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source: trunk/GSASIIphsGUI.py @ 1283

Last change on this file since 1283 was 1283, checked in by vondreele, 9 years ago
open a SASD gpx file now starts at SASD file & plot fix 2/a & 2/c lattice codes in CellSizer? more graceful when SASD least squares fails add 'Radius' to list of possibel parameters in SASD fit fix form factor volume calc for monodisperse models
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
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1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2014-04-18 16:27:12 +0000 (Fri, 18 Apr 2014) $
5	# $Author: vondreele $
6	# $Revision: 1283 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1283 2014-04-18 16:27:12Z 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 wx.lib.scrolledpanel as wxscroll
29	import matplotlib as mpl
30	import math
31	import copy
32	import time
33	import sys
34	import random as ran
35	import cPickle
36	import GSASIIpath
37	GSASIIpath.SetVersionNumber("$Revision: 1283 $")
38	import GSASIIlattice as G2lat
39	import GSASIIspc as G2spc
40	import GSASIIElem as G2elem
41	import GSASIIElemGUI as G2elemGUI
42	import GSASIIddataGUI as G2ddG
43	import GSASIIplot as G2plt
44	import GSASIIgrid as G2gd
45	import GSASIIIO as G2IO
46	import GSASIIstrMain as G2stMn
47	import GSASIImath as G2mth
48	import GSASIIpwd as G2pwd
49	import GSASIIpy3 as G2py3
50	import GSASIIobj as G2obj
51	import numpy as np
52	import numpy.linalg as nl
53	import numpy.ma as ma
54
55	VERY_LIGHT_GREY = wx.Colour(235,235,235)
56	WHITE = wx.Colour(255,255,255)
57	BLACK = wx.Colour(0,0,0)
58	WACV = wx.ALIGN_CENTER_VERTICAL
59	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
60	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
61	# trig functions in degrees
62	sind = lambda x: np.sin(x*np.pi/180.)
63	tand = lambda x: np.tan(x*np.pi/180.)
64	cosd = lambda x: np.cos(x*np.pi/180.)
65	asind = lambda x: 180.*np.arcsin(x)/np.pi
66	acosd = lambda x: 180.*np.arccos(x)/np.pi
67
68	def SetPhaseWindow(mainFrame,phasePage,mainSizer):
69	phasePage.SetSizer(mainSizer)
70	Size = mainSizer.GetMinSize()
71	Size[0] += 40
72	# Size[1] = 500
73	Size[1] = min(Size[1]+ 150,500)
74	phasePage.SetSize(Size)
75	phasePage.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
76	mainFrame.setSizePosLeft(Size)
77
78	def UpdatePhaseData(G2frame,Item,data,oldPage):
79	'''Create the data display window contents when a phase is clicked on
80	in the main (data tree) window.
81	Called only from :meth:`GSASIIgrid.MovePatternTreeToGrid`,
82	which in turn is called from :meth:`GSASII.GSASII.OnPatternTreeSelChanged`
83	when a tree item is selected.
84
85	:param wx.frame G2frame: the main GSAS-II frame object
86	:param wx.TreeItemId Item: the tree item that was selected
87	:param dict data: all the information on the phase in a dictionary
88	:param int oldPage: This sets a tab to select when moving
89	from one phase to another, in which case the same tab is selected
90	to display first. This is set only when the previous data tree
91	selection is a phase, if not the value is None. The default action
92	is to bring up the General tab.
93
94	'''
95
96	#patch
97	if 'RBModels' not in data:
98	data['RBModels'] = {}
99	if 'MCSA' not in data:
100	data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
101	if isinstance(data['MCSA']['Results'],dict):
102	data['MCSA']['Results'] = []
103	#end patch
104
105	global rbAtmDict
106	rbAtmDict = {}
107	if G2frame.dataDisplay:
108	G2frame.dataDisplay.Destroy()
109	PhaseName = G2frame.PatternTree.GetItemText(Item)
110	G2gd.SetDataMenuBar(G2frame)
111	G2frame.dataFrame.SetLabel('Phase Data for '+PhaseName)
112	G2frame.dataFrame.CreateStatusBar()
113	G2frame.dataDisplay = G2gd.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize())
114	G2frame.dataDisplay.gridList = [] # list of all grids in notebook
115	# UpdatePhaseData execution continues below
116
117	def SetupGeneral():
118	generalData = data['General']
119	atomData = data['Atoms']
120	generalData['AtomTypes'] = []
121	generalData['Isotopes'] = {}
122	# various patches
123	if 'Isotope' not in generalData:
124	generalData['Isotope'] = {}
125	if 'Data plot type' not in generalData:
126	generalData['Data plot type'] = 'Mustrain'
127	if 'POhkl' not in generalData:
128	generalData['POhkl'] = [0,0,1]
129	if 'Map' not in generalData:
130	generalData['Map'] = mapDefault
131	if 'Flip' not in generalData:
132	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
133	'k-factor':0.1,'k-Max':20.}
134	if 'doPawley' not in generalData:
135	generalData['doPawley'] = False
136	if 'Pawley dmin' not in generalData:
137	generalData['Pawley dmin'] = 1.0
138	if 'Pawley neg wt' not in generalData:
139	generalData['Pawley neg wt'] = 0.0
140	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
141	'MCSA controls' not in generalData:
142	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
143	'dmin':2.0,'Algorithm':'fast','Jump coeff':[0.95,0.5],'boltzmann':1.0,
144	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[]}
145	if 'AtomPtrs' not in generalData:
146	generalData['AtomPtrs'] = [3,1,7,9]
147	if generalData['Type'] =='macromolecular':
148	generalData['AtomPtrs'] = [6,4,10,12]
149	# end of patches
150	cx,ct,cs,cia = generalData['AtomPtrs']
151	generalData['NoAtoms'] = {}
152	generalData['BondRadii'] = []
153	generalData['AngleRadii'] = []
154	generalData['vdWRadii'] = []
155	generalData['AtomMass'] = []
156	generalData['Color'] = []
157	generalData['Mydir'] = G2frame.dirname
158	for atom in atomData:
159	atom[ct] = atom[ct].lower().capitalize() #force to standard form
160	if generalData['AtomTypes'].count(atom[ct]):
161	generalData['NoAtoms'][atom[ct]] += atom[cs-1]*float(atom[cs+1])
162	elif atom[ct] != 'UNK':
163	Info = G2elem.GetAtomInfo(atom[ct])
164	generalData['AtomTypes'].append(atom[ct])
165	generalData['Z'] = Info['Z']
166	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
167	generalData['BondRadii'].append(Info['Drad'])
168	generalData['AngleRadii'].append(Info['Arad'])
169	generalData['vdWRadii'].append(Info['Vdrad'])
170	if atom[ct] in generalData['Isotope']:
171	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]][0])
172	else:
173	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
174	generalData['AtomMass'].append(Info['Mass'])
175	generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
176	generalData['Color'].append(Info['Color'])
177	F000X = 0.
178	F000N = 0.
179	for i,elem in enumerate(generalData['AtomTypes']):
180	F000X += generalData['NoAtoms'][elem]*generalData['Z']
181	isotope = generalData['Isotope'][elem]
182	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope][1]
183	generalData['F000X'] = F000X
184	generalData['F000N'] = F000N
185
186
187	################################################################################
188	##### General phase routines
189	################################################################################
190
191	def UpdateGeneral():
192	'''Draw the controls for the General phase data subpage
193	'''
194
195	""" This is the default dictionary structure for phase data
196	(taken from GSASII.py)
197	'General':{
198	'Name':PhaseName
199	'Type':'nuclear'
200	'SGData':SGData
201	'Cell':[False,10.,10.,10.,90.,90.,90,1000.]
202	'AtomPtrs':[]
203	'Histogram list':['',]
204	'Pawley dmin':1.0,
205	'Pawley neg wt':0.0}
206	'Atoms':[]
207	'Drawing':{}
208	"""
209	# UpdateGeneral execution starts here
210	phaseTypes = ['nuclear','modulated','magnetic','macromolecular']
211	SetupGeneral()
212	generalData = data['General']
213	Map = generalData['Map']
214	Flip = generalData['Flip']
215	MCSAdata = generalData['MCSA controls']
216	PWDR = any(['PWDR' in item for item in data['Histograms'].keys()])
217	# UpdateGeneral execution continues below
218
219	def NameSizer():
220	def OnPhaseName(event):
221	oldName = generalData['Name']
222	generalData['Name'] = NameTxt.GetValue()
223	G2frame.G2plotNB.Rename(oldName,generalData['Name'])
224	G2frame.dataFrame.SetLabel('Phase Data for '+generalData['Name'])
225	G2frame.PatternTree.SetItemText(Item,generalData['Name'])
226	#Hmm, need to change phase name key in Reflection Lists for each histogram
227
228	def OnPhaseType(event):
229	if not generalData['AtomTypes']: #can change only if no atoms!
230	generalData['Type'] = TypeTxt.GetValue()
231	wx.CallAfter(UpdateGeneral)
232	else:
233	TypeTxt.SetValue(generalData['Type'])
234
235	def OnSpaceGroup(event):
236	SpcGp = SGTxt.GetValue()
237	SGErr,SGData = G2spc.SpcGroup(SpcGp)
238	# try a lookup on the user-supplied name
239	if SGErr:
240	SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
241	if SpGrpNorm:
242	E,SGData = G2spc.SpcGroup(SpGrpNorm)
243	if not E: SGErr = False
244	if SGErr:
245	text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
246	SGTxt.SetValue(generalData['SGData']['SpGrp'])
247	msg = 'Space Group Error'
248	Style = wx.ICON_EXCLAMATION
249	else:
250	text = G2spc.SGPrint(SGData)
251	generalData['SGData'] = SGData
252	msg = 'Space Group Information'
253	Style = wx.ICON_INFORMATION
254	Text = ''
255	for line in text:
256	Text += line+'\n'
257	wx.MessageBox(Text,caption=msg,style=Style)
258	wx.CallAfter(UpdateGeneral)
259
260	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
261	nameSizer.Add(wx.StaticText(General,-1,' Phase name: '),0,WACV)
262	NameTxt = wx.TextCtrl(General,-1,value=generalData['Name'],style=wx.TE_PROCESS_ENTER)
263	NameTxt.Bind(wx.EVT_TEXT_ENTER,OnPhaseName)
264	NameTxt.Bind(wx.EVT_KILL_FOCUS,OnPhaseName)
265	nameSizer.Add(NameTxt,0,WACV)
266	nameSizer.Add(wx.StaticText(General,-1,' Phase type: '),0,WACV)
267	TypeTxt = wx.ComboBox(General,-1,value=generalData['Type'],choices=phaseTypes,
268	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
269	TypeTxt.Bind(wx.EVT_COMBOBOX, OnPhaseType)
270	nameSizer.Add(TypeTxt,0,WACV)
271	nameSizer.Add(wx.StaticText(General,-1,' Space group: '),0,WACV)
272	SGTxt = wx.TextCtrl(General,-1,value=generalData['SGData']['SpGrp'],style=wx.TE_PROCESS_ENTER)
273	SGTxt.Bind(wx.EVT_TEXT_ENTER,OnSpaceGroup)
274	nameSizer.Add(SGTxt,0,WACV)
275	return nameSizer
276
277	def CellSizer():
278
279	cellGUIlist = [[['m3','m3m'],4,zip([" Unit cell: a = "," Vol = "],["%.5f","%.3f"],[True,False],[0,0])],
280	[['3R','3mR'],6,zip([" a = "," alpha = "," Vol = "],["%.5f","%.3f","%.3f"],[True,True,False],[0,2,0])],
281	[['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])],
282	[['mmm'],8,zip([" a = "," b = "," c = "," Vol = "],["%.5f","%.5f","%.5f","%.3f"],
283	[True,True,True,False],[0,1,2,0])],
284	[['2/m'+'a'],10,zip([" a = "," b = "," c = "," alpha = "," Vol = "],
285	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,5,0])],
286	[['2/m'+'b'],10,zip([" a = "," b = "," c = "," beta = "," Vol = "],
287	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
288	[['2/m'+'c'],10,zip([" a = "," b = "," c = "," gamma = "," Vol = "],
289	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,3,0])],
290	[['-1'],8,zip([" a = "," b = "," c = "," Vol = "," alpha = "," beta = "," gamma = "],
291	["%.5f","%.5f","%.5f","%.3f","%.3f","%.3f","%.3f"],
292	[True,True,True,False,True,True,True],[0,1,2,0,3,4,5])]]
293
294	def OnCellRef(event):
295	generalData['Cell'][0] = cellRef.GetValue()
296
297	def OnCellChange(event):
298	SGData = generalData['SGData']
299	laue = SGData['SGLaue']
300	if laue == '2/m':
301	laue += SGData['SGUniq']
302	cell = generalData['Cell']
303	Obj = event.GetEventObject()
304	ObjId = cellList.index(Obj.GetId())
305	try:
306	value = max(1.0,float(Obj.GetValue()))
307	except ValueError:
308	if ObjId < 3: #bad cell edge - reset
309	value = controls[6+ObjId]
310	else: #bad angle
311	value = 90.
312	if laue in ['m3','m3m']:
313	cell[1] = cell[2] = cell[3] = value
314	cell[4] = cell[5] = cell[6] = 90.0
315	Obj.SetValue("%.5f"%(cell[1]))
316	elif laue in ['3R','3mR']:
317	if ObjId == 0:
318	cell[1] = cell[2] = cell[3] = value
319	Obj.SetValue("%.5f"%(cell[1]))
320	else:
321	cell[4] = cell[5] = cell[6] = value
322	Obj.SetValue("%.5f"%(cell[4]))
323	elif laue in ['3','3m1','31m','6/m','6/mmm','4/m','4/mmm']:
324	cell[4] = cell[5] = 90.
325	cell[6] = 120.
326	if laue in ['4/m','4/mmm']:
327	cell[6] = 90.
328	if ObjId == 0:
329	cell[1] = cell[2] = value
330	Obj.SetValue("%.5f"%(cell[1]))
331	else:
332	cell[3] = value
333	Obj.SetValue("%.5f"%(cell[3]))
334	elif laue in ['mmm']:
335	cell[ObjId+1] = value
336	cell[4] = cell[5] = cell[6] = 90.
337	Obj.SetValue("%.5f"%(cell[ObjId+1]))
338	elif laue in ['2/m'+'a']:
339	cell[5] = cell[6] = 90.
340	if ObjId != 3:
341	cell[ObjId+1] = value
342	Obj.SetValue("%.5f"%(cell[ObjId+1]))
343	else:
344	cell[4] = value
345	Obj.SetValue("%.3f"%(cell[4]))
346	elif laue in ['2/m'+'b']:
347	cell[4] = cell[6] = 90.
348	if ObjId != 3:
349	cell[ObjId+1] = value
350	Obj.SetValue("%.5f"%(cell[ObjId+1]))
351	else:
352	cell[5] = value
353	Obj.SetValue("%.3f"%(cell[5]))
354	elif laue in ['2/m'+'c']:
355	cell[5] = cell[6] = 90.
356	if ObjId != 3:
357	cell[ObjId+1] = value
358	Obj.SetValue("%.5f"%(cell[ObjId+1]))
359	else:
360	cell[6] = value
361	Obj.SetValue("%.3f"%(cell[6]))
362	else:
363	cell[ObjId+1] = value
364	if ObjId < 3:
365	Obj.SetValue("%.5f"%(cell[1+ObjId]))
366	else:
367	Obj.SetValue("%.3f"%(cell[1+ObjId]))
368	cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
369	volVal.SetValue("%.3f"%(cell[7]))
370	density,mattCoeff = G2mth.getDensity(generalData)
371	if denSizer:
372	denSizer[1].SetValue('%.3f'%(density))
373	if denSizer[2]:
374	denSizer[2].SetValue('%.3f'%(mattCoeff))
375	generalData['Cell'] = cell
376
377	cell = generalData['Cell']
378	laue = generalData['SGData']['SGLaue']
379	if laue == '2/m':
380	laue += generalData['SGData']['SGUniq']
381	for cellGUI in cellGUIlist:
382	if laue in cellGUI[0]:
383	useGUI = cellGUI
384	cellSizer = wx.FlexGridSizer(2,useGUI[1]+1,5,5)
385	if PWDR:
386	cellRef = wx.CheckBox(General,-1,label='Refine unit cell:')
387	cellSizer.Add(cellRef,0,WACV)
388	cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef)
389	cellRef.SetValue(cell[0])
390	cellList = []
391	for txt,fmt,ifEdit,Id in useGUI[2]:
392	cellSizer.Add(wx.StaticText(General,label=txt),0,WACV)
393	if ifEdit: #a,b,c,etc.
