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source: trunk/GSASIIphsGUI.py @ 1060

Last change on this file since 1060 was 1060, checked in by vondreele, 10 years ago
mods to MC/SA stuff - some speedup done
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1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2013-09-19 21:31:46 +0000 (Thu, 19 Sep 2013) $
5	# $Author: vondreele $
6	# $Revision: 1060 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1060 2013-09-19 21:31:46Z 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: 1060 $")
37	import GSASIIlattice as G2lat
38	import GSASIIspc as G2spc
39	import GSASIIElem as G2elem
40	import GSASIIElemGUI as G2elemGUI
41	import GSASIIddataGUI as G2ddG
42	import GSASIIplot as G2plt
43	import GSASIIgrid as G2gd
44	import GSASIIIO as G2IO
45	import GSASIIstrMain as G2stMn
46	import GSASIImath as G2mth
47	import GSASIIpwd as G2pwd
48	import numpy as np
49	import numpy.linalg as nl
50	import numpy.ma as ma
51
52	VERY_LIGHT_GREY = wx.Colour(235,235,235)
53	WHITE = wx.Colour(255,255,255)
54	BLACK = wx.Colour(0,0,0)
55	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
56	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
57	# trig functions in degrees
58	sind = lambda x: np.sin(x*np.pi/180.)
59	tand = lambda x: np.tan(x*np.pi/180.)
60	cosd = lambda x: np.cos(x*np.pi/180.)
61	asind = lambda x: 180.*np.arcsin(x)/np.pi
62	acosd = lambda x: 180.*np.arccos(x)/np.pi
63
64	def SetPhaseWindow(mainFrame,phasePage,mainSizer):
65	phasePage.SetSizer(mainSizer)
66	Size = mainSizer.GetMinSize()
67	Size[0] += 40
68	Size[1] = max(Size[1],430) + 35
69	phasePage.SetSize(Size)
70	phasePage.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
71	mainFrame.setSizePosLeft(Size)
72
73	def UpdatePhaseData(G2frame,Item,data,oldPage):
74	'''Create the data display window contents when a phase is clicked on
75	in the man (data tree) window.
76	Called only from :meth:`GSASIIgrid.MovePatternTreeToGrid`,
77	which in turn is called from :meth:`GSASII.GSASII.OnPatternTreeSelChanged`
78	when a tree item is selected.
79
80	:param wx.frame G2frame: the main GSAS-II frame object
81	:param wx.TreeItemId Item: the tree item that was selected
82	:param dict data: all the information on the phase in a dictionary
83	:param int oldPage: This sets a tab to select when moving
84	from one phase to another, in which case the same tab is selected
85	to display first. This is set only when the previous data tree
86	selection is a phase, if not the value is None. The default action
87	is to bring up the General tab.
88
89	'''
90
91	#patch
92	if 'RBModels' not in data:
93	data['RBModels'] = {}
94	if 'MCSA' not in data:
95	data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[0.3,3.],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
96	if isinstance(data['MCSA']['Results'],dict):
97	data['MCSA']['Results'] = []
98	#end patch
99
100	global rbAtmDict
101	rbAtmDict = {}
102	if G2frame.dataDisplay:
103	G2frame.dataDisplay.Destroy()
104	PhaseName = G2frame.PatternTree.GetItemText(Item)
105	G2gd.SetDataMenuBar(G2frame)
106	G2frame.dataFrame.SetLabel('Phase Data for '+PhaseName)
107	G2frame.dataFrame.CreateStatusBar()
108	G2frame.dataDisplay = G2gd.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize())
109	G2frame.dataDisplay.gridList = [] # list of all grids in notebook
110
111	def SetupGeneral():
112	generalData = data['General']
113	atomData = data['Atoms']
114	generalData['AtomTypes'] = []
115	generalData['Isotopes'] = {}
116	# various patches
117	if 'Isotope' not in generalData:
118	generalData['Isotope'] = {}
119	if 'Data plot type' not in generalData:
120	generalData['Data plot type'] = 'Mustrain'
121	if 'POhkl' not in generalData:
122	generalData['POhkl'] = [0,0,1]
123	if 'Map' not in generalData:
124	generalData['Map'] = mapDefault
125	if 'Flip' not in generalData:
126	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
127	'k-factor':0.1,'k-Max':20.}
128	if 'doPawley' not in generalData:
129	generalData['doPawley'] = False
130	if 'Pawley dmin' not in generalData:
131	generalData['Pawley dmin'] = 1.0
132	if 'Pawley neg wt' not in generalData:
133	generalData['Pawley neg wt'] = 0.0
134	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
135	'MCSA controls' not in generalData:
136	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
137	'dmin':2.0,'Algorithm':'fast','Jump coeff':[0.95,0.5],'boltzmann':1.0,
138	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[]}
139	# end of patches
140	generalData['NoAtoms'] = {}
141	generalData['BondRadii'] = []
142	generalData['AngleRadii'] = []
143	generalData['vdWRadii'] = []
144	generalData['AtomMass'] = []
145	generalData['Color'] = []
146	generalData['Mydir'] = G2frame.dirname
147	cx,ct,cs,cia = [3,1,7,9]
148	if generalData['Type'] =='macromolecular':
149	cx,ct,cs,cia = [6,4,10,12]
150	generalData['AtomPtrs'] = [cx,ct,cs,cia]
151	for atom in atomData:
152	atom[ct] = atom[ct].lower().capitalize() #force to standard form
153	if generalData['AtomTypes'].count(atom[ct]):
154	generalData['NoAtoms'][atom[ct]] += atom[cs-1]*float(atom[cs+1])
155	elif atom[ct] != 'UNK':
156	Info = G2elem.GetAtomInfo(atom[ct])
157	generalData['AtomTypes'].append(atom[ct])
158	generalData['Z'] = Info['Z']
159	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
160	generalData['BondRadii'].append(Info['Drad'])
161	generalData['AngleRadii'].append(Info['Arad'])
162	generalData['vdWRadii'].append(Info['Vdrad'])
163	if atom[ct] in generalData['Isotope']:
164	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]][0])
165	else:
166	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
167	generalData['AtomMass'].append(Info['Mass'])
168	generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
169	generalData['Color'].append(Info['Color'])
170	F000X = 0.
171	F000N = 0.
172	for i,elem in enumerate(generalData['AtomTypes']):
173	F000X += generalData['NoAtoms'][elem]*generalData['Z']
174	isotope = generalData['Isotope'][elem]
175	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope][1]
176	generalData['F000X'] = F000X
177	generalData['F000N'] = F000N
178
179
180	################################################################################
181	##### General phase routines
182	################################################################################
183
184	def UpdateGeneral():
185	'''Draw the controls for the General phase data subpage
186	'''
187
188	""" This is the default dictionary structure for phase data
189	(taken from GSASII.py)
190	'General':{
191	'Name':PhaseName
192	'Type':'nuclear'
193	'SGData':SGData
194	'Cell':[False,10.,10.,10.,90.,90.,90,1000.]
195	'AtomPtrs':[]
196	'Histogram list':['',]
197	'Pawley dmin':1.0,
198	'Pawley neg wt':0.0}
199	'Atoms':[]
200	'Drawing':{}
201	"""
202	# UpdateGeneral execution starts here
203	phaseTypes = ['nuclear','modulated','magnetic','macromolecular']
204	SetupGeneral()
205	generalData = data['General']
206	Map = generalData['Map']
207	Flip = generalData['Flip']
208	MCSAdata = generalData['MCSA controls']
209	PWDR = any(['PWDR' in item for item in data['Histograms'].keys()])
210	# UpdateGeneral execution continues below
211
212	def NameSizer():
213	def OnPhaseName(event):
214	oldName = generalData['Name']
215	generalData['Name'] = NameTxt.GetValue()
216	G2frame.G2plotNB.Rename(oldName,generalData['Name'])
217	G2frame.dataFrame.SetLabel('Phase Data for '+generalData['Name'])
218	G2frame.PatternTree.SetItemText(Item,generalData['Name'])
219	#Hmm, need to change phase name key in Reflection Lists for each histogram
220
221	def OnPhaseType(event):
222	if not generalData['AtomTypes']: #can change only if no atoms!
223	generalData['Type'] = TypeTxt.GetValue()
224	wx.CallAfter(UpdateGeneral)
225	else:
226	TypeTxt.SetValue(generalData['Type'])
227
228	def OnSpaceGroup(event):
229	SpcGp = SGTxt.GetValue()
230	SGErr,SGData = G2spc.SpcGroup(SpcGp)
231	# try a lookup on the user-supplied name
232	if SGErr:
233	SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
234	if SpGrpNorm:
235	E,SGData = G2spc.SpcGroup(SpGrpNorm)
236	if not E: SGErr = False
237	if SGErr:
238	text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
239	SGTxt.SetValue(generalData['SGData']['SpGrp'])
240	msg = 'Space Group Error'
241	Style = wx.ICON_EXCLAMATION
242	else:
243	text = G2spc.SGPrint(SGData)
244	generalData['SGData'] = SGData
245	msg = 'Space Group Information'
246	Style = wx.ICON_INFORMATION
247	Text = ''
248	for line in text:
249	Text += line+'\n'
250	wx.MessageBox(Text,caption=msg,style=Style)
251	# General.DestroyChildren() #needed to clear away bad cellSizer, etc.
252	wx.CallAfter(UpdateGeneral)
253
254	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
255	nameSizer.Add(wx.StaticText(General,-1,' Phase name: '),0,wx.ALIGN_CENTER_VERTICAL)
256	NameTxt = wx.TextCtrl(General,-1,value=generalData['Name'],style=wx.TE_PROCESS_ENTER)
257	NameTxt.Bind(wx.EVT_TEXT_ENTER,OnPhaseName)
258	NameTxt.Bind(wx.EVT_KILL_FOCUS,OnPhaseName)
259	nameSizer.Add(NameTxt,0,wx.ALIGN_CENTER_VERTICAL)
260	nameSizer.Add(wx.StaticText(General,-1,' Phase type: '),0,wx.ALIGN_CENTER_VERTICAL)
261	TypeTxt = wx.ComboBox(General,-1,value=generalData['Type'],choices=phaseTypes,
262	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
263	TypeTxt.Bind(wx.EVT_COMBOBOX, OnPhaseType)
264	nameSizer.Add(TypeTxt,0,wx.ALIGN_CENTER_VERTICAL)
265	nameSizer.Add(wx.StaticText(General,-1,' Space group: '),0,wx.ALIGN_CENTER_VERTICAL)
266	SGTxt = wx.TextCtrl(General,-1,value=generalData['SGData']['SpGrp'],style=wx.TE_PROCESS_ENTER)
267	SGTxt.Bind(wx.EVT_TEXT_ENTER,OnSpaceGroup)
268	nameSizer.Add(SGTxt,0,wx.ALIGN_CENTER_VERTICAL)
269	return nameSizer
270
271	def CellSizer():
272
273	cellGUIlist = [[['m3','m3m'],4,zip([" Unit cell: a = "," Vol = "],["%.5f","%.3f"],[True,False],[0,0])],
274	[['3R','3mR'],6,zip([" a = "," alpha = "," Vol = "],["%.5f","%.3f","%.3f"],[True,True,False],[0,2,0])],
275	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],6,zip([" a = "," c = "," Vol = "],["%.5f","%.5f","%.3f"],[True,True,False],[0,2,0])],
276	[['mmm'],8,zip([" a = "," b = "," c = "," Vol = "],["%.5f","%.5f","%.5f","%.3f"],
277	[True,True,True,False],[0,1,2,0])],
278	[['2/m'+'a'],10,zip([" a = "," b = "," c = "," alpha = "," Vol = "],
279	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
280	[['2/m'+'b'],10,zip([" a = "," b = "," c = "," beta = "," Vol = "],
281	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
282	[['2/m'+'c'],10,zip([" a = "," b = "," c = "," gamma = "," Vol = "],
283	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
284	[['-1'],8,zip([" a = "," b = "," c = "," Vol = "," alpha = "," beta = "," gamma = "],
285	["%.5f","%.5f","%.5f","%.3f","%.3f","%.3f","%.3f"],
286	[True,True,True,False,True,True,True],[0,1,2,0,3,4,5])]]
287
288	def OnCellRef(event):
289	generalData['Cell'][0] = cellRef.GetValue()
290
291	def OnCellChange(event):
292	SGData = generalData['SGData']
293	laue = SGData['SGLaue']
294	if laue == '2/m':
295	laue += SGData['SGUniq']
296	cell = generalData['Cell']
297	Obj = event.GetEventObject()
298	ObjId = cellList.index(Obj.GetId())
299	try:
300	value = max(1.0,float(Obj.GetValue()))
301	except ValueError:
302	if ObjId < 3: #bad cell edge - reset
303	value = controls[6+ObjId]
304	else: #bad angle
305	value = 90.
306	if laue in ['m3','m3m']:
307	cell[1] = cell[2] = cell[3] = value
308	cell[4] = cell[5] = cell[6] = 90.0
309	Obj.SetValue("%.5f"%(cell[1]))
310	elif laue in ['3R','3mR']:
311	if ObjId == 0:
312	cell[1] = cell[2] = cell[3] = value
313	Obj.SetValue("%.5f"%(cell[1]))
314	else:
315	cell[4] = cell[5] = cell[6] = value
316	Obj.SetValue("%.5f"%(cell[4]))
317	elif laue in ['3','3m1','31m','6/m','6/mmm','4/m','4/mmm']:
318	cell[4] = cell[5] = 90.
319	cell[6] = 120.
320	if laue in ['4/m','4/mmm']:
321	cell[6] = 90.
322	if ObjId == 0:
323	cell[1] = cell[2] = value
324	Obj.SetValue("%.5f"%(cell[1]))
325	else:
326	cell[3] = value
327	Obj.SetValue("%.5f"%(cell[3]))
328	elif laue in ['mmm']:
329	cell[ObjId+1] = value
330	cell[4] = cell[5] = cell[6] = 90.
331	Obj.SetValue("%.5f"%(cell[ObjId+1]))
332	elif laue in ['2/m'+'a']:
333	cell[5] = cell[6] = 90.
334	if ObjId != 3:
335	cell[ObjId+1] = value
336	Obj.SetValue("%.5f"%(cell[ObjId+1]))
337	else:
338	cell[4] = value
339	Obj.SetValue("%.3f"%(cell[4]))
340	elif laue in ['2/m'+'b']:
341	cell[4] = cell[6] = 90.
342	if ObjId != 3:
343	cell[ObjId+1] = value
344	Obj.SetValue("%.5f"%(cell[ObjId+1]))
345	else:
346	cell[5] = value
347	Obj.SetValue("%.3f"%(cell[5]))
348	elif laue in ['2/m'+'c']:
349	cell[5] = cell[6] = 90.
350	if ObjId != 3:
351	cell[ObjId+1] = value
352	Obj.SetValue("%.5f"%(cell[ObjId+1]))
353	else:
354	cell[6] = value
355	Obj.SetValue("%.3f"%(cell[6]))
356	else:
357	cell[ObjId+1] = value
358	if ObjId < 3:
359	Obj.SetValue("%.5f"%(cell[1+ObjId]))
360	else:
361	Obj.SetValue("%.3f"%(cell[1+ObjId]))
362	cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
363	volVal.SetValue("%.3f"%(cell[7]))
364	density,mattCoeff = G2mth.getDensity(generalData)
365	if denSizer:
366	denSizer[1].SetValue('%.3f'%(density))
367	if denSizer[2]:
368	denSizer[2].SetValue('%.3f'%(mattCoeff))
369	generalData['Cell'] = cell
370
371	cell = generalData['Cell']
372	laue = generalData['SGData']['SGLaue']
373	if laue == '2/m':
374	laue += generalData['SGData']['SGUniq']
375	for cellGUI in cellGUIlist:
376	if laue in cellGUI[0]:
377	useGUI = cellGUI
378	cellSizer = wx.FlexGridSizer(2,useGUI[1]+1,5,5)
379	if PWDR:
380	cellRef = wx.CheckBox(General,-1,label='Refine unit cell:')
381	cellSizer.Add(cellRef,0,wx.ALIGN_CENTER_VERTICAL)
382	cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef)
383	cellRef.SetValue(cell[0])
384	cellList = []
385	for txt,fmt,ifEdit,Id in useGUI[2]:
386	cellSizer.Add(wx.StaticText(General,label=txt),0,wx.ALIGN_CENTER_VERTICAL)
387	if ifEdit: #a,b,c,etc.
