239	thermSizer = wx.FlexGridSizer(1,9,5,5)
3240	model = RBObj['ThermalMotion']
3241	if model[0] == 'Uiso':
3242	names = ['Uiso',]
3243	elif 'T' in model[0]:
3244	names = ['T11','T22','T33','T12','T13','T23']
3245	if 'L' in model[0]:
3246	names += ['L11','L22','L33','L12','L13','L23']
3247	if 'S' in model[0]:
3248	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3249	for i,name in enumerate(names):
3250	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,wx.ALIGN_CENTER_VERTICAL)
3251	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3252	style=wx.TE_PROCESS_ENTER)
3253	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3254	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3255	Indx[thermVal.GetId()] = i
3256	thermSizer.Add(thermVal)
3257	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3258	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3259	Tcheck.SetValue(model[2][i])
3260	Indx[Tcheck.GetId()] = i
3261	thermSizer.Add(Tcheck,0,wx.ALIGN_CENTER_VERTICAL)
3262	return thermSizer
3263
3264	def LocationSizer(RBObj,rbType):
3265
3266	def OnOrigRef(event):
3267	RBObj['Orig'][1] = Ocheck.GetValue()
3268
3269	def OnOrienRef(event):
3270	RBObj['Orient'][1] = Qcheck.GetValue()
3271
3272	def OnOrigX(event):
3273	Obj = event.GetEventObject()
3274	item = Indx[Obj.GetId()]
3275	try:
3276	val = float(Obj.GetValue())
3277	RBObj['Orig'][0][item] = val
3278	Obj.SetValue('%8.5f'%(val))
3279	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3280	for i,id in enumerate(RBObj['Ids']):
3281	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3282	data['Drawing']['Atoms'] = []
3283	UpdateDrawAtoms(atomStyle)
3284	G2plt.PlotStructure(G2frame,data)
3285	except ValueError:
3286	pass
3287
3288	def OnOrien(event):
3289	Obj = event.GetEventObject()
3290	item = Indx[Obj.GetId()]
3291	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3292	V = np.inner(Bmat,V)
3293	try:
3294	val = float(Obj.GetValue())
3295	if item:
3296	V[item-1] = val
3297	else:
3298	A = val
3299	Obj.SetValue('%8.5f'%(val))
3300	V = np.inner(Amat,V)
3301	Q = G2mth.AVdeg2Q(A,V)
3302	if not any(Q):
3303	raise ValueError
3304	RBObj['Orient'][0] = Q
3305	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3306	for i,id in enumerate(RBObj['Ids']):
3307	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3308	data['Drawing']['Atoms'] = []
3309	UpdateDrawAtoms(atomStyle)
3310	G2plt.PlotStructure(G2frame,data)
3311	except ValueError:
3312	pass
3313
3314	topSizer = wx.FlexGridSizer(2,6,5,5)
3315	Orig = RBObj['Orig'][0]
3316	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3317	Orien = [Orien,]
3318	Orien.extend(OrienV/nl.norm(OrienV))
3319	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,wx.ALIGN_CENTER_VERTICAL)
3320	for ix,x in enumerate(Orig):
3321	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3322	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3323	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3324	Indx[origX.GetId()] = ix
3325	topSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3326	topSizer.Add((5,0),)
3327	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3328	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3329	Ocheck.SetValue(RBObj['Orig'][1])
3330	topSizer.Add(Ocheck,0,wx.ALIGN_CENTER_VERTICAL)
3331	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,wx.ALIGN_CENTER_VERTICAL)
3332	for ix,x in enumerate(Orien):
3333	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3334	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3335	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3336	Indx[orien.GetId()] = ix
3337	topSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3338	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3339	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3340	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3341	Qcheck.SetValue(RBObj['Orient'][1])
3342	topSizer.Add(Qcheck)
3343	return topSizer
3344
3345	def ResrbSizer(RBObj):
3346	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3347
3348	def OnTorsionRef(event):
3349	Obj = event.GetEventObject()
3350	item = Indx[Obj.GetId()]
3351	RBObj['Torsions'][item][1] = Obj.GetValue()
3352
3353	def OnTorsion(event):
3354	Obj = event.GetEventObject()
3355	item = Indx[Obj.GetId()]
3356	try:
3357	val = float(Obj.GetValue())
3358	RBObj['Torsions'][item][0] = val
3359	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3360	for i,id in enumerate(RBObj['Ids']):
3361	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3362	except ValueError:
3363	pass
3364	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3365	data['Drawing']['Atoms'] = []
3366	UpdateDrawAtoms(atomStyle)
3367	drawAtoms.ClearSelection()
3368	G2plt.PlotStructure(G2frame,data)
3369
3370	def OnDelResRB(event):
3371	Obj = event.GetEventObject()
3372	RBId = Indx[Obj.GetId()]
3373	RBData['Residue'][RBId]['useCount'] -= 1
3374	RBObjs = data['RBModels']['Residue']
3375	for rbObj in RBObjs:
3376	if RBId == rbObj['RBId']:
3377	data['RBModels']['Residue'].remove(rbObj)
3378	G2plt.PlotStructure(G2frame,data)
3379	wx.CallAfter(FillRigidBodyGrid,True)
3380
3381	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3382	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3383	topLine = wx.BoxSizer(wx.HORIZONTAL)
3384	topLine.Add(wx.StaticText(RigidBodies,-1,
3385	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3386	rbId = RBObj['RBId']
3387	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3388	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3389	Indx[delRB.GetId()] = rbId
3390	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3391	resrbSizer.Add(topLine)
3392	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3393	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,wx.ALIGN_CENTER_VERTICAL)
3394	torSizer = wx.FlexGridSizer(1,6,5,5)
3395	for itors,tors in enumerate(RBObj['Torsions']):
3396	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,wx.ALIGN_CENTER_VERTICAL)
3397	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3398	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3399	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3400	Indx[torsTxt.GetId()] = itors
3401	torSizer.Add(torsTxt)
3402	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3403	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3404	torCheck.SetValue(tors[1])
3405	Indx[torCheck.GetId()] = itors
3406	torSizer.Add(torCheck,0,wx.ALIGN_CENTER_VERTICAL)
3407	resrbSizer.Add(torSizer)
3408	tchoice = ['None','Uiso','T','TL','TLS']
3409	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3410	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3411	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3412	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3413	Indx[thermSel.GetId()] = RBObj
3414	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3415	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3416	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3417	resrbSizer.Add(thermSizer)
3418	if RBObj['ThermalMotion'][0] != 'None':
3419	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3420	return resrbSizer
3421
3422	def VecrbSizer(RBObj):
3423	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3424
3425	def OnDelVecRB(event):
3426	Obj = event.GetEventObject()
3427	RBId = Indx[Obj.GetId()]
3428	RBData['Vector'][RBId]['useCount'] -= 1
3429	RBObjs = data['RBModels']['Vector']
3430	for rbObj in RBObjs:
3431	if RBId == rbObj['RBId']:
3432	data['RBModels']['Vector'].remove(rbObj)
3433	G2plt.PlotStructure(G2frame,data)
3434	wx.CallAfter(FillRigidBodyGrid,True)
3435
3436	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3437	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3438	topLine = wx.BoxSizer(wx.HORIZONTAL)
3439	topLine.Add(wx.StaticText(RigidBodies,-1,
3440	'Name: '+RBObj['RBname']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3441	rbId = RBObj['RBId']
3442	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3443	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3444	Indx[delRB.GetId()] = rbId
3445	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3446	vecrbSizer.Add(topLine)
3447	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3448	tchoice = ['None','Uiso','T','TL','TLS']
3449	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3450	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3451	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3452	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3453	Indx[thermSel.GetId()] = RBObj
3454	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3455	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3456	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3457	vecrbSizer.Add(thermSizer)
3458	if RBObj['ThermalMotion'][0] != 'None':
3459	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3460	return vecrbSizer
3461
3462	# FillRigidBodyGrid executable code starts here
3463	if refresh:
3464	RigidBodies.DestroyChildren()
3465	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3466	general = data['General']
3467	cx = general['AtomPtrs'][0]
3468	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3469	RBData = G2frame.PatternTree.GetItemPyData(
3470	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3471	Indx = {}
3472	atomStyle = 'balls & sticks'
3473	if 'macro' in general['Type']:
3474	atomStyle = 'sticks'
3475	G2frame.dataFrame.SetStatusText('')
3476	mainSizer = wx.BoxSizer(wx.VERTICAL)
3477	if not data['RBModels']:
3478	mainSizer.Add((5,5),0)
3479	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,wx.ALIGN_CENTER_VERTICAL)
3480	mainSizer.Add((5,5),0)
3481	if 'Residue' in data['RBModels']:
3482	mainSizer.Add((5,5),0)
3483	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3484	mainSizer.Add((5,5),0)
3485	for RBObj in data['RBModels']['Residue']:
3486	mainSizer.Add(ResrbSizer(RBObj))
3487	if 'Vector' in data['RBModels']:
3488	mainSizer.Add((5,5),0)
3489	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3490	mainSizer.Add((5,5),0)
3491	for RBObj in data['RBModels']['Vector']:
3492	mainSizer.Add(VecrbSizer(RBObj))
3493
3494	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3495
3496	def OnRBCopyParms(event):
3497	RBObjs = []
3498	for rbType in ['Vector','Residue']:
3499	RBObjs += data['RBModels'].get(rbType,[])
3500	if not len(RBObjs):
3501	print '** ERROR - no rigid bodies defined **'
3502	return
3503	if len(RBObjs) == 1:
3504	print '** INFO - only one rigid body defined; nothing to copy to **'
3505	return
3506	Source = []
3507	sourceRB = {}
3508	for RBObj in RBObjs:
3509	Source.append(RBObj['RBname'])
3510	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3511	if dlg.ShowModal() == wx.ID_OK:
3512	sel = dlg.GetSelection()
3513	name = Source[sel]
3514	for item in ['Orig','Orient','ThermalMotion']:
3515	sourceRB.update({item:RBObjs[sel][item],})
3516	dlg.Destroy()
3517	if not sourceRB:
3518	return
3519	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3520	if dlg.ShowModal() == wx.ID_OK:
3521	sel = dlg.GetSelections()
3522	for x in sel:
3523	RBObjs[x].update(copy.copy(sourceRB))
3524	G2plt.PlotStructure(G2frame,data)
3525	wx.CallAfter(FillRigidBodyGrid(True))
3526
3527	def OnRBAssign(event):
3528
3529	G2frame.dataFrame.SetStatusText('')
3530	RBData = G2frame.PatternTree.GetItemPyData(
3531	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3532	rbNames = {}
3533	for rbVec in RBData['Vector']:
3534	if rbVec != 'AtInfo':
3535	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3536	for rbRes in RBData['Residue']:
3537	if rbRes != 'AtInfo':
3538	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3539	if not rbNames:
3540	print '** ERROR - no rigid bodies defined **'
3541	return
3542	general = data['General']
3543	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3544	cx,ct = general['AtomPtrs'][:2]