394	cellVal = wx.TextCtrl(General,value=(fmt%(cell[Id+1])),
395	style=wx.TE_PROCESS_ENTER)
396	cellVal.Bind(wx.EVT_TEXT_ENTER,OnCellChange)
397	cellVal.Bind(wx.EVT_KILL_FOCUS,OnCellChange)
398	cellSizer.Add(cellVal,0,WACV)
399	cellList.append(cellVal.GetId())
400	else: #volume
401	volVal = wx.TextCtrl(General,value=(fmt%(cell[7])),style=wx.TE_READONLY)
402	volVal.SetBackgroundColour(VERY_LIGHT_GREY)
403	cellSizer.Add(volVal,0,WACV)
404	return cellSizer
405
406	def ElemSizer():
407
408	def OnIsotope(event):
409	Obj = event.GetEventObject()
410	item = Indx[Obj.GetId()]
411	isotope = Obj.GetValue()
412	generalData['Isotope'][item] = isotope
413	indx = generalData['AtomTypes'].index(item)
414	data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope][0]
415	density,mattCoeff = G2mth.getDensity(generalData)
416	denSizer[1].SetValue('%.3f'%(density))
417	if denSizer[2]:
418	denSizer[2].SetValue('%.3f'%(mattCoeff))
419
420	elemSizer = wx.FlexGridSizer(8,len(generalData['AtomTypes'])+1,1,1)
421	elemSizer.Add(wx.StaticText(General,label=' Elements'),0,WACV)
422	for elem in generalData['AtomTypes']:
423	typTxt = wx.TextCtrl(General,value=elem,style=wx.TE_READONLY)
424	typTxt.SetBackgroundColour(VERY_LIGHT_GREY)
425	elemSizer.Add(typTxt,0,WACV)
426	elemSizer.Add(wx.StaticText(General,label=' Isotope'),0,WACV)
427	for elem in generalData['AtomTypes']:
428	choices = generalData['Isotopes'][elem].keys()
429	isoSel = wx.ComboBox(General,-1,value=generalData['Isotope'][elem],choices=choices,
430	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
431	isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope)
432	Indx[isoSel.GetId()] = elem
433	elemSizer.Add(isoSel,1,WACV\|wx.EXPAND)
434	elemSizer.Add(wx.StaticText(General,label=' No. per cell'),0,WACV)
435	for elem in generalData['AtomTypes']:
436	numbTxt = wx.TextCtrl(General,value='%.1f'%(generalData['NoAtoms'][elem]),
437	style=wx.TE_READONLY)
438	numbTxt.SetBackgroundColour(VERY_LIGHT_GREY)
439	elemSizer.Add(numbTxt,0,WACV)
440	elemSizer.Add(wx.StaticText(General,label=' Atom weight'),0,WACV)
441	for wt in generalData['AtomMass']:
442	wtTxt = wx.TextCtrl(General,value='%.3f'%(wt),style=wx.TE_READONLY)
443	wtTxt.SetBackgroundColour(VERY_LIGHT_GREY)
444	elemSizer.Add(wtTxt,0,WACV)
445	elemSizer.Add(wx.StaticText(General,label=' Bond radii'),0,WACV)
446	for rad in generalData['BondRadii']:
447	bondRadii = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
448	bondRadii.SetBackgroundColour(VERY_LIGHT_GREY)
449	elemSizer.Add(bondRadii,0,WACV)
450	elemSizer.Add(wx.StaticText(General,label=' Angle radii'),0,WACV)
451	for rad in generalData['AngleRadii']:
452	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
453	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
454	elemSizer.Add(elemTxt,0,WACV)
455	elemSizer.Add(wx.StaticText(General,label=' van der Waals radii'),0,WACV)
456	for rad in generalData['vdWRadii']:
457	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
458	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
459	elemSizer.Add(elemTxt,0,WACV)
460	elemSizer.Add(wx.StaticText(General,label=' Default color'),0,WACV)
461	for R,G,B in generalData['Color']:
462	colorTxt = wx.TextCtrl(General,value='',style=wx.TE_READONLY)
463	colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
464	elemSizer.Add(colorTxt,0,WACV)
465	return elemSizer
466
467	def DenSizer():
468
469	mass = G2mth.getMass(generalData)
470	density,mattCoeff = G2mth.getDensity(generalData)
471	denSizer = wx.BoxSizer(wx.HORIZONTAL)
472	denSizer.Add(wx.StaticText(General,-1,' Density: '),0,WACV)
473	denTxt = wx.TextCtrl(General,-1,'%.3f'%(density),style=wx.TE_READONLY)
474	denTxt.SetBackgroundColour(VERY_LIGHT_GREY)
475	denSizer.Add(denTxt,0,WACV)
476	mattTxt = None
477	if generalData['Type'] == 'macromolecular' and mass > 0.0:
478	denSizer.Add(wx.StaticText(General,-1,' Matthews coeff.: '),
479	0,WACV)
480	mattTxt = wx.TextCtrl(General,-1,'%.3f'%(mattCoeff),style=wx.TE_READONLY)
481	mattTxt.SetBackgroundColour(VERY_LIGHT_GREY)
482	denSizer.Add(mattTxt,0,WACV)
483	return denSizer,denTxt,mattTxt
484
485	def PawleySizer():
486
487	def OnPawleyRef(event):
488	generalData['doPawley'] = pawlRef.GetValue()
489
490	def OnPawleyVal(event):
491	try:
492	dmin = float(pawlVal.GetValue())
493	if 0.25 <= dmin <= 20.:
494	generalData['Pawley dmin'] = dmin
495	except ValueError:
496	pass
497	pawlVal.SetValue("%.3f"%(generalData['Pawley dmin'])) #reset in case of error
498
499	def OnPawleyNegWt(event):
500	try:
501	wt = float(pawlNegWt.GetValue())
502	if 0. <= wt <= 1.:
503	generalData['Pawley neg wt'] = wt
504	except ValueError:
505	pass
506	pawlNegWt.SetValue("%.4f"%(generalData['Pawley neg wt'])) #reset in case of error
507
508	pawleySizer = wx.BoxSizer(wx.HORIZONTAL)
509	pawleySizer.Add(wx.StaticText(General,label=' Pawley controls: '),0,WACV)
510	pawlRef = wx.CheckBox(General,-1,label=' Do Pawley refinement?')
511	pawlRef.SetValue(generalData['doPawley'])
512	pawlRef.Bind(wx.EVT_CHECKBOX,OnPawleyRef)
513	pawleySizer.Add(pawlRef,0,WACV)
514	pawleySizer.Add(wx.StaticText(General,label=' Pawley dmin: '),0,WACV)
515	pawlVal = wx.TextCtrl(General,value='%.3f'%(generalData['Pawley dmin']),style=wx.TE_PROCESS_ENTER)
516	pawlVal.Bind(wx.EVT_TEXT_ENTER,OnPawleyVal)
517	pawlVal.Bind(wx.EVT_KILL_FOCUS,OnPawleyVal)
518	pawleySizer.Add(pawlVal,0,WACV)
519	pawleySizer.Add(wx.StaticText(General,label=' Pawley neg. wt.: '),0,WACV)
520	pawlNegWt = wx.TextCtrl(General,value='%.4f'%(generalData['Pawley neg wt']),style=wx.TE_PROCESS_ENTER)
521	pawlNegWt.Bind(wx.EVT_TEXT_ENTER,OnPawleyNegWt)
522	pawlNegWt.Bind(wx.EVT_KILL_FOCUS,OnPawleyNegWt)
523	pawleySizer.Add(pawlNegWt,0,WACV)
524	return pawleySizer
525
526	def MapSizer():
527
528	def OnMapType(event):
529	Map['MapType'] = mapType.GetValue()
530
531	def OnRefList(event):
532	Map['RefList'] = refList.GetValue()
533
534	def OnResVal(event):
535	try:
536	res = float(mapRes.GetValue())
537	if 0.25 <= res <= 20.:
538	Map['Resolution'] = res
539	except ValueError:
540	pass
541	mapRes.SetValue("%.2f"%(Map['Resolution'])) #reset in case of error
542
543	def OnCutOff(event):
544	try:
545	res = float(cutOff.GetValue())
546	if 10.0 <= res <= 100.:
547	Map['cutOff'] = res
548	except ValueError:
549	pass
550	cutOff.SetValue("%.1f"%(Map['cutOff'])) #reset in case of error
551
552	#patch
553	if 'cutOff' not in Map:
554	Map['cutOff'] = 100.0
555	mapTypes = ['Fobs','Fcalc','delt-F','2*Fo-Fc','Omit','2Fo-Fc Omit','Patterson']
556	refList = data['Histograms'].keys()
557	if not generalData['AtomTypes']:
558	mapTypes = ['Patterson',]
559	Map['MapType'] = 'Patterson'
560	mapSizer = wx.BoxSizer(wx.VERTICAL)
561	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
562	lineSizer.Add(wx.StaticText(General,label=' Fourier map controls: Map type: '),0,WACV)
563	mapType = wx.ComboBox(General,-1,value=Map['MapType'],choices=mapTypes,
564	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
565	mapType.Bind(wx.EVT_COMBOBOX,OnMapType)
566	lineSizer.Add(mapType,0,WACV)
567	lineSizer.Add(wx.StaticText(General,label=' Reflection set from: '),0,WACV)
568	refList = wx.ComboBox(General,-1,value=Map['RefList'],choices=refList,
569	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
570	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
571	lineSizer.Add(refList,0,WACV)
572	mapSizer.Add(lineSizer,0,WACV)
573	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
574	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,WACV)
575	mapRes = wx.TextCtrl(General,value='%.2f'%(Map['Resolution']),style=wx.TE_PROCESS_ENTER)
576	mapRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
577	mapRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
578	line2Sizer.Add(mapRes,0,WACV)
579	line2Sizer.Add(wx.StaticText(General,label=' Peak cutoff %: '),0,WACV)
580	cutOff = wx.TextCtrl(General,value='%.1f'%(Map['cutOff']),style=wx.TE_PROCESS_ENTER)
581	cutOff.Bind(wx.EVT_TEXT_ENTER,OnCutOff)
582	cutOff.Bind(wx.EVT_KILL_FOCUS,OnCutOff)
583	line2Sizer.Add(cutOff,0,WACV)
584	mapSizer.Add(line2Sizer,0,WACV)
585	return mapSizer
586
587	def FlipSizer():
588	if 'k-Max' not in Flip: Flip['k-Max'] = 20.
589
590	def OnRefList(event):
591	Flip['RefList'] = refList.GetValue()
592
593	def OnNormElem(event):
594	PE = G2elemGUI.PickElement(G2frame,ifNone=True)
595	if PE.ShowModal() == wx.ID_OK:
596	Flip['Norm element'] = PE.Elem.strip()
597	normElem.SetLabel(Flip['Norm element'])
598	PE.Destroy()
599
600	def OnResVal(event):
601	try:
602	res = float(flipRes.GetValue())
603	if 0.25 <= res <= 20.:
604	Flip['Resolution'] = res
605	except ValueError:
606	pass
607	flipRes.SetValue("%.2f"%(Flip['Resolution'])) #reset in case of error
608
609	def OnkFactor(event):
610	try:
611	res = float(kFactor.GetValue())
612	if 0.1 <= res <= 1.2:
613	Flip['k-factor'] = res
614	except ValueError:
615	pass
616	kFactor.SetValue("%.3f"%(Flip['k-factor'])) #reset in case of error
617
618	def OnkMax(event):
619	try:
620	res = float(kMax.GetValue())
621	if res >= 10.:
622	Flip['k-Max'] = res
623	except ValueError:
624	pass
625	kMax.SetValue("%.1f"%(Flip['k-Max'])) #reset in case of error
626
627	refList = data['Histograms'].keys()
628	flipSizer = wx.BoxSizer(wx.VERTICAL)
629	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
630	lineSizer.Add(wx.StaticText(General,label=' Charge flip controls: Reflection set from: '),0,WACV)
631	refList = wx.ComboBox(General,-1,value=Flip['RefList'],choices=refList,
632	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
633	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
634	lineSizer.Add(refList,0,WACV)
635	lineSizer.Add(wx.StaticText(General,label=' Normalizing element: '),0,WACV)
636	normElem = wx.Button(General,label=Flip['Norm element'],style=wx.TE_READONLY)
637	normElem.Bind(wx.EVT_BUTTON,OnNormElem)
638	lineSizer.Add(normElem,0,WACV)
639	flipSizer.Add(lineSizer,0,WACV)
640	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
641	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,WACV)
642	flipRes = wx.TextCtrl(General,value='%.2f'%(Flip['Resolution']),style=wx.TE_PROCESS_ENTER)
643	flipRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
644	flipRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
645	line2Sizer.Add(flipRes,0,WACV)
646	line2Sizer.Add(wx.StaticText(General,label=' k-Factor (0.1-1.2): '),0,WACV)
647	kFactor = wx.TextCtrl(General,value='%.3f'%(Flip['k-factor']),style=wx.TE_PROCESS_ENTER)
648	kFactor.Bind(wx.EVT_TEXT_ENTER,OnkFactor)
649	kFactor.Bind(wx.EVT_KILL_FOCUS,OnkFactor)
650	line2Sizer.Add(kFactor,0,WACV)
651	line2Sizer.Add(wx.StaticText(General,label=' k-Max (>=10.0): '),0,WACV)
652	kMax = wx.TextCtrl(General,value='%.1f'%(Flip['k-Max']),style=wx.TE_PROCESS_ENTER)
653	kMax.Bind(wx.EVT_TEXT_ENTER,OnkMax)
654	kMax.Bind(wx.EVT_KILL_FOCUS,OnkMax)
655	line2Sizer.Add(kMax,0,WACV)
656	flipSizer.Add(line2Sizer,0,WACV)
657	return flipSizer
658
659	def MCSASizer():
660	Ind = {}
661
662	def OnRefList(event):
663	MCSAdata['Data source'] = refList.GetValue()
664
665	def OnDmin(event):
666	try:
667	val = float(dmin.GetValue())
668	if 1.0 <= val < 5.0:
669	MCSAdata['dmin'] = val
670	except ValueError:
671	pass
672	dmin.SetValue("%.3f"%(MCSAdata['dmin'])) #reset in case of error
673	MCSAdata['newDmin'] = True
674
675	def OnCycles(event):
676	MCSAdata['Cycles'] = int(cycles.GetValue())
677
678	def OnAlist(event):
679	MCSAdata['Algorithm'] = Alist.GetValue()
680	wx.CallAfter(UpdateGeneral)
681
682	def OnSlope(event):
683	try:
684	val = float(slope.GetValue())
685	if .25 <= val < 1.0:
686	MCSAdata['log slope'] = val
687	except ValueError:
688	pass
689	slope.SetValue("%.3f"%(MCSAdata['log slope'])) #reset in case of error
690
691	def OnAjump(event):
692	Obj = event.GetEventObject()
693	name,ind = Indx[Obj.GetId()]
694	try:
695	val = float(Obj.GetValue())
696	if .0 <= val <= 1.0:
697	MCSAdata[name][ind] = val
698	except ValueError:
699	pass
700	Obj.SetValue("%.3f"%(MCSAdata[name][ind]))
701
702	def OnRanStart(event):
703	MCSAdata['ranStart'] = ranStart.GetValue()
704
705	def OnAutoRan(event):
706	MCSAdata['autoRan'] = autoRan.GetValue()
707
708	def OnRanRange(event):
709	try:
710	val = float(ranRange.GetValue())/100
711	if 0.01 <= val <= 0.99:
712	MCSAdata['ranRange'] = val
713	except ValueError:
714	pass
715	ranRange.SetValue('%.1f'%(MCSAdata['ranRange']*100.))