388	cellVal = wx.TextCtrl(General,value=(fmt%(cell[Id+1])),
389	style=wx.TE_PROCESS_ENTER)
390	cellVal.Bind(wx.EVT_TEXT_ENTER,OnCellChange)
391	cellVal.Bind(wx.EVT_KILL_FOCUS,OnCellChange)
392	cellSizer.Add(cellVal,0,wx.ALIGN_CENTER_VERTICAL)
393	cellList.append(cellVal.GetId())
394	else: #volume
395	volVal = wx.TextCtrl(General,value=(fmt%(cell[7])),style=wx.TE_READONLY)
396	volVal.SetBackgroundColour(VERY_LIGHT_GREY)
397	cellSizer.Add(volVal,0,wx.ALIGN_CENTER_VERTICAL)
398	return cellSizer
399
400	def ElemSizer():
401
402	def OnIsotope(event):
403	Obj = event.GetEventObject()
404	item = Indx[Obj.GetId()]
405	isotope = Obj.GetValue()
406	generalData['Isotope'][item] = isotope
407	indx = generalData['AtomTypes'].index(item)
408	data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope][0]
409	density,mattCoeff = G2mth.getDensity(generalData)
410	denSizer[1].SetValue('%.3f'%(density))
411	if denSizer[2]:
412	denSizer[2].SetValue('%.3f'%(mattCoeff))
413
414	elemSizer = wx.FlexGridSizer(8,len(generalData['AtomTypes'])+1,1,1)
415	elemSizer.Add(wx.StaticText(General,label=' Elements'),0,wx.ALIGN_CENTER_VERTICAL)
416	for elem in generalData['AtomTypes']:
417	typTxt = wx.TextCtrl(General,value=elem,style=wx.TE_READONLY)
418	typTxt.SetBackgroundColour(VERY_LIGHT_GREY)
419	elemSizer.Add(typTxt,0,wx.ALIGN_CENTER_VERTICAL)
420	elemSizer.Add(wx.StaticText(General,label=' Isotope'),0,wx.ALIGN_CENTER_VERTICAL)
421	for elem in generalData['AtomTypes']:
422	choices = generalData['Isotopes'][elem].keys()
423	isoSel = wx.ComboBox(General,-1,value=generalData['Isotope'][elem],choices=choices,
424	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
425	isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope)
426	Indx[isoSel.GetId()] = elem
427	elemSizer.Add(isoSel,1,wx.ALIGN_CENTER_VERTICAL\|wx.EXPAND)
428	elemSizer.Add(wx.StaticText(General,label=' No. per cell'),0,wx.ALIGN_CENTER_VERTICAL)
429	for elem in generalData['AtomTypes']:
430	numbTxt = wx.TextCtrl(General,value='%.1f'%(generalData['NoAtoms'][elem]),
431	style=wx.TE_READONLY)
432	numbTxt.SetBackgroundColour(VERY_LIGHT_GREY)
433	elemSizer.Add(numbTxt,0,wx.ALIGN_CENTER_VERTICAL)
434	elemSizer.Add(wx.StaticText(General,label=' Atom weight'),0,wx.ALIGN_CENTER_VERTICAL)
435	for wt in generalData['AtomMass']:
436	wtTxt = wx.TextCtrl(General,value='%.3f'%(wt),style=wx.TE_READONLY)
437	wtTxt.SetBackgroundColour(VERY_LIGHT_GREY)
438	elemSizer.Add(wtTxt,0,wx.ALIGN_CENTER_VERTICAL)
439	elemSizer.Add(wx.StaticText(General,label=' Bond radii'),0,wx.ALIGN_CENTER_VERTICAL)
440	for rad in generalData['BondRadii']:
441	bondRadii = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
442	bondRadii.SetBackgroundColour(VERY_LIGHT_GREY)
443	elemSizer.Add(bondRadii,0,wx.ALIGN_CENTER_VERTICAL)
444	elemSizer.Add(wx.StaticText(General,label=' Angle radii'),0,wx.ALIGN_CENTER_VERTICAL)
445	for rad in generalData['AngleRadii']:
446	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
447	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
448	elemSizer.Add(elemTxt,0,wx.ALIGN_CENTER_VERTICAL)
449	elemSizer.Add(wx.StaticText(General,label=' van der Waals radii'),0,wx.ALIGN_CENTER_VERTICAL)
450	for rad in generalData['vdWRadii']:
451	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
452	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
453	elemSizer.Add(elemTxt,0,wx.ALIGN_CENTER_VERTICAL)
454	elemSizer.Add(wx.StaticText(General,label=' Default color'),0,wx.ALIGN_CENTER_VERTICAL)
455	for R,G,B in generalData['Color']:
456	colorTxt = wx.TextCtrl(General,value='',style=wx.TE_READONLY)
457	colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
458	elemSizer.Add(colorTxt,0,wx.ALIGN_CENTER_VERTICAL)
459	return elemSizer
460
461	def DenSizer():
462
463	mass = G2mth.getMass(generalData)
464	density,mattCoeff = G2mth.getDensity(generalData)
465	denSizer = wx.BoxSizer(wx.HORIZONTAL)
466	denSizer.Add(wx.StaticText(General,-1,' Density: '),0,wx.ALIGN_CENTER_VERTICAL)
467	denTxt = wx.TextCtrl(General,-1,'%.3f'%(density),style=wx.TE_READONLY)
468	denTxt.SetBackgroundColour(VERY_LIGHT_GREY)
469	denSizer.Add(denTxt,0,wx.ALIGN_CENTER_VERTICAL)
470	mattTxt = None
471	if generalData['Type'] == 'macromolecular' and mass > 0.0:
472	denSizer.Add(wx.StaticText(General,-1,' Matthews coeff.: '),
473	0,wx.ALIGN_CENTER_VERTICAL)
474	mattTxt = wx.TextCtrl(General,-1,'%.3f'%(mattCoeff),style=wx.TE_READONLY)
475	mattTxt.SetBackgroundColour(VERY_LIGHT_GREY)
476	denSizer.Add(mattTxt,0,wx.ALIGN_CENTER_VERTICAL)
477	return denSizer,denTxt,mattTxt
478
479	def PawleySizer():
480
481	def OnPawleyRef(event):
482	generalData['doPawley'] = pawlRef.GetValue()
483
484	def OnPawleyVal(event):
485	try:
486	dmin = float(pawlVal.GetValue())
487	if 0.25 <= dmin <= 20.:
488	generalData['Pawley dmin'] = dmin
489	except ValueError:
490	pass
491	pawlVal.SetValue("%.3f"%(generalData['Pawley dmin'])) #reset in case of error
492
493	def OnPawleyNegWt(event):
494	try:
495	wt = float(pawlNegWt.GetValue())
496	if 0. <= wt <= 1.:
497	generalData['Pawley neg wt'] = wt
498	except ValueError:
499	pass
500	pawlNegWt.SetValue("%.4f"%(generalData['Pawley neg wt'])) #reset in case of error
501
502	pawleySizer = wx.BoxSizer(wx.HORIZONTAL)
503	pawleySizer.Add(wx.StaticText(General,label=' Pawley controls: '),0,wx.ALIGN_CENTER_VERTICAL)
504	pawlRef = wx.CheckBox(General,-1,label=' Do Pawley refinement?')
505	pawlRef.SetValue(generalData['doPawley'])
506	pawlRef.Bind(wx.EVT_CHECKBOX,OnPawleyRef)
507	pawleySizer.Add(pawlRef,0,wx.ALIGN_CENTER_VERTICAL)
508	pawleySizer.Add(wx.StaticText(General,label=' Pawley dmin: '),0,wx.ALIGN_CENTER_VERTICAL)
509	pawlVal = wx.TextCtrl(General,value='%.3f'%(generalData['Pawley dmin']),style=wx.TE_PROCESS_ENTER)
510	pawlVal.Bind(wx.EVT_TEXT_ENTER,OnPawleyVal)
511	pawlVal.Bind(wx.EVT_KILL_FOCUS,OnPawleyVal)
512	pawleySizer.Add(pawlVal,0,wx.ALIGN_CENTER_VERTICAL)
513	pawleySizer.Add(wx.StaticText(General,label=' Pawley neg. wt.: '),0,wx.ALIGN_CENTER_VERTICAL)
514	pawlNegWt = wx.TextCtrl(General,value='%.4f'%(generalData['Pawley neg wt']),style=wx.TE_PROCESS_ENTER)
515	pawlNegWt.Bind(wx.EVT_TEXT_ENTER,OnPawleyNegWt)
516	pawlNegWt.Bind(wx.EVT_KILL_FOCUS,OnPawleyNegWt)
517	pawleySizer.Add(pawlNegWt,0,wx.ALIGN_CENTER_VERTICAL)
518	return pawleySizer
519
520	def MapSizer():
521
522	def OnMapType(event):
523	Map['MapType'] = mapType.GetValue()
524
525	def OnRefList(event):
526	Map['RefList'] = refList.GetValue()
527
528	def OnResVal(event):
529	try:
530	res = float(mapRes.GetValue())
531	if 0.25 <= res <= 20.:
532	Map['Resolution'] = res
533	except ValueError:
534	pass
535	mapRes.SetValue("%.2f"%(Map['Resolution'])) #reset in case of error
536
537	def OnCutOff(event):
538	try:
539	res = float(cutOff.GetValue())
540	if 10.0 <= res <= 100.:
541	Map['cutOff'] = res
542	except ValueError:
543	pass
544	cutOff.SetValue("%.1f"%(Map['cutOff'])) #reset in case of error
545
546	#patch
547	if 'cutOff' not in Map:
548	Map['cutOff'] = 100.0
549	mapTypes = ['Fobs','Fcalc','delt-F','2*Fo-Fc','Omit','Patterson']
550	refList = data['Histograms'].keys()
551	if not generalData['AtomTypes']:
552	mapTypes = ['Patterson',]
553	Map['MapType'] = 'Patterson'
554	mapSizer = wx.BoxSizer(wx.VERTICAL)
555	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
556	lineSizer.Add(wx.StaticText(General,label=' Fourier map controls: Map type: '),0,wx.ALIGN_CENTER_VERTICAL)
557	mapType = wx.ComboBox(General,-1,value=Map['MapType'],choices=mapTypes,
558	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
559	mapType.Bind(wx.EVT_COMBOBOX,OnMapType)
560	lineSizer.Add(mapType,0,wx.ALIGN_CENTER_VERTICAL)
561	lineSizer.Add(wx.StaticText(General,label=' Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
562	refList = wx.ComboBox(General,-1,value=Map['RefList'],choices=refList,
563	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
564	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
565	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
566	mapSizer.Add(lineSizer,0,wx.ALIGN_CENTER_VERTICAL)
567	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
568	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,wx.ALIGN_CENTER_VERTICAL)
569	mapRes = wx.TextCtrl(General,value='%.2f'%(Map['Resolution']),style=wx.TE_PROCESS_ENTER)
570	mapRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
571	mapRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
572	line2Sizer.Add(mapRes,0,wx.ALIGN_CENTER_VERTICAL)
573	line2Sizer.Add(wx.StaticText(General,label=' Peak cutoff %: '),0,wx.ALIGN_CENTER_VERTICAL)
574	cutOff = wx.TextCtrl(General,value='%.1f'%(Map['cutOff']),style=wx.TE_PROCESS_ENTER)
575	cutOff.Bind(wx.EVT_TEXT_ENTER,OnCutOff)
576	cutOff.Bind(wx.EVT_KILL_FOCUS,OnCutOff)
577	line2Sizer.Add(cutOff,0,wx.ALIGN_CENTER_VERTICAL)
578	mapSizer.Add(line2Sizer,0,wx.ALIGN_CENTER_VERTICAL)
579	return mapSizer
580
581	def FlipSizer():
582	if 'k-Max' not in Flip: Flip['k-Max'] = 20.
583
584	def OnRefList(event):
585	Flip['RefList'] = refList.GetValue()
586
587	def OnNormElem(event):
588	PE = G2elemGUI.PickElement(G2frame,ifNone=True)
589	if PE.ShowModal() == wx.ID_OK:
590	Flip['Norm element'] = PE.Elem.strip()
591	normElem.SetLabel(Flip['Norm element'])
592	PE.Destroy()
593
594	def OnResVal(event):
595	try:
596	res = float(flipRes.GetValue())
597	if 0.25 <= res <= 20.:
598	Flip['Resolution'] = res
599	except ValueError:
600	pass
601	flipRes.SetValue("%.2f"%(Flip['Resolution'])) #reset in case of error
602
603	def OnkFactor(event):
604	try:
605	res = float(kFactor.GetValue())
606	if 0.1 <= res <= 1.2:
607	Flip['k-factor'] = res
608	except ValueError:
609	pass
610	kFactor.SetValue("%.3f"%(Flip['k-factor'])) #reset in case of error
611
612	def OnkMax(event):
613	try:
614	res = float(kMax.GetValue())
615	if res >= 10.:
616	Flip['k-Max'] = res
617	except ValueError:
618	pass
619	kMax.SetValue("%.1f"%(Flip['k-Max'])) #reset in case of error
620
621	refList = data['Histograms'].keys()
622	flipSizer = wx.BoxSizer(wx.VERTICAL)
623	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
624	lineSizer.Add(wx.StaticText(General,label=' Charge flip controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
625	refList = wx.ComboBox(General,-1,value=Flip['RefList'],choices=refList,
626	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
627	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
628	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
629	lineSizer.Add(wx.StaticText(General,label=' Normalizing element: '),0,wx.ALIGN_CENTER_VERTICAL)
630	normElem = wx.Button(General,label=Flip['Norm element'],style=wx.TE_READONLY)
631	normElem.Bind(wx.EVT_BUTTON,OnNormElem)
632	lineSizer.Add(normElem,0,wx.ALIGN_CENTER_VERTICAL)
633	flipSizer.Add(lineSizer,0,wx.ALIGN_CENTER_VERTICAL)
634	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
635	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,wx.ALIGN_CENTER_VERTICAL)
636	flipRes = wx.TextCtrl(General,value='%.2f'%(Flip['Resolution']),style=wx.TE_PROCESS_ENTER)
637	flipRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
638	flipRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
639	line2Sizer.Add(flipRes,0,wx.ALIGN_CENTER_VERTICAL)
640	line2Sizer.Add(wx.StaticText(General,label=' k-Factor (0.1-1.2): '),0,wx.ALIGN_CENTER_VERTICAL)
641	kFactor = wx.TextCtrl(General,value='%.3f'%(Flip['k-factor']),style=wx.TE_PROCESS_ENTER)
642	kFactor.Bind(wx.EVT_TEXT_ENTER,OnkFactor)
643	kFactor.Bind(wx.EVT_KILL_FOCUS,OnkFactor)
644	line2Sizer.Add(kFactor,0,wx.ALIGN_CENTER_VERTICAL)
645	line2Sizer.Add(wx.StaticText(General,label=' k-Max (>=10.0): '),0,wx.ALIGN_CENTER_VERTICAL)
646	kMax = wx.TextCtrl(General,value='%.1f'%(Flip['k-Max']),style=wx.TE_PROCESS_ENTER)
647	kMax.Bind(wx.EVT_TEXT_ENTER,OnkMax)
648	kMax.Bind(wx.EVT_KILL_FOCUS,OnkMax)
649	line2Sizer.Add(kMax,0,wx.ALIGN_CENTER_VERTICAL)
650	flipSizer.Add(line2Sizer,0,wx.ALIGN_CENTER_VERTICAL)
651	return flipSizer
652
653	def MCSASizer():
654	Ind = {}
655
656	def OnRefList(event):
657	MCSAdata['Data source'] = refList.GetValue()
658
659	def OnDmin(event):
660	try:
661	val = float(dmin.GetValue())
662	if 1.0 <= val < 5.0:
663	MCSAdata['dmin'] = val
664	except ValueError:
665	pass
666	dmin.SetValue("%.3f"%(MCSAdata['dmin'])) #reset in case of error
667	MCSAdata['newDmin'] = True
668
669	def OnCycles(event):
670	MCSAdata['Cycles'] = int(cycles.GetValue())
671
672	def OnAlist(event):
673	MCSAdata['Algorithm'] = Alist.GetValue()
674	wx.CallAfter(UpdateGeneral)
675
676	def OnSlope(event):
677	try:
678	val = float(slope.GetValue())
679	if .25 <= val < 1.0:
680	MCSAdata['log slope'] = val
681	except ValueError:
682	pass
683	slope.SetValue("%.3f"%(MCSAdata['log slope'])) #reset in case of error
684
685	def OnAjump(event):
686	Obj = event.GetEventObject()
687	name,ind = Indx[Obj.GetId()]
688	try:
689	val = float(Obj.GetValue())
690	if .0 <= val <= 1.0:
691	MCSAdata[name][ind] = val
692	except ValueError:
693	pass
694	Obj.SetValue("%.3f"%(MCSAdata[name][ind]))
695
696	def OnRanStart(event):
697	MCSAdata['ranStart'] = ranStart.GetValue()
698
699	def OnAnneal(event):
700	Obj = event.GetEventObject()
701	ind,fmt = Indx[Obj.GetId()]
702	if ind == 2: #No. trials
703	try:
704	val = int(Obj.GetValue())
705	if 1 <= val:
706	MCSAdata['Annealing'][ind] = val
707	except ValueError:
708	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
709	else:
710	try:
711	val = float(Obj.GetValue())
712	if .0 <= val:
713	MCSAdata['Annealing'][ind] = val
714	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
715	except ValueError:
716	MCSAdata['Annealing'][ind] = None
717	Obj.SetValue(str(MCSAdata['Annealing'][ind]))
718
719	refList = []
720	if len(data['Pawley ref']):
721	refList = ['Pawley reflections']
722	for item in data['Histograms'].keys():
723	if 'HKLF' in item or 'PWDR' in item:
724	refList.append(item)
725	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
726	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
727	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,wx.ALIGN_CENTER_VERTICAL)
728	refList = wx.ComboBox(General,-1,value=MCSAdata['Data source'],choices=refList,
729	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
730	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
731	lineSizer.Add(refList,0,wx.ALIGN_CENTER_VERTICAL)
732	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,wx.ALIGN_CENTER_VERTICAL)
733	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['dmin']),style=wx.TE_PROCESS_ENTER)
734	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
735	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
736	lineSizer.Add(dmin,0,wx.ALIGN_CENTER_VERTICAL)
737	mcsaSizer.Add(lineSizer)
738	mcsaSizer.Add((5,5),)
739	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
740	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,wx.ALIGN_CENTER_VERTICAL)
741	Cchoice = ['1','2','3','6','10','20','30','60','100']
742	cycles = wx.ComboBox(General,-1,value=str(MCSAdata.get('Cycles',1)),choices=Cchoice,
743	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
744	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
745	line2Sizer.Add(cycles,0,wx.ALIGN_CENTER_VERTICAL)
746	line2Sizer.Add((5,0),)
747	ranStart = wx.CheckBox(General,-1,label=' Random start? (ignored if Start temp = None)')
748	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
749	ranStart.SetValue(MCSAdata.get('ranStart',True))
750	line2Sizer.Add(ranStart,0,wx.ALIGN_CENTER_VERTICAL)
751	mcsaSizer.Add(line2Sizer)
752	mcsaSizer.Add((5,5),)
753	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
754	Achoice = ['log','fast'] #these work
755	# Achoice = ['log','fast','cauchy','boltzmann']
756	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
757	Alist = wx.ComboBox(General,-1,value=MCSAdata['Algorithm'],choices=Achoice,
758	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
759	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
760	line3Sizer.Add(Alist,0,wx.ALIGN_CENTER_VERTICAL)
761	if MCSAdata['Algorithm'] in ['fast','boltzmann','cauchy']:
762	Names = [' A-jump: ',' B-jump: ']
763	parms = 'Jump coeff'
764	if MCSAdata['Algorithm'] in ['boltzmann','cauchy']:
765	Names = [' A-jump: ']
766	elif 'fast' in MCSAdata['Algorithm']:
767	Names = [' quench: ',' m-factor: ',' n-factor: ']
768	parms = 'fast parms'
769	for i,name in enumerate(Names):
770	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
771	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata[parms][i]),style=wx.TE_PROCESS_ENTER)
772	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
773	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
774	Indx[Ajump.GetId()] = [parms,i]
775	line3Sizer.Add(Ajump,0,wx.ALIGN_CENTER_VERTICAL)
776	elif 'log' in MCSAdata['Algorithm']:
777	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,wx.ALIGN_CENTER_VERTICAL)
778	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['log slope']),style=wx.TE_PROCESS_ENTER)
779	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
780	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
781	line3Sizer.Add(slope,0,wx.ALIGN_CENTER_VERTICAL)
782	mcsaSizer.Add(line3Sizer)
783	mcsaSizer.Add((5,5),)
784	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
785	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,wx.ALIGN_CENTER_VERTICAL)
786	names = [' Start temp: ',' Final temp: ',' No. trials: ']
787	fmts = ['%.1f','%.5f','%d']
788	for i,[name,fmt] in enumerate(zip(names,fmts)):
789	if MCSAdata['Annealing'][i]:
790	text = fmt%(MCSAdata['Annealing'][i])
791	else:
792	text = 'None'
793	line3Sizer.Add(wx.StaticText(General,label=name),0,wx.ALIGN_CENTER_VERTICAL)
794	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
795	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
796	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
797	Indx[anneal.GetId()] = [i,fmt]
798	line3Sizer.Add(anneal,0,wx.ALIGN_CENTER_VERTICAL)
799	mcsaSizer.Add(line3Sizer)
800	return mcsaSizer
801
802	# UpdateGeneral execution continues here
803	if General.GetSizer():
804	General.GetSizer().Clear(True)
805	mainSizer = wx.BoxSizer(wx.VERTICAL)
806	mainSizer.Add((5,5),0)
807	mainSizer.Add(NameSizer(),0)
808	mainSizer.Add((5,5),0)
809	mainSizer.Add(CellSizer(),0)
810	mainSizer.Add((5,5),0)
811
812	Indx = {}
813	denSizer = None
814	if len(generalData['AtomTypes']):
815	denSizer = DenSizer()
816	mainSizer.Add(denSizer[0])
817	mainSizer.Add((5,5),0)
818	mainSizer.Add(ElemSizer())
819	G2gd.HorizontalLine(mainSizer,General)
820
821	mainSizer.Add(PawleySizer())
822	G2gd.HorizontalLine(mainSizer,General)
823
824	mainSizer.Add(MapSizer())
825	G2gd.HorizontalLine(mainSizer,General)
826
827	mainSizer.Add(FlipSizer())
828	G2gd.HorizontalLine(mainSizer,General)
829
830	mainSizer.Add(MCSASizer())
831	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
832	G2frame.dataFrame.SetStatusText('')
833
834	################################################################################
835	##### Atom routines
836	################################################################################
837
838	def FillAtomsGrid(Atoms):
839	'''Display the contents of the Atoms tab
840	'''
841	def RefreshAtomGrid(event):
842
843	r,c = event.GetRow(),event.GetCol()
844	if r < 0 and c < 0:
845	for row in range(Atoms.GetNumberRows()):
846	Atoms.SelectRow(row,True)
847	if r < 0: #double click on col label! Change all atoms!