3545	atomData = data['Atoms']
3546	Indx = {}
3547	atInd = [-1,-1,-1]
3548	data['testRBObj'] = {}
3549
3550	def Draw():
3551
3552	def OnOk(event):
3553	rbType = data['testRBObj']['rbType']
3554	RBObjs = data['RBModels'].get(rbType,[])
3555	rbObj = data['testRBObj']['rbObj']
3556	rbId = rbObj['RBId']
3557	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3558	Ids = []
3559	dmax = 0.0
3560	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3561	for xyz in newXYZ:
3562	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3563	dmax = max(dmax,np.min(dist))
3564	id = np.argmin(dist)
3565	Ids.append(atomData[id][-1])
3566	atomData[id][cx:cx+3] = xyz
3567	if dmax > 1.0:
3568	print '** WARNING - some atoms not found or misidentified **'
3569	print '** check torsion angles & try again **'
3570	OkBtn.SetLabel('Not Ready')
3571	OkBtn.Enable(False)
3572	return
3573	rbObj['Ids'] = Ids
3574	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3575	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3576	RBObjs.append(rbObj)
3577	data['RBModels'][rbType] = RBObjs
3578	RBData[rbType][rbId]['useCount'] += 1
3579	del data['testRBObj']
3580	G2plt.PlotStructure(G2frame,data)
3581	FillRigidBodyGrid(True)
3582
3583	def OnCancel(event):
3584	del data['testRBObj']
3585	FillRigidBodyGrid(True)
3586
3587	def OnRBSel(event):
3588	selection = rbSel.GetValue()
3589	rbType,rbId = rbNames[selection]
3590	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3591	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3592	data['testRBObj']['rbType'] = rbType
3593	data['testRBObj']['rbData'] = RBData
3594	data['testRBObj']['Sizers'] = {}
3595	rbRef = RBData[rbType][rbId]['rbRef']
3596	data['testRBObj']['rbRef'] = rbRef
3597	refType = []
3598	refName = []
3599	for ref in rbRef[:3]:
3600	reftype = data['testRBObj']['rbAtTypes'][ref]
3601	refType.append(reftype)
3602	refName.append(reftype+' '+str(rbRef[0]))
3603	atNames,AtNames = fillAtNames(refType,atomData,ct)
3604	data['testRBObj']['atNames'] = atNames
3605	data['testRBObj']['AtNames'] = AtNames
3606	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3607	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3608	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3609	data['testRBObj']['torAtms'] = []
3610	for item in RBData[rbType][rbId].get('rbSeq',[]):
3611	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3612	data['testRBObj']['torAtms'].append([-1,-1,-1])
3613	Draw()
3614
3615	def fillAtNames(refType,atomData,ct):
3616	atNames = [{},{},{}]
3617	AtNames = {}
3618	for iatm,atom in enumerate(atomData):
3619	AtNames[atom[ct-1]] = iatm
3620	for i,reftype in enumerate(refType):
3621	if atom[ct] == reftype:
3622	atNames[i][atom[ct-1]] = iatm
3623	return atNames,AtNames
3624
3625	def OnAtOrigPick(event):
3626	Obj = event.GetEventObject()
3627	item = Indx[Obj.GetId()]
3628	atName = Obj.GetValue()
3629	rbType = data['testRBObj']['rbType']
3630	atInd[0] = atNames[item][atName]
3631	if 'Vector' in rbType:
3632	rbObj = data['testRBObj']['rbObj']
3633	rbId = rbObj['RBId']
3634	rbRef = data['testRBObj']['rbRef']
3635	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3636	nref = atNames[item][atName]
3637	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3638	Nxyz = np.array(atomData[nref][cx:cx+3])
3639	Orig = Nxyz-Oxyz
3640	data['testRBObj']['rbObj']['Orig'][0] = Orig
3641	else:
3642	Orig = atomData[atNames[item][atName]][cx:cx+3]
3643	data['testRBObj']['rbObj']['Orig'][0] = Orig
3644	for x,item in zip(Orig,Xsizers):
3645	item.SetLabel('%10.5f'%(x))
3646	G2plt.PlotStructure(G2frame,data)
3647
3648	def OnAtQPick(event):
3649	Obj = event.GetEventObject()
3650	item = Indx[Obj.GetId()]
3651	atName = Obj.GetValue()
3652	atInd[item] = atNames[item][atName]
3653	if any([x<0 for x in atInd]):
3654	return
3655	OkBtn.SetLabel('OK')
3656	OkBtn.Enable(True)
3657	rbType = data['testRBObj']['rbType']
3658	rbObj = data['testRBObj']['rbObj']
3659	rbId = rbObj['RBId']
3660	rbRef = data['testRBObj']['rbRef']
3661	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3662	rbOrig = rbXYZ[rbRef[0]]
3663	VAR = rbXYZ[rbRef[1]]-rbOrig
3664	VBR = rbXYZ[rbRef[2]]-rbOrig
3665	if rbType == 'Vector':
3666	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3667	else:
3668	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3669	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3670	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3671	VCC = np.cross(VAR,VAC)
3672	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3673	VAR = G2mth.prodQVQ(QuatA,VAR)
3674	VBR = G2mth.prodQVQ(QuatA,VBR)
3675	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3676	QuatC = G2mth.prodQQ(QuatB,QuatA)
3677	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3678	for x,item in zip(QuatC,Osizers):
3679	item.SetLabel('%10.4f'%(x))
3680	if rbType == 'Vector':
3681	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3682	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3683	Orig = Nxyz-Oxyz
3684	data['testRBObj']['rbObj']['Orig'][0] = Orig
3685	for x,item in zip(Orig,Xsizers):
3686	item.SetLabel('%10.5f'%(x))
3687	G2plt.PlotStructure(G2frame,data)
3688
3689	def OnTorAngle(event):
3690	OkBtn.SetLabel('OK')
3691	OkBtn.Enable(True)
3692	Obj = event.GetEventObject()
3693	[tor,torSlide] = Indx[Obj.GetId()]
3694	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3695	try:
3696	value = float(Obj.GetValue())
3697	except ValueError:
3698	value = Tors[0]
3699	Tors[0] = value
3700	Obj.SetValue('%8.3f'%(value))
3701	torSlide.SetValue(int(value*10))
3702	G2plt.PlotStructure(G2frame,data)
3703
3704	def OnTorSlide(event):
3705	OkBtn.SetLabel('OK')
3706	OkBtn.Enable(True)
3707	Obj = event.GetEventObject()
3708	tor,ang = Indx[Obj.GetId()]
3709	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3710	val = float(Obj.GetValue())/10.
3711	Tors[0] = val
3712	ang.SetValue('%8.3f'%(val))
3713	G2plt.PlotStructure(G2frame,data)
3714
3715	if len(data['testRBObj']):
3716	G2plt.PlotStructure(G2frame,data)
3717
3718	RigidBodies.DestroyChildren()
3719	mainSizer = wx.BoxSizer(wx.VERTICAL)
3720	mainSizer.Add((5,5),0)
3721	if data['testRBObj']:
3722	Xsizers = []
3723	Osizers = []
3724	rbObj = data['testRBObj']['rbObj']
3725	rbName = rbObj['RBname']
3726	rbId = rbObj['RBId']
3727	Orig = rbObj['Orig'][0]
3728	Orien = rbObj['Orient'][0]
3729	rbRef = data['testRBObj']['rbRef']
3730	Torsions = rbObj['Torsions']
3731	refName = []
3732	for ref in rbRef:
3733	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3734	atNames = data['testRBObj']['atNames']
3735	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3736	0,wx.ALIGN_CENTER_VERTICAL)
3737	mainSizer.Add((5,5),0)
3738	OriSizer = wx.FlexGridSizer(1,5,5,5)
3739	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,wx.ALIGN_CENTER_VERTICAL)
3740	for ix,x in enumerate(Orig):
3741	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3742	OriSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3743	Xsizers.append(origX)
3744	OriSizer.Add((5,0),)
3745	if len(atomData):
3746	choice = atNames[0].keys()
3747	choice.sort()
3748	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3749	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,wx.ALIGN_CENTER_VERTICAL)
3750	for ix,x in enumerate(Orien):
3751	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3752	OriSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3753	Osizers.append(orien)
3754	data['testRBObj']['Sizers']['Osizers'] = Osizers
3755	mainSizer.Add(OriSizer)
3756	mainSizer.Add((5,5),0)
3757	RefSizer = wx.FlexGridSizer(1,7,5,5)
3758	if len(atomData):
3759	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,wx.ALIGN_CENTER_VERTICAL)
3760	for i in [0,1,2]:
3761	choice = ['',]+atNames[i].keys()
3762	choice.sort()
3763	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,wx.ALIGN_CENTER_VERTICAL)
3764	atPick = wx.ComboBox(RigidBodies,-1,value='',
3765	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3766	if i:
3767	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3768	else:
3769	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3770	Indx[atPick.GetId()] = i
3771	RefSizer.Add(atPick,0,wx.ALIGN_CENTER_VERTICAL)
3772	mainSizer.Add(RefSizer)
3773	mainSizer.Add((5,5),0)
3774	if Torsions:
3775	AtNames = data['testRBObj']['AtNames']
3776	rbAtTypes = data['testRBObj']['rbAtTypes']
3777	rbSeq = RBData['Residue'][rbId]['rbSeq']
3778	TorSizer = wx.FlexGridSizer(1,4)
3779	TorSizer.AddGrowableCol(1,1)
3780	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3781	torName = ''
3782	for item in [seq[0],seq[1],seq[3][0]]:
3783	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3784	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,wx.ALIGN_CENTER_VERTICAL)
3785	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3786	torSlide.SetRange(0,3600)
3787	torSlide.SetValue(int(torsion[0]*10.))
3788	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3789	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3790	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,wx.ALIGN_CENTER_VERTICAL)
3791	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
3792	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
3793	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
3794	Indx[torSlide.GetId()] = [t,ang]
3795	Indx[ang.GetId()] = [t,torSlide]
3796	TorSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
3797	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
3798	else:
3799	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,wx.ALIGN_CENTER_VERTICAL)
3800	else:
3801	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,wx.ALIGN_CENTER_VERTICAL)
3802	mainSizer.Add((5,5),0)
3803	topSizer = wx.BoxSizer(wx.HORIZONTAL)
3804	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,wx.ALIGN_CENTER_VERTICAL)
3805	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
3806	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3807	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
3808	topSizer.Add((5,5),0)
3809	topSizer.Add(rbSel,0,wx.ALIGN_CENTER_VERTICAL)
3810	mainSizer.Add(topSizer)
3811
3812	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
3813	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
3814	OkBtn.Enable(False)
3815	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
3816	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
3817	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
3818	btnSizer.Add((20,20),1)
3819	btnSizer.Add(OkBtn)
3820	btnSizer.Add(CancelBtn)
3821	btnSizer.Add((20,20),1)
3822	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
3823	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3824	Draw()
3825
3826	def OnAutoFindResRB(event):
3827	RBData = G2frame.PatternTree.GetItemPyData(
3828	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3829	rbKeys = RBData['Residue'].keys()
3830	rbKeys.remove('AtInfo')
3831	if not len(rbKeys):
3832	print '** ERROR - no residue rigid bodies are defined **'
3833	return
3834	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
3835	RBIds = dict(zip(RBNames,rbKeys))
3836	general = data['General']
3837	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3838	Atoms = data['Atoms']
3839	AtLookUp = G2mth.FillAtomLookUp(Atoms)
3840	if 'macro' not in general['Type']:
3841	print '** ERROR - this phase is not a macromolecule **'
3842	return
3843	if not len(Atoms):
3844	print '** ERROR - this phase has no atoms **'
3845	return
3846	RBObjs = []
3847	cx,ct = general['AtomPtrs'][:2]
3848	iatm = 0
3849	wx.BeginBusyCursor()
3850	try:
3851	while iatm < len(Atoms):
3852	atom = Atoms[iatm]
3853	res = atom[1].strip()
3854	numChain = ' %s %s'%(atom[0],atom[2])
3855	if res not in RBIds or atom[ct-1] == 'OXT':
3856	iatm += 1
3857	continue #skip for OXT, water molecules, etc.