716
717	def OnAnneal(event):
718	Obj = event.GetEventObject()
719	ind,fmt = Indx[Obj.GetId()]
720	if ind == 2: #No. trials
721	try:
722	val = int(Obj.GetValue())
723	if 1 <= val:
724	MCSAdata['Annealing'][ind] = val
725	except ValueError:
726	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
727	else:
728	try:
729	val = float(Obj.GetValue())
730	if .0 <= val:
731	MCSAdata['Annealing'][ind] = val
732	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
733	except ValueError:
734	MCSAdata['Annealing'][ind] = None
735	Obj.SetValue(str(MCSAdata['Annealing'][ind]))
736
737	refList = []
738	if len(data['Pawley ref']):
739	refList = ['Pawley reflections']
740	for item in data['Histograms'].keys():
741	if 'HKLF' in item or 'PWDR' in item:
742	refList.append(item)
743	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
744	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
745	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,WACV)
746	refList = wx.ComboBox(General,-1,value=MCSAdata['Data source'],choices=refList,
747	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
748	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
749	lineSizer.Add(refList,0,WACV)
750	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,WACV)
751	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['dmin']),style=wx.TE_PROCESS_ENTER)
752	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
753	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
754	lineSizer.Add(dmin,0,WACV)
755	mcsaSizer.Add(lineSizer)
756	mcsaSizer.Add((5,5),)
757	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
758	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,WACV)
759	Cchoice = ['1','2','4','8','16','32','64','128','256']
760	cycles = wx.ComboBox(General,-1,value=str(MCSAdata.get('Cycles',1)),choices=Cchoice,
761	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
762	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
763	line2Sizer.Add(cycles,0,WACV)
764	line2Sizer.Add((5,0),)
765	ranStart = wx.CheckBox(General,-1,label=' MC/SA Refine at ')
766	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
767	ranStart.SetValue(MCSAdata.get('ranStart',False))
768	line2Sizer.Add(ranStart,0,WACV)
769	ranRange = wx.TextCtrl(General,-1,value='%.1f'%(MCSAdata.get('ranRange',0.10)*100),style=wx.TE_PROCESS_ENTER)
770	ranRange.Bind(wx.EVT_TEXT_ENTER,OnRanRange)
771	ranRange.Bind(wx.EVT_KILL_FOCUS,OnRanRange)
772	line2Sizer.Add(ranRange,0,WACV)
773	line2Sizer.Add(wx.StaticText(General,label='% of ranges. '),0,WACV)
774	# autoRan = wx.CheckBox(General,-1,label=' Do auto range reduction? ')
775	# autoRan.Bind(wx.EVT_CHECKBOX, OnAutoRan)
776	# autoRan.SetValue(MCSAdata.get('autoRan',False))
777	# line2Sizer.Add(autoRan,0,WACV)
778	mcsaSizer.Add(line2Sizer)
779	mcsaSizer.Add((5,5),)
780	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
781	Achoice = ['log','fast'] #these work
782	# Achoice = ['log','fast','cauchy','boltzmann']
783	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,WACV)
784	Alist = wx.ComboBox(General,-1,value=MCSAdata['Algorithm'],choices=Achoice,
785	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
786	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
787	line3Sizer.Add(Alist,0,WACV)
788	if MCSAdata['Algorithm'] in ['fast','boltzmann','cauchy']:
789	Names = [' A-jump: ',' B-jump: ']
790	parms = 'Jump coeff'
791	if MCSAdata['Algorithm'] in ['boltzmann','cauchy']:
792	Names = [' A-jump: ']
793	elif 'fast' in MCSAdata['Algorithm']:
794	Names = [' quench: ',' m-factor: ',' n-factor: ']
795	parms = 'fast parms'
796	for i,name in enumerate(Names):
797	line3Sizer.Add(wx.StaticText(General,label=name),0,WACV)
798	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata[parms][i]),style=wx.TE_PROCESS_ENTER)
799	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
800	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
801	Indx[Ajump.GetId()] = [parms,i]
802	line3Sizer.Add(Ajump,0,WACV)
803	elif 'log' in MCSAdata['Algorithm']:
804	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,WACV)
805	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['log slope']),style=wx.TE_PROCESS_ENTER)
806	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
807	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
808	line3Sizer.Add(slope,0,WACV)
809	mcsaSizer.Add(line3Sizer)
810	mcsaSizer.Add((5,5),)
811	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
812	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,WACV)
813	names = [' Start temp: ',' Final temp: ',' No. trials: ']
814	fmts = ['%.1f','%.5f','%d']
815	for i,[name,fmt] in enumerate(zip(names,fmts)):
816	if MCSAdata['Annealing'][i]:
817	text = fmt%(MCSAdata['Annealing'][i])
818	else:
819	text = 'None'
820	line3Sizer.Add(wx.StaticText(General,label=name),0,WACV)
821	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
822	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
823	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
824	Indx[anneal.GetId()] = [i,fmt]
825	line3Sizer.Add(anneal,0,WACV)
826	mcsaSizer.Add(line3Sizer)
827	return mcsaSizer
828
829	# UpdateGeneral execution continues here
830	if General.GetSizer():
831	General.GetSizer().Clear(True)
832	mainSizer = wx.BoxSizer(wx.VERTICAL)
833	mainSizer.Add((5,5),0)
834	mainSizer.Add(NameSizer(),0)
835	mainSizer.Add((5,5),0)
836	mainSizer.Add(CellSizer(),0)
837	mainSizer.Add((5,5),0)
838
839	Indx = {}
840	denSizer = None
841	if len(generalData['AtomTypes']):
842	denSizer = DenSizer()
843	mainSizer.Add(denSizer[0])
844	mainSizer.Add((5,5),0)
845	mainSizer.Add(ElemSizer())
846	G2gd.HorizontalLine(mainSizer,General)
847
848	mainSizer.Add(PawleySizer())
849	G2gd.HorizontalLine(mainSizer,General)
850
851	mainSizer.Add(MapSizer())
852	G2gd.HorizontalLine(mainSizer,General)
853
854	mainSizer.Add(FlipSizer())
855	G2gd.HorizontalLine(mainSizer,General)
856
857	mainSizer.Add(MCSASizer())
858	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
859	G2frame.dataFrame.SetStatusText('')
860
861	################################################################################
862	##### Atom routines
863	################################################################################
864
865	def FillAtomsGrid(Atoms):
866	'''Display the contents of the Atoms tab
867	'''
868	def RefreshAtomGrid(event):
869
870	r,c = event.GetRow(),event.GetCol()
871	if r < 0 and c < 0:
872	for row in range(Atoms.GetNumberRows()):
873	Atoms.SelectRow(row,True)
874	if r < 0: #double click on col label! Change all atoms!
875	sel = -1
876	noSkip = True
877	if Atoms.GetColLabelValue(c) == 'refine':
878	Type = generalData['Type']
879	if Type in ['nuclear','macromolecular']:
880	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
881	elif Type in ['magnetic',]:
882	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
883	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
884	if dlg.ShowModal() == wx.ID_OK:
885	sel = dlg.GetSelections()
886	parms = ''
887	for x in sel:
888	parms += choice[x][0]
889	dlg.Destroy()
890	elif Atoms.GetColLabelValue(c) == 'I/A':
891	choice = ['Isotropic','Anisotropic']
892	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
893	if dlg.ShowModal() == wx.ID_OK:
894	sel = dlg.GetSelection()
895	parms = choice[sel][0]
896	dlg.Destroy()
897	elif Atoms.GetColLabelValue(c) == 'Type':
898	choice = generalData['AtomTypes']
899	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
900	if dlg.ShowModal() == wx.ID_OK:
901	sel = dlg.GetSelection()
902	parms = choice[sel]
903	noSkip = False
904	Atoms.ClearSelection()
905	for row in range(Atoms.GetNumberRows()):
906	if parms == atomData[row][c]:
907	Atoms.SelectRow(row,True)
908	dlg.Destroy()
909	SetupGeneral()
910	elif Atoms.GetColLabelValue(c) == 'residue':
911	choice = []
912	for r in range(Atoms.GetNumberRows()):
913	if str(atomData[r][c]) not in choice:
914	choice.append(str(atomData[r][c]))
915	choice.sort()
916	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
917	if dlg.ShowModal() == wx.ID_OK:
918	sel = dlg.GetSelection()
919	parms = choice[sel]
920	noSkip = False
921	Atoms.ClearSelection()
922	for row in range(Atoms.GetNumberRows()):
923	if parms == atomData[row][c]:
924	Atoms.SelectRow(row,True)
925	dlg.Destroy()
926	elif Atoms.GetColLabelValue(c) == 'res no':
927	choice = []
928	for r in range(Atoms.GetNumberRows()):
929	if str(atomData[r][c]) not in choice:
930	choice.append(str(atomData[r][c]))
931	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
932	if dlg.ShowModal() == wx.ID_OK:
933	sel = dlg.GetSelection()
934	parms = choice[sel]
935	noSkip = False
936	Atoms.ClearSelection()
937	for row in range(Atoms.GetNumberRows()):
938	if int(parms) == atomData[row][c]:
939	Atoms.SelectRow(row,True)
940	dlg.Destroy()
941	elif Atoms.GetColLabelValue(c) == 'chain':
942	choice = []
943	for r in range(Atoms.GetNumberRows()):
944	if atomData[r][c] not in choice:
945	choice.append(atomData[r][c])
946	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
947	if dlg.ShowModal() == wx.ID_OK:
948	sel = dlg.GetSelection()
949	parms = choice[sel]
950	noSkip = False
951	Atoms.ClearSelection()
952	for row in range(Atoms.GetNumberRows()):
953	if parms == atomData[row][c]:
954	Atoms.SelectRow(row,True)
955	dlg.Destroy()
956	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
957	pass #& then change all 'I' atoms
958	if sel >= 0 and noSkip:
959	ui = colLabels.index('U11')
960	us = colLabels.index('Uiso')
961	ss = colLabels.index('site sym')
962	for r in range(Atoms.GetNumberRows()):
963	ID = atomData[r][-1]
964	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
965	if parms == 'A': #'I' --> 'A'
966	Uiso = float(Atoms.GetCellValue(r,us))
967	sytsym = atomData[r][ss]
968	CSI = G2spc.GetCSuinel(sytsym)
969	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
970	atomData[r][us] = 0.0
971	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
972	for i in range(6):
973	ci = ui+i
974	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
975	if CSI[2][i]:
976	Atoms.SetCellStyle(r,ci,WHITE,False)
977	else: #'A' --> 'I'
978	Uij = atomData[r][ui:ui+6]
979	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
980	atomData[r][us] = Uiso
981	Atoms.SetCellStyle(r,us,WHITE,False)
982	for i in range(6):
983	ci = ui+i
984	atomData[r][ci] = 0.0
985	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
986	if not Atoms.IsReadOnly(r,c):
987	if Atoms.GetColLabelValue(c) == 'refine':
988	rbExcl = rbAtmDict.get(atomData[r][-1],'')
989	if rbExcl:
990	for excl in rbExcl:
991	atomData[r][c] = parms.replace(excl,'')
992	else:
993	atomData[r][c] = parms
994	else:
995	atomData[r][c] = parms
996	if 'Atoms' in data['Drawing']:
997	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
998	wx.CallAfter(Paint)
999
1000	def ChangeAtomCell(event):
1001
1002	def chkUij(Uij,CSI): #needs to do something!!!
1003	return Uij
1004
1005	r,c = event.GetRow(),event.GetCol()
1006	if r >= 0 and c >= 0:
1007	ID = atomData[r][-1]
1008	if Atoms.GetColLabelValue(c) in ['x','y','z']:
1009	ci = colLabels.index('x')
1010	XYZ = atomData[r][ci:ci+3]
1011	if None in XYZ:
1012	XYZ = [0,0,0]
1013	SScol = colLabels.index('site sym')
1014	Mulcol = colLabels.index('mult')
1015	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1016	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
1017	atomData[r][SScol] = Sytsym
1018	atomData[r][Mulcol] = Mult
1019	if atomData[r][colLabels.index('I/A')] == 'A':
1020	ui = colLabels.index('U11')
1021	CSI = G2spc.GetCSuinel(Sytsym)
1022	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
1023	for i in range(6):
1024	ci = i+ui
1025	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1026	if CSI[2][i]:
1027	Atoms.SetCellStyle(r,ci,WHITE,False)
1028	SetupGeneral()
1029	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1030	if atomData[r][c] == 'I':
1031	Uij = atomData[r][c+2:c+8]
1032	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1033	Atoms.SetCellStyle(r,c+1,WHITE,False)
1034	Atoms.SetCellTextColour(r,c+1,BLACK)
1035	for i in range(6):
1036	ci = i+colLabels.index('U11')
1037	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1038	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1039	atomData[r][ci] = 0.0
1040	else:
1041	value = atomData[r][c+1]
1042	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1043	atomData[r][c+1] = 0.0
1044	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1045	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1046	for i in range(6):
1047	ci = i+colLabels.index('U11')
1048	atomData[r][ci] = value*CSI[3][i]
1049	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1050	Atoms.SetCellTextColour(r,ci,BLACK)
1051	if CSI[2][i]:
1052	Atoms.SetCellStyle(r,ci,WHITE,False)
1053	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1054	value = atomData[r][c]
1055	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1056	iUij = CSI[0][c-colLabels.index('U11')]
1057	for i in range(6):
1058	if iUij == CSI[0][i]:
1059	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1060	elif Atoms.GetColLabelValue(c) == 'refine':
1061	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1062	if 'Atoms' in data['Drawing']:
1063	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1064	wx.CallAfter(Paint)
1065
1066	def AtomTypeSelect(event):
1067	r,c = event.GetRow(),event.GetCol()
1068	if Atoms.GetColLabelValue(c) == 'Type':
1069	PE = G2elemGUI.PickElement(G2frame)
1070	if PE.ShowModal() == wx.ID_OK:
1071	if PE.Elem != 'None':
1072	atomData[r][c] = PE.Elem.strip()
1073	name = atomData[r][c]
1074	if len(name) in [2,4]:
1075	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1076	else:
1077	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1078	PE.Destroy()
1079	SetupGeneral()
1080	wx.CallAfter(Paint)
1081	value = Atoms.GetCellValue(r,c)
1082	atomData[r][c] = value
1083	ID = atomData[r][-1]
1084	if 'Atoms' in data['Drawing']:
1085	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1086	SetupGeneral()
1087	else:
1088	event.Skip()
1089
1090	def RowSelect(event):
1091	r,c = event.GetRow(),event.GetCol()
1092	if not event.AltDown():
1093	Atoms.frm = -1
1094	G2frame.dataFrame.SetStatusText('')
1095	if r < 0 and c < 0:
1096	if Atoms.IsSelection():
1097	Atoms.ClearSelection()
1098	elif c < 0: #only row clicks
1099	if event.ControlDown():
1100	if r in Atoms.GetSelectedRows():
1101	Atoms.DeselectRow(r)
1102	else:
1103	Atoms.SelectRow(r,True)
1104	elif event.ShiftDown():
1105	indxs = Atoms.GetSelectedRows()
1106	Atoms.ClearSelection()
1107	ibeg = 0
1108	if indxs:
1109	ibeg = indxs[-1]
1110	for row in range(ibeg,r+1):
1111	Atoms.SelectRow(row,True)
1112	elif event.AltDown():
1113	if atomData[r][-1] in rbAtmDict:
1114	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1115	Atoms.frm = -1
1116	Atoms.ClearSelection()
1117	else:
1118	if Atoms.frm < 0: #pick atom to be moved
1119	Atoms.frm = r
1120	Atoms.SelectRow(r,True)
1121	n = colLabels.index('Name')
1122	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1123	else: #move it
1124	item = atomData.pop(Atoms.frm)
1125	atomData.insert(r,item)
1126	Atoms.frm = -1
1127	G2frame.dataFrame.SetStatusText('')
1128	wx.CallAfter(Paint)
1129	else:
1130	Atoms.ClearSelection()
1131	Atoms.SelectRow(r,True)
1132
1133	def ChangeSelection(event):
1134	r,c = event.GetRow(),event.GetCol()
1135	if r < 0 and c < 0:
1136	Atoms.ClearSelection()
1137	if c < 0:
1138	if r in Atoms.GetSelectedRows():
1139	Atoms.DeselectRow(r)
1140	else:
1141	Atoms.SelectRow(r,True)
1142	if r < 0:
1143	if c in Atoms.GetSelectedCols():
1144	Atoms.DeselectCol(c)
1145	else:
1146	Atoms.SelectCol(c,True)
1147
1148	def Paint():
1149
1150	table = []
1151	rowLabels = []
1152	for i,atom in enumerate(atomData):
1153	table.append(atom)
1154	rowLabels.append(str(i))
1155	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1156	Atoms.SetTable(atomTable, True)
1157	Atoms.frm = -1
1158	colType = colLabels.index('Type')
1159	colR = colLabels.index('refine')
1160	colSS = colLabels.index('site sym')
1161	colX = colLabels.index('x')
1162	colIA = colLabels.index('I/A')
1163	colU11 = colLabels.index('U11')
1164	colUiso = colLabels.index('Uiso')
1165	attr = wx.grid.GridCellAttr()
1166	attr.IncRef() #fix from Jim Hester
1167	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1168	for c in range(colX,colX+3):