848	sel = -1
849	noSkip = True
850	if Atoms.GetColLabelValue(c) == 'refine':
851	Type = generalData['Type']
852	if Type in ['nuclear','macromolecular']:
853	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
854	elif Type in ['magnetic',]:
855	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
856	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
857	if dlg.ShowModal() == wx.ID_OK:
858	sel = dlg.GetSelections()
859	parms = ''
860	for x in sel:
861	parms += choice[x][0]
862	dlg.Destroy()
863	elif Atoms.GetColLabelValue(c) == 'I/A':
864	choice = ['Isotropic','Anisotropic']
865	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
866	if dlg.ShowModal() == wx.ID_OK:
867	sel = dlg.GetSelection()
868	parms = choice[sel][0]
869	dlg.Destroy()
870	elif Atoms.GetColLabelValue(c) == 'Type':
871	choice = generalData['AtomTypes']
872	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
873	if dlg.ShowModal() == wx.ID_OK:
874	sel = dlg.GetSelection()
875	parms = choice[sel]
876	noSkip = False
877	Atoms.ClearSelection()
878	for row in range(Atoms.GetNumberRows()):
879	if parms == atomData[row][c]:
880	Atoms.SelectRow(row,True)
881	dlg.Destroy()
882	SetupGeneral()
883	elif Atoms.GetColLabelValue(c) == 'residue':
884	choice = []
885	for r in range(Atoms.GetNumberRows()):
886	if str(atomData[r][c]) not in choice:
887	choice.append(str(atomData[r][c]))
888	choice.sort()
889	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
890	if dlg.ShowModal() == wx.ID_OK:
891	sel = dlg.GetSelection()
892	parms = choice[sel]
893	noSkip = False
894	Atoms.ClearSelection()
895	for row in range(Atoms.GetNumberRows()):
896	if parms == atomData[row][c]:
897	Atoms.SelectRow(row,True)
898	dlg.Destroy()
899	elif Atoms.GetColLabelValue(c) == 'res no':
900	choice = []
901	for r in range(Atoms.GetNumberRows()):
902	if str(atomData[r][c]) not in choice:
903	choice.append(str(atomData[r][c]))
904	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
905	if dlg.ShowModal() == wx.ID_OK:
906	sel = dlg.GetSelection()
907	parms = choice[sel]
908	noSkip = False
909	Atoms.ClearSelection()
910	for row in range(Atoms.GetNumberRows()):
911	if int(parms) == atomData[row][c]:
912	Atoms.SelectRow(row,True)
913	dlg.Destroy()
914	elif Atoms.GetColLabelValue(c) == 'chain':
915	choice = []
916	for r in range(Atoms.GetNumberRows()):
917	if atomData[r][c] not in choice:
918	choice.append(atomData[r][c])
919	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
920	if dlg.ShowModal() == wx.ID_OK:
921	sel = dlg.GetSelection()
922	parms = choice[sel]
923	noSkip = False
924	Atoms.ClearSelection()
925	for row in range(Atoms.GetNumberRows()):
926	if parms == atomData[row][c]:
927	Atoms.SelectRow(row,True)
928	dlg.Destroy()
929	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
930	pass #& then change all 'I' atoms
931	if sel >= 0 and noSkip:
932	ui = colLabels.index('U11')
933	us = colLabels.index('Uiso')
934	ss = colLabels.index('site sym')
935	for r in range(Atoms.GetNumberRows()):
936	ID = atomData[r][-1]
937	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
938	if parms == 'A': #'I' --> 'A'
939	Uiso = float(Atoms.GetCellValue(r,us))
940	sytsym = atomData[r][ss]
941	CSI = G2spc.GetCSuinel(sytsym)
942	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
943	atomData[r][us] = 0.0
944	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
945	for i in range(6):
946	ci = ui+i
947	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
948	if CSI[2][i]:
949	Atoms.SetCellStyle(r,ci,WHITE,False)
950	else: #'A' --> 'I'
951	Uij = atomData[r][ui:ui+6]
952	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
953	atomData[r][us] = Uiso
954	Atoms.SetCellStyle(r,us,WHITE,False)
955	for i in range(6):
956	ci = ui+i
957	atomData[r][ci] = 0.0
958	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
959	if not Atoms.IsReadOnly(r,c):
960	if Atoms.GetColLabelValue(c) == 'refine':
961	rbExcl = rbAtmDict.get(atomData[r][-1],'')
962	if rbExcl:
963	for excl in rbExcl:
964	atomData[r][c] = parms.replace(excl,'')
965	else:
966	atomData[r][c] = parms
967	else:
968	atomData[r][c] = parms
969	if 'Atoms' in data['Drawing']:
970	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
971	wx.CallAfter(Paint)
972
973	def ChangeAtomCell(event):
974
975	def chkUij(Uij,CSI): #needs to do something!!!
976	return Uij
977
978	r,c = event.GetRow(),event.GetCol()
979	if r >= 0 and c >= 0:
980	ID = atomData[r][-1]
981	if Atoms.GetColLabelValue(c) in ['x','y','z']:
982	ci = colLabels.index('x')
983	XYZ = atomData[r][ci:ci+3]
984	if None in XYZ:
985	XYZ = [0,0,0]
986	SScol = colLabels.index('site sym')
987	Mulcol = colLabels.index('mult')
988	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
989	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
990	atomData[r][SScol] = Sytsym
991	atomData[r][Mulcol] = Mult
992	if atomData[r][colLabels.index('I/A')] == 'A':
993	ui = colLabels.index('U11')
994	CSI = G2spc.GetCSuinel(Sytsym)
995	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
996	for i in range(6):
997	ci = i+ui
998	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
999	if CSI[2][i]:
1000	Atoms.SetCellStyle(r,ci,WHITE,False)
1001	SetupGeneral()
1002	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1003	if atomData[r][c] == 'I':
1004	Uij = atomData[r][c+2:c+8]
1005	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1006	Atoms.SetCellStyle(r,c+1,WHITE,False)
1007	Atoms.SetCellTextColour(r,c+1,BLACK)
1008	for i in range(6):
1009	ci = i+colLabels.index('U11')
1010	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1011	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1012	atomData[r][ci] = 0.0
1013	else:
1014	value = atomData[r][c+1]
1015	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1016	atomData[r][c+1] = 0.0
1017	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1018	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1019	for i in range(6):
1020	ci = i+colLabels.index('U11')
1021	atomData[r][ci] = value*CSI[3][i]
1022	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1023	Atoms.SetCellTextColour(r,ci,BLACK)
1024	if CSI[2][i]:
1025	Atoms.SetCellStyle(r,ci,WHITE,False)
1026	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1027	value = atomData[r][c]
1028	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1029	iUij = CSI[0][c-colLabels.index('U11')]
1030	for i in range(6):
1031	if iUij == CSI[0][i]:
1032	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1033	elif Atoms.GetColLabelValue(c) == 'refine':
1034	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1035	if 'Atoms' in data['Drawing']:
1036	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1037	wx.CallAfter(Paint)
1038
1039	def AtomTypeSelect(event):
1040	r,c = event.GetRow(),event.GetCol()
1041	if Atoms.GetColLabelValue(c) == 'Type':
1042	PE = G2elemGUI.PickElement(G2frame)
1043	if PE.ShowModal() == wx.ID_OK:
1044	if PE.Elem != 'None':
1045	atomData[r][c] = PE.Elem.strip()
1046	name = atomData[r][c]
1047	if len(name) in [2,4]:
1048	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1049	else:
1050	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1051	PE.Destroy()
1052	SetupGeneral()
1053	wx.CallAfter(Paint)
1054	value = Atoms.GetCellValue(r,c)
1055	atomData[r][c] = value
1056	ID = atomData[r][-1]
1057	if 'Atoms' in data['Drawing']:
1058	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1059	SetupGeneral()
1060	else:
1061	event.Skip()
1062
1063	def RowSelect(event):
1064	r,c = event.GetRow(),event.GetCol()
1065	if not event.AltDown():
1066	Atoms.frm = -1
1067	G2frame.dataFrame.SetStatusText('')
1068	if r < 0 and c < 0:
1069	if Atoms.IsSelection():
1070	Atoms.ClearSelection()
1071	elif c < 0: #only row clicks
1072	if event.ControlDown():
1073	if r in Atoms.GetSelectedRows():
1074	Atoms.DeselectRow(r)
1075	else:
1076	Atoms.SelectRow(r,True)
1077	elif event.ShiftDown():
1078	indxs = Atoms.GetSelectedRows()
1079	Atoms.ClearSelection()
1080	ibeg = 0
1081	if indxs:
1082	ibeg = indxs[-1]
1083	for row in range(ibeg,r+1):
1084	Atoms.SelectRow(row,True)
1085	elif event.AltDown():
1086	if atomData[r][-1] in rbAtmDict:
1087	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1088	Atoms.frm = -1
1089	Atoms.ClearSelection()
1090	else:
1091	if Atoms.frm < 0: #pick atom to be moved
1092	Atoms.frm = r
1093	Atoms.SelectRow(r,True)
1094	n = colLabels.index('Name')
1095	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1096	else: #move it
1097	item = atomData.pop(Atoms.frm)
1098	atomData.insert(r,item)
1099	Atoms.frm = -1
1100	G2frame.dataFrame.SetStatusText('')
1101	wx.CallAfter(Paint)
1102	else:
1103	Atoms.ClearSelection()
1104	Atoms.SelectRow(r,True)
1105
1106	def ChangeSelection(event):
1107	r,c = event.GetRow(),event.GetCol()
1108	if r < 0 and c < 0:
1109	Atoms.ClearSelection()
1110	if c < 0:
1111	if r in Atoms.GetSelectedRows():
1112	Atoms.DeselectRow(r)
1113	else:
1114	Atoms.SelectRow(r,True)
1115	if r < 0:
1116	if c in Atoms.GetSelectedCols():
1117	Atoms.DeselectCol(c)
1118	else:
1119	Atoms.SelectCol(c,True)
1120
1121	def Paint():
1122
1123	table = []
1124	rowLabels = []
1125	for i,atom in enumerate(atomData):
1126	table.append(atom)
1127	rowLabels.append(str(i))
1128	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1129	Atoms.SetTable(atomTable, True)
1130	Atoms.frm = -1
1131	colType = colLabels.index('Type')
1132	colR = colLabels.index('refine')
1133	colSS = colLabels.index('site sym')
1134	colX = colLabels.index('x')
1135	colIA = colLabels.index('I/A')
1136	colU11 = colLabels.index('U11')
1137	colUiso = colLabels.index('Uiso')
1138	attr = wx.grid.GridCellAttr()
1139	attr.IncRef() #fix from Jim Hester
1140	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1141	for c in range(colX,colX+3):
1142	Atoms.SetColAttr(c, attr)
1143	for i in range(colU11-1,colU11+6):
1144	Atoms.SetColSize(i,50)
1145	for row in range(Atoms.GetNumberRows()):
1146	atId = atomData[row][-1]
1147	rbExcl = rbAtmDict.get(atId,'')
1148	Atoms.SetReadOnly(row,colSS,True) #site sym
1149	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1150	if Atoms.GetCellValue(row,colIA) == 'A':
1151	CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')])
1152	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1153	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1154	for i in range(6):
1155	ci = colU11+i
1156	Atoms.SetCellTextColour(row,ci,BLACK)
1157	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1158	if CSI[2][i] and 'U' not in rbExcl:
1159	Atoms.SetCellStyle(row,ci,WHITE,False)
1160	else:
1161	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1162	Atoms.SetCellTextColour(row,colUiso,BLACK)
1163	if 'U' in rbExcl:
1164	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1165	for i in range(6):
1166	ci = colU11+i
1167	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1168	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1169	if 'X' in rbExcl:
1170	for c in range(0,colX+3):
1171	if c != colR:
1172	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1173	Atoms.AutoSizeColumns(False)
1174
1175	# FillAtomsGrid executable code starts here
1176	generalData = data['General']
1177	atomData = data['Atoms']
1178	DData = data['Drawing']
1179	resRBData = data['RBModels'].get('Residue',[])
1180	vecRBData = data['RBModels'].get('Vector',[])
1181	rbAtmDict = {}
1182	for rbObj in resRBData+vecRBData:
1183	exclList = ['X' for i in range(len(rbObj['Ids']))]
1184	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1185	if rbObj['ThermalMotion'][0] != 'None':
1186	for id in rbObj['Ids']:
1187	rbAtmDict[id] += 'U'
1188	# exclList will be 'x' or 'xu' if TLS used in RB
1189	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1190	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1191	if atomData:
1192	for item in Items:
1193	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1194	else:
1195	for item in Items:
1196	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1197	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1198	if 'showABC' in data['Drawing']:
1199	for item in Items:
1200	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1201	else:
1202	for item in Items:
1203	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1204
1205	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1206	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1207	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1208	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1209	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1210	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1211	if generalData['Type'] == 'magnetic':
1212	colLabels += ['Mx','My','Mz']
1213	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1214	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1215	elif generalData['Type'] == 'macromolecular':
1216	colLabels = ['res no','residue','chain'] + colLabels
1217	Types = [wg.GRID_VALUE_STRING,
1218	wg.GRID_VALUE_CHOICE+AAchoice,
1219	wg.GRID_VALUE_STRING] + Types
1220	elif generalData['Type'] == 'modulated':
1221	Types += []
1222	colLabels += []
1223	SGData = data['General']['SGData']
1224	G2frame.dataFrame.SetStatusText('')
1225	if SGData['SGPolax']:
1226	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1227	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1228	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1229	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1230	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1231	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1232	Atoms.SetMargins(0,0)
1233
1234	G2frame.dataFrame.setSizePosLeft([700,300])
1235	Paint()
1236
1237	def OnAtomAdd(event):
1238	AtomAdd(0,0,0)
1239	FillAtomsGrid(Atoms)
1240	event.StopPropagation()
1241	if data['Drawing']:
1242	G2plt.PlotStructure(G2frame,data)
1243
1244	def OnAtomViewAdd(event):
1245	try:
1246	drawData = data['Drawing']
1247	x,y,z = drawData['viewPoint'][0]
1248	AtomAdd(x,y,z)
1249	except:
1250	AtomAdd(0,0,0)
1251	FillAtomsGrid(Atoms)
1252	event.StopPropagation()
1253	G2plt.PlotStructure(G2frame,data)
1254
1255	def AtomAdd(x,y,z,El='H',Name='UNK'):
1256	atomData = data['Atoms']
1257	generalData = data['General']
1258	Ncol = Atoms.GetNumberCols()
1259	atId = ran.randint(0,sys.maxint)
1260	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1261	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1262	if generalData['Type'] == 'macromolecular':
1263	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1264	elif generalData['Type'] == 'nuclear':
1265	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1266	elif generalData['Type'] == 'magnetic':
1267	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1268	SetupGeneral()
1269	if 'Atoms' in data['Drawing']:
1270	DrawAtomAdd(data['Drawing'],atomData[-1])
1271
1272	def OnAtomInsert(event):
1273	AtomInsert(0,0,0)
1274	FillAtomsGrid(Atoms)
1275	event.StopPropagation()
1276	G2plt.PlotStructure(G2frame,data)
1277
1278	def OnAtomViewInsert(event):
1279	if 'Drawing' in data:
1280	drawData = data['Drawing']
1281	x,y,z = drawData['viewPoint'][0]
1282	AtomAdd(x,y,z)
1283	FillAtomsGrid(Atoms)
1284	event.StopPropagation()
1285
1286	def OnAtomMove(event):
1287	drawData = data['Drawing']
1288	atomData = data['Atoms']
1289	x,y,z = drawData['viewPoint'][0]
1290	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1291	cx = colLabels.index('x')
1292	indx = Atoms.GetSelectedRows()
1293	if len(indx) != 1:
1294	print '** ERROR - only one atom can be moved **'
1295	elif atomData[indx[0]][-1] in rbAtmDict:
1296	print '** ERROR - Atoms in rigid bodies can not be moved **'
1297	else:
1298	atomData[indx[0]][cx:cx+3] = [x,y,z]
1299	SetupGeneral()
1300	FillAtomsGrid(Atoms)
1301	ID = atomData[indx[0]][-1]
1302	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1303	G2plt.PlotStructure(G2frame,data)
1304	event.StopPropagation()
1305
1306	def DrawAtomsReplaceByID(drawingData,atom,ID):
1307	IDs = [ID,]
1308	atomData = drawingData['Atoms']
1309	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1310	for ind in indx:
1311	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1312
1313	def MakeDrawAtom(atom,oldatom=None):
1314	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1315	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1316	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1317	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1318	generalData = data['General']
1319	SGData = generalData['SGData']
1320	if generalData['Type'] == 'nuclear':
1321	if oldatom:
1322	opr = oldatom[5]
1323	if atom[9] == 'A':
1324	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1325	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1326	else:
1327	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1328	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1329	else:
1330	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1331	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1332	ct,cs = [1,8] #type & color
1333	elif generalData['Type'] == 'macromolecular':
1334	try:
1335	oneLetter = AA3letter.index(atom[1])
1336	except ValueError:
1337	oneLetter = -1
1338	atomInfo = [[atom[1].strip()+atom[0],]+
1339	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1340	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1341	ct,cs = [4,11] #type & color
1342	elif generalData['Type'] == 'magnetic':
1343	if oldatom:
1344	atomInfo = [atom[:2]+oldatom[3:]][0]
1345	else:
1346	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1347	ct,cs = [1,8] #type & color
1348	# elif generalData['Type'] == 'modulated':
1349	# ????? for future
1350	atNum = generalData['AtomTypes'].index(atom[ct])
1351	atomInfo[cs] = list(generalData['Color'][atNum])
1352	return atomInfo
1353
1354	def AtomInsert(x,y,z):
1355	indx = Atoms.GetSelectedRows()
1356	if indx:
1357	indx = indx[0]
1358	atomData = data['Atoms']
1359	generalData = data['General']
1360	Ncol = Atoms.GetNumberCols()
1361	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1362	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1363	atId = ran.randint(0,sys.maxint)
1364	if generalData['Type'] == 'macromolecular':
1365	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1366	elif generalData['Type'] == 'nuclear':
1367	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1368	elif generalData['Type'] == 'magnetic':
1369	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])
1370	SetupGeneral()
1371
1372	def AtomDelete(event):
1373	indx = Atoms.GetSelectedRows()
1374	IDs = []
1375	if indx:
1376	atomData = data['Atoms']
1377	indx.reverse()
1378	for ind in indx:
1379	atom = atomData[ind]
1380	if atom[-1] in rbAtmDict:
1381	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1382	else:
1383	IDs.append(atom[-1])
1384	del atomData[ind]
1385	if 'Atoms' in data['Drawing']:
1386	DrawAtomsDeleteByIDs(IDs)
1387	wx.CallAfter(FillAtomsGrid,Atoms)
1388	G2plt.PlotStructure(G2frame,data)
1389	SetupGeneral()
1390	event.StopPropagation()
1391
1392	def AtomRefine(event):
1393	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1394	c = colLabels.index('refine')
1395	indx = Atoms.GetSelectedRows()
1396	if indx:
1397	atomData = data['Atoms']
1398	generalData = data['General']
1399	Type = generalData['Type']
1400	if Type in ['nuclear','macromolecular']:
1401	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1402	elif Type == 'magnetic':
1403	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1404	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1405	if dlg.ShowModal() == wx.ID_OK:
1406	sel = dlg.GetSelections()
1407	parms = ''
1408	for x in sel:
1409	parms += choice[x][0]
1410	for r in indx:
1411	if not Atoms.IsReadOnly(r,c):
1412	atomData[r][c] = parms
1413	Atoms.ForceRefresh()
1414	dlg.Destroy()
1415
1416	def AtomModify(event):
1417	indx = Atoms.GetSelectedRows()
1418	if indx:
1419	atomData = data['Atoms']
1420	generalData = data['General']
1421	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1422	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1423	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1424	parm = ''
1425	if dlg.ShowModal() == wx.ID_OK:
1426	sel = dlg.GetSelection()
1427	parm = choices[sel]
1428	cid = colLabels.index(parm)
1429	dlg.Destroy()
1430	if parm in ['Type']:
1431	dlg = G2elemGUI.PickElement(G2frame)
1432	if dlg.ShowModal() == wx.ID_OK:
1433	if dlg.Elem not in ['None']:
1434	El = dlg.Elem.strip()
1435	for r in indx:
1436	if not Atoms.IsReadOnly(r,cid):
1437	atomData[r][cid] = El
1438	if len(El) in [2,4]:
1439	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1440	else:
1441	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1442	SetupGeneral()
1443	if 'Atoms' in data['Drawing']:
1444	for r in indx:
1445	ID = atomData[r][-1]
1446	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1447	FillAtomsGrid(Atoms)
1448	dlg.Destroy()
1449	elif parm in ['Name',]:
1450	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1451	wx.YES_NO \| wx.ICON_QUESTION)
1452	try:
1453	result = dlg.ShowModal()
1454	if result == wx.ID_YES:
1455	for r in indx:
1456	if not Atoms.IsReadOnly(r,cid+1):
1457	El = atomData[r][cid+1]
1458	if len(El) in [2,4]:
1459	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1460	else:
1461	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1462	FillAtomsGrid(Atoms)
1463	finally:
1464	dlg.Destroy()
1465
1466	elif parm in ['I/A']:
1467	choices = ['Isotropic','Anisotropic']
1468	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1469	if dlg.ShowModal() == wx.ID_OK:
1470	sel = dlg.GetSelection()
1471	parm = choices[sel][0]
1472	for r in indx:
1473	if not Atoms.IsReadOnly(r,cid):
1474	atomData[r][cid] = parm
1475	FillAtomsGrid(Atoms)
1476	dlg.Destroy()
1477	elif parm in ['frac','Uiso']:
1478	limits = [0.,1.]