3858	rbRes = RBData['Residue'][RBIds[res]]
3859	rbRef = rbRes['rbRef']
3860	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
3861	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
3862	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
3863	rbAtoms = []
3864	rbIds = []
3865	for iratm in range(len(rbRes['atNames'])):
3866	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
3867	rbIds.append(Atoms[iatm][20])
3868	iatm += 1 #puts this at beginning of next residue?
3869	Orig = rbAtoms[rbRef[0]]
3870	rbObj['RBId'] = RBIds[res]
3871	rbObj['Ids'] = rbIds
3872	rbObj['Orig'] = [Orig,False]
3873	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
3874	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
3875	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
3876	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
3877	VCC = np.cross(VAR,VAC)
3878	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3879	VAR = G2mth.prodQVQ(QuatA,VAR)
3880	VBR = G2mth.prodQVQ(QuatA,VBR)
3881	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3882	QuatC = G2mth.prodQQ(QuatB,QuatA)
3883	rbObj['Orient'] = [QuatC,' ']
3884	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3885	SXYZ = []
3886	TXYZ = []
3887	rbObj['Torsions'] = []
3888	for i,xyz in enumerate(rbRes['rbXYZ']):
3889	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
3890	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
3891	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
3892	VBR = SXYZ[Oatm]-SXYZ[Patm]
3893	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
3894	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
3895	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
3896	ang = 180.*D/np.pi
3897	rbObj['Torsions'].append([ang,False])
3898	for ride in Riders:
3899	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
3900	rbRes['useCount'] += 1
3901	RBObjs.append(rbObj)
3902	data['RBModels']['Residue'] = RBObjs
3903	for RBObj in RBObjs:
3904	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3905	for i,id in enumerate(RBObj['Ids']):
3906	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3907	finally:
3908	wx.EndBusyCursor()
3909	wx.CallAfter(FillRigidBodyGrid,True)
3910
3911	def OnRBRemoveAll(event):
3912	data['RBModels']['Residue'] = []
3913	data['RBModels']['Vector'] = []
3914	RBData = G2frame.PatternTree.GetItemPyData(
3915	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3916	for RBType in ['Vector','Residue']:
3917	for rbId in RBData[RBType]:
3918	RBData[RBType][rbId]['useCount'] = 0
3919	FillRigidBodyGrid(True)
3920
3921	def OnGlobalResRBTherm(event):
3922	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3923	RBObjs = data['RBModels']['Residue']
3924	names = ['None','Uiso','T','TL','TLS']
3925	cia = data['General']['AtomPtrs'][3]
3926	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
3927	if dlg.ShowModal() == wx.ID_OK:
3928	sel = dlg.GetSelection()
3929	parm = names[sel]
3930	Ttype = 'A'
3931	if parm == 'Uiso':
3932	Ttype = 'I'
3933	for rbObj in RBObjs:
3934	rbObj['ThermalMotion'][0] = parm
3935	if parm != 'None':
3936	for i,id in enumerate(rbObj['Ids']):
3937	data['Atoms'][AtLookUp[id]][cia] = Ttype
3938	dlg.Destroy()
3939	wx.CallAfter(FillRigidBodyGrid,True)
3940
3941	def OnGlobalResRBRef(event):
3942	RBObjs = data['RBModels']['Residue']
3943	names = ['Origin','Orient. angle','Full Orient.']
3944	nTor = 0
3945	for rbObj in RBObjs:
3946	nTor = max(nTor,len(rbObj['Torsions']))
3947	names += ['Torsion '+str(i) for i in range(nTor)]
3948	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
3949	names += ['Uiso',]
3950	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
3951	names += ['Tii','Tij','Lii','Lij','Sij']
3952	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
3953	names += ['Tii','Tij','Lii','Lij']
3954	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
3955	names += ['Tii','Tij']
3956
3957	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
3958	if dlg.ShowModal() == wx.ID_OK:
3959	sel = dlg.GetSelections()
3960	parms = []
3961	for x in sel:
3962	parms.append(names[x])
3963	wx.BeginBusyCursor()
3964	try:
3965	for rbObj in RBObjs:
3966	if 'Origin' in parms:
3967	rbObj['Orig'][1] = True
3968	else:
3969	rbObj['Orig'][1] = False
3970	if 'Full Orient.' in parms:
3971	rbObj['Orient'][1] = 'AV'
3972	elif 'Orient. angle' in parms:
3973	rbObj['Orient'][1] = 'A'
3974	else:
3975	rbObj['Orient'][1] = ' '
3976	for i in range(len(rbObj['Torsions'])):
3977	if 'Torsion '+str(i) in parms:
3978	rbObj['Torsions'][i][1] = True
3979	else:
3980	rbObj['Torsions'][i][1] = False
3981	if rbObj['ThermalMotion'][0] == 'Uiso':
3982	if 'Uiso' in parms:
3983	rbObj['ThermalMotion'][2][0] = True
3984	else:
3985	rbObj['ThermalMotion'][2][0] = False
3986	elif 'T' in rbObj['ThermalMotion'][0]:
3987	if 'Tii' in parms:
3988	rbObj['ThermalMotion'][2][0:2] = [True,True,True]
3989	else:
3990	rbObj['ThermalMotion'][2][0:2] = [False,False,False]
3991	if 'Tij' in parms:
3992	rbObj['ThermalMotion'][2][3:6] = [True,True,True]
3993	else:
3994	rbObj['ThermalMotion'][2][3:6] = [False,False,False]
3995	elif 'L' in rbObj['ThermalMotion'][0]:
3996	if 'Lii' in parms:
3997	rbObj['ThermalMotion'][2][6:9] = [True,True,True]
3998	else:
3999	rbObj['ThermalMotion'][2][6:9] = [False,False,False]
4000	if 'Lij' in parms:
4001	rbObj['ThermalMotion'][2][9:12] = [True,True,True]
4002	else:
4003	rbObj['ThermalMotion'][2][9:12] = [False,False,False]
4004	elif 'S' in rbObj['ThermalMotion'][0]:
4005	if 'Sij' in parms:
4006	rbObj['ThermalMotion'][2][12:20] = [True,True,True,True,True,True,True,True]
4007	else:
4008	rbObj['ThermalMotion'][2][12:20] = [False,False,False,False,False,False,False,False]
4009	finally:
4010	wx.EndBusyCursor()
4011	FillRigidBodyGrid()
4012
4013	################################################################################
4014	##### MC/SA routines
4015	################################################################################
4016
4017	def UpdateMCSA(Scroll=0):
4018	Indx = {}
4019
4020	def OnPosRef(event):
4021	Obj = event.GetEventObject()
4022	model,item,ix = Indx[Obj.GetId()]
4023	model[item][1][ix] = Obj.GetValue()
4024
4025	def OnPosVal(event):
4026	Obj = event.GetEventObject()
4027	model,item,ix = Indx[Obj.GetId()]
4028	try:
4029	model[item][0][ix] = float(Obj.GetValue())
4030	except ValueError:
4031	pass
4032	Obj.SetValue("%.4f"%(model[item][0][ix]))
4033	G2plt.PlotStructure(G2frame,data)
4034
4035	def OnPosRange(event):
4036	Obj = event.GetEventObject()
4037	model,item,ix = Indx[Obj.GetId()]
4038	Range = Obj.GetValue().split()
4039	try:
4040	rmin,rmax = [float(Range[i]) for i in range(2)]
4041	if rmin >= rmax:
4042	raise ValueError
4043	except (ValueError,IndexError):
4044	rmin,rmax = model[item][2][ix]
4045	model[item][2][ix] = [rmin,rmax]
4046	Obj.SetValue('%.3f %.3f'%(rmin,rmax))
4047
4048	def atomSizer(model):
4049
4050	atomsizer = wx.FlexGridSizer(1,7,5,5)
4051	atomsizer.Add(wx.StaticText(MCSA,-1,' Atom: '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4052	for ix,item in enumerate(['x','y','z']):
4053	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4054	posRef.SetValue(model['Pos'][1][ix])
4055	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4056	Indx[posRef.GetId()] = [model,'Pos',ix]
4057	atomsizer.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4058	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4059	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4060	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4061	Indx[posVal.GetId()] = [model,'Pos',ix]
4062	atomsizer.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4063	atomsizer.Add((5,5),0)
4064	for ix,item in enumerate(['x','y','z']):
4065	atomsizer.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4066	rmin,rmax = model['Pos'][2][ix]
4067	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4068	Indx[posRange.GetId()] = [model,'Pos',ix]
4069	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4070	posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4071	atomsizer.Add(posRange,0,wx.ALIGN_CENTER_VERTICAL)
4072	return atomsizer
4073
4074	def rbSizer(model):
4075
4076	def OnOrVar(event):
4077	Obj = event.GetEventObject()
4078	model = Indx[Obj.GetId()]
4079	model['Ovar'] = Obj.GetValue()
4080
4081	def OnOriVal(event):
4082	Obj = event.GetEventObject()
4083	model,ix,ObjA,ObjV = Indx[Obj.GetId()]
4084	A = model['Ori'][0][0]
4085	V = model['Ori'][0][1:]
4086	if ix:
4087	Anew = A
4088	Vec = ObjV.GetValue().split()
4089	try:
4090	Vnew = [float(Vec[i]) for i in range(3)]
4091	except ValueError:
4092	Vnew = V
4093	else:
4094	Vnew = V
4095	try:
4096	Anew = float(ObjA.GetValue())
4097	if not Anew: #==0.0!