1169	Atoms.SetColAttr(c, attr)
1170	for i in range(colU11-1,colU11+6):
1171	Atoms.SetColSize(i,50)
1172	for row in range(Atoms.GetNumberRows()):
1173	atId = atomData[row][-1]
1174	rbExcl = rbAtmDict.get(atId,'')
1175	Atoms.SetReadOnly(row,colSS,True) #site sym
1176	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1177	if Atoms.GetCellValue(row,colIA) == 'A':
1178	CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')])
1179	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1180	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1181	for i in range(6):
1182	ci = colU11+i
1183	Atoms.SetCellTextColour(row,ci,BLACK)
1184	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1185	if CSI[2][i] and 'U' not in rbExcl:
1186	Atoms.SetCellStyle(row,ci,WHITE,False)
1187	else:
1188	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1189	Atoms.SetCellTextColour(row,colUiso,BLACK)
1190	if 'U' in rbExcl:
1191	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1192	for i in range(6):
1193	ci = colU11+i
1194	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1195	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1196	if 'X' in rbExcl:
1197	for c in range(0,colX+3):
1198	if c != colR:
1199	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1200	Atoms.AutoSizeColumns(False)
1201
1202	# FillAtomsGrid executable code starts here
1203	generalData = data['General']
1204	atomData = data['Atoms']
1205	DData = data['Drawing']
1206	resRBData = data['RBModels'].get('Residue',[])
1207	vecRBData = data['RBModels'].get('Vector',[])
1208	rbAtmDict = {}
1209	for rbObj in resRBData+vecRBData:
1210	exclList = ['X' for i in range(len(rbObj['Ids']))]
1211	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1212	if rbObj['ThermalMotion'][0] != 'None':
1213	for id in rbObj['Ids']:
1214	rbAtmDict[id] += 'U'
1215	# exclList will be 'x' or 'xu' if TLS used in RB
1216	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1217	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1218	if atomData:
1219	for item in Items:
1220	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1221	else:
1222	for item in Items:
1223	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1224	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1225	if 'showABC' in data['Drawing']:
1226	for item in Items:
1227	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1228	else:
1229	for item in Items:
1230	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1231
1232	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1233	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1234	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1235	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1236	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1237	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1238	if generalData['Type'] == 'magnetic':
1239	colLabels += ['Mx','My','Mz']
1240	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1241	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1242	elif generalData['Type'] == 'macromolecular':
1243	colLabels = ['res no','residue','chain'] + colLabels
1244	Types = [wg.GRID_VALUE_STRING,
1245	wg.GRID_VALUE_CHOICE+AAchoice,
1246	wg.GRID_VALUE_STRING] + Types
1247	elif generalData['Type'] == 'modulated':
1248	Types += []
1249	colLabels += []
1250	SGData = data['General']['SGData']
1251	G2frame.dataFrame.SetStatusText('')
1252	if SGData['SGPolax']:
1253	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1254	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1255	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1256	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1257	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1258	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1259	Atoms.SetMargins(0,0)
1260
1261	G2frame.dataFrame.setSizePosLeft([700,300])
1262	Paint()
1263
1264	def OnAtomAdd(event):
1265	AtomAdd(0,0,0)
1266	FillAtomsGrid(Atoms)
1267	event.StopPropagation()
1268	if data['Drawing']:
1269	G2plt.PlotStructure(G2frame,data)
1270
1271	def OnAtomViewAdd(event):
1272	try:
1273	drawData = data['Drawing']
1274	x,y,z = drawData['viewPoint'][0]
1275	AtomAdd(x,y,z)
1276	except:
1277	AtomAdd(0,0,0)
1278	FillAtomsGrid(Atoms)
1279	event.StopPropagation()
1280	G2plt.PlotStructure(G2frame,data)
1281
1282	def AtomAdd(x,y,z,El='H',Name='UNK'):
1283	atomData = data['Atoms']
1284	generalData = data['General']
1285	Ncol = Atoms.GetNumberCols()
1286	atId = ran.randint(0,sys.maxint)
1287	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1288	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1289	if generalData['Type'] == 'macromolecular':
1290	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1291	elif generalData['Type'] == 'nuclear':
1292	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1293	elif generalData['Type'] == 'magnetic':
1294	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1295	SetupGeneral()
1296	if 'Atoms' in data['Drawing']:
1297	DrawAtomAdd(data['Drawing'],atomData[-1])
1298
1299	def OnAtomInsert(event):
1300	AtomInsert(0,0,0)
1301	FillAtomsGrid(Atoms)
1302	event.StopPropagation()
1303	G2plt.PlotStructure(G2frame,data)
1304
1305	def OnAtomViewInsert(event):
1306	if 'Drawing' in data:
1307	drawData = data['Drawing']
1308	x,y,z = drawData['viewPoint'][0]
1309	AtomAdd(x,y,z)
1310	FillAtomsGrid(Atoms)
1311	event.StopPropagation()
1312
1313	def OnAtomMove(event):
1314	drawData = data['Drawing']
1315	atomData = data['Atoms']
1316	x,y,z = drawData['viewPoint'][0]
1317	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1318	cx = colLabels.index('x')
1319	indx = Atoms.GetSelectedRows()
1320	if len(indx) != 1:
1321	print '** ERROR - only one atom can be moved **'
1322	elif atomData[indx[0]][-1] in rbAtmDict:
1323	print '** ERROR - Atoms in rigid bodies can not be moved **'
1324	else:
1325	atomData[indx[0]][cx:cx+3] = [x,y,z]
1326	SetupGeneral()
1327	FillAtomsGrid(Atoms)
1328	ID = atomData[indx[0]][-1]
1329	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1330	G2plt.PlotStructure(G2frame,data)
1331	event.StopPropagation()
1332
1333	def DrawAtomsReplaceByID(drawingData,atom,ID):
1334	IDs = [ID,]
1335	atomData = drawingData['Atoms']
1336	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1337	for ind in indx:
1338	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1339
1340	def MakeDrawAtom(atom,oldatom=None):
1341	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1342	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1343	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1344	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1345	generalData = data['General']
1346	SGData = generalData['SGData']
1347	if generalData['Type'] == 'nuclear':
1348	if oldatom:
1349	opr = oldatom[5]
1350	if atom[9] == 'A':
1351	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1352	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1353	else:
1354	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1355	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1356	else:
1357	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1358	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1359	ct,cs = [1,8] #type & color
1360	elif generalData['Type'] == 'macromolecular':
1361	try:
1362	oneLetter = AA3letter.index(atom[1])
1363	except ValueError:
1364	oneLetter = -1
1365	atomInfo = [[atom[1].strip()+atom[0],]+
1366	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1367	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1368	ct,cs = [4,11] #type & color
1369	elif generalData['Type'] == 'magnetic':
1370	if oldatom:
1371	atomInfo = [atom[:2]+oldatom[3:]][0]
1372	else:
1373	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1374	ct,cs = [1,8] #type & color
1375	# elif generalData['Type'] == 'modulated':
1376	# ????? for future
1377	atNum = generalData['AtomTypes'].index(atom[ct])
1378	atomInfo[cs] = list(generalData['Color'][atNum])
1379	return atomInfo
1380
1381	def AtomInsert(x,y,z):
1382	indx = Atoms.GetSelectedRows()
1383	if indx:
1384	indx = indx[0]
1385	atomData = data['Atoms']
1386	generalData = data['General']
1387	Ncol = Atoms.GetNumberCols()
1388	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1389	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1390	atId = ran.randint(0,sys.maxint)
1391	if generalData['Type'] == 'macromolecular':
1392	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1393	elif generalData['Type'] == 'nuclear':
1394	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1395	elif generalData['Type'] == 'magnetic':
1396	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])
1397	SetupGeneral()
1398
1399	def AtomDelete(event):
1400	indx = Atoms.GetSelectedRows()
1401	IDs = []
1402	if indx:
1403	atomData = data['Atoms']
1404	indx.reverse()
1405	for ind in indx:
1406	atom = atomData[ind]
1407	if atom[-1] in rbAtmDict:
1408	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1409	else:
1410	IDs.append(atom[-1])
1411	del atomData[ind]
1412	if 'Atoms' in data['Drawing']:
1413	DrawAtomsDeleteByIDs(IDs)
1414	wx.CallAfter(FillAtomsGrid,Atoms)
1415	G2plt.PlotStructure(G2frame,data)
1416	SetupGeneral()
1417	event.StopPropagation()
1418
1419	def AtomRefine(event):
1420	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1421	c = colLabels.index('refine')
1422	indx = Atoms.GetSelectedRows()
1423	if indx:
1424	atomData = data['Atoms']
1425	generalData = data['General']
1426	Type = generalData['Type']
1427	if Type in ['nuclear','macromolecular']:
1428	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1429	elif Type == 'magnetic':
1430	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1431	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1432	if dlg.ShowModal() == wx.ID_OK:
1433	sel = dlg.GetSelections()
1434	parms = ''
1435	for x in sel:
1436	parms += choice[x][0]
1437	for r in indx:
1438	if not Atoms.IsReadOnly(r,c):
1439	atomData[r][c] = parms
1440	Atoms.ForceRefresh()
1441	dlg.Destroy()
1442
1443	def AtomModify(event):
1444	indx = Atoms.GetSelectedRows()
1445	if indx:
1446	atomData = data['Atoms']
1447	generalData = data['General']
1448	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1449	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1450	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1451	parm = ''
1452	if dlg.ShowModal() == wx.ID_OK:
1453	sel = dlg.GetSelection()
1454	parm = choices[sel]
1455	cid = colLabels.index(parm)
1456	dlg.Destroy()
1457	if parm in ['Type']:
1458	dlg = G2elemGUI.PickElement(G2frame)
1459	if dlg.ShowModal() == wx.ID_OK:
1460	if dlg.Elem not in ['None']:
1461	El = dlg.Elem.strip()
1462	for r in indx:
1463	if not Atoms.IsReadOnly(r,cid):
1464	atomData[r][cid] = El
1465	if len(El) in [2,4]:
1466	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1467	else:
1468	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1469	SetupGeneral()
1470	if 'Atoms' in data['Drawing']:
1471	for r in indx:
1472	ID = atomData[r][-1]
1473	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1474	FillAtomsGrid(Atoms)
1475	dlg.Destroy()
1476	elif parm in ['Name',]:
1477	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1478	wx.YES_NO \| wx.ICON_QUESTION)
1479	try:
1480	result = dlg.ShowModal()
1481	if result == wx.ID_YES:
1482	for r in indx:
1483	if not Atoms.IsReadOnly(r,cid+1):
1484	El = atomData[r][cid+1]
1485	if len(El) in [2,4]:
1486	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1487	else:
1488	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1489	FillAtomsGrid(Atoms)
1490	finally:
1491	dlg.Destroy()
1492
1493	elif parm in ['I/A']:
1494	choices = ['Isotropic','Anisotropic']
1495	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1496	if dlg.ShowModal() == wx.ID_OK:
1497	sel = dlg.GetSelection()
1498	parm = choices[sel][0]
1499	for r in indx:
1500	if not Atoms.IsReadOnly(r,cid):
1501	atomData[r][cid] = parm
1502	FillAtomsGrid(Atoms)
1503	dlg.Destroy()
1504	elif parm in ['frac','Uiso']:
1505	limits = [0.,1.]
1506	val = 1.0
1507	if parm in ['Uiso']:
1508	limits = [0.,0.25]
1509	val = 0.01
1510	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1511	if dlg.ShowModal() == wx.ID_OK:
1512	parm = dlg.GetValue()
1513	for r in indx:
1514	if not Atoms.IsReadOnly(r,cid):
1515	atomData[r][cid] = parm
1516	SetupGeneral()
1517	FillAtomsGrid(Atoms)
1518	dlg.Destroy()
1519	elif parm in ['x','y','z']:
1520	limits = [-1.,1.]
1521	val = 0.
1522	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1523	if dlg.ShowModal() == wx.ID_OK:
1524	parm = dlg.GetValue()
1525	for r in indx:
1526	if not Atoms.IsReadOnly(r,cid):
1527	atomData[r][cid] += parm
1528	SetupGeneral()
1529	FillAtomsGrid(Atoms)
1530	dlg.Destroy()
1531
1532	def AtomTransform(event):
1533	indx = Atoms.GetSelectedRows()
1534	if indx:
1535	generalData = data['General']
1536	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1537	cx = colLabels.index('x')
1538	cuia = colLabels.index('I/A')
1539	cuij = colLabels.index('U11')
1540	css = colLabels.index('site sym')
1541	atomData = data['Atoms']
1542	generalData = data['General']
1543	SGData = generalData['SGData']
1544	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1545	New = False
1546	try:
1547	if dlg.ShowModal() == wx.ID_OK:
1548	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1549	Cell = np.array(Cell)
1550	cent = SGData['SGCen'][Cent]
1551	M,T = SGData['SGOps'][Opr]
1552	for ind in indx:
1553	XYZ = np.array(atomData[ind][cx:cx+3])
1554	XYZ = np.inner(M,XYZ)+T
1555	if Inv:
1556	XYZ = -XYZ
1557	XYZ = XYZ+cent+Cell
1558	if Force:
1559	XYZ = G2spc.MoveToUnitCell(XYZ)
1560	if New:
1561	atom = copy.copy(atomData[ind])
1562	else:
1563	atom = atomData[ind]
1564	atom[cx:cx+3] = XYZ
1565	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1566	if atom[cuia] == 'A':
1567	Uij = atom[cuij:cuij+6]
1568	U = G2spc.Uij2U(Uij)
1569	U = np.inner(np.inner(M,U),M)
1570	Uij = G2spc.U2Uij(U)
1571	atom[cuij:cuij+6] = Uij
1572	if New:
1573	atomData.append(atom)
1574	finally:
1575	dlg.Destroy()
1576	Atoms.ClearSelection()
1577	if New:
1578	FillAtomsGrid(Atoms)
1579	else:
1580	Atoms.ForceRefresh()
1581
1582	def OnDistAnglePrt(event):
1583	'save distances and angles to a file'
1584	fp = file(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile
1585	)[0]+'.disagl'),'w')
1586	OnDistAngle(event,fp=fp)
1587	fp.close()
1588
1589	def OnDistAngle(event,fp=None):
1590	'Compute distances and angles'
1591	indx = Atoms.GetSelectedRows()
1592	Oxyz = []
1593	xyz = []
1594	DisAglData = {}
1595	DisAglCtls = {}
1596	if indx:
1597	generalData = data['General']
1598	DisAglData['OrigIndx'] = indx
1599	if 'DisAglCtls' in generalData:
1600	DisAglCtls = generalData['DisAglCtls']
1601	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1602	if dlg.ShowModal() == wx.ID_OK:
1603	DisAglCtls = dlg.GetData()
1604	else:
1605	dlg.Destroy()
1606	return
1607	dlg.Destroy()
1608	generalData['DisAglCtls'] = DisAglCtls
1609	atomData = data['Atoms']
1610	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1611	cx = colLabels.index('x')
1612	cn = colLabels.index('Name')
1613	for i,atom in enumerate(atomData):
1614	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1615	if i in indx:
1616	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1617	DisAglData['OrigAtoms'] = Oxyz
1618	DisAglData['TargAtoms'] = xyz
1619	generalData = data['General']
1620	DisAglData['SGData'] = generalData['SGData']
1621	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1622	if 'pId' in data:
1623	DisAglData['pId'] = data['pId']
1624	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1625	try:
1626	if fp:
1627	G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
1628	else:
1629	G2stMn.PrintDistAngle(DisAglCtls,DisAglData)
1630	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1631	G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types')
1632	else:
1633	print "select one or more rows of atoms"
1634	G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
1635
1636	def OnIsoDistortCalc(event):
1637	'''Compute the ISODISTORT mode values from the current coordinates.
1638	Called in response to the (Phase/Atoms tab) AtomCompute
1639	"Compute ISODISTORT mode values" menu item, which should be enabled
1640	only when Phase['ISODISTORT'] is defined.