1479	val = 1.0
1480	if parm in ['Uiso']:
1481	limits = [0.,0.25]
1482	val = 0.01
1483	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1484	if dlg.ShowModal() == wx.ID_OK:
1485	parm = dlg.GetValue()
1486	for r in indx:
1487	if not Atoms.IsReadOnly(r,cid):
1488	atomData[r][cid] = parm
1489	SetupGeneral()
1490	FillAtomsGrid(Atoms)
1491	dlg.Destroy()
1492	elif parm in ['x','y','z']:
1493	limits = [-1.,1.]
1494	val = 0.
1495	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1496	if dlg.ShowModal() == wx.ID_OK:
1497	parm = dlg.GetValue()
1498	for r in indx:
1499	if not Atoms.IsReadOnly(r,cid):
1500	atomData[r][cid] += parm
1501	SetupGeneral()
1502	FillAtomsGrid(Atoms)
1503	dlg.Destroy()
1504
1505	def AtomTransform(event):
1506	indx = Atoms.GetSelectedRows()
1507	if indx:
1508	generalData = data['General']
1509	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1510	cx = colLabels.index('x')
1511	cuia = colLabels.index('I/A')
1512	cuij = colLabels.index('U11')
1513	css = colLabels.index('site sym')
1514	atomData = data['Atoms']
1515	generalData = data['General']
1516	SGData = generalData['SGData']
1517	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1518	New = False
1519	try:
1520	if dlg.ShowModal() == wx.ID_OK:
1521	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1522	Cell = np.array(Cell)
1523	cent = SGData['SGCen'][Cent]
1524	M,T = SGData['SGOps'][Opr]
1525	for ind in indx:
1526	XYZ = np.array(atomData[ind][cx:cx+3])
1527	XYZ = np.inner(M,XYZ)+T
1528	if Inv:
1529	XYZ = -XYZ
1530	XYZ = XYZ+cent+Cell
1531	if Force:
1532	XYZ = G2spc.MoveToUnitCell(XYZ)
1533	if New:
1534	atom = copy.copy(atomData[ind])
1535	else:
1536	atom = atomData[ind]
1537	atom[cx:cx+3] = XYZ
1538	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1539	if atom[cuia] == 'A':
1540	Uij = atom[cuij:cuij+6]
1541	U = G2spc.Uij2U(Uij)
1542	U = np.inner(np.inner(M,U),M)
1543	Uij = G2spc.U2Uij(U)
1544	atom[cuij:cuij+6] = Uij
1545	if New:
1546	atomData.append(atom)
1547	finally:
1548	dlg.Destroy()
1549	Atoms.ClearSelection()
1550	if New:
1551	FillAtomsGrid(Atoms)
1552	else:
1553	Atoms.ForceRefresh()
1554
1555	def OnDistAnglePrt(event):
1556	fp = file(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile
1557	)[0]+'.disagl'),'w')
1558	OnDistAngle(event,fp=fp)
1559	fp.close()
1560
1561	def OnDistAngle(event,fp=None):
1562	indx = Atoms.GetSelectedRows()
1563	Oxyz = []
1564	xyz = []
1565	DisAglData = {}
1566	DisAglCtls = {}
1567	if indx:
1568	generalData = data['General']
1569	DisAglData['OrigIndx'] = indx
1570	if 'DisAglCtls' in generalData:
1571	DisAglCtls = generalData['DisAglCtls']
1572	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1573	if dlg.ShowModal() == wx.ID_OK:
1574	DisAglCtls = dlg.GetData()
1575	else:
1576	dlg.Destroy()
1577	return
1578	dlg.Destroy()
1579	generalData['DisAglCtls'] = DisAglCtls
1580	atomData = data['Atoms']
1581	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1582	cx = colLabels.index('x')
1583	cn = colLabels.index('Name')
1584	for i,atom in enumerate(atomData):
1585	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1586	if i in indx:
1587	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1588	DisAglData['OrigAtoms'] = Oxyz
1589	DisAglData['TargAtoms'] = xyz
1590	generalData = data['General']
1591	DisAglData['SGData'] = generalData['SGData']
1592	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1593	if 'pId' in data:
1594	DisAglData['pId'] = data['pId']
1595	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1596	try:
1597	if fp:
1598	G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
1599	else:
1600	G2stMn.PrintDistAngle(DisAglCtls,DisAglData)
1601	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1602	G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types')
1603	else:
1604	print "select one or more rows of atoms"
1605	G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
1606
1607	def OnReImport(event):
1608	print 'reimport atoms from file to be developed'
1609	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1610	rdlist = G2frame.OnImportGeneric(reqrdr,
1611	G2frame.ImportPhaseReaderlist,
1612	'phase')
1613	if len(rdlist) == 0: return
1614	# for now rdlist is only expected to have one element
1615	# for now always use the first phase for when multiple phases are ever implemented
1616	# but it would be better to loop until we find a phase that matches the one in data
1617	for rd in rdlist:
1618	# rd contains all info for a phase
1619	PhaseName = rd.Phase['General']['Name']
1620	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1621	print rd.Phase['Atoms']
1622	return
1623
1624	################################################################################
1625	#Structure drawing GUI stuff
1626	################################################################################
1627
1628	def SetupDrawingData():
1629	generalData = data['General']
1630	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1631	atomData = data['Atoms']
1632	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1633	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1634	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1635	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1636	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1637	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1638	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1639	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1640	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1641	'bondList':{},'viewDir':[1,0,0]}
1642	V0 = np.array([0,0,1])
1643	V = np.inner(Amat,V0)
1644	V /= np.sqrt(np.sum(V**2))
1645	A = np.arccos(np.sum(V*V0))
1646	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1647	try:
1648	drawingData = data['Drawing']
1649	except KeyError:
1650	data['Drawing'] = {}
1651	drawingData = data['Drawing']
1652	if not drawingData: #fill with defaults if empty
1653	drawingData.update(defaultDrawing)
1654	if 'Zstep' not in drawingData:
1655	drawingData['Zstep'] = 0.5
1656	if 'contourLevel' not in drawingData:
1657	drawingData['contourLevel'] = 1.
1658	if 'viewDir' not in drawingData:
1659	drawingData['viewDir'] = [0,0,1]
1660	if 'Quaternion' not in drawingData:
1661	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1662	if 'showRigidBodies' not in drawingData:
1663	drawingData['showRigidBodies'] = True
1664	cx,ct,cs,ci = [0,0,0,0]
1665	if generalData['Type'] == 'nuclear':
1666	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1667	elif generalData['Type'] == 'macromolecular':
1668	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1669	elif generalData['Type'] == 'magnetic':
1670	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1671	# elif generalData['Type'] == 'modulated':
1672	# ????? for future
1673	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1674	if not drawingData.get('Atoms'):
1675	for atom in atomData:
1676	DrawAtomAdd(drawingData,atom)
1677	data['Drawing'] = drawingData
1678
1679	def DrawAtomAdd(drawingData,atom):
1680	drawingData['Atoms'].append(MakeDrawAtom(atom))
1681
1682	def OnRestraint(event):
1683	indx = drawAtoms.GetSelectedRows()
1684	restData = G2frame.PatternTree.GetItemPyData(
1685	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1686	drawingData = data['Drawing']
1687	generalData = data['General']
1688	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1689	cx,ct,cs,ci = drawingData['atomPtrs']
1690	atomData = drawingData['Atoms']
1691	atNames = []
1692	atXYZ = []
1693	atSymOp = []
1694	atIndx = []
1695	for item in indx:
1696	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1697	atSymOp.append(atomData[item][cs-1])
1698	atIndx.append(atomData[item][ci])
1699	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1700	try:
1701	bondData = restData[PhaseName]['Bond']
1702	except KeyError:
1703	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1704	restData[PhaseName] = {}
1705	restData[PhaseName]['Bond'] = bondData
1706	dist = G2mth.getRestDist(atXYZ,Amat)
1707	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1708	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1709	try:
1710	angleData = restData[PhaseName]['Angle']
1711	except KeyError:
1712	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1713	restData[PhaseName] = {}
1714	restData[PhaseName]['Angle'] = angleData
1715	angle = G2mth.getRestAngle(atXYZ,Amat)
1716	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1717	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1718	try:
1719	planeData = restData[PhaseName]['Plane']
1720	except KeyError:
1721	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1722	restData[PhaseName] = {}
1723	restData[PhaseName]['Plane'] = planeData
1724	plane = G2mth.getRestPlane(atXYZ,Amat)
1725	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1726	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1727	try:
1728	chiralData = restData[PhaseName]['Chiral']
1729	except KeyError:
1730	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1731	restData[PhaseName] = {}
1732	restData[PhaseName]['Chiral'] = chiralData
1733	volume = G2mth.getRestChiral(atXYZ,Amat)
1734	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1735	else:
1736	print '**** ERROR wrong number of atoms selected for this restraint'
1737	return
1738	G2frame.PatternTree.SetItemPyData(
1739	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1740
1741	def OnDefineRB(event):
1742	indx = drawAtoms.GetSelectedRows()
1743	indx.sort()
1744	RBData = G2frame.PatternTree.GetItemPyData(
1745	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1746	drawingData = data['Drawing']
1747	generalData = data['General']
1748	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1749	cx,ct,cs,ci = drawingData['atomPtrs']
1750	atomData = drawingData['Atoms']
1751	rbXYZ = []
1752	rbType = []
1753	atNames = []
1754	AtInfo = RBData['Residue']['AtInfo']
1755	for i,item in enumerate(indx):
1756	rbtype = atomData[item][ct]
1757	atNames.append(rbtype+str(i))
1758	rbType.append(rbtype)
1759	if rbtype not in AtInfo:
1760	Info = G2elem.GetAtomInfo(rbtype)
1761	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1762	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1763	rbXYZ = np.array(rbXYZ)
1764	rbXYZ -= rbXYZ[0]
1765	rbId = ran.randint(0,sys.maxint)
1766	rbName = 'UNKRB'
1767	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1768	'Edit rigid body name',rbName ,style=wx.OK)
1769	if dlg.ShowModal() == wx.ID_OK:
1770	rbName = dlg.GetValue()
1771	dlg.Destroy()
1772	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1773	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1774	RBData['RBIds']['Residue'].append(rbId)
1775	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1776
1777	################################################################################
1778	##### Atom draw routines
1779	################################################################################
1780
1781	def UpdateDrawAtoms(atomStyle=''):
1782	def RefreshAtomGrid(event):
1783	def SetChoice(name,c,n=0):
1784	choice = []
1785	for r in range(len(atomData)):
1786	if n:
1787	srchStr = str(atomData[r][c][:n])
1788	else:
1789	srchStr = str(atomData[r][c])
1790	if srchStr not in choice:
1791	if n:
1792	choice.append(str(atomData[r][c][:n]))
1793	else:
1794	choice.append(str(atomData[r][c]))
1795	choice.sort()
1796
1797	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
1798	if dlg.ShowModal() == wx.ID_OK:
1799	sel = dlg.GetSelections()
1800	parms = []
1801	for x in sel:
1802	parms.append(choice[x])
1803	noSkip = False
1804	drawAtoms.ClearSelection()
1805	drawingData['selectedAtoms'] = []
1806	for row in range(len(atomData)):
1807	test = atomData[row][c]
1808	if n:
1809	test = test[:n]
1810	if test in parms:
1811	drawAtoms.SelectRow(row,True)
1812	drawingData['selectedAtoms'].append(row)
1813	G2plt.PlotStructure(G2frame,data)
1814	dlg.Destroy()
1815
1816	r,c = event.GetRow(),event.GetCol()
1817	if r < 0 and c < 0:
1818	for row in range(drawAtoms.GetNumberRows()):
1819	drawingData['selectedAtoms'].append(row)
1820	drawAtoms.SelectRow(row,True)
1821	elif r < 0: #dclick on col label
1822	sel = -1
1823	Parms = False
1824	noSkip = True
1825	if drawAtoms.GetColLabelValue(c) == 'Style':
1826	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1827	if dlg.ShowModal() == wx.ID_OK:
1828	sel = dlg.GetSelection()
1829	parms = styleChoice[sel]
1830	for r in range(len(atomData)):
1831	atomData[r][c] = parms
1832	drawAtoms.SetCellValue(r,c,parms)
1833	FindBondsDraw()
1834	G2plt.PlotStructure(G2frame,data)
1835	dlg.Destroy()
1836	elif drawAtoms.GetColLabelValue(c) == 'Label':
1837	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
1838	if dlg.ShowModal() == wx.ID_OK:
1839	sel = dlg.GetSelection()
1840	parms = labelChoice[sel]
1841	for r in range(len(atomData)):
1842	atomData[r][c] = parms
1843	drawAtoms.SetCellValue(r,c,parms)
1844	dlg.Destroy()
1845	elif drawAtoms.GetColLabelValue(c) == 'Color':
1846	dlg = wx.ColourDialog(G2frame)
1847	if dlg.ShowModal() == wx.ID_OK:
1848	color = dlg.GetColourData().GetColour()
1849	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1850	attr.SetReadOnly(True)
1851	attr.SetBackgroundColour(color)
1852	for r in range(len(atomData)):
1853	atomData[r][c] = color
1854	drawingData['Atoms'][r][c] = color
1855	drawAtoms.SetAttr(r,c,attr)
1856	UpdateDrawAtoms()
1857	dlg.Destroy()
1858	elif drawAtoms.GetColLabelValue(c) == 'Residue':
1859	SetChoice('Residue',c,3)
1860	elif drawAtoms.GetColLabelValue(c) == '1-letter':
1861	SetChoice('1-letter',c,1)
1862	elif drawAtoms.GetColLabelValue(c) == 'Chain':
1863	SetChoice('Chain',c)
1864	elif drawAtoms.GetColLabelValue(c) == 'Name':
1865	SetChoice('Name',c)
1866	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
1867	SetChoice('Name',c)
1868	elif drawAtoms.GetColLabelValue(c) == 'Type':
1869	SetChoice('Type',c)
1870	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
1871	drawAtoms.ClearSelection()
1872	else:
1873	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
1874	atomData[r][c] = drawAtoms.GetCellValue(r,c)
1875	FindBondsDraw()
1876	elif drawAtoms.GetColLabelValue(c) == 'Color':
1877	dlg = wx.ColourDialog(G2frame)
1878	if dlg.ShowModal() == wx.ID_OK:
1879	color = dlg.GetColourData().GetColour()
1880	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1881	attr.SetReadOnly(True)
1882	attr.SetBackgroundColour(color)
1883	atomData[r][c] = color
1884	drawingData['Atoms'][r][c] = color
1885	drawAtoms.SetAttr(i,cs+2,attr)
1886	dlg.Destroy()
1887	UpdateDrawAtoms()
1888	G2plt.PlotStructure(G2frame,data)
1889
1890	def RowSelect(event):
1891	r,c = event.GetRow(),event.GetCol()
1892	if r < 0 and c < 0:
1893	if drawAtoms.IsSelection():
1894	drawAtoms.ClearSelection()
1895	elif c < 0: #only row clicks
1896	if event.ControlDown():
1897	if r in drawAtoms.GetSelectedRows():
1898	drawAtoms.DeselectRow(r)
1899	else:
1900	drawAtoms.SelectRow(r,True)
1901	elif event.ShiftDown():
1902	indxs = drawAtoms.GetSelectedRows()
1903	drawAtoms.ClearSelection()
1904	ibeg = 0
1905	if indxs:
1906	ibeg = indxs[-1]
1907	for row in range(ibeg,r+1):
1908	drawAtoms.SelectRow(row,True)
1909	else:
1910	drawAtoms.ClearSelection()
1911	drawAtoms.SelectRow(r,True)
1912	drawingData['selectedAtoms'] = []
1913	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
1914	G2plt.PlotStructure(G2frame,data)
1915
1916	# UpdateDrawAtoms executable code starts here
1917	G2frame.dataFrame.SetStatusText('')
1918	generalData = data['General']
1919	SetupDrawingData()
1920	drawingData = data['Drawing']
1921	cx,ct,cs,ci = drawingData['atomPtrs']
1922	atomData = drawingData['Atoms']
1923	if atomStyle:
1924	for atom in atomData:
1925	atom[cs] = atomStyle
1926	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
1927	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
1928	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
1929	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1930	labelChoice = [' ','type','name','number']
1931	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
1932	if generalData['Type'] == 'macromolecular':
1933	colLabels = ['Residue','1-letter','Chain'] + colLabels
1934	Types = 3*[wg.GRID_VALUE_STRING,]+Types
1935	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
1936	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
1937	labelChoice = [' ','type','name','number','residue','1-letter','chain']
1938	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
1939	# elif generalData['Type'] == 'modulated':
1940	# Types += []
1941	# colLabels += []
1942	table = []
1943	rowLabels = []
1944	for i,atom in enumerate(drawingData['Atoms']):
1945	table.append(atom[:colLabels.index('I/A')+1])
1946	rowLabels.append(str(i))
1947
1948	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1949	drawAtoms.SetTable(atomTable, True)
1950	drawAtoms.SetMargins(0,0)
1951	drawAtoms.AutoSizeColumns(True)
1952	drawAtoms.SetColSize(colLabels.index('Style'),80)
1953	drawAtoms.SetColSize(colLabels.index('Color'),50)
1954	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
1955	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1956	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
1957	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1958	for i,atom in enumerate(drawingData['Atoms']):
1959	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1960	attr.SetReadOnly(True)
1961	attr.SetBackgroundColour(atom[cs+2])
1962	drawAtoms.SetAttr(i,cs+2,attr)
1963	drawAtoms.SetCellValue(i,cs+2,'')
1964	indx = drawingData['selectedAtoms']
1965	if indx:
1966	for r in range(len(atomData)):
1967	if r in indx:
1968	drawAtoms.SelectRow(r)
1969	for c in range(len(colLabels)):
1970	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
1971	attr.SetReadOnly(True)
1972	attr.SetBackgroundColour(VERY_LIGHT_GREY)
1973	if colLabels[c] not in ['Style','Label','Color']:
1974	drawAtoms.SetColAttr(c,attr)
1975	G2frame.dataFrame.setSizePosLeft([600,300])
1976
1977	FindBondsDraw()
1978	drawAtoms.ClearSelection()
1979	# G2plt.PlotStructure(G2frame,data)
1980
1981	def DrawAtomStyle(event):
1982	indx = drawAtoms.GetSelectedRows()
1983	if indx:
1984	generalData = data['General']
1985	atomData = data['Drawing']['Atoms']
1986	cx,ct,cs,ci = data['Drawing']['atomPtrs']
1987	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
1988	if generalData['Type'] == 'macromolecular':
1989	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
1990	'backbone','ribbons','schematic']
1991	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
1992	if dlg.ShowModal() == wx.ID_OK:
1993	sel = dlg.GetSelection()
1994	parms = styleChoice[sel]
1995	for r in indx:
1996	atomData[r][cs] = parms
1997	drawAtoms.SetCellValue(r,cs,parms)
1998	dlg.Destroy()
1999	FindBondsDraw()
2000	drawAtoms.ClearSelection()
2001	G2plt.PlotStructure(G2frame,data)
2002
2003	def DrawAtomLabel(event):
2004	indx = drawAtoms.GetSelectedRows()
2005	if indx:
2006	generalData = data['General']
2007	atomData = data['Drawing']['Atoms']
2008	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2009	styleChoice = [' ','type','name','number']
2010	if generalData['Type'] == 'macromolecular':
2011	styleChoice = [' ','type','name','number','residue','1-letter','chain']
2012	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
2013	if dlg.ShowModal() == wx.ID_OK:
2014	sel = dlg.GetSelection()
2015	parms = styleChoice[sel]
2016	for r in indx:
2017	atomData[r][cs+1] = parms
2018	drawAtoms.SetCellValue(r,cs+1,parms)
2019	dlg.Destroy()
2020	drawAtoms.ClearSelection()
2021	G2plt.PlotStructure(G2frame,data)
2022
2023	def DrawAtomColor(event):
2024
2025	indx = drawAtoms.GetSelectedRows()
2026	if indx:
2027	if len(indx) > 1:
2028	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2029	else:
2030	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2031	generalData = data['General']
2032	atomData = data['Drawing']['Atoms']
2033	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2034	atmColors = []
2035	atmTypes = []
2036	for r in indx:
2037	if atomData[r][cs+2] not in atmColors:
2038	atmColors.append(atomData[r][cs+2])
2039	atmTypes.append(atomData[r][ct])
2040	if len(atmColors) > 16:
2041	break
2042	colors = wx.ColourData()
2043	colors.SetChooseFull(True)
2044	dlg = wx.ColourDialog(G2frame)
2045	if dlg.ShowModal() == wx.ID_OK:
2046	for i in range(len(atmColors)):
2047	atmColors[i] = dlg.GetColourData().GetColour()
2048	colorDict = dict(zip(atmTypes,atmColors))
2049	for r in indx:
2050	color = colorDict[atomData[r][ct]]
2051	atomData[r][cs+2] = color
2052	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2053	attr.SetBackgroundColour(color)
2054	drawAtoms.SetAttr(r,cs+2,attr)
2055	data['Drawing']['Atoms'][r][cs+2] = color
2056	drawAtoms.ClearSelection()
2057	dlg.Destroy()
2058	G2frame.dataFrame.SetStatusText('')
2059	G2plt.PlotStructure(G2frame,data)
2060
2061	def ResetAtomColors(event):
2062	generalData = data['General']
2063	atomData = data['Drawing']['Atoms']
2064	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2065	for atom in atomData:
2066	atNum = generalData['AtomTypes'].index(atom[ct])
2067	atom[cs+2] = list(generalData['Color'][atNum])
2068	UpdateDrawAtoms()
2069	drawAtoms.ClearSelection()
2070	G2plt.PlotStructure(G2frame,data)
2071
2072	def SetViewPoint(event):
2073	indx = drawAtoms.GetSelectedRows()
2074	if indx:
2075	atomData = data['Drawing']['Atoms']
2076	cx = data['Drawing']['atomPtrs'][0]
2077	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2078	drawAtoms.ClearSelection() #do I really want to do this?