4098	Anew = 360.
4099	except ValueError:
4100	Anew = A
4101	Q = G2mth.AVdeg2Q(Anew,Vnew)
4102	A,V = G2mth.Q2AVdeg(Q)
4103	model['Ori'][0][0] = A
4104	model['Ori'][0][1:] = V
4105	if ix:
4106	ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2]))
4107	else:
4108	ObjA.SetValue('%.5f'%(A))
4109	ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2]))
4110	G2plt.PlotStructure(G2frame,data)
4111	# UpdateMCSA()
4112
4113	def OnMolCent(event):
4114	Obj = event.GetEventObject()
4115	model = Indx[Obj.GetId()]
4116	model['MolCent'][1] = Obj.GetValue()
4117	if model['MolCent'][1]:
4118	G2mth.SetMolCent(model,RBData)
4119	G2plt.PlotStructure(G2frame,data)
4120
4121	rbsizer = wx.BoxSizer(wx.VERTICAL)
4122	rbsizer1 = wx.FlexGridSizer(1,7,5,5)
4123	rbsizer1.Add(wx.StaticText(MCSA,-1,model['Type']+': '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4124	for ix,item in enumerate(['x','y','z']):
4125	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4126	posRef.SetValue(model['Pos'][1][ix])
4127	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4128	Indx[posRef.GetId()] = [model,'Pos',ix]
4129	rbsizer1.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4130	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4131	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4132	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4133	Indx[posVal.GetId()] = [model,'Pos',ix]
4134	rbsizer1.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4135	molcent = wx.CheckBox(MCSA,-1,label=' Use mol. center? ')
4136	molcent.SetValue(model['MolCent'][1])
4137	molcent.Bind(wx.EVT_CHECKBOX,OnMolCent)
4138	Indx[molcent.GetId()] = model
4139	rbsizer1.Add(molcent,0,wx.ALIGN_CENTER_VERTICAL)
4140	for ix,item in enumerate(['x','y','z']):
4141	rbsizer1.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4142	rmin,rmax = model['Pos'][2][ix]
4143	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4144	Indx[posRange.GetId()] = [model,'Pos',ix]
4145	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4146	posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4147	rbsizer1.Add(posRange,0,wx.ALIGN_CENTER_VERTICAL)
4148
4149	rbsizer2 = wx.FlexGridSizer(1,6,5,5)
4150	Ori = model['Ori'][0]
4151	rbsizer2.Add(wx.StaticText(MCSA,-1,'Oa: '),0,wx.ALIGN_CENTER_VERTICAL)
4152	angVal = wx.TextCtrl(MCSA,-1,'%.5f'%(Ori[0]),style=wx.TE_PROCESS_ENTER)
4153	angVal.Bind(wx.EVT_TEXT_ENTER,OnOriVal)
4154	angVal.Bind(wx.EVT_KILL_FOCUS,OnOriVal)
4155	rbsizer2.Add(angVal,0,wx.ALIGN_CENTER_VERTICAL)
4156	rbsizer2.Add(wx.StaticText(MCSA,-1,'Oi,Oj,Ok: '),0,wx.ALIGN_CENTER_VERTICAL)
4157	vecVal = wx.TextCtrl(MCSA,-1,'%.3f %.3f %.3f'%(Ori[1],Ori[2],Ori[3]),style=wx.TE_PROCESS_ENTER)
4158	vecVal.Bind(wx.EVT_TEXT_ENTER,OnOriVal)
4159	vecVal.Bind(wx.EVT_KILL_FOCUS,OnOriVal)
4160	Indx[angVal.GetId()] = [model,0,angVal,vecVal]
4161	Indx[vecVal.GetId()] = [model,1,angVal,vecVal]
4162	rbsizer2.Add(vecVal,0,wx.ALIGN_CENTER_VERTICAL)
4163	rbsizer2.Add(wx.StaticText(MCSA,-1,' Vary? '),0,wx.ALIGN_CENTER_VERTICAL)
4164	choice = [' ','A','AV']
4165	orvar = wx.ComboBox(MCSA,-1,value=model['Ovar'],choices=choice,
4166	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
4167	orvar.Bind(wx.EVT_COMBOBOX, OnOrVar)
4168	Indx[orvar.GetId()] = model
4169	rbsizer2.Add(orvar,0,wx.ALIGN_CENTER_VERTICAL)
4170	rbsizer2.Add(wx.StaticText(MCSA,-1,' Range: Oa: '),0,wx.ALIGN_CENTER_VERTICAL)
4171	Rge = model['Ori'][2]
4172	angRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(Rge[0][0],Rge[0][1]),style=wx.TE_PROCESS_ENTER)
4173	Indx[angRange.GetId()] = [model,'Ori',0]
4174	angRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4175	angRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4176	rbsizer2.Add(angRange,0,wx.ALIGN_CENTER_VERTICAL)
4177	rbsizer2.Add(wx.StaticText(MCSA,-1,'Oi,Oj,Ok: '),0,wx.ALIGN_CENTER_VERTICAL)
4178	for io,item in enumerate(['Oi','Oj','Ok']):
4179	rmin,rmax = Rge[io+1]
4180	vecRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f '%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4181	Indx[vecRange.GetId()] = [model,'Ori',io+1]
4182	vecRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4183	vecRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4184	rbsizer2.Add(vecRange,0,wx.ALIGN_CENTER_VERTICAL)
4185	rbsizer.Add(rbsizer1)
4186	rbsizer.Add(rbsizer2)
4187	if model['Type'] == 'Residue':
4188	atNames = RBData['Residue'][model['RBId']]['atNames']
4189	rbsizer.Add(wx.StaticText(MCSA,-1,'Torsions:'),0,wx.ALIGN_CENTER_VERTICAL)
4190	rbsizer3 = wx.FlexGridSizer(1,8,5,5)
4191	for it,tor in enumerate(model['Tor'][0]):
4192	iBeg,iFin = RBData['Residue'][model['RBId']]['rbSeq'][it][:2]
4193	name = atNames[iBeg]+'-'+atNames[iFin]
4194	torRef = wx.CheckBox(MCSA,-1,label=' %s: '%(name))
4195	torRef.SetValue(model['Tor'][1][it])
4196	torRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4197	Indx[torRef.GetId()] = [model,'Tor',it]
4198	rbsizer3.Add(torRef,0,wx.ALIGN_CENTER_VERTICAL)
4199	torVal = wx.TextCtrl(MCSA,-1,'%.4f'%(tor),style=wx.TE_PROCESS_ENTER)
4200	torVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4201	torVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4202	Indx[torVal.GetId()] = [model,'Tor',it]
4203	rbsizer3.Add(torVal,0,wx.ALIGN_CENTER_VERTICAL)
4204	rbsizer3.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4205	rmin,rmax = model['Tor'][2][it]
4206	torRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4207	Indx[torRange.GetId()] = [model,'Tor',it]
4208	torRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4209	torRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4210	rbsizer3.Add(torRange,0,wx.ALIGN_CENTER_VERTICAL)
4211	rbsizer.Add(rbsizer3)
4212
4213	return rbsizer
4214
4215	def MDSizer(POData):
4216
4217	def OnPORef(event):
4218	POData['Coef'][1] = poRef.GetValue()
4219
4220	def OnPOVal(event):
4221	try:
4222	mdVal = float(poVal.GetValue())
4223	if mdVal > 0:
4224	POData['Coef'][0] = mdVal
4225	except ValueError:
4226	pass
4227	poVal.SetValue("%.3f"%(POData['Coef'][0]))
4228
4229	def OnPORange(event):
4230	Range = poRange.GetValue().split()
4231	try:
4232	rmin,rmax = [float(Range[i]) for i in range(2)]
4233	if 0. < rmin < rmax:
4234	pass
4235	else:
4236	raise ValueError
4237	except (ValueError,IndexError):
4238	rmin,rmax = POData['Coef'][2]
4239	POData['Coef'][2] = [rmin,rmax]
4240	poRange.SetValue('%.3f %.3f'%(rmin,rmax))
4241
4242	def OnPOAxis(event):
4243	Saxis = poAxis.GetValue().split()
4244	try:
4245	hkl = [int(Saxis[i]) for i in range(3)]
4246	except (ValueError,IndexError):
4247	hkl = POData['axis']
4248	if not np.any(np.array(hkl)):
4249	hkl = POData['axis']
4250	POData['axis'] = hkl
4251	h,k,l = hkl
4252	poAxis.SetValue('%3d %3d %3d'%(h,k,l))
4253
4254	poSizer = wx.BoxSizer(wx.HORIZONTAL)
4255	poRef = wx.CheckBox(MCSA,-1,label=' March-Dollase ratio: ')
4256	poRef.SetValue(POData['Coef'][1])
4257	poRef.Bind(wx.EVT_CHECKBOX,OnPORef)
4258	poSizer.Add(poRef,0,wx.ALIGN_CENTER_VERTICAL)
4259	poVal = wx.TextCtrl(MCSA,-1,'%.3f'%(POData['Coef'][0]),style=wx.TE_PROCESS_ENTER)
4260	poVal.Bind(wx.EVT_TEXT_ENTER,OnPOVal)
4261	poVal.Bind(wx.EVT_KILL_FOCUS,OnPOVal)
4262	poSizer.Add(poVal,0,wx.ALIGN_CENTER_VERTICAL)
4263	poSizer.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4264	rmin,rmax = POData['Coef'][2]
4265	poRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4266	poRange.Bind(wx.EVT_TEXT_ENTER,OnPORange)
4267	poRange.Bind(wx.EVT_KILL_FOCUS,OnPORange)
4268	poSizer.Add(poRange,0,wx.ALIGN_CENTER_VERTICAL)
4269	poSizer.Add(wx.StaticText(MCSA,-1,' Unique axis, H K L: '),0,wx.ALIGN_CENTER_VERTICAL)
4270	h,k,l = POData['axis']
4271	poAxis = wx.TextCtrl(MCSA,-1,'%3d %3d %3d'%(h,k,l),style=wx.TE_PROCESS_ENTER)
4272	poAxis.Bind(wx.EVT_TEXT_ENTER,OnPOAxis)
4273	poAxis.Bind(wx.EVT_KILL_FOCUS,OnPOAxis)
4274	poSizer.Add(poAxis,0,wx.ALIGN_CENTER_VERTICAL)
4275	return poSizer
4276
4277	def ResultsSizer(Results):
4278
4279	def OnCellChange(event):
4280	r,c = event.GetRow(),event.GetCol()
4281	if c == 0:
4282	for row in range(resultsGrid.GetNumberRows()):
4283	resultsTable.SetValue(row,c,False)
4284	Results[row][0] = False
4285	result = Results[r]
4286	Models = data['MCSA']['Models']
4287	SetSolution(result,Models)
4288	Results[r][0] = True
4289	resultsTable.SetValue(r,0,True)
4290	G2plt.PlotStructure(G2frame,data)
4291	wx.CallAfter(UpdateMCSA,MCSA.GetScrollPos(wx.VERTICAL))
4292	resultsGrid.ForceRefresh()
4293	elif c == 1:
4294	if Results[r][1]:
4295	Results[r][1] = False
4296	else:
4297	Results[r][1] = True
4298	resultsTable.SetValue(r,c,Results[r][1])
4299	resultsGrid.ForceRefresh()
4300
4301	resultsSizer = wx.BoxSizer(wx.VERTICAL)
4302	maxVary = 0
4303	resultVals = []
4304	for result in Results:
4305	maxVary = max(maxVary,len(result[-1]))
4306	resultVals.append(result[:-1])
4307	rowLabels = []
4308	for i in range(len(Results)): rowLabels.append(str(i))
4309	colLabels = ['Select','Keep','Residual','Tmin',]
4310	for item in result[-1]: colLabels.append(item) #from last result from for loop above
4311	Types = [wg.GRID_VALUE_BOOL,wg.GRID_VALUE_BOOL,wg.GRID_VALUE_FLOAT+':10,4',
4312	wg.GRID_VALUE_FLOAT+':10,4',]+maxVary*[wg.GRID_VALUE_FLOAT+':10,5',]
4313	resultsTable = G2gd.Table(resultVals,rowLabels=rowLabels,colLabels=colLabels,types=Types)
4314	resultsGrid = G2gd.GSGrid(MCSA)
4315	resultsGrid.SetTable(resultsTable, True)
4316	resultsGrid.Bind(wg.EVT_GRID_CELL_LEFT_CLICK, OnCellChange)
4317	resultsGrid.AutoSizeColumns(True)
4318	for r in range(resultsGrid.GetNumberRows()):
4319	for c in range(resultsGrid.GetNumberCols()):
4320	if c in [0,1]:
4321	resultsGrid.SetReadOnly(r,c,isReadOnly=False)
4322	else:
4323	resultsGrid.SetCellStyle(r,c,VERY_LIGHT_GREY,True)
4324	resultsSizer.Add(resultsGrid)
4325	return resultsSizer
4326
4327	# UpdateMCSA executable code starts here
4328	MCSA.DestroyChildren()
4329	general = data['General']
4330	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
4331	RBData = G2frame.PatternTree.GetItemPyData(
4332	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4333	Indx = {}
4334	atomStyle = 'balls & sticks'
4335	if 'macro' in general['Type']:
4336	atomStyle = 'sticks'
4337	G2frame.dataFrame.SetStatusText('')
4338	mainSizer = wx.BoxSizer(wx.VERTICAL)
4339	if not data['MCSA']['Models']:
4340	mainSizer.Add((5,5),0)
4341	mainSizer.Add(wx.StaticText(MCSA,-1,'No MC/SA models:'),0,wx.ALIGN_CENTER_VERTICAL)
4342	mainSizer.Add((5,5),0)
4343	else:
4344	mainSizer.Add((5,5),0)
4345	mainSizer.Add(wx.StaticText(MCSA,-1,'MC/SA models:'),0,wx.ALIGN_CENTER_VERTICAL)
4346	mainSizer.Add((5,5),0)
4347	for model in data['MCSA']['Models']:
4348	Xsize = 500
4349	if model['Type'] == 'MD':
4350	mainSizer.Add(MDSizer(model))
4351	elif model['Type'] == 'Atom':
4352	Asizer = atomSizer(model)
4353	mainSizer.Add(Asizer)
4354	Xsize = max(Asizer.GetMinSize()[0],Xsize)
4355	else:
4356	Rsizer = rbSizer(model)
4357	mainSizer.Add(Rsizer)
4358	Xsize = max(Rsizer.GetMinSize()[0],Xsize)
4359	G2gd.HorizontalLine(mainSizer,MCSA)
4360
4361	if not data['MCSA']['Results']:
4362	mainSizer.Add((5,5),0)
4363	mainSizer.Add(wx.StaticText(MCSA,-1,'No MC/SA results:'),0,wx.ALIGN_CENTER_VERTICAL)
4364	mainSizer.Add((5,5),0)
4365	else:
4366	mainSizer.Add((5,5),0)
4367	mainSizer.Add(wx.StaticText(MCSA,-1,'MC/SA results:'),0,wx.ALIGN_CENTER_VERTICAL)
4368	mainSizer.Add((5,5),0)
4369	Results = data['MCSA']['Results']
4370	mainSizer.Add(ResultsSizer(Results))
4371
4372	SetPhaseWindow(G2frame.dataFrame,MCSA,mainSizer)
4373	Size = MCSA.GetSize()
4374	Size[0] = Xsize+40
4375	G2frame.dataFrame.SetSize(Size)
4376	MCSA.Scroll(0,Scroll)
4377
4378	def SetSolution(result,Models):
4379	for key,val in zip(result[-1],result[4:-1]):
4380	vals = key.split(':')
4381	nObj,name = int(vals[0]),vals[1]
4382	if 'A' in name:
4383	ind = ['Ax','Ay','Az'].index(name)
4384	Models[nObj]['Pos'][0][ind] = val
4385	elif 'Q' in name:
4386	ind = ['Qa','Qi','Qj','Qk'].index(name)
4387	Models[nObj]['Ori'][0][ind] = val
4388	elif 'P' in name:
4389	ind = ['Px','Py','Pz'].index(name)
4390	Models[nObj]['Pos'][0][ind] = val
4391	elif 'T' in name:
4392	tnum = int(name.split('Tor')[1])
4393	Models[nObj]['Tor'][0][tnum] = val
4394	else: #March Dollase
4395	Models[0]['Coef'][0] = val
4396
4397	def OnRunMultiMCSA(event):
4398	RunMCSA('multi')
4399
4400	def OnRunSingleMCSA(event):
4401	RunMCSA('single')
4402
4403	def RunMCSA(process):
4404	generalData = data['General']
4405	mcsaControls = generalData['MCSA controls']
4406	reflName = mcsaControls['Data source']
4407	phaseName = generalData['Name']
4408	MCSAdata = data['MCSA']
4409	saveResult = []
4410	for result in MCSAdata['Results']:
4411	if result[1]: #keep?