1641	'''
1642	def _onClose(event):
1643	dlg.EndModal(wx.ID_CANCEL)
1644	def fmtHelp(item,fullname):
1645	helptext = "A new variable"
1646	if item[-3]:
1647	helptext += " named "+str(item[-3])
1648	helptext += " is a linear combination of the following parameters:\n"
1649	first = True
1650	for term in item[:-3]:
1651	line = ''
1652	var = str(term[1])
1653	m = term[0]
1654	if first:
1655	first = False
1656	line += ' = '
1657	else:
1658	if m >= 0:
1659	line += ' + '
1660	else:
1661	line += ' - '
1662	m = abs(m)
1663	line += '%.3f*%s '%(m,var)
1664	varMean = G2obj.fmtVarDescr(var)
1665	helptext += "\n" + line + " ("+ varMean + ")"
1666	helptext += '\n\nISODISTORT full name: '+str(fullname)
1667	return helptext
1668
1669	if 'ISODISTORT' not in data:
1670	raise Exception,"Should not happen: 'ISODISTORT' not in data"
1671	if len(data.get('Histograms',[])) == 0:
1672	G2frame.ErrorDialog(
1673	'No data',
1674	'Sorry, this computation requires that a histogram first be added to the phase'
1675	)
1676	return
1677	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() # init for constraint
1678	# make a lookup table for constraints
1679	sub = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Constraints')
1680	Constraints = G2frame.PatternTree.GetItemPyData(sub)
1681	constDict = {}
1682	for item in Constraints:
1683	if item.startswith('_'): continue
1684	for c in Constraints[item]:
1685	if c[-1] != 'f' or not c[-3]: continue
1686	constDict[c[-3]] = c
1687
1688	ISO = data['ISODISTORT']
1689	parmDict,varyList = G2frame.MakeLSParmDict()
1690
1691	dlg = wx.Dialog(G2frame,wx.ID_ANY,'ISODISTORT mode values',#size=(630,400),
1692	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
1693	mainSizer = wx.BoxSizer(wx.VERTICAL)
1694	mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,
1695	'ISODISTORT mode computation for cordinates in phase '+
1696	str(data['General'].get('Name'))))
1697	aSizer = wx.BoxSizer(wx.HORIZONTAL)
1698	panel1 = wxscroll.ScrolledPanel(
1699	dlg, wx.ID_ANY,#size=(100,200),
1700	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
1701	subSizer1 = wx.FlexGridSizer(rows=1,cols=2,hgap=5,vgap=2)
1702	panel2 = wxscroll.ScrolledPanel(
1703	dlg, wx.ID_ANY,#size=(100,200),
1704	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
1705	subSizer2 = wx.FlexGridSizer(rows=1,cols=3,hgap=5,vgap=2)
1706	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'Parameter name '))
1707	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
1708	subSizer2.Add((-1,-1))
1709	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'Mode name '))
1710	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
1711
1712	if 'G2VarList' in ISO:
1713	deltaList = []
1714	for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']):
1715	dvar = gv.varname()
1716	var = dvar.replace('::dA','::A')
1717	albl = Ilbl[:Ilbl.rfind('_')]
1718	v = Ilbl[Ilbl.rfind('_')+1:]
1719	pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)]
1720	if var in parmDict:
1721	cval = parmDict[var][0]
1722	else:
1723	dlg.EndModal(wx.ID_CANCEL)
1724	G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var))
1725	return
1726	deltaList.append(cval-pval)
1727	modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList)
1728	for lbl,xyz,var,val,G2var in zip(ISO['IsoVarList'],deltaList,
1729	ISO['IsoModeList'],modeVals,ISO['G2ModeList']):
1730	if G2var in constDict:
1731	ch = G2gd.HelpButton(panel2,fmtHelp(constDict[G2var],var))
1732	subSizer2.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
1733	else:
1734	subSizer2.Add((-1,-1))
1735	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
1736	try:
1737	value = G2py3.FormatSigFigs(xyz)
1738	except TypeError:
1739	value = str(xyz)
1740	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1741	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
1742	try:
1743	value = G2py3.FormatSigFigs(val)
1744	except TypeError:
1745	value = str(val)
1746	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1747	if 'G2OccVarList' in ISO:
1748	deltaList = []
1749	for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']):
1750	var = gv.varname()
1751	albl = Ilbl[:Ilbl.rfind('_')]
1752	#v = Ilbl[Ilbl.rfind('_')+1:]
1753	pval = ISO['BaseOcc'][albl]
1754	if var in parmDict:
1755	cval = parmDict[var][0]
1756	else:
1757	dlg.EndModal(wx.ID_CANCEL)
1758	G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var))
1759	return
1760	deltaList.append(cval-pval)
1761	modeVals = np.inner(ISO['Var2OccMatrix'],deltaList)
1762	for lbl,xyz,var,val,G2var in zip(ISO['OccVarList'],deltaList,
1763	ISO['OccModeList'],modeVals,ISO['G2OccModeList']):
1764	if G2var in constDict:
1765	ch = G2gd.HelpButton(panel2,fmtHelp(constDict[G2var],var))
1766	subSizer2.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
1767	else:
1768	subSizer2.Add((-1,-1))
1769	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
1770	try:
1771	value = G2py3.FormatSigFigs(xyz)
1772	except TypeError:
1773	value = str(xyz)
1774	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1775	#subSizer.Add((10,-1))
1776	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
1777	try:
1778	value = G2py3.FormatSigFigs(val)
1779	except TypeError:
1780	value = str(val)
1781	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1782
1783	# finish up ScrolledPanel
1784	panel1.SetSizer(subSizer1)
1785	panel2.SetSizer(subSizer2)
1786	panel1.SetAutoLayout(1)
1787	panel1.SetupScrolling()
1788	panel2.SetAutoLayout(1)
1789	panel2.SetupScrolling()
1790	# Allow window to be enlarged but not made smaller
1791	dlg.SetSizer(mainSizer)
1792	w1,l1 = subSizer1.GetSize()
1793	w2,l2 = subSizer2.GetSize()
1794	panel1.SetMinSize((w1+10,200))
1795	panel2.SetMinSize((w2+20,200))
1796	aSizer.Add(panel1,1, wx.ALL\|wx.EXPAND,1)
1797	aSizer.Add(panel2,2, wx.ALL\|wx.EXPAND,1)
1798	mainSizer.Add(aSizer,1, wx.ALL\|wx.EXPAND,1)
1799
1800	# make OK button
1801	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
1802	btn = wx.Button(dlg, wx.ID_CLOSE)
1803	btn.Bind(wx.EVT_BUTTON,_onClose)
1804	btnsizer.Add(btn)
1805	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1806
1807	mainSizer.Fit(dlg)
1808	dlg.SetMinSize(dlg.GetSize())
1809	dlg.ShowModal()
1810	dlg.Destroy()
1811
1812	def OnReImport(event):
1813	generalData = data['General']
1814	cx,ct,cs,cia = generalData['AtomPtrs']
1815	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1816	rdlist = G2frame.OnImportGeneric(reqrdr,
1817	G2frame.ImportPhaseReaderlist,'phase')
1818	if len(rdlist) == 0: return
1819	# rdlist is only expected to have one element
1820	rd = rdlist[0]
1821	G2frame.OnFileSave(event)
1822	# rd contains all info for a phase
1823	PhaseName = rd.Phase['General']['Name']
1824	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1825	atomData = data['Atoms']
1826	atomNames = []
1827	for atom in atomData:
1828	atomNames.append(atom[:ct+1])
1829	for atom in rd.Phase['Atoms']:
1830	try:
1831	idx = atomNames.index(atom[:ct+1])
1832	atomData[idx][:-1] = atom[:-1]
1833	except ValueError:
1834	print atom[:ct+1], 'not in Atom array; not updated'
1835	wx.CallAfter(FillAtomsGrid,Atoms)
1836
1837
1838	################################################################################
1839	#Structure drawing GUI stuff
1840	################################################################################
1841
1842	def SetupDrawingData():
1843	generalData = data['General']
1844	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1845	atomData = data['Atoms']
1846	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1847	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1848	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1849	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1850	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1851	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1852	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1853	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1854	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1855	'bondList':{},'viewDir':[1,0,0]}
1856	V0 = np.array([0,0,1])
1857	V = np.inner(Amat,V0)
1858	V /= np.sqrt(np.sum(V**2))
1859	A = np.arccos(np.sum(V*V0))
1860	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1861	try:
1862	drawingData = data['Drawing']
1863	except KeyError:
1864	data['Drawing'] = {}
1865	drawingData = data['Drawing']
1866	if not drawingData: #fill with defaults if empty
1867	drawingData.update(defaultDrawing)
1868	if 'Zstep' not in drawingData:
1869	drawingData['Zstep'] = 0.5
1870	if 'contourLevel' not in drawingData:
1871	drawingData['contourLevel'] = 1.
1872	if 'viewDir' not in drawingData:
1873	drawingData['viewDir'] = [0,0,1]
1874	if 'Quaternion' not in drawingData:
1875	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1876	if 'showRigidBodies' not in drawingData:
1877	drawingData['showRigidBodies'] = True
1878	cx,ct,cs,ci = [0,0,0,0]
1879	if generalData['Type'] == 'nuclear':
1880	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1881	elif generalData['Type'] == 'macromolecular':
1882	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1883	elif generalData['Type'] == 'magnetic':
1884	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1885	# elif generalData['Type'] == 'modulated':
1886	# ????? for future
1887	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1888	if not drawingData.get('Atoms'):
1889	for atom in atomData:
1890	DrawAtomAdd(drawingData,atom)
1891	data['Drawing'] = drawingData
1892
1893	def DrawAtomAdd(drawingData,atom):
1894	drawingData['Atoms'].append(MakeDrawAtom(atom))
1895
1896	def OnRestraint(event):
1897	indx = drawAtoms.GetSelectedRows()
1898	restData = G2frame.PatternTree.GetItemPyData(
1899	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1900	drawingData = data['Drawing']
1901	generalData = data['General']
1902	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1903	cx,ct,cs,ci = drawingData['atomPtrs']
1904	atomData = drawingData['Atoms']
1905	atNames = []
1906	atXYZ = []
1907	atSymOp = []
1908	atIndx = []
1909	for item in indx:
1910	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1911	atSymOp.append(atomData[item][cs-1])
1912	atIndx.append(atomData[item][ci])
1913	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1914	try:
1915	bondData = restData[PhaseName]['Bond']
1916	except KeyError:
1917	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1918	restData[PhaseName] = {}
1919	restData[PhaseName]['Bond'] = bondData
1920	dist = G2mth.getRestDist(atXYZ,Amat)
1921	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1922	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1923	try:
1924	angleData = restData[PhaseName]['Angle']
1925	except KeyError:
1926	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1927	restData[PhaseName] = {}
1928	restData[PhaseName]['Angle'] = angleData
1929	angle = G2mth.getRestAngle(atXYZ,Amat)
1930	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1931	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1932	try:
1933	planeData = restData[PhaseName]['Plane']
1934	except KeyError:
1935	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1936	restData[PhaseName] = {}
1937	restData[PhaseName]['Plane'] = planeData
1938	plane = G2mth.getRestPlane(atXYZ,Amat)
1939	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1940	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1941	try:
1942	chiralData = restData[PhaseName]['Chiral']
1943	except KeyError:
1944	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1945	restData[PhaseName] = {}
1946	restData[PhaseName]['Chiral'] = chiralData
1947	volume = G2mth.getRestChiral(atXYZ,Amat)
1948	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1949	else:
1950	print '**** ERROR wrong number of atoms selected for this restraint'
1951	return
1952	G2frame.PatternTree.SetItemPyData(
1953	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1954
1955	def OnDefineRB(event):
1956	indx = drawAtoms.GetSelectedRows()
1957	indx.sort()
1958	RBData = G2frame.PatternTree.GetItemPyData(
1959	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1960	drawingData = data['Drawing']
1961	generalData = data['General']
1962	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1963	cx,ct,cs,ci = drawingData['atomPtrs']
1964	atomData = drawingData['Atoms']
1965	rbXYZ = []
1966	rbType = []
1967	atNames = []
1968	AtInfo = RBData['Residue']['AtInfo']
1969	for i,item in enumerate(indx):
1970	rbtype = atomData[item][ct]
1971	atNames.append(rbtype+str(i))
1972	rbType.append(rbtype)
1973	if rbtype not in AtInfo:
1974	Info = G2elem.GetAtomInfo(rbtype)
1975	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1976	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1977	rbXYZ = np.array(rbXYZ)
1978	rbXYZ -= rbXYZ[0]
1979	rbId = ran.randint(0,sys.maxint)
1980	rbName = 'UNKRB'
1981	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1982	'Edit rigid body name',rbName ,style=wx.OK)
1983	if dlg.ShowModal() == wx.ID_OK:
1984	rbName = dlg.GetValue()
1985	dlg.Destroy()
1986	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1987	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1988	RBData['RBIds']['Residue'].append(rbId)
1989	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1990
1991	################################################################################
1992	##### Atom draw routines
1993	################################################################################
1994
1995	def UpdateDrawAtoms(atomStyle=''):
1996	def RefreshAtomGrid(event):
1997	def SetChoice(name,c,n=0):
1998	choice = []
1999	for r in range(len(atomData)):
2000	if n:
2001	srchStr = str(atomData[r][c][:n])
2002	else:
2003	srchStr = str(atomData[r][c])
2004	if srchStr not in choice:
2005	if n:
2006	choice.append(str(atomData[r][c][:n]))
2007	else:
2008	choice.append(str(atomData[r][c]))
2009	choice.sort()
2010
2011	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
2012	if dlg.ShowModal() == wx.ID_OK:
2013	sel = dlg.GetSelections()
2014	parms = []
2015	for x in sel:
2016	parms.append(choice[x])
2017	noSkip = False
2018	drawAtoms.ClearSelection()
2019	drawingData['selectedAtoms'] = []
2020	for row in range(len(atomData)):
2021	test = atomData[row][c]
2022	if n:
2023	test = test[:n]
2024	if test in parms:
2025	drawAtoms.SelectRow(row,True)
2026	drawingData['selectedAtoms'].append(row)
2027	G2plt.PlotStructure(G2frame,data)
2028	dlg.Destroy()
2029
2030	r,c = event.GetRow(),event.GetCol()
2031	if r < 0 and c < 0:
2032	for row in range(drawAtoms.GetNumberRows()):
2033	drawingData['selectedAtoms'].append(row)
2034	drawAtoms.SelectRow(row,True)
2035	elif r < 0: #dclick on col label
2036	sel = -1
2037	Parms = False
2038	noSkip = True
2039	if drawAtoms.GetColLabelValue(c) == 'Style':
2040	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2041	if dlg.ShowModal() == wx.ID_OK:
2042	sel = dlg.GetSelection()
2043	parms = styleChoice[sel]
2044	for r in range(len(atomData)):
2045	atomData[r][c] = parms
2046	drawAtoms.SetCellValue(r,c,parms)
2047	FindBondsDraw()
2048	G2plt.PlotStructure(G2frame,data)
2049	dlg.Destroy()
2050	elif drawAtoms.GetColLabelValue(c) == 'Label':
2051	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
2052	if dlg.ShowModal() == wx.ID_OK:
2053	sel = dlg.GetSelection()
2054	parms = labelChoice[sel]
2055	for r in range(len(atomData)):
2056	atomData[r][c] = parms
2057	drawAtoms.SetCellValue(r,c,parms)
2058	dlg.Destroy()
2059	elif drawAtoms.GetColLabelValue(c) == 'Color':
2060	dlg = wx.ColourDialog(G2frame)
2061	if dlg.ShowModal() == wx.ID_OK:
2062	color = dlg.GetColourData().GetColour()
2063	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2064	attr.SetReadOnly(True)
2065	attr.SetBackgroundColour(color)
2066	for r in range(len(atomData)):
2067	atomData[r][c] = color
2068	drawingData['Atoms'][r][c] = color
2069	drawAtoms.SetAttr(r,c,attr)
2070	UpdateDrawAtoms()
2071	dlg.Destroy()
2072	elif drawAtoms.GetColLabelValue(c) == 'Residue':
2073	SetChoice('Residue',c,3)
2074	elif drawAtoms.GetColLabelValue(c) == '1-letter':
2075	SetChoice('1-letter',c,1)
2076	elif drawAtoms.GetColLabelValue(c) == 'Chain':
2077	SetChoice('Chain',c)
2078	elif drawAtoms.GetColLabelValue(c) == 'Name':
2079	SetChoice('Name',c)
2080	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
2081	SetChoice('Name',c)
2082	elif drawAtoms.GetColLabelValue(c) == 'Type':
2083	SetChoice('Type',c)
2084	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
2085	drawAtoms.ClearSelection()
2086	else:
2087	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
2088	atomData[r][c] = drawAtoms.GetCellValue(r,c)
2089	FindBondsDraw()
2090	elif drawAtoms.GetColLabelValue(c) == 'Color':
2091	dlg = wx.ColourDialog(G2frame)
2092	if dlg.ShowModal() == wx.ID_OK:
2093	color = dlg.GetColourData().GetColour()
2094	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2095	attr.SetReadOnly(True)
2096	attr.SetBackgroundColour(color)
2097	atomData[r][c] = color
2098	drawingData['Atoms'][r][c] = color
2099	drawAtoms.SetAttr(i,cs+2,attr)
2100	dlg.Destroy()
2101	UpdateDrawAtoms()
2102	G2plt.PlotStructure(G2frame,data)
2103
2104	def RowSelect(event):
2105	r,c = event.GetRow(),event.GetCol()
2106	if r < 0 and c < 0:
2107	if drawAtoms.IsSelection():
2108	drawAtoms.ClearSelection()
2109	elif c < 0: #only row clicks
2110	if event.ControlDown():
2111	if r in drawAtoms.GetSelectedRows():
2112	drawAtoms.DeselectRow(r)
2113	else:
2114	drawAtoms.SelectRow(r,True)
2115	elif event.ShiftDown():
2116	indxs = drawAtoms.GetSelectedRows()
2117	drawAtoms.ClearSelection()
2118	ibeg = 0
2119	if indxs:
2120	ibeg = indxs[-1]
2121	for row in range(ibeg,r+1):
2122	drawAtoms.SelectRow(row,True)
2123	else:
2124	drawAtoms.ClearSelection()
2125	drawAtoms.SelectRow(r,True)
2126	drawingData['selectedAtoms'] = []
2127	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
2128	G2plt.PlotStructure(G2frame,data)
2129
2130	# UpdateDrawAtoms executable code starts here
2131	G2frame.dataFrame.SetStatusText('')
2132	generalData = data['General']
2133	SetupDrawingData()
2134	drawingData = data['Drawing']
2135	cx,ct,cs,ci = drawingData['atomPtrs']
2136	atomData = drawingData['Atoms']
2137	if atomStyle:
2138	for atom in atomData:
2139	atom[cs] = atomStyle
2140	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
2141	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
2142	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
2143	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2144	labelChoice = [' ','type','name','number']
2145	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
2146	if generalData['Type'] == 'macromolecular':
2147	colLabels = ['Residue','1-letter','Chain'] + colLabels
2148	Types = 3*[wg.GRID_VALUE_STRING,]+Types
2149	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
2150	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
2151	labelChoice = [' ','type','name','number','residue','1-letter','chain']
2152	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
2153	# elif generalData['Type'] == 'modulated':
2154	# Types += []
2155	# colLabels += []
2156	table = []
2157	rowLabels = []
2158	for i,atom in enumerate(drawingData['Atoms']):
2159	table.append(atom[:colLabels.index('I/A')+1])
2160	rowLabels.append(str(i))
2161
2162	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
2163	drawAtoms.SetTable(atomTable, True)
2164	drawAtoms.SetMargins(0,0)
2165	drawAtoms.AutoSizeColumns(True)
2166	drawAtoms.SetColSize(colLabels.index('Style'),80)
2167	drawAtoms.SetColSize(colLabels.index('Color'),50)
2168	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
2169	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
2170	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
2171	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
2172	for i,atom in enumerate(drawingData['Atoms']):
2173	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2174	attr.SetReadOnly(True)
2175	attr.SetBackgroundColour(atom[cs+2])
2176	drawAtoms.SetAttr(i,cs+2,attr)
2177	drawAtoms.SetCellValue(i,cs+2,'')
2178	indx = drawingData['selectedAtoms']
2179	if indx:
2180	for r in range(len(atomData)):
2181	if r in indx:
2182	drawAtoms.SelectRow(r)
2183	for c in range(len(colLabels)):
2184	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2185	attr.SetReadOnly(True)
2186	attr.SetBackgroundColour(VERY_LIGHT_GREY)
2187	if colLabels[c] not in ['Style','Label','Color']:
2188	drawAtoms.SetColAttr(c,attr)
2189	G2frame.dataFrame.setSizePosLeft([600,300])
2190
2191	FindBondsDraw()
2192	drawAtoms.ClearSelection()
2193	# G2plt.PlotStructure(G2frame,data)
2194
2195	def DrawAtomStyle(event):
2196	indx = drawAtoms.GetSelectedRows()
2197	if indx:
2198	generalData = data['General']
2199	atomData = data['Drawing']['Atoms']
2200	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2201	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2202	if generalData['Type'] == 'macromolecular':
2203	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
2204	'backbone','ribbons','schematic']
2205	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2206	if dlg.ShowModal() == wx.ID_OK:
2207	sel = dlg.GetSelection()
2208	parms = styleChoice[sel]
2209	for r in indx:
2210	atomData[r][cs] = parms
2211	drawAtoms.SetCellValue(r,cs,parms)
2212	dlg.Destroy()
2213	FindBondsDraw()
2214	drawAtoms.ClearSelection()
2215	G2plt.PlotStructure(G2frame,data)
2216
2217	def DrawAtomLabel(event):
2218	indx = drawAtoms.GetSelectedRows()
2219	if indx:
2220	generalData = data['General']
2221	atomData = data['Drawing']['Atoms']
2222	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2223	styleChoice = [' ','type','name','number']
2224	if generalData['Type'] == 'macromolecular':
2225	styleChoice = [' ','type','name','number','residue','1-letter','chain']
2226	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
2227	if dlg.ShowModal() == wx.ID_OK:
2228	sel = dlg.GetSelection()
2229	parms = styleChoice[sel]
2230	for r in indx:
2231	atomData[r][cs+1] = parms
2232	drawAtoms.SetCellValue(r,cs+1,parms)
2233	dlg.Destroy()
2234	drawAtoms.ClearSelection()
2235	G2plt.PlotStructure(G2frame,data)
2236
2237	def DrawAtomColor(event):
2238
2239	indx = drawAtoms.GetSelectedRows()
2240	if indx:
2241	if len(indx) > 1:
2242	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2243	else:
2244	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2245	generalData = data['General']
2246	atomData = data['Drawing']['Atoms']
2247	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2248	atmColors = []
2249	atmTypes = []
2250	for r in indx:
2251	if atomData[r][cs+2] not in atmColors:
2252	atmColors.append(atomData[r][cs+2])
2253	atmTypes.append(atomData[r][ct])
2254	if len(atmColors) > 16:
2255	break
2256	colors = wx.ColourData()
2257	colors.SetChooseFull(True)
2258	dlg = wx.ColourDialog(G2frame)
2259	if dlg.ShowModal() == wx.ID_OK:
2260	for i in range(len(atmColors)):
2261	atmColors[i] = dlg.GetColourData().GetColour()
2262	colorDict = dict(zip(atmTypes,atmColors))
2263	for r in indx:
2264	color = colorDict[atomData[r][ct]]
2265	atomData[r][cs+2] = color
2266	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2267	attr.SetBackgroundColour(color)
2268	drawAtoms.SetAttr(r,cs+2,attr)
2269	data['Drawing']['Atoms'][r][cs+2] = color
2270	drawAtoms.ClearSelection()
2271	dlg.Destroy()
2272	G2frame.dataFrame.SetStatusText('')
2273	G2plt.PlotStructure(G2frame,data)
2274
2275	def ResetAtomColors(event):
2276	generalData = data['General']
2277	atomData = data['Drawing']['Atoms']
2278	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2279	for atom in atomData:
2280	atNum = generalData['AtomTypes'].index(atom[ct])
2281	atom[cs+2] = list(generalData['Color'][atNum])
2282	UpdateDrawAtoms()
2283	drawAtoms.ClearSelection()
2284	G2plt.PlotStructure(G2frame,data)
2285
2286	def SetViewPoint(event):
2287	indx = drawAtoms.GetSelectedRows()
2288	if indx:
2289	atomData = data['Drawing']['Atoms']
2290	cx = data['Drawing']['atomPtrs'][0]
2291	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2292	drawAtoms.ClearSelection() #do I really want to do this?