2079	G2plt.PlotStructure(G2frame,data)
2080
2081	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2082	cx = data['Drawing']['atomPtrs'][0]
2083	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2084	return False
2085	else:
2086	return True
2087
2088	def AddSymEquiv(event):
2089	indx = drawAtoms.GetSelectedRows()
2090	indx.sort()
2091	if indx:
2092	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2093	cx = colLabels.index('x')
2094	cuia = colLabels.index('I/A')
2095	cuij = cuia+2
2096	atomData = data['Drawing']['Atoms']
2097	generalData = data['General']
2098	SGData = generalData['SGData']
2099	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2100	try:
2101	if dlg.ShowModal() == wx.ID_OK:
2102	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2103	Cell = np.array(Cell)
2104	cent = SGData['SGCen'][Cent]
2105	M,T = SGData['SGOps'][Opr]
2106	for ind in indx:
2107	XYZ = np.array(atomData[ind][cx:cx+3])
2108	XYZ = np.inner(M,XYZ)+T
2109	if Inv:
2110	XYZ = -XYZ
2111	XYZ = XYZ+cent+Cell
2112	if Force:
2113	XYZ = G2spc.MoveToUnitCell(XYZ)
2114	if noDuplicate(XYZ,atomData):
2115	atom = copy.copy(atomData[ind])
2116	atom[cx:cx+3] = XYZ
2117	atomOp = atom[cx+3]
2118	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2119	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2120	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2121	if atom[cuia] == 'A':
2122	Uij = atom[cuij:cuij+6]
2123	U = G2spc.Uij2U(Uij)
2124	U = np.inner(np.inner(M,U),M)
2125	Uij = G2spc.U2Uij(U)
2126	atom[cuij:cuij+6] = Uij
2127	atomData.append(atom)
2128	finally:
2129	dlg.Destroy()
2130	UpdateDrawAtoms()
2131	drawAtoms.ClearSelection()
2132	G2plt.PlotStructure(G2frame,data)
2133
2134	def TransformSymEquiv(event):
2135	indx = drawAtoms.GetSelectedRows()
2136	indx.sort()
2137	if indx:
2138	atomData = data['Drawing']['Atoms']
2139	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2140	cx = colLabels.index('x')
2141	cuia = colLabels.index('I/A')
2142	cuij = cuia+2
2143	atomData = data['Drawing']['Atoms']
2144	generalData = data['General']
2145	SGData = generalData['SGData']
2146	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2147	try:
2148	if dlg.ShowModal() == wx.ID_OK:
2149	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2150	Cell = np.array(Cell)
2151	cent = SGData['SGCen'][Cent]
2152	M,T = SGData['SGOps'][Opr]
2153	for ind in indx:
2154	XYZ = np.array(atomData[ind][cx:cx+3])
2155	XYZ = np.inner(M,XYZ)+T
2156	if Inv:
2157	XYZ = -XYZ
2158	XYZ = XYZ+cent+Cell
2159	if Force:
2160	XYZ = G2spc.MoveToUnitCell(XYZ)
2161	atom = atomData[ind]
2162	atom[cx:cx+3] = XYZ
2163	atomOp = atom[cx+3]
2164	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2165	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2166	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2167	if atom[cuia] == 'A':
2168	Uij = atom[cuij:cuij+6]
2169	U = G2spc.Uij2U(Uij)
2170	U = np.inner(np.inner(M,U),M)
2171	Uij = G2spc.U2Uij(U)
2172	atom[cuij:cuij+6] = Uij
2173	data['Drawing']['Atoms'] = atomData
2174	finally:
2175	dlg.Destroy()
2176	UpdateDrawAtoms()
2177	drawAtoms.ClearSelection()
2178	G2plt.PlotStructure(G2frame,data)
2179
2180	def FillCoordSphere(event):
2181	generalData = data['General']
2182	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2183	radii = generalData['BondRadii']
2184	atomTypes = generalData['AtomTypes']
2185	try:
2186	indH = atomTypes.index('H')
2187	radii[indH] = 0.5
2188	except:
2189	pass
2190	indx = drawAtoms.GetSelectedRows()
2191	if indx:
2192	indx.sort()
2193	atomData = data['Drawing']['Atoms']
2194	numAtoms = len(atomData)
2195	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2196	generalData = data['General']
2197	SGData = generalData['SGData']
2198	cellArray = G2lat.CellBlock(1)
2199	wx.BeginBusyCursor()
2200	try:
2201	for ind in indx:
2202	atomA = atomData[ind]
2203	xyzA = np.array(atomA[cx:cx+3])
2204	indA = atomTypes.index(atomA[ct])
2205	for atomB in atomData[:numAtoms]:
2206	indB = atomTypes.index(atomB[ct])
2207	sumR = radii[indA]+radii[indB]
2208	xyzB = np.array(atomB[cx:cx+3])
2209	for xyz in cellArray+xyzB:
2210	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2211	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2212	if noDuplicate(xyz,atomData):
2213	oprB = atomB[cx+3]
2214	C = xyz-xyzB
2215	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2216	newAtom = atomB[:]
2217	newAtom[cx:cx+3] = xyz
2218	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2219	atomData.append(newAtom)
2220	finally:
2221	wx.EndBusyCursor()
2222	data['Drawing']['Atoms'] = atomData
2223	UpdateDrawAtoms()
2224	drawAtoms.ClearSelection()
2225	G2plt.PlotStructure(G2frame,data)
2226
2227	def FillUnitCell(event):
2228	indx = drawAtoms.GetSelectedRows()
2229	indx.sort()
2230	if indx:
2231	atomData = data['Drawing']['Atoms']
2232	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2233	cx = colLabels.index('x')
2234	cuia = colLabels.index('I/A')
2235	cuij = cuia+2
2236	generalData = data['General']
2237	SGData = generalData['SGData']
2238	wx.BeginBusyCursor()
2239	try:
2240	for ind in indx:
2241	atom = atomData[ind]
2242	XYZ = np.array(atom[cx:cx+3])
2243	if atom[cuia] == 'A':
2244	Uij = atom[cuij:cuij+6]
2245	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2246	for item in result:
2247	atom = copy.copy(atomData[ind])
2248	atom[cx:cx+3] = item[0]
2249	atom[cx+3] = str(item[2])+'+' \
2250	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2251	atom[cuij:cuij+6] = item[1]
2252	Opp = G2spc.Opposite(item[0])
2253	for xyz in Opp:
2254	if noDuplicate(xyz,atomData):
2255	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2256	cell = '1'+'+'+ \
2257	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2258	atom[cx:cx+3] = xyz
2259	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2260	atomData.append(atom[:])
2261	else:
2262	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2263	for item in result:
2264	atom = copy.copy(atomData[ind])
2265	atom[cx:cx+3] = item[0]
2266	atom[cx+3] = str(item[1])+'+' \
2267	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2268	Opp = G2spc.Opposite(item[0])
2269	for xyz in Opp:
2270	if noDuplicate(xyz,atomData):
2271	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2272	cell = '1'+'+'+ \
2273	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2274	atom[cx:cx+3] = xyz
2275	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2276	atomData.append(atom[:])
2277	data['Drawing']['Atoms'] = atomData
2278	finally:
2279	wx.EndBusyCursor()
2280	UpdateDrawAtoms()
2281	drawAtoms.ClearSelection()
2282	G2plt.PlotStructure(G2frame,data)
2283
2284	def FindBondsToo(): #works but slow for large structures - keep as reference
2285	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2286	atomData = data['Drawing']['Atoms']
2287	generalData = data['General']
2288	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2289	radii = generalData['BondRadii']
2290	atomTypes = generalData['AtomTypes']
2291	try:
2292	indH = atomTypes.index('H')
2293	radii[indH] = 0.5
2294	except:
2295	pass
2296	for atom in atomData:
2297	atom[-1] = []
2298	Atoms = []
2299	for i,atom in enumerate(atomData):
2300	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2301	for atomA in Atoms:
2302	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2303	for atomB in Atoms:
2304	Dx = atomB[1]-atomA[1]
2305	DX = np.inner(Amat,Dx)
2306	dist = np.sqrt(np.sum(DX**2))
2307	sumR = atomA[3]+atomB[3]
2308	if 0.5 < dist <= 0.85*sumR:
2309	i = atomA[0]
2310	if atomA[2] == 'polyhedra':
2311	atomData[i][-1].append(DX)
2312	elif atomB[1] != 'polyhedra':
2313	j = atomB[0]
2314	atomData[i][-1].append(Dx*atomA[3]/sumR)
2315	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2316
2317	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2318	import numpy.ma as ma
2319	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2320	hydro = data['Drawing']['showHydrogen']
2321	atomData = data['Drawing']['Atoms']
2322	generalData = data['General']
2323	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2324	radii = generalData['BondRadii']
2325	atomTypes = generalData['AtomTypes']
2326	try:
2327	indH = atomTypes.index('H')
2328	radii[indH] = 0.5
2329	except:
2330	pass
2331	for atom in atomData:
2332	atom[-2] = [] #clear out old bonds/polyhedra
2333	atom[-1] = []
2334	Indx = range(len(atomData))
2335	Atoms = []
2336	Styles = []
2337	Radii = []
2338	for atom in atomData:
2339	Atoms.append(np.array(atom[cx:cx+3]))
2340	Styles.append(atom[cs])
2341	try:
2342	if not hydro and atom[ct] == 'H':
2343	Radii.append(0.0)
2344	else:
2345	Radii.append(radii[atomTypes.index(atom[ct])])
2346	except ValueError: #changed atom type!
2347	Radii.append(0.20)
2348	Atoms = np.array(Atoms)
2349	Radii = np.array(Radii)
2350	IASR = zip(Indx,Atoms,Styles,Radii)
2351	for atomA in IASR:
2352	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2353	Dx = Atoms-atomA[1]
2354	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
2355	sumR = atomA[3]+Radii
2356	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2357	i = atomA[0]
2358	for j in IndB[0]:
2359	if Styles[i] == 'polyhedra':
2360	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2361	elif Styles[j] != 'polyhedra' and j > i:
2362	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2363	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2364	if Styles[i] == 'polyhedra':
2365	Bonds = atomData[i][-2]
2366	Faces = []
2367	if len(Bonds) > 2:
2368	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2369	for face in FaceGen:
2370	vol = nl.det(face)
2371	if abs(vol) > 1. or len(Bonds) == 3:
2372	if vol < 0.:
2373	face = [face[0],face[2],face[1]]
2374	face = np.array(face)
2375	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2376	norm = np.cross(face[1]-face[0],face[2]-face[0])
2377	norm /= np.sqrt(np.sum(norm**2))
2378	Faces.append([face,norm])
2379	atomData[i][-1] = Faces
2380
2381	def DrawAtomsDelete(event):
2382	indx = drawAtoms.GetSelectedRows()
2383	indx.sort()
2384	if indx:
2385	atomData = data['Drawing']['Atoms']
2386	indx.reverse()
2387	for ind in indx:
2388	del atomData[ind]
2389	UpdateDrawAtoms()
2390	drawAtoms.ClearSelection()
2391	G2plt.PlotStructure(G2frame,data)
2392	event.StopPropagation()
2393
2394	def OnReloadDrawAtoms(event):
2395	data['Drawing']['Atoms'] = []
2396	UpdateDrawAtoms()
2397	drawAtoms.ClearSelection()
2398	G2plt.PlotStructure(G2frame,data)
2399	event.StopPropagation()
2400
2401	def DrawAtomsDeleteByIDs(IDs):
2402	atomData = data['Drawing']['Atoms']
2403	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2404	indx.reverse()
2405	for ind in indx:
2406	del atomData[ind]
2407
2408	def ChangeDrawAtomsByIDs(colName,IDs,value):
2409	atomData = data['Drawing']['Atoms']
2410	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2411	if colName == 'Name':
2412	col = ct-1
2413	elif colName == 'Type':
2414	col = ct
2415	elif colName == 'I/A':
2416	col = cs
2417	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2418	for ind in indx:
2419	atomData[ind][col] = value
2420
2421	def OnDrawPlane(event):
2422	indx = drawAtoms.GetSelectedRows()
2423	if len(indx) < 4:
2424	print '**** ERROR - need 4+ atoms for plane calculation'
2425	return
2426	PlaneData = {}
2427	drawingData = data['Drawing']
2428	atomData = drawingData['Atoms']
2429	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2430	cx = colLabels.index('x')
2431	cn = colLabels.index('Name')
2432	xyz = []
2433	for i,atom in enumerate(atomData):
2434	if i in indx:
2435	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2436	generalData = data['General']
2437	PlaneData['Name'] = generalData['Name']
2438	PlaneData['Atoms'] = xyz
2439	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2440	G2stMn.BestPlane(PlaneData)
2441
2442	def OnDrawDistVP(event):
2443	# distance to view point
2444	indx = drawAtoms.GetSelectedRows()
2445	if not indx:
2446	print '***** ERROR - no atoms selected'
2447	return
2448	generalData = data['General']
2449	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2450	drawingData = data['Drawing']
2451	viewPt = np.array(drawingData['viewPoint'][0])
2452	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2453	atomDData = drawingData['Atoms']
2454	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2455	cx = colLabels.index('x')
2456	cn = colLabels.index('Name')
2457	for i in indx:
2458	atom = atomDData[i]
2459	Dx = np.array(atom[cx:cx+3])-viewPt
2460	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2461	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2462
2463	def OnDrawDAT(event):
2464	#distance, angle, torsion
2465	indx = drawAtoms.GetSelectedRows()
2466	if len(indx) not in [2,3,4]:
2467	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2468	return
2469	DATData = {}
2470	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2471	drawingData = data['Drawing']
2472	atomData = data['Atoms']
2473	atomDData = drawingData['Atoms']
2474	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2475	cx = colLabels.index('x')
2476	cn = colLabels.index('Name')
2477	cid = colLabels.index('I/A')+8
2478	xyz = []
2479	Oxyz = []
2480	DATData['Natoms'] = len(indx)
2481	for i in indx:
2482	atom = atomDData[i]
2483	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2484	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2485	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2486	DATData['Datoms'] = xyz
2487	DATData['Oatoms'] = Oxyz
2488	generalData = data['General']
2489	DATData['Name'] = generalData['Name']
2490	DATData['SGData'] = generalData['SGData']
2491	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2492	if 'pId' in data:
2493	DATData['pId'] = data['pId']
2494	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2495	G2stMn.DisAglTor(DATData)
2496
2497	################################################################################
2498	#### Draw Options page
2499	################################################################################
2500
2501	def UpdateDrawOptions():
2502	import copy
2503	import wx.lib.colourselect as wcs
2504	def SlopSizer():
2505	def OnCameraPos(event):
2506	drawingData['cameraPos'] = cameraPos.GetValue()
2507	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2508	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2509	G2plt.PlotStructure(G2frame,data)
2510
2511	def OnZclip(event):
2512	drawingData['Zclip'] = Zclip.GetValue()
2513	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2514	G2plt.PlotStructure(G2frame,data)
2515
2516	def OnZstep(event):
2517	try:
2518	step = float(Zstep.GetValue())
2519	if not (0.01 <= step <= 1.0):
2520	raise ValueError
2521	except ValueError:
2522	step = drawingData['Zstep']
2523	drawingData['Zstep'] = step
2524	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2525
2526	def OnMoveZ(event):
2527	move = MoveZ.GetValue()*drawingData['Zstep']
2528	MoveZ.SetValue(0)
2529	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2530	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2531	VD /= np.sqrt(np.sum(VD**2))
2532	VP += move*VD
2533	VP = np.inner(Bmat,VP)
2534	drawingData['viewPoint'][0] = VP
2535	panel = drawOptions.GetChildren()
2536	names = [child.GetName() for child in panel]
2537	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2538	G2plt.PlotStructure(G2frame,data)
2539
2540	def OnVdWScale(event):
2541	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2542	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2543	G2plt.PlotStructure(G2frame,data)
2544
2545	def OnEllipseProb(event):
2546	drawingData['ellipseProb'] = ellipseProb.GetValue()
2547	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2548	G2plt.PlotStructure(G2frame,data)
2549
2550	def OnBallScale(event):
2551	drawingData['ballScale'] = ballScale.GetValue()/100.