4412	saveResult.append(result)
4413	MCSAdata['Results'] = saveResult
4414	covData = {}
4415	if 'PWDR' in reflName:
4416	PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, reflName)
4417	reflSets = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
4418	try: #patch for old reflection data
4419	reflData = reflSets[phaseName]['RefList']
4420	except TypeError:
4421	reflData = reflSets[phaseName]
4422	reflType = 'PWDR'
4423	elif 'HKLF' in reflName:
4424	PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, reflName)
4425	try:
4426	reflData = G2frame.PatternTree.GetItemPyData(PatternId)[1]['RefList']
4427	except TypeError:
4428	reflData = G2frame.PatternTree.GetItemPyData(PatternId)[1]
4429	reflType = 'HKLF'
4430	elif reflName == 'Pawley reflections':
4431	reflData = data['Pawley ref']
4432	covData = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
4433	reflType = 'Pawley'
4434	else:
4435	print '**** ERROR - No data defined for MC/SA run'
4436	return
4437	print 'MC/SA run:'
4438	print 'Reflection type:',reflType,' Total No. reflections: ',len(reflData)
4439	RBdata = G2frame.PatternTree.GetItemPyData(
4440	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4441	MCSAmodels = MCSAdata['Models']
4442	if not len(MCSAmodels):
4443	print '** ERROR - no models defined for MC/SA run**'
4444	return
4445	time1 = time.time()
4446	if process == 'single':
4447	pgbar = wx.ProgressDialog('MC/SA','Residual Rcf =',101.0,
4448	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
4449	screenSize = wx.ClientDisplayRect()
4450	Size = pgbar.GetSize()
4451	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
4452	pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
4453	pgbar.SetSize(Size)
4454	else:
4455	pgbar = None
4456	try:
4457	tsf = 0.
4458	nCyc = mcsaControls['Cycles']
4459	if process == 'single':
4460	for i in range(nCyc):
4461	Result,tsum = G2mth.mcsaSearch(data,RBdata,reflType,reflData,covData,pgbar)
4462	MCSAdata['Results'].append(Result)
4463	print ' MC/SA run completed: %d residual: %.3f%% SFcalc time: %.2fs'%(i,100*Result[2],tsum)
4464	tsf += tsum
4465	print ' Structure factor time: %.2f'%(tsf)
4466	else:
4467	MCSAdata['Results'] = G2mth.MPmcsaSearch(nCyc,data,RBdata,reflType,reflData,covData)
4468	print ' MC/SA run time: %.2f'%(time.time()-time1)
4469	finally:
4470	if process == 'single':
4471	pgbar.Destroy()
4472	MCSAdata['Results'] = G2mth.sortArray(MCSAdata['Results'],2,reverse=False)
4473	MCSAdata['Results'][0][0] = True
4474	SetSolution(MCSAdata['Results'][0],data['MCSA']['Models'])
4475	G2frame.dataDisplay.SetFocus()
4476	Page = G2frame.dataDisplay.FindPage('MC/SA')
4477	G2frame.dataDisplay.SetSelection(Page)
4478	G2plt.PlotStructure(G2frame,data)
4479	wx.CallAfter(UpdateMCSA)
4480
4481	def OnMCSAaddAtom(event):
4482	dlg = G2elemGUI.PickElement(G2frame)
4483	if dlg.ShowModal() == wx.ID_OK:
4484	El = dlg.Elem.strip()
4485	Info = G2elem.GetAtomInfo(El)
4486	dlg.Destroy()
4487
4488	atom = {'Type':'Atom','atType':El,'Pos':[[0.,0.,0.],
4489	[False,False,False],[[0.,1.],[0.,1.],[0.,1.]]],
4490	'name':El+'('+str(len(data['MCSA']['Models']))+')'}
4491	data['MCSA']['Models'].append(atom)
4492	data['MCSA']['AtInfo'][El] = [Info['Drad'],Info['Color']]
4493	G2plt.PlotStructure(G2frame,data)
4494	UpdateMCSA()
4495
4496	def OnMCSAaddRB(event):
4497	rbData = G2frame.PatternTree.GetItemPyData(
4498	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4499	rbNames = {}
4500	for rbVec in rbData['Vector']:
4501	if rbVec != 'AtInfo':
4502	rbNames[rbData['Vector'][rbVec]['RBname']] = ['Vector',rbVec]
4503	for rbRes in rbData['Residue']:
4504	if rbRes != 'AtInfo':
4505	rbNames[rbData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
4506	if not rbNames:
4507	print '** ERROR - no rigid bodies defined **'
4508	return
4509	dlg = wx.SingleChoiceDialog(G2frame.dataFrame,'Select','Rigid body',rbNames.keys())
4510	if dlg.ShowModal() == wx.ID_OK:
4511	sel = dlg.GetSelection()
4512	rbname = rbNames.keys()[sel]
4513	rbType,rbId = rbNames[rbname]
4514	RB = rbData[rbType][rbId]
4515	body = {'name':RB['RBname']+'('+str(len(data['MCSA']['Models']))+')','RBId':rbId,'Type':rbType,
4516	'Pos':[[0.,0.,0.],[False,False,False],[[0.,1.],[0.,1.],[0.,1.]]],'Ovar':'','MolCent':[[0.,0.,0.],False],
4517	'Ori':[[180.,0.,0.,1.],[False,False,False,False],[[0.,360.],[-1.,1.],[-1.,1.],[-1.,1.]]]}
4518	if rbType == 'Residue':
4519	body['Tor'] = [[],[],[]]
4520	for i,tor in enumerate(RB['rbSeq']):
4521	body['Tor'][0].append(0.0)
4522	body['Tor'][1].append(False)
4523	body['Tor'][2].append([0.,360.])