2293	G2plt.PlotStructure(G2frame,data)
2294
2295	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2296	cx = data['Drawing']['atomPtrs'][0]
2297	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2298	return False
2299	else:
2300	return True
2301
2302	def AddSymEquiv(event):
2303	indx = drawAtoms.GetSelectedRows()
2304	indx.sort()
2305	if indx:
2306	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2307	cx = colLabels.index('x')
2308	cuia = colLabels.index('I/A')
2309	cuij = cuia+2
2310	atomData = data['Drawing']['Atoms']
2311	generalData = data['General']
2312	SGData = generalData['SGData']
2313	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2314	try:
2315	if dlg.ShowModal() == wx.ID_OK:
2316	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2317	Cell = np.array(Cell)
2318	cent = SGData['SGCen'][Cent]
2319	M,T = SGData['SGOps'][Opr]
2320	for ind in indx:
2321	XYZ = np.array(atomData[ind][cx:cx+3])
2322	XYZ = np.inner(M,XYZ)+T
2323	if Inv:
2324	XYZ = -XYZ
2325	XYZ = XYZ+cent+Cell
2326	if Force:
2327	XYZ = G2spc.MoveToUnitCell(XYZ)
2328	if noDuplicate(XYZ,atomData):
2329	atom = copy.copy(atomData[ind])
2330	atom[cx:cx+3] = XYZ
2331	atomOp = atom[cx+3]
2332	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2333	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2334	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2335	if atom[cuia] == 'A':
2336	Uij = atom[cuij:cuij+6]
2337	U = G2spc.Uij2U(Uij)
2338	U = np.inner(np.inner(M,U),M)
2339	Uij = G2spc.U2Uij(U)
2340	atom[cuij:cuij+6] = Uij
2341	atomData.append(atom)
2342	finally:
2343	dlg.Destroy()
2344	UpdateDrawAtoms()
2345	drawAtoms.ClearSelection()
2346	G2plt.PlotStructure(G2frame,data)
2347
2348	def TransformSymEquiv(event):
2349	indx = drawAtoms.GetSelectedRows()
2350	indx.sort()
2351	if indx:
2352	atomData = data['Drawing']['Atoms']
2353	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2354	cx = colLabels.index('x')
2355	cuia = colLabels.index('I/A')
2356	cuij = cuia+2
2357	atomData = data['Drawing']['Atoms']
2358	generalData = data['General']
2359	SGData = generalData['SGData']
2360	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2361	try:
2362	if dlg.ShowModal() == wx.ID_OK:
2363	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2364	Cell = np.array(Cell)
2365	cent = SGData['SGCen'][Cent]
2366	M,T = SGData['SGOps'][Opr]
2367	for ind in indx:
2368	XYZ = np.array(atomData[ind][cx:cx+3])
2369	XYZ = np.inner(M,XYZ)+T
2370	if Inv:
2371	XYZ = -XYZ
2372	XYZ = XYZ+cent+Cell
2373	if Force:
2374	XYZ = G2spc.MoveToUnitCell(XYZ)
2375	atom = atomData[ind]
2376	atom[cx:cx+3] = XYZ
2377	atomOp = atom[cx+3]
2378	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2379	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2380	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2381	if atom[cuia] == 'A':
2382	Uij = atom[cuij:cuij+6]
2383	U = G2spc.Uij2U(Uij)
2384	U = np.inner(np.inner(M,U),M)
2385	Uij = G2spc.U2Uij(U)
2386	atom[cuij:cuij+6] = Uij
2387	data['Drawing']['Atoms'] = atomData
2388	finally:
2389	dlg.Destroy()
2390	UpdateDrawAtoms()
2391	drawAtoms.ClearSelection()
2392	G2plt.PlotStructure(G2frame,data)
2393
2394	def FillCoordSphere(event):
2395	generalData = data['General']
2396	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2397	radii = generalData['BondRadii']
2398	atomTypes = generalData['AtomTypes']
2399	try:
2400	indH = atomTypes.index('H')
2401	radii[indH] = 0.5
2402	except:
2403	pass
2404	indx = drawAtoms.GetSelectedRows()
2405	if indx:
2406	indx.sort()
2407	atomData = data['Drawing']['Atoms']
2408	numAtoms = len(atomData)
2409	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2410	generalData = data['General']
2411	SGData = generalData['SGData']
2412	cellArray = G2lat.CellBlock(1)
2413	wx.BeginBusyCursor()
2414	try:
2415	for ind in indx:
2416	atomA = atomData[ind]
2417	xyzA = np.array(atomA[cx:cx+3])
2418	indA = atomTypes.index(atomA[ct])
2419	for atomB in atomData[:numAtoms]:
2420	indB = atomTypes.index(atomB[ct])
2421	sumR = radii[indA]+radii[indB]
2422	xyzB = np.array(atomB[cx:cx+3])
2423	for xyz in cellArray+xyzB:
2424	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2425	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2426	if noDuplicate(xyz,atomData):
2427	oprB = atomB[cx+3]
2428	C = xyz-xyzB
2429	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2430	newAtom = atomB[:]
2431	newAtom[cx:cx+3] = xyz
2432	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2433	atomData.append(newAtom)
2434	finally:
2435	wx.EndBusyCursor()
2436	data['Drawing']['Atoms'] = atomData
2437	UpdateDrawAtoms()
2438	drawAtoms.ClearSelection()
2439	G2plt.PlotStructure(G2frame,data)
2440
2441	def FillUnitCell(event):
2442	indx = drawAtoms.GetSelectedRows()
2443	indx.sort()
2444	if indx:
2445	atomData = data['Drawing']['Atoms']
2446	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2447	cx = colLabels.index('x')
2448	cuia = colLabels.index('I/A')
2449	cuij = cuia+2
2450	generalData = data['General']
2451	SGData = generalData['SGData']
2452	wx.BeginBusyCursor()
2453	try:
2454	for ind in indx:
2455	atom = atomData[ind]
2456	XYZ = np.array(atom[cx:cx+3])
2457	if atom[cuia] == 'A':
2458	Uij = atom[cuij:cuij+6]
2459	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2460	for item in result:
2461	atom = copy.copy(atomData[ind])
2462	atom[cx:cx+3] = item[0]
2463	atom[cx+3] = str(item[2])+'+' \
2464	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2465	atom[cuij:cuij+6] = item[1]
2466	Opp = G2spc.Opposite(item[0])
2467	for xyz in Opp:
2468	if noDuplicate(xyz,atomData):
2469	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2470	cell = '1'+'+'+ \
2471	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2472	atom[cx:cx+3] = xyz
2473	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2474	atomData.append(atom[:])
2475	else:
2476	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2477	for item in result:
2478	atom = copy.copy(atomData[ind])
2479	atom[cx:cx+3] = item[0]
2480	atom[cx+3] = str(item[1])+'+' \
2481	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2482	Opp = G2spc.Opposite(item[0])
2483	for xyz in Opp:
2484	if noDuplicate(xyz,atomData):
2485	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2486	cell = '1'+'+'+ \
2487	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2488	atom[cx:cx+3] = xyz
2489	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2490	atomData.append(atom[:])
2491	data['Drawing']['Atoms'] = atomData
2492	finally:
2493	wx.EndBusyCursor()
2494	UpdateDrawAtoms()
2495	drawAtoms.ClearSelection()
2496	G2plt.PlotStructure(G2frame,data)
2497
2498	def FindBondsToo(): #works but slow for large structures - keep as reference
2499	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2500	atomData = data['Drawing']['Atoms']
2501	generalData = data['General']
2502	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2503	radii = generalData['BondRadii']
2504	atomTypes = generalData['AtomTypes']
2505	try:
2506	indH = atomTypes.index('H')
2507	radii[indH] = 0.5
2508	except:
2509	pass
2510	for atom in atomData:
2511	atom[-1] = []
2512	Atoms = []
2513	for i,atom in enumerate(atomData):
2514	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2515	for atomA in Atoms:
2516	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2517	for atomB in Atoms:
2518	Dx = atomB[1]-atomA[1]
2519	DX = np.inner(Amat,Dx)
2520	dist = np.sqrt(np.sum(DX**2))
2521	sumR = atomA[3]+atomB[3]
2522	if 0.5 < dist <= 0.85*sumR:
2523	i = atomA[0]
2524	if atomA[2] == 'polyhedra':
2525	atomData[i][-1].append(DX)
2526	elif atomB[1] != 'polyhedra':
2527	j = atomB[0]
2528	atomData[i][-1].append(Dx*atomA[3]/sumR)
2529	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2530
2531	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2532	import numpy.ma as ma
2533	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2534	hydro = data['Drawing']['showHydrogen']
2535	atomData = data['Drawing']['Atoms']
2536	generalData = data['General']
2537	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2538	radii = generalData['BondRadii']
2539	atomTypes = generalData['AtomTypes']
2540	try:
2541	indH = atomTypes.index('H')
2542	radii[indH] = 0.5
2543	except:
2544	pass
2545	for atom in atomData:
2546	atom[-2] = [] #clear out old bonds/polyhedra
2547	atom[-1] = []
2548	Indx = range(len(atomData))
2549	Atoms = []
2550	Styles = []
2551	Radii = []
2552	for atom in atomData:
2553	Atoms.append(np.array(atom[cx:cx+3]))
2554	Styles.append(atom[cs])
2555	try:
2556	if not hydro and atom[ct] == 'H':
2557	Radii.append(0.0)
2558	else:
2559	Radii.append(radii[atomTypes.index(atom[ct])])
2560	except ValueError: #changed atom type!
2561	Radii.append(0.20)
2562	Atoms = np.array(Atoms)
2563	Radii = np.array(Radii)
2564	IASR = zip(Indx,Atoms,Styles,Radii)
2565	for atomA in IASR:
2566	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2567	Dx = Atoms-atomA[1]
2568	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
2569	sumR = atomA[3]+Radii
2570	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2571	i = atomA[0]
2572	for j in IndB[0]:
2573	if Styles[i] == 'polyhedra':
2574	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2575	elif Styles[j] != 'polyhedra' and j > i:
2576	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2577	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2578	if Styles[i] == 'polyhedra':
2579	Bonds = atomData[i][-2]
2580	Faces = []
2581	if len(Bonds) > 2:
2582	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2583	for face in FaceGen:
2584	vol = nl.det(face)
2585	if abs(vol) > 1. or len(Bonds) == 3:
2586	if vol < 0.:
2587	face = [face[0],face[2],face[1]]
2588	face = np.array(face)
2589	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2590	norm = np.cross(face[1]-face[0],face[2]-face[0])
2591	norm /= np.sqrt(np.sum(norm**2))
2592	Faces.append([face,norm])
2593	atomData[i][-1] = Faces
2594
2595	def DrawAtomsDelete(event):
2596	indx = drawAtoms.GetSelectedRows()
2597	indx.sort()
2598	if indx:
2599	atomData = data['Drawing']['Atoms']
2600	indx.reverse()
2601	for ind in indx:
2602	del atomData[ind]
2603	UpdateDrawAtoms()
2604	drawAtoms.ClearSelection()
2605	G2plt.PlotStructure(G2frame,data)
2606	event.StopPropagation()
2607
2608	def OnReloadDrawAtoms(event):
2609	data['Drawing']['Atoms'] = []
2610	UpdateDrawAtoms()
2611	drawAtoms.ClearSelection()
2612	G2plt.PlotStructure(G2frame,data)
2613	event.StopPropagation()
2614
2615	def DrawAtomsDeleteByIDs(IDs):
2616	atomData = data['Drawing']['Atoms']
2617	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2618	indx.reverse()
2619	for ind in indx:
2620	del atomData[ind]
2621
2622	def ChangeDrawAtomsByIDs(colName,IDs,value):
2623	atomData = data['Drawing']['Atoms']
2624	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2625	if colName == 'Name':
2626	col = ct-1
2627	elif colName == 'Type':
2628	col = ct
2629	elif colName == 'I/A':
2630	col = cs
2631	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2632	for ind in indx:
2633	atomData[ind][col] = value
2634
2635	def OnDrawPlane(event):
2636	indx = drawAtoms.GetSelectedRows()
2637	if len(indx) < 4:
2638	print '**** ERROR - need 4+ atoms for plane calculation'
2639	return
2640	PlaneData = {}
2641	drawingData = data['Drawing']
2642	atomData = drawingData['Atoms']
2643	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2644	cx = colLabels.index('x')
2645	cn = colLabels.index('Name')
2646	xyz = []
2647	for i,atom in enumerate(atomData):
2648	if i in indx:
2649	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2650	generalData = data['General']
2651	PlaneData['Name'] = generalData['Name']
2652	PlaneData['Atoms'] = xyz
2653	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2654	G2stMn.BestPlane(PlaneData)
2655
2656	def OnDrawDistVP(event):
2657	# distance to view point
2658	indx = drawAtoms.GetSelectedRows()
2659	if not indx:
2660	print '***** ERROR - no atoms selected'
2661	return
2662	generalData = data['General']
2663	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2664	drawingData = data['Drawing']
2665	viewPt = np.array(drawingData['viewPoint'][0])
2666	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2667	atomDData = drawingData['Atoms']
2668	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2669	cx = colLabels.index('x')
2670	cn = colLabels.index('Name')
2671	for i in indx:
2672	atom = atomDData[i]
2673	Dx = np.array(atom[cx:cx+3])-viewPt
2674	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2675	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2676
2677	def OnDrawDAT(event):
2678	#distance, angle, torsion
2679	indx = drawAtoms.GetSelectedRows()
2680	if len(indx) not in [2,3,4]:
2681	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2682	return
2683	DATData = {}
2684	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2685	drawingData = data['Drawing']
2686	atomData = data['Atoms']
2687	atomDData = drawingData['Atoms']
2688	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2689	cx = colLabels.index('x')
2690	cn = colLabels.index('Name')
2691	cid = colLabels.index('I/A')+8
2692	xyz = []
2693	Oxyz = []
2694	DATData['Natoms'] = len(indx)
2695	for i in indx:
2696	atom = atomDData[i]
2697	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2698	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2699	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2700	DATData['Datoms'] = xyz
2701	DATData['Oatoms'] = Oxyz
2702	generalData = data['General']
2703	DATData['Name'] = generalData['Name']
2704	DATData['SGData'] = generalData['SGData']
2705	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2706	if 'pId' in data:
2707	DATData['pId'] = data['pId']
2708	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2709	G2stMn.DisAglTor(DATData)
2710
2711	################################################################################
2712	#### Draw Options page
2713	################################################################################
2714
2715	def UpdateDrawOptions():
2716	import copy
2717	import wx.lib.colourselect as wcs
2718	def SlopSizer():
2719	def OnCameraPos(event):
2720	drawingData['cameraPos'] = cameraPos.GetValue()
2721	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2722	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2723	G2plt.PlotStructure(G2frame,data)
2724
2725	def OnZclip(event):
2726	drawingData['Zclip'] = Zclip.GetValue()
2727	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2728	G2plt.PlotStructure(G2frame,data)
2729
2730	def OnZstep(event):
2731	try:
2732	step = float(Zstep.GetValue())
2733	if not (0.01 <= step <= 1.0):
2734	raise ValueError
2735	except ValueError:
2736	step = drawingData['Zstep']
2737	drawingData['Zstep'] = step
2738	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2739
2740	def OnMoveZ(event):
2741	move = MoveZ.GetValue()*drawingData['Zstep']
2742	MoveZ.SetValue(0)
2743	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2744	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2745	VD /= np.sqrt(np.sum(VD**2))
2746	VP += move*VD
2747	VP = np.inner(Bmat,VP)
2748	drawingData['viewPoint'][0] = VP
2749	panel = drawOptions.GetChildren()
2750	names = [child.GetName() for child in panel]
2751	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2752	G2plt.PlotStructure(G2frame,data)
2753
2754	def OnVdWScale(event):
2755	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2756	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2757	G2plt.PlotStructure(G2frame,data)
2758
2759	def OnEllipseProb(event):
2760	drawingData['ellipseProb'] = ellipseProb.GetValue()
2761	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2762	G2plt.PlotStructure(G2frame,data)
2763
2764	def OnBallScale(event):
2765	drawingData['ballScale'] = ballScale.GetValue()/100.