2552	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2553	G2plt.PlotStructure(G2frame,data)
2554
2555	def OnBondRadius(event):
2556	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2557	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2558	G2plt.PlotStructure(G2frame,data)
2559
2560	def OnContourLevel(event):
2561	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2562	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2563	G2plt.PlotStructure(G2frame,data)
2564
2565	def OnMapSize(event):
2566	drawingData['mapSize'] = mapSize.GetValue()/10.
2567	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2568	G2plt.PlotStructure(G2frame,data)
2569
2570
2571	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2572	slideSizer = wx.FlexGridSizer(7,2)
2573	slideSizer.AddGrowableCol(1,1)
2574
2575	cameraPosTxt = wx.StaticText(drawOptions,-1,
2576	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2577	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2578	slideSizer.Add(cameraPosTxt,0,wx.ALIGN_CENTER_VERTICAL)
2579	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2580	cameraPos.SetRange(10,500)
2581	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2582	G2frame.dataDisplay.cameraSlider = cameraPos
2583	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2584
2585	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2586	slideSizer.Add(ZclipTxt,0,wx.ALIGN_CENTER_VERTICAL)
2587	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2588	Zclip.SetRange(1,99)
2589	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2590	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2591
2592	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2593	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,wx.ALIGN_CENTER_VERTICAL)
2594	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2595	style=wx.TE_PROCESS_ENTER)
2596	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2597	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2598	ZstepSizer.Add(Zstep,0,wx.ALIGN_CENTER_VERTICAL)
2599	slideSizer.Add(ZstepSizer)
2600	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2601	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,wx.ALIGN_CENTER_VERTICAL)
2602	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2603	MoveZ.SetValue(0)
2604	MoveZ.SetRange(-1,1)
2605	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2606	MoveSizer.Add(MoveZ)
2607	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2608
2609	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2610	slideSizer.Add(vdwScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2611	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2612	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2613	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2614
2615	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2616	slideSizer.Add(ellipseProbTxt,0,wx.ALIGN_CENTER_VERTICAL)
2617	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2618	ellipseProb.SetRange(1,99)
2619	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2620	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2621
2622	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2623	slideSizer.Add(ballScaleTxt,0,wx.ALIGN_CENTER_VERTICAL)
2624	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2625	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2626	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2627
2628	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2629	slideSizer.Add(bondRadiusTxt,0,wx.ALIGN_CENTER_VERTICAL)
2630	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2631	bondRadius.SetRange(1,25)
2632	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2633	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2634
2635	if generalData['Map']['rhoMax']:
2636	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2637	slideSizer.Add(contourLevelTxt,0,wx.ALIGN_CENTER_VERTICAL)
2638	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2639	contourLevel.SetRange(1,100)
2640	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2641	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2642	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2643	slideSizer.Add(mapSizeTxt,0,wx.ALIGN_CENTER_VERTICAL)
2644	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2645	mapSize.SetRange(1,100)
2646	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2647	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2648
2649	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2650	slopSizer.Add((10,5),0)
2651	slopSizer.SetMinSize(wx.Size(350,10))
2652	return slopSizer
2653
2654	def ShowSizer():
2655
2656	def OnBackColor(event):
2657	drawingData['backColor'] = event.GetValue()
2658	G2plt.PlotStructure(G2frame,data)
2659
2660	def OnShowABC(event):
2661	drawingData['showABC'] = showABC.GetValue()
2662	G2plt.PlotStructure(G2frame,data)
2663
2664	def OnShowUnitCell(event):
2665	drawingData['unitCellBox'] = unitCellBox.GetValue()
2666	G2plt.PlotStructure(G2frame,data)
2667
2668	def OnShowHyd(event):
2669	drawingData['showHydrogen'] = showHydrogen.GetValue()
2670	FindBondsDraw()
2671	G2plt.PlotStructure(G2frame,data)
2672
2673	def OnShowRB(event):
2674	drawingData['showRigidBodies'] = showRB.GetValue()
2675	FindBondsDraw()
2676	G2plt.PlotStructure(G2frame,data)
2677
2678	def OnViewPoint(event):
2679	Obj = event.GetEventObject()
2680	viewPt = Obj.GetValue().split()
2681	try:
2682	VP = [float(viewPt[i]) for i in range(3)]
2683	except (ValueError,IndexError):
2684	VP = drawingData['viewPoint'][0]
2685	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2686	drawingData['viewPoint'][0] = VP
2687	G2plt.PlotStructure(G2frame,data)
2688
2689	def OnViewDir(event):
2690	Obj = event.GetEventObject()
2691	viewDir = Obj.GetValue().split()
2692	try:
2693	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2694	VD = np.array([float(viewDir[i]) for i in range(3)])
2695	VC = np.inner(Amat,VD)
2696	VC /= np.sqrt(np.sum(VC**2))
2697	V = np.array(drawingData['viewDir'])
2698	VB = np.inner(Amat,V)
2699	VB /= np.sqrt(np.sum(VB**2))
2700	VX = np.cross(VC,VB)
2701	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2702	QV = G2mth.AVdeg2Q(A,VX)
2703	Q = drawingData['Quaternion']
2704	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2705	except (ValueError,IndexError):
2706	VD = drawingData['viewDir']
2707	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2708	drawingData['viewDir'] = VD
2709	G2plt.PlotStructure(G2frame,data)
2710
2711	showSizer = wx.BoxSizer(wx.VERTICAL)
2712	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2713	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,wx.ALIGN_CENTER_VERTICAL)
2714	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2715	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2716	lineSizer.Add(backColor,0,wx.ALIGN_CENTER_VERTICAL)
2717	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,wx.ALIGN_CENTER_VERTICAL)
2718	VD = drawingData['viewDir']
2719	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2720	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2721	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2722	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2723	G2frame.dataDisplay.viewDir = viewDir
2724	lineSizer.Add(viewDir,0,wx.ALIGN_CENTER_VERTICAL)
2725	showSizer.Add(lineSizer)
2726	showSizer.Add((0,5),0)
2727
2728	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2729	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2730	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2731	showABC.SetValue(drawingData['showABC'])
2732	lineSizer.Add(showABC,0,wx.ALIGN_CENTER_VERTICAL)
2733	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,wx.ALIGN_CENTER_VERTICAL)
2734	VP = drawingData['viewPoint'][0]
2735	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2736	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2737	G2frame.dataDisplay.viewPoint = viewPoint
2738	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2739	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2740	lineSizer.Add(viewPoint,0,wx.ALIGN_CENTER_VERTICAL)
2741	showSizer.Add(lineSizer)
2742	showSizer.Add((0,5),0)
2743
2744	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2745
2746	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2747	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2748	unitCellBox.SetValue(drawingData['unitCellBox'])
2749	line2Sizer.Add(unitCellBox,0,wx.ALIGN_CENTER_VERTICAL)
2750
2751	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2752	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2753	showHydrogen.SetValue(drawingData['showHydrogen'])
2754	line2Sizer.Add(showHydrogen,0,wx.ALIGN_CENTER_VERTICAL)
2755
2756	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2757	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2758	showRB.SetValue(drawingData['showRigidBodies'])
2759	line2Sizer.Add(showRB,0,wx.ALIGN_CENTER_VERTICAL)
2760
2761	showSizer.Add(line2Sizer)
2762	return showSizer
2763
2764	def RadSizer():
2765
2766	def OnSizeHatoms(event):
2767	try:
2768	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2769	except ValueError:
2770	value = 0.5
2771	drawingData['sizeH'] = value
2772	sizeH.SetValue("%.2f"%(value))
2773	G2plt.PlotStructure(G2frame,data)
2774
2775	def OnRadFactor(event):
2776	try:
2777	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2778	except ValueError:
2779	value = 0.85
2780	drawingData['radiusFactor'] = value
2781	radFactor.SetValue("%.2f"%(value))
2782	FindBondsDraw()
2783	G2plt.PlotStructure(G2frame,data)
2784
2785	radSizer = wx.BoxSizer(wx.HORIZONTAL)
2786	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,wx.ALIGN_CENTER_VERTICAL)
2787	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2788	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
2789	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
2790	radSizer.Add(sizeH,0,wx.ALIGN_CENTER_VERTICAL)
2791
2792	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,wx.ALIGN_CENTER_VERTICAL)
2793	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2794	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
2795	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
2796	radSizer.Add(radFactor,0,wx.ALIGN_CENTER_VERTICAL)
2797	return radSizer
2798
2799	# UpdateDrawOptions exectable code starts here
2800	generalData = data['General']
2801	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2802	SetupDrawingData()
2803	drawingData = data['Drawing']
2804	if generalData['Type'] == 'nuclear':
2805	pickChoice = ['Atoms','Bonds','Torsions','Planes']
2806	elif generalData['Type'] == 'macromolecular':
2807	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
2808
2809	G2frame.dataFrame.SetStatusText('')
2810	if drawOptions.GetSizer():
2811	drawOptions.GetSizer().Clear(True)
2812	mainSizer = wx.BoxSizer(wx.VERTICAL)
2813	mainSizer.Add((5,5),0)
2814	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,wx.ALIGN_CENTER_VERTICAL)
2815	mainSizer.Add((5,5),0)
2816	mainSizer.Add(SlopSizer(),0)
2817	mainSizer.Add((5,5),0)
2818	mainSizer.Add(ShowSizer(),0,)
2819	mainSizer.Add((5,5),0)
2820	mainSizer.Add(RadSizer(),0,)
2821	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
2822
2823	################################################################################
2824	#### Texture routines
2825	################################################################################
2826
2827	def UpdateTexture():
2828	def SetSHCoef():
2829	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
2830	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
2831	SHCoeff = textureData['SH Coeff'][1]
2832	for cofName in SHCoeff:
2833	if cofName in cofNames:
2834	newSHCoef[cofName] = SHCoeff[cofName]
2835	return newSHCoef
2836
2837	def OnShOrder(event):
2838	Obj = event.GetEventObject()
2839	textureData['Order'] = int(Obj.GetValue())
2840	textureData['SH Coeff'][1] = SetSHCoef()
2841	wx.CallAfter(UpdateTexture)
2842	G2plt.PlotTexture(G2frame,data)
2843
2844	def OnShModel(event):
2845	Obj = event.GetEventObject()
2846	textureData['Model'] = Obj.GetValue()
2847	textureData['SH Coeff'][1] = SetSHCoef()
2848	wx.CallAfter(UpdateTexture)
2849	G2plt.PlotTexture(G2frame,data)
2850
2851	def OnSHRefine(event):
2852	Obj = event.GetEventObject()
2853	textureData['SH Coeff'][0] = Obj.GetValue()
2854
2855	def OnSHShow(event):
2856	Obj = event.GetEventObject()
2857	textureData['SHShow'] = Obj.GetValue()
2858	wx.CallAfter(UpdateTexture)
2859
2860	def OnProjSel(event):
2861	Obj = event.GetEventObject()
2862	G2frame.Projection = Obj.GetValue()
2863	G2plt.PlotTexture(G2frame,data)
2864
2865	def OnColorSel(event):
2866	Obj = event.GetEventObject()
2867	G2frame.ContourColor = Obj.GetValue()
2868	G2plt.PlotTexture(G2frame,data)
2869
2870	def OnAngRef(event):
2871	Obj = event.GetEventObject()
2872	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
2873
2874	def OnAngValue(event):
2875	Obj = event.GetEventObject()
2876	try:
2877	value = float(Obj.GetValue())
2878	except ValueError:
2879	value = textureData[valIndx[Obj.GetId()]][1]
2880	Obj.SetValue('%8.2f'%(value))
2881	textureData[valIndx[Obj.GetId()]][1] = value
2882
2883	def OnODFValue(event):
2884	Obj = event.GetEventObject()
2885	try:
2886	value = float(Obj.GetValue())
2887	except ValueError:
2888	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
2889	Obj.SetValue('%8.3f'%(value))
2890	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
2891	G2plt.PlotTexture(G2frame,data)
2892
2893	def OnPfType(event):
2894	Obj = event.GetEventObject()
2895	textureData['PlotType'] = Obj.GetValue()
2896	wx.CallAfter(UpdateTexture)
2897	G2plt.PlotTexture(G2frame,data)
2898
2899	def OnPFValue(event):
2900	Obj = event.GetEventObject()
2901	Saxis = Obj.GetValue().split()
2902	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2903	try:
2904	hkl = [int(Saxis[i]) for i in range(3)]
2905	except (ValueError,IndexError):
2906	hkl = textureData['PFhkl']
2907	if not np.any(np.array(hkl)): #can't be all zeros!
2908	hkl = textureData['PFhkl']
2909	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
2910	textureData['PFhkl'] = hkl
2911	else:
2912	try:
2913	xyz = [float(Saxis[i]) for i in range(3)]
2914	except (ValueError,IndexError):
2915	xyz = textureData['PFxyz']
2916	if not np.any(np.array(xyz)): #can't be all zeros!
2917	xyz = textureData['PFxyz']
2918	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
2919	textureData['PFxyz'] = xyz
2920	G2plt.PlotTexture(G2frame,data)
2921
2922	# UpdateTexture executable starts here
2923	G2frame.dataFrame.SetStatusText('')
2924	generalData = data['General']
2925	SGData = generalData['SGData']
2926	try:
2927	textureData = generalData['SH Texture']
2928	except KeyError: #fix old files!
2929	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
2930	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
2931	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
2932	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
2933	if 'SHShow' not in textureData: #another fix
2934	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2935	try: #another fix!
2936	x = textureData['PlotType']
2937	except KeyError:
2938	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
2939	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
2940	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
2941	if generalData['doPawley'] and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Sequental results'):
2942	G2frame.dataFrame.RefineTexture.Enable(True)
2943	shAngles = ['omega','chi','phi']
2944	if Texture.GetSizer():
2945	Texture.GetSizer().Clear(True)
2946	mainSizer = wx.BoxSizer(wx.VERTICAL)
2947	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
2948	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,wx.ALIGN_CENTER_VERTICAL)
2949	titleSizer.Add(wx.StaticText(Texture,-1,
2950	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
2951	0,wx.ALIGN_CENTER_VERTICAL)
2952	mainSizer.Add(titleSizer,0)
2953	mainSizer.Add((0,5),0)
2954	shSizer = wx.FlexGridSizer(1,6,5,5)
2955	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,wx.ALIGN_CENTER_VERTICAL)
2956	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
2957	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2958	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
2959	shSizer.Add(shModel,0,wx.ALIGN_CENTER_VERTICAL)
2960	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,wx.ALIGN_CENTER_VERTICAL)
2961	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
2962	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2963	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
2964	shSizer.Add(shOrder,0,wx.ALIGN_CENTER_VERTICAL)
2965	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
2966	shRef.SetValue(textureData['SH Coeff'][0])
2967	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
2968	shSizer.Add(shRef,0,wx.ALIGN_CENTER_VERTICAL)
2969	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
2970	shShow.SetValue(textureData['SHShow'])
2971	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
2972	shSizer.Add(shShow,0,wx.ALIGN_CENTER_VERTICAL)
2973	mainSizer.Add(shSizer,0,0)
2974	mainSizer.Add((0,5),0)
2975	PTSizer = wx.FlexGridSizer(2,4,5,5)
2976	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,wx.ALIGN_CENTER_VERTICAL)
2977	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
2978	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
2979	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2980	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
2981	PTSizer.Add(pfType,0,wx.ALIGN_CENTER_VERTICAL)
2982	if 'Axial' not in textureData['PlotType']:
2983	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,wx.ALIGN_CENTER_VERTICAL)
2984	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
2985	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2986	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
2987	PTSizer.Add(projSel,0,wx.ALIGN_CENTER_VERTICAL)
2988	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
2989	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,wx.ALIGN_CENTER_VERTICAL)
2990	PH = textureData['PFhkl']
2991	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
2992	else:
2993	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,wx.ALIGN_CENTER_VERTICAL)
2994	PX = textureData['PFxyz']
2995	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
2996	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
2997	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
2998	PTSizer.Add(pfVal,0,wx.ALIGN_CENTER_VERTICAL)
2999	if 'Axial' not in textureData['PlotType']:
3000	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,wx.ALIGN_CENTER_VERTICAL)
3001	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3002	choice.sort()
3003	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
3004	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3005	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
3006	PTSizer.Add(colorSel,0,wx.ALIGN_CENTER_VERTICAL)
3007	mainSizer.Add(PTSizer,0,wx.ALIGN_CENTER_VERTICAL)
3008	mainSizer.Add((0,5),0)
3009	if textureData['SHShow']:
3010	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,wx.ALIGN_CENTER_VERTICAL)
3011	mainSizer.Add((0,5),0)
3012	ODFSizer = wx.FlexGridSizer(2,8,2,2)
3013	ODFIndx = {}
3014	ODFkeys = textureData['SH Coeff'][1].keys()
3015	ODFkeys.sort()
3016	for item in ODFkeys:
3017	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,wx.ALIGN_CENTER_VERTICAL)
3018	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3019	ODFIndx[ODFval.GetId()] = item
3020	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3021	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3022	ODFSizer.Add(ODFval,0,wx.ALIGN_CENTER_VERTICAL)
3023	mainSizer.Add(ODFSizer,0,wx.ALIGN_CENTER_VERTICAL)
3024	mainSizer.Add((0,5),0)
3025	mainSizer.Add((0,5),0)
3026	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,wx.ALIGN_CENTER_VERTICAL)
3027	mainSizer.Add((0,5),0)
3028	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3029	angIndx = {}
3030	valIndx = {}
3031	for item in ['Sample omega','Sample chi','Sample phi']:
3032	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3033	angRef.SetValue(textureData[item][0])
3034	angIndx[angRef.GetId()] = item
3035	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3036	angSizer.Add(angRef,0,wx.ALIGN_CENTER_VERTICAL)
3037	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3038	valIndx[angVal.GetId()] = item
3039	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3040	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3041	angSizer.Add(angVal,0,wx.ALIGN_CENTER_VERTICAL)
3042	angSizer.Add((5,0),0)
3043	mainSizer.Add(angSizer,0,wx.ALIGN_CENTER_VERTICAL)
3044	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3045
3046	################################################################################
3047	##### DData routines - GUI stuff in GSASIIddataGUI.py
3048	################################################################################
3049
3050	def OnHklfAdd(event):
3051	UseList = data['Histograms']
3052	keyList = UseList.keys()
3053	TextList = []
3054	if G2frame.PatternTree.GetCount():
3055	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3056	while item:
3057	name = G2frame.PatternTree.GetItemText(item)
3058	if name not in keyList and 'HKLF' in name:
3059	TextList.append(name)
3060	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3061	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3062	try:
3063	if dlg.ShowModal() == wx.ID_OK:
3064	result = dlg.GetSelections()
3065	for i in result:
3066	histoName = TextList[i]
3067	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3068	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3069	'Extinction':['Lorentzian','None',
3070	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3071	wx.BeginBusyCursor()
3072	UpdateHKLFdata(histoName)
3073	wx.EndBusyCursor()
3074	data['Histograms'] = UseList
3075	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3076	finally:
3077	dlg.Destroy()
3078
3079	def UpdateHKLFdata(histoName):
3080	generalData = data['General']
3081	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3082	refDict,reflData = G2frame.PatternTree.GetItemPyData(Id)
3083	SGData = generalData['SGData']
3084	Cell = generalData['Cell'][1:7]
3085	G,g = G2lat.cell2Gmat(Cell)
3086	for ref in reflData:
3087	H = ref[:3]
3088	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3089	iabsnt,ref[3],ref[11],ref[12] = G2spc.GenHKLf(H,SGData)
3090	G2frame.PatternTree.SetItemPyData(Id,[refDict,reflData])
3091
3092	def OnPwdrAdd(event):
3093	generalData = data['General']
3094	SGData = generalData['SGData']
3095	UseList = data['Histograms']
3096	newList = []
3097	NShkl = len(G2spc.MustrainNames(SGData))
3098	NDij = len(G2spc.HStrainNames(SGData))
3099	keyList = UseList.keys()
3100	TextList = ['All PWDR']
3101	if G2frame.PatternTree.GetCount():
3102	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3103	while item:
3104	name = G2frame.PatternTree.GetItemText(item)
3105	if name not in keyList and 'PWDR' in name:
3106	TextList.append(name)
3107	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3108	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3109	try:
3110	if dlg.ShowModal() == wx.ID_OK:
3111	result = dlg.GetSelections()
3112	for i in result: newList.append(TextList[i])
3113	if 'All PWDR' in newList:
3114	newList = TextList[1:]
3115	for histoName in newList:
3116	pId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3117	UseList[histoName] = {'Histogram':histoName,'Show':False,
3118	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3119	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3120	[1.,1.,1.,0.,0.,0.],6*[False,]],
3121	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3122	NShkl[0.01,],NShkl[False,]],
3123	'HStrain':[NDij[0.0,],NDij[False,]],
3124	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3125	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,pId,'Reflection Lists'))
3126	refList[generalData['Name']] = []
3127	data['Histograms'] = UseList
3128	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3129	finally:
3130	dlg.Destroy()
3131
3132	def OnDataDelete(event):
3133	UseList = data['Histograms']
3134	keyList = ['All',]+UseList.keys()
3135	keyList.sort()
3136	DelList = []
3137	if UseList:
3138	DelList = []
3139	dlg = wx.MultiChoiceDialog(G2frame,
3140	'Which histogram to delete from this phase?', 'Delete histogram',
3141	keyList, wx.CHOICEDLG_STYLE)
3142	try:
3143	if dlg.ShowModal() == wx.ID_OK:
3144	result = dlg.GetSelections()
3145	for i in result:
3146	DelList.append(keyList[i])
3147	if 'All' in DelList:
3148	DelList = keyList[1:]
3149	for i in DelList:
3150	del UseList[i]
3151	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3152	finally:
3153	dlg.Destroy()
3154
3155	################################################################################
3156	##### Rigid bodies
3157	################################################################################
3158
3159	def FillRigidBodyGrid(refresh=True):
3160	'''Fill the Rigid Body Phase information tab page.