4524	data['MCSA']['Models'].append(body)
4525	data['MCSA']['rbData'] = rbData
4526	data['MCSA']['AtInfo'].update(rbData[rbType]['AtInfo'])
4527	G2plt.PlotStructure(G2frame,data)
4528	UpdateMCSA()
4529
4530	def OnMCSAclear(event):
4531	data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
4532	G2plt.PlotStructure(G2frame,data)
4533	UpdateMCSA()
4534
4535	def OnMCSAmove(event):
4536	general = data['General']
4537	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
4538	xyz,aTypes = G2mth.UpdateMCSAxyz(Bmat,data['MCSA'])
4539	for iat,atype in enumerate(aTypes):
4540	x,y,z = xyz[iat]
4541	AtomAdd(x,y,z,atype,Name=atype+'(%d)'%(iat+1))
4542	G2plt.PlotStructure(G2frame,data)
4543
4544	def OnClearResults(event):
4545	data['MCSA']['Results'] = []
4546	UpdateMCSA()
4547
4548	################################################################################
4549	##### Pawley routines
4550	################################################################################
4551
4552	def FillPawleyReflectionsGrid():
4553	def KeyEditPawleyGrid(event):
4554	colList = G2frame.PawleyRefl.GetSelectedCols()
4555	rowList = G2frame.PawleyRefl.GetSelectedRows()
4556	PawleyPeaks = data['Pawley ref']
4557	if event.GetKeyCode() == wx.WXK_RETURN:
4558	event.Skip(True)
4559	elif event.GetKeyCode() == wx.WXK_CONTROL:
4560	event.Skip(True)
4561	elif event.GetKeyCode() == wx.WXK_SHIFT:
4562	event.Skip(True)
4563	elif colList:
4564	G2frame.PawleyRefl.ClearSelection()
4565	key = event.GetKeyCode()
4566	for col in colList:
4567	if PawleyTable.GetTypeName(0,col) == wg.GRID_VALUE_BOOL:
4568	if key == 89: #'Y'
4569	for row in range(PawleyTable.GetNumberRows()): PawleyPeaks[row][col]=True
4570	elif key == 78: #'N'
4571	for row in range(PawleyTable.GetNumberRows()): PawleyPeaks[row][col]=False
4572	FillPawleyReflectionsGrid()
4573	elif rowList:
4574	if event.GetKeyCode() == wx.WXK_DELETE:
4575	rowList.reverse()
4576	for row in rowList:
4577	del(PawleyPeaks[row])
4578	FillPawleyReflectionsGrid()
4579
4580	# FillPawleyReflectionsGrid executable starts here
4581	G2frame.dataFrame.SetStatusText('To delete a few Pawley reflections: select rows & press Delete')
4582	if 'Pawley ref' in data:
4583	PawleyPeaks = data['Pawley ref']
4584	rowLabels = []
4585	for i in range(len(PawleyPeaks)): rowLabels.append(str(i))
4586	colLabels = ['h','k','l','mul','d','refine','Fsq(hkl)','sig(Fsq)']
4587	Types = 4*[wg.GRID_VALUE_LONG,]+[wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL,]+ \
4588	2*[wg.GRID_VALUE_FLOAT+':10,2',]
4589	PawleyTable = G2gd.Table(PawleyPeaks,rowLabels=rowLabels,colLabels=colLabels,types=Types)
4590	G2frame.PawleyRefl.SetTable(PawleyTable, True)
4591	G2frame.PawleyRefl.Bind(wx.EVT_KEY_DOWN, KeyEditPawleyGrid)
4592	for r in range(G2frame.PawleyRefl.GetNumberRows()):
4593	for c in range(G2frame.PawleyRefl.GetNumberCols()):
4594	if c in [5,6]:
4595	G2frame.PawleyRefl.SetReadOnly(r,c,isReadOnly=False)
4596	else:
4597	G2frame.PawleyRefl.SetCellStyle(r,c,VERY_LIGHT_GREY,True)
4598	G2frame.PawleyRefl.SetMargins(0,0)
4599	G2frame.PawleyRefl.AutoSizeColumns(False)
4600	G2frame.dataFrame.setSizePosLeft([450,300])
4601
4602	def OnPawleyLoad(event):
4603	generalData = data['General']
4604	dmin = generalData['Pawley dmin']
4605	cell = generalData['Cell'][1:7]
4606	A = G2lat.cell2A(cell)
4607	SGData = generalData['SGData']
4608	HKLd = np.array(G2lat.GenHLaue(dmin,SGData,A))
4609	PawleyPeaks = []
4610	wx.BeginBusyCursor()
4611	try:
4612	for h,k,l,d in HKLd:
4613	ext,mul = G2spc.GenHKLf([h,k,l],SGData)[:2]
4614	if not ext:
4615	mul *= 2 #for powder multiplicity
4616	PawleyPeaks.append([h,k,l,mul,d,False,100.0,1.0])
4617	finally:
4618	wx.EndBusyCursor()
4619	data['Pawley ref'] = PawleyPeaks
4620	FillPawleyReflectionsGrid()
4621
4622	def OnPawleyEstimate(event):
4623	try:
4624	Refs = data['Pawley ref']
4625	Histograms = data['Histograms']
4626	except KeyError:
4627	G2frame.ErrorDialog('Pawley estimate','No histograms defined for this phase')
4628	return
4629	HistoNames = Histograms.keys()
4630	PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,HistoNames[0])
4631	xdata = G2frame.PatternTree.GetItemPyData(PatternId)[1]
4632	Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Instrument Parameters'))[0]
4633	Sample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Sample Parameters'))
4634	wave = G2mth.getWave(Inst)
4635	posCorr = Inst['Zero'][1]
4636	const = 9.e-2/(np.pi*Sample['Gonio. radius']) #shifts in microns
4637
4638	wx.BeginBusyCursor()
4639	try:
4640	for ref in Refs:
4641	pos = 2.0asind(wave/(2.0ref[4]))
4642	if 'Bragg' in Sample['Type']:
4643	pos -= const(4.Sample['Shift'][0]*cosd(pos/2.0)+ \
4644	Sample['Transparency'][0]sind(pos)100.0) #trans(=1/mueff) in cm
4645	else: #Debye-Scherrer - simple but maybe not right
4646	pos -= const(Sample['DisplaceX'][0]cosd(pos)+Sample['DisplaceY'][0]*sind(pos))
4647	indx = np.searchsorted(xdata[0],pos)
4648	try:
4649	FWHM = max(0.001,G2pwd.getFWHM(pos,Inst))/2.
4650	dx = xdata[0][indx+1]-xdata[0][indx]
4651	ref[6] = FWHM(xdata[1][indx]-xdata[4][indx])cosd(pos/2.)**3/dx
4652	Lorenz = 1./(2.sind(xdata[0][indx]/2.)2cosd(xdata[0][indx]/2.)) #Lorentz correction
4653	pola,dIdPola = G2pwd.Polarization(Inst['Polariz.'][1],xdata[0][indx],Inst['Azimuth'][1])
4654	ref[6] /= (Lorenzpolaref[3])
4655	except IndexError:
4656	pass
4657	finally:
4658	wx.EndBusyCursor()
4659	FillPawleyReflectionsGrid()
4660
4661	def OnPawleyUpdate(event):
4662	'''This is the place for any reflection modification trick
4663	Patterson squared, leBail extraction, etc.
4664	'''
4665	try:
4666	Refs = data['Pawley ref']
4667	Histograms = data['Histograms']
4668	except KeyError:
4669	G2frame.ErrorDialog('Pawley update','No histograms defined for this phase')
4670	return
4671	HistoNames = Histograms.keys()
4672	PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,HistoNames[0])
4673	refData = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))[PhaseName]
4674	Inv = data['General']['SGData']['SGInv']
4675	mult = 0.5
4676	if Inv:
4677	mult = 0.3
4678	wx.BeginBusyCursor()
4679	try:
4680	for iref,ref in enumerate(Refs):
4681	try:
4682	if ref[6] < 0.:
4683	ref[6] *= -mult
4684	refData[iref][8] *= -mult
4685	refData[iref][9] *= -mult
4686	ref[5] = False
4687	ref[7] = 1.0
4688	except IndexError:
4689	print 'skipped',ref
4690	pass
4691	finally:
4692	wx.EndBusyCursor()
4693	wx.CallAfter(FillPawleyReflectionsGrid)
4694
4695	################################################################################
4696	##### Fourier routines
4697	################################################################################
4698
4699	def FillMapPeaksGrid():
4700
4701	def RowSelect(event):
4702	r,c = event.GetRow(),event.GetCol()
4703	if r < 0 and c < 0:
4704	if MapPeaks.IsSelection():
4705	MapPeaks.ClearSelection()
4706	else:
4707	for row in range(MapPeaks.GetNumberRows()):
4708	MapPeaks.SelectRow(row,True)
4709
4710	elif c < 0: #only row clicks
4711	if event.ControlDown():
4712	if r in MapPeaks.GetSelectedRows():
4713	MapPeaks.DeselectRow(r)
4714	else:
4715	MapPeaks.SelectRow(r,True)
4716	elif event.ShiftDown():
4717	indxs = MapPeaks.GetSelectedRows()
4718	MapPeaks.ClearSelection()
4719	ibeg = 0
4720	if indxs:
4721	ibeg = indxs[-1]
4722	for row in range(ibeg,r+1):
4723	MapPeaks.SelectRow(row,True)
4724	else:
4725	MapPeaks.ClearSelection()
4726	MapPeaks.SelectRow(r,True)
4727	elif r < 0: #a column pick
4728	mapPeaks = data['Map Peaks']
4729	c = event.GetCol()
4730	if colLabels[c] == 'mag':
4731	mapPeaks = G2mth.sortArray(mapPeaks,c,reverse=True)
4732	elif colLabels[c] in ['x','y','z','dzero']:
4733	mapPeaks = G2mth.sortArray(mapPeaks,c)
4734	else:
4735	return
4736	data['Map Peaks'] = mapPeaks
4737	wx.CallAfter(FillMapPeaksGrid)
4738	G2plt.PlotStructure(G2frame,data)
4739
4740	G2frame.dataFrame.setSizePosLeft([450,300])
4741	G2frame.dataFrame.SetStatusText('')
4742	if 'Map Peaks' in data:
4743	G2frame.dataFrame.SetStatusText('Select mag or dzero columns to sort')
4744	mapPeaks = data['Map Peaks']
4745	rowLabels = []
4746	for i in range(len(mapPeaks)): rowLabels.append(str(i))
4747	colLabels = ['mag','x','y','z','dzero']
4748	Types = 5*[wg.GRID_VALUE_FLOAT+':10,4',]
4749	G2frame.MapPeaksTable = G2gd.Table(mapPeaks,rowLabels=rowLabels,colLabels=colLabels,types=Types)
4750	MapPeaks.SetTable(G2frame.MapPeaksTable, True)
4751	MapPeaks.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
4752	for r in range(MapPeaks.GetNumberRows()):
4753	for c in range(MapPeaks.GetNumberCols()):
4754	MapPeaks.SetCellStyle(r,c,VERY_LIGHT_GREY,True)
4755	MapPeaks.SetMargins(0,0)
4756	MapPeaks.AutoSizeColumns(False)
4757
4758	def OnPeaksMove(event):
4759	if 'Map Peaks' in data:
4760	mapPeaks = np.array(data['Map Peaks'])
4761	peakMax = np.max(mapPeaks.T[0])
4762	Ind = MapPeaks.GetSelectedRows()
4763	for ind in Ind:
4764	mag,x,y,z,d = mapPeaks[ind]
4765	AtomAdd(x,y,z,'H',Name='M '+'%d'%(int(100*mag/peakMax)))
4766	G2plt.PlotStructure(G2frame,data)
4767
4768	def OnPeaksClear(event):
4769	data['Map Peaks'] = []
4770	FillMapPeaksGrid()
4771	G2plt.PlotStructure(G2frame,data)
4772
4773	def OnPeaksDelete(event):
4774	if 'Map Peaks' in data:
4775	mapPeaks = data['Map Peaks']
4776	Ind = MapPeaks.GetSelectedRows()
4777	Ind.sort()
4778	Ind.reverse()
4779	for ind in Ind:
4780	mapPeaks = np.delete(mapPeaks,ind,0)
4781	data['Map Peaks'] = mapPeaks
4782	FillMapPeaksGrid()
4783	G2plt.PlotStructure(G2frame,data)
4784
4785	def OnPeaksEquiv(event):
4786	if 'Map Peaks' in data:
4787	mapPeaks = data['Map Peaks']
4788	Ind = MapPeaks.GetSelectedRows()
4789	if Ind:
4790	wx.BeginBusyCursor()
4791	try:
4792	Ind = G2mth.PeaksEquiv(data,Ind)
4793	for r in range(MapPeaks.GetNumberRows()):
4794	if r in Ind:
4795	MapPeaks.SelectRow(r,addToSelected=True)
4796	else:
4797	MapPeaks.DeselectRow(r)
4798	finally:
4799	wx.EndBusyCursor()
4800	G2plt.PlotStructure(G2frame,data)
4801
4802	def OnShowBonds(event):
4803	generalData = data['General']
4804	if generalData['Map'].get('Show bonds',False):
4805	generalData['Map']['Show bonds'] = False
4806	G2frame.dataFrame.MapPeaksEdit.SetLabel(G2gd.wxID_SHOWBONDS,'Show bonds')
4807	else:
4808	generalData['Map']['Show bonds'] = True
4809	G2frame.dataFrame.MapPeaksEdit.SetLabel(G2gd.wxID_SHOWBONDS,'Hide bonds')
4810	FillMapPeaksGrid()
4811	G2plt.PlotStructure(G2frame,data)
4812
4813	def OnPeaksUnique(event):
4814	if 'Map Peaks' in data:
4815	mapPeaks = data['Map Peaks']
4816	Ind = MapPeaks.GetSelectedRows()
4817	if Ind:
4818	wx.BeginBusyCursor()
4819	try:
4820	Ind = G2mth.PeaksUnique(data,Ind)
4821	for r in range(MapPeaks.GetNumberRows()):
4822	if r in Ind:
4823	MapPeaks.SelectRow(r,addToSelected=True)
4824	else:
4825	MapPeaks.DeselectRow(r)
4826	finally:
4827	wx.EndBusyCursor()
4828	G2plt.PlotStructure(G2frame,data)
4829
4830	def OnPeaksViewPoint(event):
4831	# set view point
4832	indx = MapPeaks.GetSelectedRows()
4833	if not indx:
4834	G2frame.ErrorDialog('Set viewpoint','No peaks selected')
4835	return
4836	mapPeaks = data['Map Peaks']
4837	drawingData = data['Drawing']
4838	drawingData['viewPoint'][0] = mapPeaks[indx[0]][1:4]
4839	G2plt.PlotStructure(G2frame,data)
4840
4841	def OnPeaksDistVP(event):
4842	# distance to view point
4843	indx = MapPeaks.GetSelectedRows()
4844	if not indx:
4845	G2frame.ErrorDialog('Peak distance','No peaks selected')
4846	return
4847	generalData = data['General']
4848	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
4849	mapPeaks = data['Map Peaks']
4850	drawingData = data['Drawing']
4851	viewPt = np.array(drawingData['viewPoint'][0])
4852	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
4853	colLabels = [MapPeaks.GetColLabelValue(c) for c in range(MapPeaks.GetNumberCols())]
4854	cx = colLabels.index('x')
4855	cm = colLabels.index('mag')
4856	for i in indx:
4857	peak = mapPeaks[i]
4858	Dx = np.array(peak[cx:cx+3])-viewPt
4859	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
4860	print 'Peak: %5d mag= %8.2f distance = %.3f'%(i,peak[cm],dist)
4861
4862	def OnPeaksDA(event):
4863	#distance, angle
4864	indx = MapPeaks.GetSelectedRows()
4865	if len(indx) not in [2,3]:
4866	G2frame.ErrorDialog('Peak distance/angle','Wrong number of atoms for distance or angle calculation')
4867	return
4868	generalData = data['General']
4869	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
4870	mapPeaks = data['Map Peaks']
4871	xyz = []
4872	for i in indx:
4873	xyz.append(mapPeaks[i][1:4])
4874	if len(indx) == 2:
4875	print ' distance for atoms %s = %.3f'%(str(indx),G2mth.getRestDist(xyz,Amat))
4876	else:
4877	print ' angle for atoms %s = %.2f'%(str(indx),G2mth.getRestAngle(xyz,Amat))
4878
4879	def OnFourierMaps(event):
4880	generalData = data['General']
4881	mapData = generalData['Map']
4882	reflName = mapData['RefList']
4883	if not reflName:
4884	G2frame.ErrorDialog('Fourier map','No reflections defined for Fourier map')
4885	return
4886	phaseName = generalData['Name']
4887	if 'PWDR' in reflName:
4888	PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, reflName)
4889	reflSets = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
4890	reflData = reflSets[phaseName]
4891	if isinstance(reflData,list): #patch for old reflection data
4892	RefData = {'RefList':[],'FF':[]}
4893	for ref in reflData:
4894	RefData['RefList'].append(ref[:11]+[ref[13],])
4895	RefData['FF'].append(ref[14])
4896	RefData['RefList'] = np.array(RefData['RefList'])
4897	reflData = RefData
4898	elif 'HKLF' in reflName:
4899	PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, reflName)
4900	reflData = G2frame.PatternTree.GetItemPyData(PatternId)[1]
4901	if 'Omit' in mapData['MapType']:
4902	pgbar = wx.ProgressDialog('Omit map','Blocks done',65,
4903	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE)
4904	mapData.update(G2mth.OmitMap(data,reflData,pgbar))
4905	pgbar.Destroy()
4906	else:
4907	mapData.update(G2mth.FourierMap(data,reflData))
4908	mapData['Flip'] = False
4909	mapSig = np.std(mapData['rho'])
4910	if not data['Drawing']: #if new drawing - no drawing data!