2766	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2767	G2plt.PlotStructure(G2frame,data)
2768
2769	def OnBondRadius(event):
2770	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2771	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2772	G2plt.PlotStructure(G2frame,data)
2773
2774	def OnContourLevel(event):
2775	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2776	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2777	G2plt.PlotStructure(G2frame,data)
2778
2779	def OnMapSize(event):
2780	drawingData['mapSize'] = mapSize.GetValue()/10.
2781	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2782	G2plt.PlotStructure(G2frame,data)
2783
2784
2785	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2786	slideSizer = wx.FlexGridSizer(7,2)
2787	slideSizer.AddGrowableCol(1,1)
2788
2789	cameraPosTxt = wx.StaticText(drawOptions,-1,
2790	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2791	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2792	slideSizer.Add(cameraPosTxt,0,WACV)
2793	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2794	cameraPos.SetRange(10,500)
2795	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2796	G2frame.dataDisplay.cameraSlider = cameraPos
2797	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2798
2799	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2800	slideSizer.Add(ZclipTxt,0,WACV)
2801	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2802	Zclip.SetRange(1,99)
2803	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2804	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2805
2806	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2807	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,WACV)
2808	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2809	style=wx.TE_PROCESS_ENTER)
2810	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2811	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2812	ZstepSizer.Add(Zstep,0,WACV)
2813	slideSizer.Add(ZstepSizer)
2814	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2815	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,WACV)
2816	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2817	MoveZ.SetValue(0)
2818	MoveZ.SetRange(-1,1)
2819	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2820	MoveSizer.Add(MoveZ)
2821	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2822
2823	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2824	slideSizer.Add(vdwScaleTxt,0,WACV)
2825	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2826	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2827	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2828
2829	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2830	slideSizer.Add(ellipseProbTxt,0,WACV)
2831	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2832	ellipseProb.SetRange(1,99)
2833	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2834	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2835
2836	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2837	slideSizer.Add(ballScaleTxt,0,WACV)
2838	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2839	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2840	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2841
2842	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2843	slideSizer.Add(bondRadiusTxt,0,WACV)
2844	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2845	bondRadius.SetRange(1,25)
2846	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2847	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2848
2849	if generalData['Map']['rhoMax']:
2850	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2851	slideSizer.Add(contourLevelTxt,0,WACV)
2852	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2853	contourLevel.SetRange(1,100)
2854	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2855	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2856	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2857	slideSizer.Add(mapSizeTxt,0,WACV)
2858	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2859	mapSize.SetRange(1,100)
2860	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2861	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2862
2863	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2864	slopSizer.Add((10,5),0)
2865	slopSizer.SetMinSize(wx.Size(350,10))
2866	return slopSizer
2867
2868	def ShowSizer():
2869
2870	def OnBackColor(event):
2871	drawingData['backColor'] = event.GetValue()
2872	G2plt.PlotStructure(G2frame,data)
2873
2874	def OnShowABC(event):
2875	drawingData['showABC'] = showABC.GetValue()
2876	G2plt.PlotStructure(G2frame,data)
2877
2878	def OnShowUnitCell(event):
2879	drawingData['unitCellBox'] = unitCellBox.GetValue()
2880	G2plt.PlotStructure(G2frame,data)
2881
2882	def OnShowHyd(event):
2883	drawingData['showHydrogen'] = showHydrogen.GetValue()
2884	FindBondsDraw()
2885	G2plt.PlotStructure(G2frame,data)
2886
2887	def OnShowRB(event):
2888	drawingData['showRigidBodies'] = showRB.GetValue()
2889	FindBondsDraw()
2890	G2plt.PlotStructure(G2frame,data)
2891
2892	def OnViewPoint(event):
2893	Obj = event.GetEventObject()
2894	viewPt = Obj.GetValue().split()
2895	try:
2896	VP = [float(viewPt[i]) for i in range(3)]
2897	except (ValueError,IndexError):
2898	VP = drawingData['viewPoint'][0]
2899	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2900	drawingData['viewPoint'][0] = VP
2901	G2plt.PlotStructure(G2frame,data)
2902
2903	def OnViewDir(event):
2904	Obj = event.GetEventObject()
2905	viewDir = Obj.GetValue().split()
2906	try:
2907	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2908	VD = np.array([float(viewDir[i]) for i in range(3)])
2909	VC = np.inner(Amat,VD)
2910	VC /= np.sqrt(np.sum(VC**2))
2911	V = np.array(drawingData['viewDir'])
2912	VB = np.inner(Amat,V)
2913	VB /= np.sqrt(np.sum(VB**2))
2914	VX = np.cross(VC,VB)
2915	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2916	QV = G2mth.AVdeg2Q(A,VX)
2917	Q = drawingData['Quaternion']
2918	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2919	except (ValueError,IndexError):
2920	VD = drawingData['viewDir']
2921	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2922	drawingData['viewDir'] = VD
2923	G2plt.PlotStructure(G2frame,data)
2924
2925	showSizer = wx.BoxSizer(wx.VERTICAL)
2926	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2927	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,WACV)
2928	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2929	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2930	lineSizer.Add(backColor,0,WACV)
2931	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,WACV)
2932	VD = drawingData['viewDir']
2933	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2934	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2935	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2936	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2937	G2frame.dataDisplay.viewDir = viewDir
2938	lineSizer.Add(viewDir,0,WACV)
2939	showSizer.Add(lineSizer)
2940	showSizer.Add((0,5),0)
2941
2942	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2943	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2944	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2945	showABC.SetValue(drawingData['showABC'])
2946	lineSizer.Add(showABC,0,WACV)
2947	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,WACV)
2948	VP = drawingData['viewPoint'][0]
2949	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2950	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2951	G2frame.dataDisplay.viewPoint = viewPoint
2952	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2953	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2954	lineSizer.Add(viewPoint,0,WACV)
2955	showSizer.Add(lineSizer)
2956	showSizer.Add((0,5),0)
2957
2958	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2959
2960	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2961	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2962	unitCellBox.SetValue(drawingData['unitCellBox'])
2963	line2Sizer.Add(unitCellBox,0,WACV)
2964
2965	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2966	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2967	showHydrogen.SetValue(drawingData['showHydrogen'])
2968	line2Sizer.Add(showHydrogen,0,WACV)
2969
2970	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2971	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2972	showRB.SetValue(drawingData['showRigidBodies'])
2973	line2Sizer.Add(showRB,0,WACV)
2974
2975	showSizer.Add(line2Sizer)
2976	return showSizer
2977
2978	def RadSizer():
2979
2980	def OnSizeHatoms(event):
2981	try:
2982	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2983	except ValueError:
2984	value = 0.5
2985	drawingData['sizeH'] = value
2986	sizeH.SetValue("%.2f"%(value))
2987	G2plt.PlotStructure(G2frame,data)
2988
2989	def OnRadFactor(event):
2990	try:
2991	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2992	except ValueError:
2993	value = 0.85
2994	drawingData['radiusFactor'] = value
2995	radFactor.SetValue("%.2f"%(value))
2996	FindBondsDraw()
2997	G2plt.PlotStructure(G2frame,data)
2998
2999	radSizer = wx.BoxSizer(wx.HORIZONTAL)
3000	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,WACV)
3001	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
3002	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
3003	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
3004	radSizer.Add(sizeH,0,WACV)
3005
3006	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,WACV)
3007	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
3008	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
3009	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
3010	radSizer.Add(radFactor,0,WACV)
3011	return radSizer
3012
3013	# UpdateDrawOptions exectable code starts here
3014	generalData = data['General']
3015	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
3016	SetupDrawingData()
3017	drawingData = data['Drawing']
3018	if generalData['Type'] == 'nuclear':
3019	pickChoice = ['Atoms','Bonds','Torsions','Planes']
3020	elif generalData['Type'] == 'macromolecular':
3021	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
3022
3023	G2frame.dataFrame.SetStatusText('')
3024	if drawOptions.GetSizer():
3025	drawOptions.GetSizer().Clear(True)
3026	mainSizer = wx.BoxSizer(wx.VERTICAL)
3027	mainSizer.Add((5,5),0)
3028	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,WACV)
3029	mainSizer.Add((5,5),0)
3030	mainSizer.Add(SlopSizer(),0)
3031	mainSizer.Add((5,5),0)
3032	mainSizer.Add(ShowSizer(),0,)
3033	mainSizer.Add((5,5),0)
3034	mainSizer.Add(RadSizer(),0,)
3035	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
3036
3037	################################################################################
3038	#### Texture routines
3039	################################################################################
3040
3041	def UpdateTexture():
3042	def SetSHCoef():
3043	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
3044	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
3045	SHCoeff = textureData['SH Coeff'][1]
3046	for cofName in SHCoeff:
3047	if cofName in cofNames:
3048	newSHCoef[cofName] = SHCoeff[cofName]
3049	return newSHCoef
3050
3051	def OnShOrder(event):
3052	Obj = event.GetEventObject()
3053	textureData['Order'] = int(Obj.GetValue())
3054	textureData['SH Coeff'][1] = SetSHCoef()
3055	wx.CallAfter(UpdateTexture)
3056	G2plt.PlotTexture(G2frame,data)
3057
3058	def OnShModel(event):
3059	Obj = event.GetEventObject()
3060	textureData['Model'] = Obj.GetValue()
3061	textureData['SH Coeff'][1] = SetSHCoef()
3062	wx.CallAfter(UpdateTexture)
3063	G2plt.PlotTexture(G2frame,data)
3064
3065	def OnSHRefine(event):
3066	Obj = event.GetEventObject()
3067	textureData['SH Coeff'][0] = Obj.GetValue()
3068
3069	def OnSHShow(event):
3070	Obj = event.GetEventObject()
3071	textureData['SHShow'] = Obj.GetValue()
3072	wx.CallAfter(UpdateTexture)
3073
3074	def OnProjSel(event):
3075	Obj = event.GetEventObject()
3076	G2frame.Projection = Obj.GetValue()
3077	G2plt.PlotTexture(G2frame,data)
3078
3079	def OnColorSel(event):
3080	Obj = event.GetEventObject()
3081	G2frame.ContourColor = Obj.GetValue()
3082	G2plt.PlotTexture(G2frame,data)
3083
3084	def OnAngRef(event):
3085	Obj = event.GetEventObject()
3086	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
3087
3088	def OnAngValue(event):
3089	Obj = event.GetEventObject()
3090	try:
3091	value = float(Obj.GetValue())
3092	except ValueError:
3093	value = textureData[valIndx[Obj.GetId()]][1]
3094	Obj.SetValue('%8.2f'%(value))
3095	textureData[valIndx[Obj.GetId()]][1] = value
3096
3097	def OnODFValue(event):
3098	Obj = event.GetEventObject()
3099	try:
3100	value = float(Obj.GetValue())
3101	except ValueError:
3102	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
3103	Obj.SetValue('%8.3f'%(value))
3104	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
3105	G2plt.PlotTexture(G2frame,data)
3106
3107	def OnPfType(event):
3108	Obj = event.GetEventObject()
3109	textureData['PlotType'] = Obj.GetValue()
3110	wx.CallAfter(UpdateTexture)
3111	G2plt.PlotTexture(G2frame,data)
3112
3113	def OnPFValue(event):
3114	Obj = event.GetEventObject()
3115	Saxis = Obj.GetValue().split()
3116	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3117	try:
3118	hkl = [int(Saxis[i]) for i in range(3)]
3119	except (ValueError,IndexError):
3120	hkl = textureData['PFhkl']
3121	if not np.any(np.array(hkl)): #can't be all zeros!
3122	hkl = textureData['PFhkl']
3123	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
3124	textureData['PFhkl'] = hkl
3125	else:
3126	try:
3127	xyz = [float(Saxis[i]) for i in range(3)]
3128	except (ValueError,IndexError):
3129	xyz = textureData['PFxyz']
3130	if not np.any(np.array(xyz)): #can't be all zeros!
3131	xyz = textureData['PFxyz']
3132	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
3133	textureData['PFxyz'] = xyz
3134	G2plt.PlotTexture(G2frame,data)
3135
3136	# UpdateTexture executable starts here
3137	G2frame.dataFrame.SetStatusText('')
3138	generalData = data['General']
3139	SGData = generalData['SGData']
3140	try:
3141	textureData = generalData['SH Texture']
3142	except KeyError: #fix old files!
3143	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
3144	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
3145	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
3146	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
3147	if 'SHShow' not in textureData: #another fix
3148	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
3149	try: #another fix!