3161	Note that the page is a ScrolledWindow, not a Grid
3162	'''
3163	def OnThermSel(event): #needs to be seen by VecRbSizer!
3164	Obj = event.GetEventObject()
3165	RBObj = Indx[Obj.GetId()]
3166	val = Obj.GetValue()
3167	Ttype = 'A'
3168	if val == 'Uiso':
3169	Ttype = 'I'
3170	RBObj['ThermalMotion'][0] = 'Uiso'
3171	elif val == 'T':
3172	RBObj['ThermalMotion'][0] = 'T'
3173	elif val == 'TL':
3174	RBObj['ThermalMotion'][0] = 'TL'
3175	elif val == 'TLS':
3176	RBObj['ThermalMotion'][0] = 'TLS'
3177	wx.CallAfter(FillRigidBodyGrid,True)
3178	if val != 'None':
3179	cia = data['General']['AtomPtrs'][3]
3180	for i,id in enumerate(RBObj['Ids']):
3181	data['Atoms'][AtLookUp[id]][cia] = Ttype
3182	G2plt.PlotStructure(G2frame,data)
3183
3184	def ThermDataSizer(RBObj,rbType):
3185
3186	def OnThermval(event):
3187	Obj = event.GetEventObject()
3188	item = Indx[Obj.GetId()]
3189	try:
3190	val = float(Obj.GetValue())
3191	RBObj['ThermalMotion'][1][item] = val
3192	except ValueError:
3193	pass
3194	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3195	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3196	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3197	cia = data['General']['AtomPtrs'][3]
3198	for i,id in enumerate(RBObj['Ids']):
3199	if Uout[i][0] == 'I':
3200	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3201	else:
3202	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3203	G2plt.PlotStructure(G2frame,data)
3204
3205	def OnTLSRef(event):
3206	Obj = event.GetEventObject()
3207	item = Indx[Obj.GetId()]
3208	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3209
3210	thermSizer = wx.FlexGridSizer(1,9,5,5)
3211	model = RBObj['ThermalMotion']
3212	if model[0] == 'Uiso':
3213	names = ['Uiso',]
3214	elif 'T' in model[0]:
3215	names = ['T11','T22','T33','T12','T13','T23']
3216	if 'L' in model[0]:
3217	names += ['L11','L22','L33','L12','L13','L23']
3218	if 'S' in model[0]:
3219	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3220	for i,name in enumerate(names):
3221	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,wx.ALIGN_CENTER_VERTICAL)
3222	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3223	style=wx.TE_PROCESS_ENTER)
3224	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3225	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3226	Indx[thermVal.GetId()] = i
3227	thermSizer.Add(thermVal)
3228	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3229	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3230	Tcheck.SetValue(model[2][i])
3231	Indx[Tcheck.GetId()] = i
3232	thermSizer.Add(Tcheck,0,wx.ALIGN_CENTER_VERTICAL)
3233	return thermSizer
3234
3235	def LocationSizer(RBObj,rbType):
3236
3237	def OnOrigRef(event):
3238	RBObj['Orig'][1] = Ocheck.GetValue()
3239
3240	def OnOrienRef(event):
3241	RBObj['Orient'][1] = Qcheck.GetValue()
3242
3243	def OnOrigX(event):
3244	Obj = event.GetEventObject()
3245	item = Indx[Obj.GetId()]
3246	try:
3247	val = float(Obj.GetValue())
3248	RBObj['Orig'][0][item] = val
3249	Obj.SetValue('%8.5f'%(val))
3250	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3251	for i,id in enumerate(RBObj['Ids']):
3252	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3253	data['Drawing']['Atoms'] = []
3254	UpdateDrawAtoms(atomStyle)
3255	G2plt.PlotStructure(G2frame,data)
3256	except ValueError:
3257	pass
3258
3259	def OnOrien(event):
3260	Obj = event.GetEventObject()
3261	item = Indx[Obj.GetId()]
3262	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3263	V = np.inner(Bmat,V)
3264	try:
3265	val = float(Obj.GetValue())
3266	if item:
3267	V[item-1] = val
3268	else:
3269	A = val
3270	Obj.SetValue('%8.5f'%(val))
3271	V = np.inner(Amat,V)
3272	Q = G2mth.AVdeg2Q(A,V)
3273	if not any(Q):
3274	raise ValueError
3275	RBObj['Orient'][0] = Q
3276	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3277	for i,id in enumerate(RBObj['Ids']):
3278	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3279	data['Drawing']['Atoms'] = []
3280	UpdateDrawAtoms(atomStyle)
3281	G2plt.PlotStructure(G2frame,data)
3282	except ValueError:
3283	pass
3284
3285	topSizer = wx.FlexGridSizer(2,6,5,5)
3286	Orig = RBObj['Orig'][0]
3287	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3288	Orien = [Orien,]
3289	Orien.extend(OrienV/nl.norm(OrienV))
3290	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,wx.ALIGN_CENTER_VERTICAL)
3291	for ix,x in enumerate(Orig):
3292	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3293	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3294	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3295	Indx[origX.GetId()] = ix
3296	topSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3297	topSizer.Add((5,0),)
3298	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3299	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3300	Ocheck.SetValue(RBObj['Orig'][1])
3301	topSizer.Add(Ocheck,0,wx.ALIGN_CENTER_VERTICAL)
3302	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,wx.ALIGN_CENTER_VERTICAL)
3303	for ix,x in enumerate(Orien):
3304	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3305	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3306	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3307	Indx[orien.GetId()] = ix
3308	topSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3309	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3310	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3311	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3312	Qcheck.SetValue(RBObj['Orient'][1])
3313	topSizer.Add(Qcheck)
3314	return topSizer
3315
3316	def ResrbSizer(RBObj):
3317	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3318
3319	def OnTorsionRef(event):
3320	Obj = event.GetEventObject()
3321	item = Indx[Obj.GetId()]
3322	RBObj['Torsions'][item][1] = Obj.GetValue()
3323
3324	def OnTorsion(event):
3325	Obj = event.GetEventObject()
3326	item = Indx[Obj.GetId()]
3327	try:
3328	val = float(Obj.GetValue())
3329	RBObj['Torsions'][item][0] = val
3330	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3331	for i,id in enumerate(RBObj['Ids']):
3332	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3333	except ValueError:
3334	pass
3335	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3336	data['Drawing']['Atoms'] = []
3337	UpdateDrawAtoms(atomStyle)
3338	drawAtoms.ClearSelection()
3339	G2plt.PlotStructure(G2frame,data)
3340
3341	def OnDelResRB(event):
3342	Obj = event.GetEventObject()
3343	RBId = Indx[Obj.GetId()]
3344	RBData['Residue'][RBId]['useCount'] -= 1
3345	RBObjs = data['RBModels']['Residue']
3346	for rbObj in RBObjs:
3347	if RBId == rbObj['RBId']:
3348	data['RBModels']['Residue'].remove(rbObj)
3349	G2plt.PlotStructure(G2frame,data)
3350	wx.CallAfter(FillRigidBodyGrid,True)
3351
3352	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3353	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3354	topLine = wx.BoxSizer(wx.HORIZONTAL)
3355	topLine.Add(wx.StaticText(RigidBodies,-1,
3356	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3357	rbId = RBObj['RBId']
3358	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3359	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3360	Indx[delRB.GetId()] = rbId
3361	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3362	resrbSizer.Add(topLine)
3363	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3364	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,wx.ALIGN_CENTER_VERTICAL)
3365	torSizer = wx.FlexGridSizer(1,6,5,5)
3366	for itors,tors in enumerate(RBObj['Torsions']):
3367	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,wx.ALIGN_CENTER_VERTICAL)
3368	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3369	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3370	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3371	Indx[torsTxt.GetId()] = itors
3372	torSizer.Add(torsTxt)
3373	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3374	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3375	torCheck.SetValue(tors[1])
3376	Indx[torCheck.GetId()] = itors
3377	torSizer.Add(torCheck,0,wx.ALIGN_CENTER_VERTICAL)
3378	resrbSizer.Add(torSizer)
3379	tchoice = ['None','Uiso','T','TL','TLS']
3380	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3381	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3382	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3383	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3384	Indx[thermSel.GetId()] = RBObj
3385	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3386	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3387	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3388	resrbSizer.Add(thermSizer)
3389	if RBObj['ThermalMotion'][0] != 'None':
3390	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3391	return resrbSizer
3392
3393	def VecrbSizer(RBObj):
3394	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3395
3396	def OnDelVecRB(event):
3397	Obj = event.GetEventObject()
3398	RBId = Indx[Obj.GetId()]
3399	RBData['Vector'][RBId]['useCount'] -= 1
3400	RBObjs = data['RBModels']['Vector']
3401	for rbObj in RBObjs:
3402	if RBId == rbObj['RBId']:
3403	data['RBModels']['Vector'].remove(rbObj)
3404	G2plt.PlotStructure(G2frame,data)
3405	wx.CallAfter(FillRigidBodyGrid,True)
3406
3407	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3408	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3409	topLine = wx.BoxSizer(wx.HORIZONTAL)
3410	topLine.Add(wx.StaticText(RigidBodies,-1,
3411	'Name: '+RBObj['RBname']+' '),0,wx.ALIGN_CENTER_VERTICAL)
3412	rbId = RBObj['RBId']
3413	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3414	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3415	Indx[delRB.GetId()] = rbId
3416	topLine.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
3417	vecrbSizer.Add(topLine)
3418	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3419	tchoice = ['None','Uiso','T','TL','TLS']
3420	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3421	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,wx.ALIGN_CENTER_VERTICAL)
3422	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3423	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3424	Indx[thermSel.GetId()] = RBObj
3425	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3426	thermSizer.Add(thermSel,0,wx.ALIGN_CENTER_VERTICAL)
3427	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,wx.ALIGN_CENTER_VERTICAL)
3428	vecrbSizer.Add(thermSizer)
3429	if RBObj['ThermalMotion'][0] != 'None':
3430	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3431	return vecrbSizer
3432
3433	# FillRigidBodyGrid executable code starts here
3434	if refresh:
3435	RigidBodies.DestroyChildren()
3436	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3437	general = data['General']
3438	cx = general['AtomPtrs'][0]
3439	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3440	RBData = G2frame.PatternTree.GetItemPyData(
3441	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3442	Indx = {}
3443	atomStyle = 'balls & sticks'
3444	if 'macro' in general['Type']:
3445	atomStyle = 'sticks'
3446	G2frame.dataFrame.SetStatusText('')
3447	mainSizer = wx.BoxSizer(wx.VERTICAL)
3448	if not data['RBModels']:
3449	mainSizer.Add((5,5),0)
3450	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,wx.ALIGN_CENTER_VERTICAL)
3451	mainSizer.Add((5,5),0)
3452	if 'Residue' in data['RBModels']:
3453	mainSizer.Add((5,5),0)
3454	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3455	mainSizer.Add((5,5),0)
3456	for RBObj in data['RBModels']['Residue']:
3457	mainSizer.Add(ResrbSizer(RBObj))
3458	if 'Vector' in data['RBModels']:
3459	mainSizer.Add((5,5),0)
3460	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,wx.ALIGN_CENTER_VERTICAL)
3461	mainSizer.Add((5,5),0)
3462	for RBObj in data['RBModels']['Vector']:
3463	mainSizer.Add(VecrbSizer(RBObj))
3464
3465	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3466
3467	def OnRBCopyParms(event):
3468	RBObjs = []
3469	for rbType in ['Vector','Residue']:
3470	RBObjs += data['RBModels'].get(rbType,[])
3471	if not len(RBObjs):
3472	print '** ERROR - no rigid bodies defined **'
3473	return
3474	if len(RBObjs) == 1:
3475	print '** INFO - only one rigid body defined; nothing to copy to **'
3476	return
3477	Source = []
3478	sourceRB = {}
3479	for RBObj in RBObjs:
3480	Source.append(RBObj['RBname'])
3481	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3482	if dlg.ShowModal() == wx.ID_OK:
3483	sel = dlg.GetSelection()
3484	name = Source[sel]
3485	for item in ['Orig','Orient','ThermalMotion']:
3486	sourceRB.update({item:RBObjs[sel][item],})
3487	dlg.Destroy()
3488	if not sourceRB:
3489	return
3490	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3491	if dlg.ShowModal() == wx.ID_OK:
3492	sel = dlg.GetSelections()
3493	for x in sel:
3494	RBObjs[x].update(copy.copy(sourceRB))
3495	G2plt.PlotStructure(G2frame,data)
3496	wx.CallAfter(FillRigidBodyGrid(True))
3497
3498	def OnRBAssign(event):
3499
3500	G2frame.dataFrame.SetStatusText('')
3501	RBData = G2frame.PatternTree.GetItemPyData(
3502	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3503	rbNames = {}
3504	for rbVec in RBData['Vector']:
3505	if rbVec != 'AtInfo':
3506	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3507	for rbRes in RBData['Residue']:
3508	if rbRes != 'AtInfo':
3509	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3510	if not rbNames:
3511	print '** ERROR - no rigid bodies defined **'
3512	return
3513	general = data['General']
3514	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3515	cx,ct = general['AtomPtrs'][:2]
3516	atomData = data['Atoms']
3517	Indx = {}
3518	atInd = [-1,-1,-1]
3519	data['testRBObj'] = {}
3520
3521	def Draw():
3522
3523	def OnOk(event):
3524	rbType = data['testRBObj']['rbType']
3525	RBObjs = data['RBModels'].get(rbType,[])
3526	rbObj = data['testRBObj']['rbObj']
3527	rbId = rbObj['RBId']
3528	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3529	Ids = []
3530	dmax = 0.0
3531	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3532	for xyz in newXYZ:
3533	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3534	dmax = max(dmax,np.min(dist))
3535	id = np.argmin(dist)
3536	Ids.append(atomData[id][-1])
3537	atomData[id][cx:cx+3] = xyz
3538	if dmax > 0.5:
3539	print '** WARNING - some atoms not found or misidentified **'
3540	print '** check torsion angles & try again **'
3541	OkBtn.SetLabel('Not Ready')
3542	OkBtn.Enable(False)
3543	return
3544	rbObj['Ids'] = Ids
3545	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3546	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3547	RBObjs.append(rbObj)
3548	data['RBModels'][rbType] = RBObjs
3549	RBData[rbType][rbId]['useCount'] += 1
3550	del data['testRBObj']
3551	G2plt.PlotStructure(G2frame,data)
3552	FillRigidBodyGrid(True)
3553
3554	def OnCancel(event):
3555	del data['testRBObj']
3556	FillRigidBodyGrid(True)
3557
3558	def OnRBSel(event):
3559	selection = rbSel.GetValue()
3560	rbType,rbId = rbNames[selection]
3561	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3562	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3563	data['testRBObj']['rbType'] = rbType
3564	data['testRBObj']['rbData'] = RBData
3565	data['testRBObj']['Sizers'] = {}
3566	rbRef = RBData[rbType][rbId]['rbRef']
3567	data['testRBObj']['rbRef'] = rbRef
3568	refType = []
3569	refName = []
3570	for ref in rbRef[:3]:
3571	reftype = data['testRBObj']['rbAtTypes'][ref]
3572	refType.append(reftype)
3573	refName.append(reftype+' '+str(rbRef[0]))
3574	atNames,AtNames = fillAtNames(refType,atomData,ct)
3575	data['testRBObj']['atNames'] = atNames
3576	data['testRBObj']['AtNames'] = AtNames
3577	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3578	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3579	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3580	data['testRBObj']['torAtms'] = []
3581	for item in RBData[rbType][rbId].get('rbSeq',[]):
3582	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3583	data['testRBObj']['torAtms'].append([-1,-1,-1])
3584	Draw()
3585
3586	def fillAtNames(refType,atomData,ct):
3587	atNames = [{},{},{}]
3588	AtNames = {}
3589	for iatm,atom in enumerate(atomData):
3590	AtNames[atom[ct-1]] = iatm
3591	for i,reftype in enumerate(refType):
3592	if atom[ct] == reftype:
3593	atNames[i][atom[ct-1]] = iatm
3594	return atNames,AtNames
3595
3596	def OnAtOrigPick(event):
3597	Obj = event.GetEventObject()
3598	item = Indx[Obj.GetId()]
3599	atName = Obj.GetValue()
3600	rbType = data['testRBObj']['rbType']
3601	atInd[0] = atNames[item][atName]
3602	if 'Vector' in rbType:
3603	rbObj = data['testRBObj']['rbObj']
3604	rbId = rbObj['RBId']
3605	rbRef = data['testRBObj']['rbRef']
3606	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3607	nref = atNames[item][atName]
3608	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3609	Nxyz = np.array(atomData[nref][cx:cx+3])
3610	Orig = Nxyz-Oxyz
3611	data['testRBObj']['rbObj']['Orig'][0] = Orig
3612	else:
3613	Orig = atomData[atNames[item][atName]][cx:cx+3]
3614	data['testRBObj']['rbObj']['Orig'][0] = Orig
3615	for x,item in zip(Orig,Xsizers):
3616	item.SetLabel('%10.5f'%(x))
3617	G2plt.PlotStructure(G2frame,data)
3618
3619	def OnAtQPick(event):
3620	Obj = event.GetEventObject()
3621	item = Indx[Obj.GetId()]
3622	atName = Obj.GetValue()
3623	atInd[item] = atNames[item][atName]
3624	if any([x<0 for x in atInd]):
3625	return
3626	OkBtn.SetLabel('OK')
3627	OkBtn.Enable(True)
3628	rbType = data['testRBObj']['rbType']
3629	rbObj = data['testRBObj']['rbObj']
3630	rbId = rbObj['RBId']
3631	rbRef = data['testRBObj']['rbRef']
3632	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3633	rbOrig = rbXYZ[rbRef[0]]
3634	VAR = rbXYZ[rbRef[1]]-rbOrig
3635	VBR = rbXYZ[rbRef[2]]-rbOrig
3636	if rbType == 'Vector':
3637	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3638	else:
3639	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3640	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3641	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3642	VCC = np.cross(VAR,VAC)
3643	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3644	VAR = G2mth.prodQVQ(QuatA,VAR)
3645	VBR = G2mth.prodQVQ(QuatA,VBR)
3646	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3647	QuatC = G2mth.prodQQ(QuatB,QuatA)
3648	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3649	for x,item in zip(QuatC,Osizers):
3650	item.SetLabel('%10.4f'%(x))
3651	if rbType == 'Vector':
3652	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3653	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3654	Orig = Nxyz-Oxyz
3655	data['testRBObj']['rbObj']['Orig'][0] = Orig
3656	for x,item in zip(Orig,Xsizers):
3657	item.SetLabel('%10.5f'%(x))
3658	G2plt.PlotStructure(G2frame,data)
3659
3660	def OnTorAngle(event):
3661	OkBtn.SetLabel('OK')
3662	OkBtn.Enable(True)
3663	Obj = event.GetEventObject()
3664	[tor,torSlide] = Indx[Obj.GetId()]
3665	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3666	try:
3667	value = float(Obj.GetValue())
3668	except ValueError:
3669	value = Tors[0]
3670	Tors[0] = value
3671	Obj.SetValue('%8.3f'%(value))
3672	torSlide.SetValue(int(value*10))
3673	G2plt.PlotStructure(G2frame,data)
3674
3675	def OnTorSlide(event):
3676	OkBtn.SetLabel('OK')
3677	OkBtn.Enable(True)
3678	Obj = event.GetEventObject()
3679	tor,ang = Indx[Obj.GetId()]
3680	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3681	val = float(Obj.GetValue())/10.