4911	SetupDrawingData()
4912	data['Drawing']['contourLevel'] = 1.
4913	data['Drawing']['mapSize'] = 10.
4914	print mapData['MapType']+' computed: rhomax = %.3f rhomin = %.3f sigma = %.3f'%(np.max(mapData['rho']),np.min(mapData['rho']),mapSig)
4915	UpdateDrawAtoms()
4916	G2plt.PlotStructure(G2frame,data)
4917
4918	def OnFourClear(event):
4919	generalData = data['General']
4920	generalData['Map'] = mapDefault
4921	G2plt.PlotStructure(G2frame,data)
4922
4923	def printRho(SGLaue,rho,rhoMax):
4924	# map printing for testing purposes
4925	dim = len(rho.shape)
4926	if dim == 2:
4927	ix,jy = rho.shape
4928	for j in range(jy):
4929	line = ''
4930	if SGLaue in ['3','3m1','31m','6/m','6/mmm']:
4931	line += (jy-j)*' '
4932	for i in range(ix):
4933	r = int(100*rho[i,j]/rhoMax)
4934	line += '%4d'%(r)
4935	print line+'\n'
4936	else:
4937	ix,jy,kz = rho.shape
4938	for k in range(kz):
4939	print 'k = ',k
4940	for j in range(jy):
4941	line = ''
4942	if SGLaue in ['3','3m1','31m','6/m','6/mmm']:
4943	line += (jy-j)*' '
4944	for i in range(ix):
4945	r = int(100*rho[i,j,k]/rhoMax)
4946	line += '%4d'%(r)
4947	print line+'\n'
4948	## keep this
4949
4950	def OnSearchMaps(event):
4951
4952	peaks = []
4953	mags = []
4954	print ' Begin fourier map search - can take some time'
4955	time0 = time.time()
4956	generalData = data['General']
4957	mapData = generalData['Map']
4958	if len(mapData['rho']):
4959	wx.BeginBusyCursor()
4960	try:
4961	peaks,mags,dzeros = G2mth.SearchMap(data)
4962	finally:
4963	wx.EndBusyCursor()
4964	if len(peaks):
4965	mapPeaks = np.concatenate((mags,peaks,dzeros),axis=1)
4966	data['Map Peaks'] = G2mth.sortArray(mapPeaks,0,reverse=True)
4967	print ' Map search finished, time = %.2fs'%(time.time()-time0)
4968	print ' No.peaks found:',len(peaks)
4969	Page = G2frame.dataDisplay.FindPage('Map peaks')
4970	G2frame.dataDisplay.SetSelection(Page)
4971	wx.CallAfter(FillMapPeaksGrid)
4972	UpdateDrawAtoms()
4973	else:
4974	print 'No map available'
4975
4976	def OnChargeFlip(event):
4977	generalData = data['General']
4978	mapData = generalData['Map']
4979	flipData = generalData['Flip']
4980	reflName = flipData['RefList']
4981	phaseName = generalData['Name']
4982	if 'PWDR' in reflName:
4983	PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, reflName)
4984	reflSets = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
4985	reflDict = reflSets[phaseName]
4986	if isinstance(reflDict,list): #patch for old reflection data
4987	RefData = {'RefList':[],'FF':[]}
4988	for ref in reflDict:
4989	RefData['RefList'].append(ref[:11]+[ref[13],])
4990	RefData['FF'].append(ref[14])
4991	RefData['RefList'] = np.array(RefData['RefList'])
4992	reflDict = RefData
4993	elif 'HKLF' in reflName:
4994	PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, reflName)
4995	reflDict = G2frame.PatternTree.GetItemPyData(PatternId)[1]
4996	else:
4997	print '**** ERROR - No data defined for charge flipping'
4998	return
4999	pgbar = wx.ProgressDialog('Charge flipping','Residual Rcf =',101.0,
5000	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
5001	screenSize = wx.ClientDisplayRect()
5002	Size = pgbar.GetSize()
5003	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
5004	pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
5005	pgbar.SetSize(Size)
5006	try:
5007	mapData.update(G2mth.ChargeFlip(data,reflDict,pgbar))
5008	finally:
5009	pgbar.Destroy()
5010	mapData['Flip'] = True
5011	mapSig = np.std(mapData['rho'])
5012	if not data['Drawing']: #if new drawing - no drawing data!
5013	SetupDrawingData()
5014	data['Drawing']['contourLevel'] = 1.
5015	data['Drawing']['mapSize'] = 10.
5016	print ' Charge flip map computed: rhomax = %.3f rhomin = %.3f sigma = %.3f'%(np.max(mapData['rho']),np.min(mapData['rho']),mapSig)
5017	if mapData['Rcf'] < 99.:
5018	OnSearchMaps(event) #does a plot structure at end
5019	else:
5020	print 'Bad charge flip map - no peak search done'
5021
5022	def OnTextureRefine(event):
5023	print 'refine texture?'
5024	event.Skip()
5025
5026	def OnTextureClear(event):
5027	print 'clear texture?'