3682	Tors[0] = val
3683	ang.SetValue('%8.3f'%(val))
3684	G2plt.PlotStructure(G2frame,data)
3685
3686	if len(data['testRBObj']):
3687	G2plt.PlotStructure(G2frame,data)
3688
3689	RigidBodies.DestroyChildren()
3690	mainSizer = wx.BoxSizer(wx.VERTICAL)
3691	mainSizer.Add((5,5),0)
3692	if data['testRBObj']:
3693	Xsizers = []
3694	Osizers = []
3695	rbObj = data['testRBObj']['rbObj']
3696	rbName = rbObj['RBname']
3697	rbId = rbObj['RBId']
3698	Orig = rbObj['Orig'][0]
3699	Orien = rbObj['Orient'][0]
3700	rbRef = data['testRBObj']['rbRef']
3701	Torsions = rbObj['Torsions']
3702	refName = []
3703	for ref in rbRef:
3704	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3705	atNames = data['testRBObj']['atNames']
3706	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3707	0,wx.ALIGN_CENTER_VERTICAL)
3708	mainSizer.Add((5,5),0)
3709	OriSizer = wx.FlexGridSizer(1,5,5,5)
3710	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,wx.ALIGN_CENTER_VERTICAL)
3711	for ix,x in enumerate(Orig):
3712	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3713	OriSizer.Add(origX,0,wx.ALIGN_CENTER_VERTICAL)
3714	Xsizers.append(origX)
3715	OriSizer.Add((5,0),)
3716	if len(atomData):
3717	choice = atNames[0].keys()
3718	choice.sort()
3719	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3720	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,wx.ALIGN_CENTER_VERTICAL)
3721	for ix,x in enumerate(Orien):
3722	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3723	OriSizer.Add(orien,0,wx.ALIGN_CENTER_VERTICAL)
3724	Osizers.append(orien)
3725	data['testRBObj']['Sizers']['Osizers'] = Osizers
3726	mainSizer.Add(OriSizer)
3727	mainSizer.Add((5,5),0)
3728	RefSizer = wx.FlexGridSizer(1,7,5,5)
3729	if len(atomData):
3730	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,wx.ALIGN_CENTER_VERTICAL)
3731	for i in [0,1,2]:
3732	choice = ['',]+atNames[i].keys()
3733	choice.sort()
3734	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,wx.ALIGN_CENTER_VERTICAL)
3735	atPick = wx.ComboBox(RigidBodies,-1,value='',
3736	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3737	if i:
3738	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3739	else:
3740	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3741	Indx[atPick.GetId()] = i
3742	RefSizer.Add(atPick,0,wx.ALIGN_CENTER_VERTICAL)
3743	mainSizer.Add(RefSizer)
3744	mainSizer.Add((5,5),0)
3745	if Torsions:
3746	AtNames = data['testRBObj']['AtNames']
3747	rbAtTypes = data['testRBObj']['rbAtTypes']
3748	rbSeq = RBData['Residue'][rbId]['rbSeq']
3749	TorSizer = wx.FlexGridSizer(1,4)
3750	TorSizer.AddGrowableCol(1,1)
3751	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3752	torName = ''
3753	for item in [seq[0],seq[1],seq[3][0]]:
3754	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3755	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,wx.ALIGN_CENTER_VERTICAL)
3756	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3757	torSlide.SetRange(0,3600)
3758	torSlide.SetValue(int(torsion[0]*10.))
3759	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3760	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3761	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,wx.ALIGN_CENTER_VERTICAL)
3762	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
3763	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
3764	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
3765	Indx[torSlide.GetId()] = [t,ang]
3766	Indx[ang.GetId()] = [t,torSlide]
3767	TorSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
3768	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
3769	else:
3770	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,wx.ALIGN_CENTER_VERTICAL)
3771	else:
3772	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,wx.ALIGN_CENTER_VERTICAL)
3773	mainSizer.Add((5,5),0)
3774	topSizer = wx.BoxSizer(wx.HORIZONTAL)
3775	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,wx.ALIGN_CENTER_VERTICAL)
3776	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
3777	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3778	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
3779	topSizer.Add((5,5),0)
3780	topSizer.Add(rbSel,0,wx.ALIGN_CENTER_VERTICAL)
3781	mainSizer.Add(topSizer)
3782
3783	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
3784	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
3785	OkBtn.Enable(False)
3786	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
3787	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
3788	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
3789	btnSizer.Add((20,20),1)
3790	btnSizer.Add(OkBtn)
3791	btnSizer.Add(CancelBtn)
3792	btnSizer.Add((20,20),1)
3793	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
3794	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3795	Draw()
3796
3797	def OnAutoFindResRB(event):
3798	RBData = G2frame.PatternTree.GetItemPyData(
3799	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3800	rbKeys = RBData['Residue'].keys()
3801	rbKeys.remove('AtInfo')
3802	if not len(rbKeys):
3803	print '** ERROR - no residue rigid bodies are defined **'
3804	return
3805	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
3806	RBIds = dict(zip(RBNames,rbKeys))
3807	general = data['General']
3808	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3809	Atoms = data['Atoms']
3810	AtLookUp = G2mth.FillAtomLookUp(Atoms)
3811	if 'macro' not in general['Type']:
3812	print '** ERROR - this phase is not a macromolecule **'
3813	return
3814	if not len(Atoms):
3815	print '** ERROR - this phase has no atoms **'
3816	return
3817	RBObjs = []
3818	cx,ct = general['AtomPtrs'][:2]
3819	iatm = 0
3820	wx.BeginBusyCursor()
3821	try:
3822	while iatm < len(Atoms):
3823	atom = Atoms[iatm]
3824	res = atom[1].strip()
3825	numChain = ' %s %s'%(atom[0],atom[2])
3826	if res not in RBIds or atom[ct-1] == 'OXT':
3827	iatm += 1
3828	continue #skip for OXT, water molecules, etc.
3829	rbRes = RBData['Residue'][RBIds[res]]
3830	rbRef = rbRes['rbRef']
3831	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
3832	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
3833	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
3834	rbAtoms = []
3835	rbIds = []
3836	for iratm in range(len(rbRes['atNames'])):
3837	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
3838	rbIds.append(Atoms[iatm][20])
3839	iatm += 1 #puts this at beginning of next residue?
3840	Orig = rbAtoms[rbRef[0]]
3841	rbObj['RBId'] = RBIds[res]
3842	rbObj['Ids'] = rbIds
3843	rbObj['Orig'] = [Orig,False]
3844	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
3845	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
3846	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
3847	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
3848	VCC = np.cross(VAR,VAC)
3849	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3850	VAR = G2mth.prodQVQ(QuatA,VAR)
3851	VBR = G2mth.prodQVQ(QuatA,VBR)
3852	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3853	QuatC = G2mth.prodQQ(QuatB,QuatA)
3854	rbObj['Orient'] = [QuatC,' ']
3855	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3856	SXYZ = []
3857	TXYZ = []
3858	rbObj['Torsions'] = []
3859	for i,xyz in enumerate(rbRes['rbXYZ']):
3860	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
3861	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
3862	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
3863	VBR = SXYZ[Oatm]-SXYZ[Patm]
3864	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
3865	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
3866	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
3867	ang = 180.*D/np.pi
3868	rbObj['Torsions'].append([ang,False])
3869	for ride in Riders:
3870	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
3871	rbRes['useCount'] += 1
3872	RBObjs.append(rbObj)
3873	data['RBModels']['Residue'] = RBObjs
3874	for RBObj in RBObjs:
3875	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3876	for i,id in enumerate(RBObj['Ids']):
3877	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3878	finally:
3879	wx.EndBusyCursor()
3880	wx.CallAfter(FillRigidBodyGrid,True)
3881
3882	def OnRBRemoveAll(event):
3883	data['RBModels']['Residue'] = []
3884	data['RBModels']['Vector'] = []
3885	RBData = G2frame.PatternTree.GetItemPyData(
3886	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3887	for RBType in ['Vector','Residue']:
3888	for rbId in RBData[RBType]:
3889	RBData[RBType][rbId]['useCount'] = 0
3890	FillRigidBodyGrid(True)
3891
3892	def OnGlobalResRBTherm(event):
3893	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3894	RBObjs = data['RBModels']['Residue']
3895	names = ['None','Uiso','T','TL','TLS']
3896	cia = data['General']['AtomPtrs'][3]
3897	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
3898	if dlg.ShowModal() == wx.ID_OK:
3899	sel = dlg.GetSelection()
3900	parm = names[sel]
3901	Ttype = 'A'
3902	if parm == 'Uiso':
3903	Ttype = 'I'
3904	for rbObj in RBObjs:
3905	rbObj['ThermalMotion'][0] = parm
3906	if parm != 'None':
3907	for i,id in enumerate(rbObj['Ids']):
3908	data['Atoms'][AtLookUp[id]][cia] = Ttype
3909	dlg.Destroy()
3910	wx.CallAfter(FillRigidBodyGrid,True)
3911
3912	def OnGlobalResRBRef(event):
3913	RBObjs = data['RBModels']['Residue']
3914	names = ['Origin','Orient. angle','Full Orient.']
3915	nTor = 0
3916	for rbObj in RBObjs:
3917	nTor = max(nTor,len(rbObj['Torsions']))
3918	names += ['Torsion '+str(i) for i in range(nTor)]
3919	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
3920	names += ['Uiso',]
3921	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
3922	names += ['Tii','Tij','Lii','Lij','Sij']
3923	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
3924	names += ['Tii','Tij','Lii','Lij']
3925	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
3926	names += ['Tii','Tij']
3927
3928	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
3929	if dlg.ShowModal() == wx.ID_OK:
3930	sel = dlg.GetSelections()
3931	parms = []
3932	for x in sel:
3933	parms.append(names[x])
3934	wx.BeginBusyCursor()
3935	try:
3936	for rbObj in RBObjs:
3937	if 'Origin' in parms:
3938	rbObj['Orig'][1] = True
3939	else:
3940	rbObj['Orig'][1] = False
3941	if 'Full Orient.' in parms:
3942	rbObj['Orient'][1] = 'AV'
3943	elif 'Orient. angle' in parms:
3944	rbObj['Orient'][1] = 'A'
3945	else:
3946	rbObj['Orient'][1] = ' '
3947	for i in range(len(rbObj['Torsions'])):
3948	if 'Torsion '+str(i) in parms:
3949	rbObj['Torsions'][i][1] = True
3950	else:
3951	rbObj['Torsions'][i][1] = False
3952	if rbObj['ThermalMotion'][0] == 'Uiso':
3953	if 'Uiso' in parms:
3954	rbObj['ThermalMotion'][2][0] = True
3955	else:
3956	rbObj['ThermalMotion'][2][0] = False
3957	elif 'T' in rbObj['ThermalMotion'][0]:
3958	if 'Tii' in parms:
3959	rbObj['ThermalMotion'][2][0:2] = [True,True,True]
3960	else:
3961	rbObj['ThermalMotion'][2][0:2] = [False,False,False]
3962	if 'Tij' in parms:
3963	rbObj['ThermalMotion'][2][3:6] = [True,True,True]
3964	else:
3965	rbObj['ThermalMotion'][2][3:6] = [False,False,False]
3966	elif 'L' in rbObj['ThermalMotion'][0]:
3967	if 'Lii' in parms:
3968	rbObj['ThermalMotion'][2][6:9] = [True,True,True]
3969	else:
3970	rbObj['ThermalMotion'][2][6:9] = [False,False,False]
3971	if 'Lij' in parms:
3972	rbObj['ThermalMotion'][2][9:12] = [True,True,True]
3973	else:
3974	rbObj['ThermalMotion'][2][9:12] = [False,False,False]
3975	elif 'S' in rbObj['ThermalMotion'][0]:
3976	if 'Sij' in parms:
3977	rbObj['ThermalMotion'][2][12:20] = [True,True,True,True,True,True,True,True]
3978	else:
3979	rbObj['ThermalMotion'][2][12:20] = [False,False,False,False,False,False,False,False]
3980	finally:
3981	wx.EndBusyCursor()
3982	FillRigidBodyGrid()
3983
3984	################################################################################
3985	##### MC/SA routines
3986	################################################################################
3987
3988	def UpdateMCSA(Scroll=0):
3989	Indx = {}
3990
3991	def OnPosRef(event):
3992	Obj = event.GetEventObject()
3993	model,item,ix = Indx[Obj.GetId()]
3994	model[item][1][ix] = Obj.GetValue()
3995
3996	def OnPosVal(event):
3997	Obj = event.GetEventObject()
3998	model,item,ix = Indx[Obj.GetId()]
3999	try:
4000	model[item][0][ix] = float(Obj.GetValue())
4001	except ValueError:
4002	pass
4003	Obj.SetValue("%.4f"%(model[item][0][ix]))
4004	G2plt.PlotStructure(G2frame,data)
4005
4006	def OnPosRange(event):
4007	Obj = event.GetEventObject()
4008	model,item,ix = Indx[Obj.GetId()]
4009	Range = Obj.GetValue().split()
4010	try:
4011	rmin,rmax = [float(Range[i]) for i in range(2)]
4012	if rmin >= rmax:
4013	raise ValueError
4014	except (ValueError,IndexError):
4015	rmin,rmax = model[item][2][ix]
4016	model[item][2][ix] = [rmin,rmax]
4017	Obj.SetValue('%.3f %.3f'%(rmin,rmax))
4018
4019	def atomSizer(model):
4020
4021	atomsizer = wx.FlexGridSizer(1,7,5,5)
4022	atomsizer.Add(wx.StaticText(MCSA,-1,' Atom: '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4023	for ix,item in enumerate(['x','y','z']):
4024	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4025	posRef.SetValue(model['Pos'][1][ix])
4026	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4027	Indx[posRef.GetId()] = [model,'Pos',ix]
4028	atomsizer.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4029	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4030	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4031	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4032	Indx[posVal.GetId()] = [model,'Pos',ix]
4033	atomsizer.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4034	atomsizer.Add((5,5),0)
4035	for ix,item in enumerate(['x','y','z']):
4036	atomsizer.Add(wx.StaticText(MCSA,-1,' Range: '),0,wx.ALIGN_CENTER_VERTICAL)
4037	rmin,rmax = model['Pos'][2][ix]
4038	posRange = wx.TextCtrl(MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER)
4039	Indx[posRange.GetId()] = [model,'Pos',ix]
4040	posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange)
4041	posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange)
4042	atomsizer.Add(posRange,0,wx.ALIGN_CENTER_VERTICAL)
4043	return atomsizer
4044
4045	def rbSizer(model):
4046
4047	def OnOrVar(event):
4048	Obj = event.GetEventObject()
4049	model = Indx[Obj.GetId()]
4050	model['Ovar'] = Obj.GetValue()
4051
4052	def OnOriVal(event):
4053	Obj = event.GetEventObject()
4054	model,ix,ObjA,ObjV = Indx[Obj.GetId()]
4055	A = model['Ori'][0][0]
4056	V = model['Ori'][0][1:]
4057	if ix:
4058	Anew = A
4059	Vec = ObjV.GetValue().split()
4060	try:
4061	Vnew = [float(Vec[i]) for i in range(3)]
4062	except ValueError:
4063	Vnew = V
4064	else:
4065	Vnew = V
4066	try:
4067	Anew = float(ObjA.GetValue())
4068	except ValueError:
4069	Anew = A
4070	Q = G2mth.AVdeg2Q(Anew,Vnew)
4071	A,V = G2mth.Q2AVdeg(Q)
4072	model['Ori'][0][0] = A
4073	model['Ori'][0][1:] = V
4074	if ix:
4075	ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2]))
4076	else:
4077	ObjA.SetValue('%.5f'%(A))
4078	G2plt.PlotStructure(G2frame,data)
4079	UpdateMCSA()
4080
4081	def OnMolCent(event):
4082	Obj = event.GetEventObject()
4083	model = Indx[Obj.GetId()]
4084	model['MolCent'][1] = Obj.GetValue()
4085	if model['MolCent'][1]:
4086	G2mth.SetMolCent(model,RBData)
4087	G2plt.PlotStructure(G2frame,data)
4088
4089	rbsizer = wx.BoxSizer(wx.VERTICAL)
4090	rbsizer1 = wx.FlexGridSizer(1,7,5,5)
4091	rbsizer1.Add(wx.StaticText(MCSA,-1,model['Type']+': '+model['name']+': '),0,wx.ALIGN_CENTER_VERTICAL)
4092	for ix,item in enumerate(['x','y','z']):
4093	posRef = wx.CheckBox(MCSA,-1,label=item+': ')
4094	posRef.SetValue(model['Pos'][1][ix])
4095	posRef.Bind(wx.EVT_CHECKBOX,OnPosRef)
4096	Indx[posRef.GetId()] = [model,'Pos',ix]
4097	rbsizer1.Add(posRef,0,wx.ALIGN_CENTER_VERTICAL)
4098	posVal = wx.TextCtrl(MCSA,-1,'%.4f'%(model['Pos'][0][ix]),style=wx.TE_PROCESS_ENTER)
4099	posVal.Bind(wx.EVT_TEXT_ENTER,OnPosVal)
4100	posVal.Bind(wx.EVT_KILL_FOCUS,OnPosVal)
4101	Indx[posVal.GetId()] = [model,'Pos',ix]
4102	rbsizer1.Add(posVal,0,wx.ALIGN_CENTER_VERTICAL)
4103	molcent = wx.CheckBox(MCSA,-1,label=' Use mol. center? ')
4104	molcent.SetValue(model['MolCent'][1])
4105	molcent.Bind(wx.EVT_CHECKBOX,OnMolCent)
4106	Indx[molcent.GetId()] = model
4107	rbsizer1.Add(molcent,0,wx.ALIGN_CENTER_VERTICAL)
4108	for