5028	event.Skip()
5029
5030	def FillSelectPageMenu(menuBar):
5031	'''Assign bindings to the menu buttons to switch between phase tabs;
5032	define a dictionary with the page index for each tab
5033	'''
5034	def OnSelectPage(event):
5035	'Called when an item is selected from the Select page menu'
5036	page = Pagedict.get(event.GetId())
5037	if page is not None: G2frame.dataDisplay.SetSelection(page)
5038	mid = menuBar.FindMenu('Select tab')
5039	Pagedict = {}
5040	for ipage,page in enumerate(Pages):
5041	menu = menuBar.GetMenu(mid)
5042	if menu.FindItem(page) < 0:
5043	Id = wx.NewId()
5044	menu.Append(id=Id,kind=wx.ITEM_NORMAL,text=page)
5045	G2frame.Bind(wx.EVT_MENU, OnSelectPage, id=Id)
5046	Pagedict[Id] = ipage
5047
5048
5049	def OnPageChanged(event):
5050	'''This is called every time that a Notebook tab button is pressed
5051	on a Phase data item window
5052	'''
5053	for page in G2frame.dataDisplay.gridList: # clear out all grids, forcing edits in progress to complete
5054	page.ClearGrid()
5055	wx.Frame.Unbind(G2frame.dataFrame,wx.EVT_SIZE) # ignore size events during this routine
5056	page = event.GetSelection()
5057	ChangePage(page)
5058
5059	def ChangePage(page):
5060	text = G2frame.dataDisplay.GetPageText(page)
5061	# print 'Select',page,text
5062	if text == 'General':
5063	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.DataGeneral)
5064	FillSelectPageMenu(G2frame.dataFrame.DataGeneral)
5065	G2frame.dataFrame.Bind(wx.EVT_MENU, OnFourierMaps, id=G2gd.wxID_FOURCALC)
5066	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSearchMaps, id=G2gd.wxID_FOURSEARCH)
5067	G2frame.dataFrame.Bind(wx.EVT_MENU, OnChargeFlip, id=G2gd.wxID_CHARGEFLIP)
5068	G2frame.dataFrame.Bind(wx.EVT_MENU, OnFourClear, id=G2gd.wxID_FOURCLEAR)
5069	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRunSingleMCSA, id=G2gd.wxID_SINGLEMCSA)
5070	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRunMultiMCSA, id=G2gd.wxID_MULTIMCSA)
5071	UpdateGeneral()
5072	elif text == 'Data':
5073	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.DataMenu)
5074	FillSelectPageMenu(G2frame.dataFrame.DataMenu)
5075	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPwdrAdd, id=G2gd.wxID_PWDRADD)
5076	G2frame.dataFrame.Bind(wx.EVT_MENU, OnHklfAdd, id=G2gd.wxID_HKLFADD)
5077	G2frame.dataFrame.Bind(wx.EVT_MENU, OnDataDelete, id=G2gd.wxID_DATADELETE)
5078	G2ddG.UpdateDData(G2frame,DData,data)
5079	G2plt.PlotSizeStrainPO(G2frame,data,Start=True)
5080	elif text == 'Atoms':
5081	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.AtomsMenu)
5082	FillSelectPageMenu(G2frame.dataFrame.AtomsMenu)
5083	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAtomAdd, id=G2gd.wxID_ATOMSEDITADD)
5084	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAtomViewAdd, id=G2gd.wxID_ATOMSVIEWADD)
5085	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAtomInsert, id=G2gd.wxID_ATOMSEDITINSERT)
5086	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAtomViewInsert, id=G2gd.wxID_ATOMVIEWINSERT)
5087	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAtomMove, id=G2gd.wxID_ATOMMOVE)
5088	G2frame.dataFrame.Bind(wx.EVT_MENU, AtomDelete, id=G2gd.wxID_ATOMSEDITDELETE)
5089	G2frame.dataFrame.Bind(wx.EVT_MENU, AtomRefine, id=G2gd.wxID_ATOMSREFINE)
5090	G2frame.dataFrame.Bind(wx.EVT_MENU, AtomModify, id=G2gd.wxID_ATOMSMODIFY)
5091	G2frame.dataFrame.Bind(wx.EVT_MENU, AtomTransform, id=G2gd.wxID_ATOMSTRANSFORM)
5092	G2frame.dataFrame.Bind(wx.EVT_MENU, OnReloadDrawAtoms, id=G2gd.wxID_RELOADDRAWATOMS)
5093	G2frame.dataFrame.Bind(wx.EVT_MENU, OnDistAngle, id=G2gd.wxID_ATOMSDISAGL)
5094	G2frame.dataFrame.Bind(wx.EVT_MENU, OnDistAnglePrt, id=G2gd.wxID_ATOMSPDISAGL)
5095	for id in G2frame.dataFrame.ReImportMenuId: #loop over submenu items
5096	G2frame.dataFrame.Bind(wx.EVT_MENU, OnReImport, id=id)
5097	FillAtomsGrid(Atoms)
5098	elif text == 'Draw Options':
5099	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.DataDrawOptions)
5100	FillSelectPageMenu(G2frame.dataFrame.DataDrawOptions)
5101	UpdateDrawOptions()
5102	wx.CallAfter(G2plt.PlotStructure,G2frame,data)
5103	elif text == 'Draw Atoms':
5104	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.DrawAtomsMenu)
5105	FillSelectPageMenu(G2frame.dataFrame.DrawAtomsMenu)
5106	G2frame.dataFrame.Bind(wx.EVT_MENU, DrawAtomStyle, id=G2gd.wxID_DRAWATOMSTYLE)
5107	G2frame.dataFrame.Bind(wx.EVT_MENU, DrawAtomLabel, id=G2gd.wxID_DRAWATOMLABEL)
5108	G2frame.dataFrame.Bind(wx.EVT_MENU, DrawAtomColor, id=G2gd.wxID_DRAWATOMCOLOR)
5109	G2frame.dataFrame.Bind(wx.EVT_MENU, ResetAtomColors, id=G2gd.wxID_DRAWATOMRESETCOLOR)
5110	G2frame.dataFrame.Bind(wx.EVT_MENU, SetViewPoint, id=G2gd.wxID_DRAWVIEWPOINT)
5111	G2frame.dataFrame.Bind(wx.EVT_MENU, AddSymEquiv, id=G2gd.wxID_DRAWADDEQUIV)
5112	G2frame.dataFrame.Bind(wx.EVT_MENU, TransformSymEquiv, id=G2gd.wxID_DRAWTRANSFORM)
5113	G2frame.dataFrame.Bind(wx.EVT_MENU, FillCoordSphere, id=G2gd.wxID_DRAWFILLCOORD)
5114	G2frame.dataFrame.Bind(wx.EVT_MENU, FillUnitCell, id=G2gd.wxID_DRAWFILLCELL)
5115	G2frame.dataFrame.Bind(wx.EVT_MENU, DrawAtomsDelete, id=G2gd.wxID_DRAWDELETE)
5116	G2frame.dataFrame.Bind(wx.EVT_MENU, OnDrawDistVP, id=G2gd.wxID_DRAWDISTVP)
5117	G2frame.dataFrame.Bind(wx.EVT_MENU, OnDrawDAT, id=G2gd.wxID_DRAWDISAGLTOR)
5118	G2frame.dataFrame.Bind(wx.EVT_MENU, OnDrawPlane, id=G2gd.wxID_DRAWPLANE)
5119	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRestraint, id=G2gd.wxID_DRAWRESTRBOND)
5120	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRestraint, id=G2gd.wxID_DRAWRESTRANGLE)
5121	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRestraint, id=G2gd.wxID_DRAWRESTRPLANE)
5122	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRestraint, id=G2gd.wxID_DRAWRESTRCHIRAL)
5123	G2frame.dataFrame.Bind(wx.EVT_MENU, OnDefineRB, id=G2gd.wxID_DRAWDEFINERB)
5124	UpdateDrawAtoms()
5125	wx.CallAfter(G2plt.PlotStructure,G2frame,data)
5126	elif text == 'RB Models':
5127	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.RigidBodiesMenu)
5128	FillSelectPageMenu(G2frame.dataFrame.RigidBodiesMenu)
5129	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAutoFindResRB, id=G2gd.wxID_AUTOFINDRESRB)
5130	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRBAssign, id=G2gd.wxID_ASSIGNATMS2RB)
5131	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRBCopyParms, id=G2gd.wxID_COPYRBPARMS)
5132	G2frame.dataFrame.Bind(wx.EVT_MENU, OnGlobalResRBTherm, id=G2gd.wxID_GLOBALTHERM)
5133	G2frame.dataFrame.Bind(wx.EVT_MENU, OnGlobalResRBRef, id=G2gd.wxID_GLOBALRESREFINE)
5134	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRBRemoveAll, id=G2gd.wxID_RBREMOVEALL)
5135	FillRigidBodyGrid()
5136	elif text == 'Map peaks':
5137	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.MapPeaksMenu)
5138	FillSelectPageMenu(G2frame.dataFrame.MapPeaksMenu)
5139	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksMove, id=G2gd.wxID_PEAKSMOVE)
5140	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksViewPoint, id=G2gd.wxID_PEAKSVIEWPT)
5141	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksDistVP, id=G2gd.wxID_PEAKSDISTVP)
5142	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksDA, id=G2gd.wxID_PEAKSDA)
5143	G2frame.dataFrame.Bind(wx.EVT_MENU, OnShowBonds, id=G2gd.wxID_SHOWBONDS)
5144	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksEquiv, id=G2gd.wxID_FINDEQVPEAKS)
5145	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksUnique, id=G2gd.wxID_PEAKSUNIQUE)
5146	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksDelete, id=G2gd.wxID_PEAKSDELETE)
5147	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksClear, id=G2gd.wxID_PEAKSCLEAR)
5148	FillMapPeaksGrid()
5149	wx.CallAfter(G2plt.PlotStructure,G2frame,data)
5150	elif text == 'MC/SA':
5151	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.MCSAMenu)
5152	FillSelectPageMenu(G2frame.dataFrame.MCSAMenu)
5153	G2frame.dataFrame.Bind(wx.EVT_MENU, OnMCSAaddAtom, id=G2gd.wxID_ADDMCSAATOM)
5154	G2frame.dataFrame.Bind(wx.EVT_MENU, OnMCSAaddRB, id=G2gd.wxID_ADDMCSARB)
5155	G2frame.dataFrame.Bind(wx.EVT_MENU, OnMCSAclear, id=G2gd.wxID_CLEARMCSARB)
5156	G2frame.dataFrame.Bind(wx.EVT_MENU, OnMCSAmove, id=G2gd.wxID_MOVEMCSA)
5157	G2frame.dataFrame.Bind(wx.EVT_MENU, OnClearResults, id=G2gd.wxID_MCSACLEARRESULTS)
5158	UpdateMCSA()
5159	wx.CallAfter(G2plt.PlotStructure,G2frame,data)
5160	elif text == 'Texture':
5161	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.TextureMenu)
5162	FillSelectPageMenu(G2frame.dataFrame.TextureMenu)
5163	G2frame.dataFrame.Bind(wx.EVT_MENU, OnTextureRefine, id=G2gd.wxID_REFINETEXTURE)
5164	G2frame.dataFrame.Bind(wx.EVT_MENU, OnTextureClear, id=G2gd.wxID_CLEARTEXTURE)
5165	UpdateTexture()
5166	G2plt.PlotTexture(G2frame,data,Start=True)
5167	elif text == 'Pawley reflections':
5168	G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.PawleyMenu)
5169	FillSelectPageMenu(G2frame.dataFrame.PawleyMenu)
5170	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPawleyLoad, id=G2gd.wxID_PAWLEYLOAD)
5171	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPawleyEstimate, id=G2gd.wxID_PAWLEYESTIMATE)
5172	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPawleyUpdate, id=G2gd.wxID_PAWLEYUPDATE)
5173	FillPawleyReflectionsGrid()
5174	else:
5175	G2gd.SetDataMenuBar(G2frame)
5176	Pages = []
5177	wx.Frame.Unbind(G2frame.dataFrame,wx.EVT_SIZE) # ignore size events during this routine
5178	G2frame.dataDisplay.gridList = []
5179	General = wx.ScrolledWindow(G2frame.dataDisplay)
5180	G2frame.dataDisplay.AddPage(General,'General')
5181	Pages.append('General')
5182	DData = wx.ScrolledWindow(G2frame.dataDisplay)
5183	G2frame.dataDisplay.AddPage(DData,'Data')
5184	Pages.append('Data')
5185	Atoms = G2gd.GSGrid(G2frame.dataDisplay)
5186	G2frame.dataDisplay.gridList.append(Atoms)
5187	G2frame.dataDisplay.AddPage(Atoms,'Atoms')
5188	Pages.append('Atoms')
5189	drawOptions = wx.ScrolledWindow(G2frame.dataDisplay)
5190	G2frame.dataDisplay.AddPage(drawOptions,'Draw Options')
5191	Pages.append('Draw Options')
5192	drawAtoms = G2gd.GSGrid(G2frame.dataDisplay)
5193	G2frame.dataDisplay.gridList.append(drawAtoms)
5194	G2frame.dataDisplay.AddPage(drawAtoms,'Draw Atoms')
5195	Pages.append('Draw Atoms')
5196	RigidBodies = wx.ScrolledWindow(G2frame.dataDisplay)
5197	G2frame.dataDisplay.AddPage(RigidBodies,'RB Models')
5198	Pages.append('RB Models')
5199	MapPeaks = G2gd.GSGrid(G2frame.dataDisplay)
5200	G2frame.dataDisplay.gridList.append(MapPeaks)
5201	G2frame.dataDisplay.AddPage(MapPeaks,'Map peaks')
5202	Pages.append('Map peaks')
5203	MCSA = wx.ScrolledWindow(G2frame.dataDisplay)
5204	G2frame.dataDisplay.AddPage(MCSA,'MC/SA')
5205	Pages.append('MC/SA')
5206	Texture = wx.ScrolledWindow(G2frame.dataDisplay)
5207	G2frame.dataDisplay.AddPage(Texture,'Texture')
5208	Pages.append('Texture')
5209	G2frame.PawleyRefl = G2gd.GSGrid(G2frame.dataDisplay)
5210	G2frame.dataDisplay.gridList.append(G2frame.PawleyRefl)
5211	G2frame.dataDisplay.AddPage(G2frame.PawleyRefl,'Pawley reflections')
5212	Pages.append('Pawley reflections')
5213
5214	G2frame.dataDisplay.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
5215	SetupGeneral()
5216	GeneralData = data['General']
5217	if oldPage is None:
5218	ChangePage(0)
5219	elif oldPage:
5220	G2frame.dataDisplay.SetSelection(oldPage)
5221	else:
5222	ChangePage(0)

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