3150	x = textureData['PlotType']
3151	except KeyError:
3152	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
3153	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
3154	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
3155	if generalData['doPawley'] and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Sequential results'):
3156	G2frame.dataFrame.RefineTexture.Enable(True)
3157	shAngles = ['omega','chi','phi']
3158	if Texture.GetSizer():
3159	Texture.GetSizer().Clear(True)
3160	mainSizer = wx.BoxSizer(wx.VERTICAL)
3161	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
3162	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,WACV)
3163	titleSizer.Add(wx.StaticText(Texture,-1,
3164	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
3165	0,WACV)
3166	mainSizer.Add(titleSizer,0)
3167	mainSizer.Add((0,5),0)
3168	shSizer = wx.FlexGridSizer(1,6,5,5)
3169	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,WACV)
3170	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
3171	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3172	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
3173	shSizer.Add(shModel,0,WACV)
3174	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,WACV)
3175	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
3176	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3177	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
3178	shSizer.Add(shOrder,0,WACV)
3179	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
3180	shRef.SetValue(textureData['SH Coeff'][0])
3181	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
3182	shSizer.Add(shRef,0,WACV)
3183	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
3184	shShow.SetValue(textureData['SHShow'])
3185	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
3186	shSizer.Add(shShow,0,WACV)
3187	mainSizer.Add(shSizer,0,0)
3188	mainSizer.Add((0,5),0)
3189	PTSizer = wx.FlexGridSizer(2,4,5,5)
3190	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,WACV)
3191	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
3192	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
3193	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3194	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
3195	PTSizer.Add(pfType,0,WACV)
3196	if 'Axial' not in textureData['PlotType']:
3197	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,WACV)
3198	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
3199	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3200	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
3201	PTSizer.Add(projSel,0,WACV)
3202	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3203	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,WACV)
3204	PH = textureData['PFhkl']
3205	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
3206	else:
3207	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,WACV)
3208	PX = textureData['PFxyz']
3209	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
3210	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
3211	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
3212	PTSizer.Add(pfVal,0,WACV)
3213	if 'Axial' not in textureData['PlotType']:
3214	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,WACV)
3215	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3216	choice.sort()
3217	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
3218	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3219	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
3220	PTSizer.Add(colorSel,0,WACV)
3221	mainSizer.Add(PTSizer,0,WACV)
3222	mainSizer.Add((0,5),0)
3223	if textureData['SHShow']:
3224	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,WACV)
3225	mainSizer.Add((0,5),0)
3226	ODFSizer = wx.FlexGridSizer(2,8,2,2)
3227	ODFIndx = {}
3228	ODFkeys = textureData['SH Coeff'][1].keys()
3229	ODFkeys.sort()
3230	for item in ODFkeys:
3231	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,WACV)
3232	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3233	ODFIndx[ODFval.GetId()] = item
3234	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3235	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3236	ODFSizer.Add(ODFval,0,WACV)
3237	mainSizer.Add(ODFSizer,0,WACV)
3238	mainSizer.Add((0,5),0)
3239	mainSizer.Add((0,5),0)
3240	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,WACV)
3241	mainSizer.Add((0,5),0)
3242	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3243	angIndx = {}
3244	valIndx = {}
3245	for item in ['Sample omega','Sample chi','Sample phi']:
3246	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3247	angRef.SetValue(textureData[item][0])
3248	angIndx[angRef.GetId()] = item
3249	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3250	angSizer.Add(angRef,0,WACV)
3251	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3252	valIndx[angVal.GetId()] = item
3253	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3254	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3255	angSizer.Add(angVal,0,WACV)
3256	angSizer.Add((5,0),0)
3257	mainSizer.Add(angSizer,0,WACV)
3258	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3259
3260	################################################################################
3261	##### DData routines - GUI stuff in GSASIIddataGUI.py
3262	################################################################################
3263
3264	def OnHklfAdd(event):
3265	UseList = data['Histograms']
3266	keyList = UseList.keys()
3267	TextList = []
3268	if not G2frame.PatternTree.GetCount():
3269	return
3270
3271	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3272	while item:
3273	name = G2frame.PatternTree.GetItemText(item)
3274	if name not in keyList and 'HKLF' in name:
3275	TextList.append(name)
3276	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3277	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3278	try:
3279	if dlg.ShowModal() == wx.ID_OK:
3280	result = dlg.GetSelections()
3281	else:
3282	return
3283	finally:
3284	dlg.Destroy()
3285
3286	# get the histograms used in other phases
3287	phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree()
3288	usedHKLFhists = [] # used single-crystal histograms
3289	for p in usedHistograms:
3290	for h in usedHistograms[p]:
3291	if h.startswith('HKLF ') and h not in usedHKLFhists:
3292	usedHKLFhists.append(h)
3293	# check that selected single crystal histograms are not already in use!
3294	for i in result:
3295	used = [TextList[i] for i in result if TextList[i] in usedHKLFhists]
3296	if used:
3297	msg = 'The following single crystal histogram(s) are already in use'
3298	for i in used:
3299	msg += '\n '+str(i)
3300	msg += '\nAre you sure you want to add them to this phase? '
3301	msg += 'Associating a single crystal dataset to >1 histogram is usually an error, '
3302	msg += 'so No is suggested here.'
3303	if G2frame.ErrorDialog('Likely error',msg,G2frame,wtype=wx.YES_NO) != wx.ID_YES: return
3304
3305	wx.BeginBusyCursor()
3306	for i in result:
3307	histoName = TextList[i]
3308	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3309	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3310	'Extinction':['Lorentzian','None',
3311	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3312	UpdateHKLFdata(histoName)
3313	data['Histograms'] = UseList
3314	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3315	wx.EndBusyCursor()
3316
3317	def UpdateHKLFdata(histoName):
3318	generalData = data['General']
3319	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3320	refDict,reflData = G2frame.PatternTree.GetItemPyData(Id)
3321	SGData = generalData['SGData']
3322	Cell = generalData['Cell'][1:7]
3323	G,g = G2lat.cell2Gmat(Cell)
3324	for iref,ref in enumerate(reflData['RefList']):
3325	H = list(ref[:3])
3326	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3327	iabsnt,ref[3],Uniq,phi = G2spc.GenHKLf(H,SGData)
3328	#G2frame.PatternTree.SetItemPyData(Id,[refDict,reflData]) #removed by BHT -- not needed!
3329
3330	def OnPwdrAdd(event):
3331	generalData = data['General']
3332	SGData = generalData['SGData']
3333	UseList = data['Histograms']
3334	newList = []
3335	NShkl = len(G2spc.MustrainNames(SGData))
3336	NDij = len(G2spc.HStrainNames(SGData))
3337	keyList = UseList.keys()
3338	TextList = ['All PWDR']
3339	if G2frame.PatternTree.GetCount():
3340	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3341	while item:
3342	name = G2frame.PatternTree.GetItemText(item)
3343	if name not in keyList and 'PWDR' in name:
3344	TextList.append(name)
3345	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3346	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3347	try:
3348	if dlg.ShowModal() == wx.ID_OK:
3349	result = dlg.GetSelections()
3350	for i in result: newList.append(TextList[i])
3351	if 'All PWDR' in newList:
3352	newList = TextList[1:]
3353	for histoName in newList:
3354	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3355	UseList[histoName] = {'Histogram':histoName,'Show':False,
3356	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3357	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3358	[1.,1.,1.,0.,0.,0.],6*[False,]],
3359	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3360	NShkl[0.01,],NShkl[False,]],
3361	'HStrain':[NDij[0.0,],NDij[False,]],
3362	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3363	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Reflection Lists'))
3364	refList[generalData['Name']] = []
3365	data['Histograms'] = UseList
3366	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3367	finally:
3368	dlg.Destroy()
3369
3370	def OnDataDelete(event):
3371	UseList = data['Histograms']
3372	keyList = ['All',]+UseList.keys()
3373	keyList.sort()
3374	DelList = []
3375	if UseList:
3376	DelList = []
3377	dlg = wx.MultiChoiceDialog(G2frame,
3378	'Which histogram to delete from this phase?', 'Delete histogram',
3379	keyList, wx.CHOICEDLG_STYLE)
3380	try:
3381	if dlg.ShowModal() == wx.ID_OK:
3382	result = dlg.GetSelections()
3383	for i in result:
3384	DelList.append(keyList[i])
3385	if 'All' in DelList:
3386	DelList = keyList[1:]
3387	for i in DelList:
3388	del UseList[i]
3389	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3390	finally:
3391	dlg.Destroy()
3392
3393	################################################################################
3394	##### Rigid bodies
3395	################################################################################
3396
3397	def FillRigidBodyGrid(refresh=True):
3398	'''Fill the Rigid Body Phase information tab page.
3399	Note that the page is a ScrolledWindow, not a Grid
3400	'''
3401	def OnThermSel(event): #needs to be seen by VecRbSizer!
3402	Obj = event.GetEventObject()
3403	RBObj = Indx[Obj.GetId()]
3404	val = Obj.GetValue()
3405	Ttype = 'A'
3406	if val == 'Uiso':
3407	Ttype = 'I'
3408	RBObj['ThermalMotion'][0] = 'Uiso'
3409	elif val == 'T':
3410	RBObj['ThermalMotion'][0] = 'T'
3411	elif val == 'TL':
3412	RBObj['ThermalMotion'][0] = 'TL'
3413	elif val == 'TLS':
3414	RBObj['ThermalMotion'][0] = 'TLS'
3415	wx.CallAfter(FillRigidBodyGrid,True)
3416	if val != 'None':
3417	cia = data['General']['AtomPtrs'][3]
3418	for i,id in enumerate(RBObj['Ids']):
3419	data['Atoms'][AtLookUp[id]][cia] = Ttype
3420	G2plt.PlotStructure(G2frame,data)
3421
3422	def ThermDataSizer(RBObj,rbType):
3423
3424	def OnThermval(event):
3425	Obj = event.GetEventObject()
3426	item = Indx[Obj.GetId()]
3427	try:
3428	val = float(Obj.GetValue())
3429	RBObj['ThermalMotion'][1][item] = val
3430	except ValueError:
3431	pass
3432	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3433	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3434	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3435	cia = data['General']['AtomPtrs'][3]
3436	for i,id in enumerate(RBObj['Ids']):
3437	if Uout[i][0] == 'I':
3438	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3439	else:
3440	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3441	G2plt.PlotStructure(G2frame,data)
3442
3443	def OnTLSRef(event):
3444	Obj = event.GetEventObject()
3445	item = Indx[Obj.GetId()]
3446	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3447
3448	thermSizer = wx.FlexGridSizer(1,9,5,5)
3449	model = RBObj['ThermalMotion']
3450	if model[0] == 'Uiso':
3451	names = ['Uiso',]
3452	elif 'T' in model[0]:
3453	names = ['T11','T22','T33','T12','T13','T23']
3454	if 'L' in model[0]:
3455	names += ['L11','L22','L33','L12','L13','L23']
3456	if 'S' in model[0]:
3457	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3458	for i,name in enumerate(names):
3459	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,WACV)
3460	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3461	style=wx.TE_PROCESS_ENTER)
3462	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3463	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3464	Indx[thermVal.GetId()] = i
3465	thermSizer.Add(thermVal)
3466	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3467	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3468	Tcheck.SetValue(model[2][i])
3469	Indx[Tcheck.GetId()] = i
3470	thermSizer.Add(Tcheck,0,WACV)
3471	return thermSizer
3472
3473	def LocationSizer(RBObj,rbType):
3474
3475	def OnOrigRef(event):
3476	RBObj['Orig'][1] = Ocheck.GetValue()
3477
3478	def OnOrienRef(event):
3479	RBObj['Orient'][1] = Qcheck.GetValue()
3480
3481	def OnOrigX(event):
3482	Obj = event.GetEventObject()
3483	item = Indx[Obj.GetId()]
3484	try:
3485	val = float(Obj.GetValue())
3486	RBObj['Orig'][0][item] = val
3487	Obj.SetValue('%8.5f'%(val))
3488	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3489	for i,id in enumerate(RBObj['Ids']):
3490	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3491	data['Drawing']['Atoms'] = []
3492	UpdateDrawAtoms(atomStyle)
3493	G2plt.PlotStructure(G2frame,data)
3494	except ValueError:
3495	pass
3496
3497	def OnOrien(event):
3498	Obj = event.GetEventObject()
3499	item = Indx[Obj.GetId()]
3500	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3501	V = np.inner(Bmat,V)
3502	try:
3503	val = float(Obj.GetValue())
3504	if item:
3505	V[item-1] = val
3506	else:
3507	A = val
3508	Obj.SetValue('%8.5f'%(val))
3509	V = np.inner(Amat,V)
3510	Q = G2mth.AVdeg2Q(A,V)
3511	if not any(Q):
3512	raise ValueError
3513	RBObj['Orient'][0] = Q
3514	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3515	for i,id in enumerate(RBObj['Ids']):
3516	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3517	data['Drawing']['Atoms'] = []
3518	UpdateDrawAtoms(atomStyle)
3519	G2plt.PlotStructure(G2frame,data)
3520	except ValueError:
3521	pass
3522
3523	topSizer = wx.FlexGridSizer(2,6,5,5)
3524	Orig = RBObj['Orig'][0]
3525	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3526	Orien = [Orien,]
3527	Orien.extend(OrienV/nl.norm(OrienV))
3528	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,WACV)
3529	for ix,x in enumerate(Orig):
3530	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3531	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3532	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3533	Indx[origX.GetId()] = ix
3534	topSizer.Add(origX,0,WACV)
3535	topSizer.Add((5,0),)
3536	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3537	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3538	Ocheck.SetValue(RBObj['Orig'][1])
3539	topSizer.Add(Ocheck,0,WACV)
3540	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,WACV)
3541	for ix,x in enumerate(Orien):
3542	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3543	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3544	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3545	Indx[orien.GetId()] = ix
3546	topSizer.Add(orien,0,WACV)
3547	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3548	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3549	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3550	Qcheck.SetValue(RBObj['Orient'][1])
3551	topSizer.Add(Qcheck)
3552	return topSizer
3553
3554	def ResrbSizer(RBObj):
3555	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3556
3557	def OnTorsionRef(event):
3558	Obj = event.GetEventObject()
3559	item = Indx[Obj.GetId()]
3560	RBObj['Torsions'][item][1] = Obj.GetValue()
3561
3562	def OnTorsion(event):
3563	Obj = event.GetEventObject()
3564	item = Indx[Obj.GetId()]
3565	try:
3566	val = float(Obj.GetValue())
3567	RBObj['Torsions'][item][0] = val
3568	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3569	for i,id in enumerate(RBObj['Ids']):
3570	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3571	except ValueError:
3572	pass
3573	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3574	data['Drawing']['Atoms'] = []
3575	UpdateDrawAtoms(atomStyle)
3576	drawAtoms.ClearSelection()
3577	G2plt.PlotStructure(G2frame,data)
3578
3579	def OnDelResRB(event):
3580	Obj = event.GetEventObject()
3581	RBId = Indx[Obj.GetId()]
3582	RBData['Residue'][RBId]['useCount'] -= 1
3583	RBObjs = data['RBModels']['Residue']
3584	for rbObj in RBObjs:
3585	if RBId == rbObj['RBId']:
3586	data['RBModels']['Residue'].remove(rbObj)
3587	G2plt.PlotStructure(G2frame,data)
3588	wx.CallAfter(FillRigidBodyGrid,True)
3589
3590	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3591	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3592	topLine = wx.BoxSizer(wx.HORIZONTAL)
3593	topLine.Add(wx.StaticText(RigidBodies,-1,
3594	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,WACV)
3595	rbId = RBObj['RBId']
3596	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3597	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3598	Indx[delRB.GetId()] = rbId
3599	topLine.Add(delRB,0,WACV)
3600	resrbSizer.Add(topLine)
3601	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3602	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,WACV)
3603	torSizer = wx.FlexGridSizer(1,6,5,5)
3604	for itors,tors in enumerate(RBObj['Torsions']):
3605	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,WACV)
3606	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3607	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3608	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3609	Indx[torsTxt.GetId()] = itors
3610	torSizer.Add(torsTxt)
3611	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3612	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3613	torCheck.SetValue(tors[1])
3614	Indx[torCheck.GetId()] = itors
3615	torSizer.Add(torCheck,0,WACV)
3616	resrbSizer.Add(torSizer)
3617	tchoice = ['None','Uiso','T','TL','TLS']
3618	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3619	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,WACV)
3620	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3621	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3622	Indx[thermSel.GetId()] = RBObj
3623	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3624	thermSizer.Add(thermSel,0,WACV)
3625	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,WACV)
3626	resrbSizer.Add(thermSizer)
3627	if RBObj['ThermalMotion'][0] != 'None':
3628	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3629	return resrbSizer
3630
3631	def VecrbSizer(RBObj):
3632	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3633
3634	def OnDelVecRB(event):
3635	Obj = event.GetEventObject()
3636	RBId = Indx[Obj.GetId()]
3637	RBData['Vector'][RBId]['useCount'] -= 1
3638	RBObjs = data['RBModels']['Vector']
3639	for rbObj in RBObjs:
3640	if RBId == rbObj['RBId']:
3641	data['RBModels']['Vector'].remove(rbObj)
3642	G2plt.PlotStructure(G2frame,data)
3643	wx.CallAfter(FillRigidBodyGrid,True)
3644
3645	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3646	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3647	topLine = wx.BoxSizer(wx.HORIZONTAL)
3648	topLine.Add(wx.StaticText(RigidBodies,-1,
3649	'Name: '+RBObj['RBname']+' '),0,WACV)
3650	rbId = RBObj['RBId']
3651	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3652	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3653	Indx[delRB.GetId()] = rbId
3654	topLine.Add(delRB,0,WACV)
3655	vecrbSizer.Add(topLine)
3656	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3657	tchoice = ['None','Uiso','T','TL','TLS']
3658	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3659	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,WACV)
3660	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3661	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3662	Indx[thermSel.GetId()] = RBObj
3663	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3664	thermSizer.Add(thermSel,0,WACV)
3665	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,WACV)
3666	vecrbSizer.Add(thermSizer)
3667	if RBObj['ThermalMotion'][0] != 'None':
3668	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3669	return vecrbSizer
3670
3671	# FillRigidBodyGrid executable code starts here
3672	if refresh:
3673	RigidBodies.DestroyChildren()
3674	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3675	general = data['General']
3676	cx = general['AtomPtrs'][0]
3677	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3678	RBData = G2frame.PatternTree.GetItemPyData(
3679	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3680	Indx = {}
3681	atomStyle = 'balls & sticks'
3682	if 'macro' in general['Type']:
3683	atomStyle = 'sticks'
3684	G2frame.dataFrame.SetStatusText('')
3685	mainSizer = wx.BoxSizer(wx.VERTICAL)
3686	if not data['RBModels']:
3687	mainSizer.Add((5,5),0)
3688	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,WACV)
3689	mainSizer.Add((5,5),0)
3690	if 'Residue' in data['RBModels']:
3691	mainSizer.Add((5,5),0)
3692	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,WACV)
3693	mainSizer.Add((5,5),0)
3694	for RBObj in data['RBModels']['Residue']:
3695	mainSizer.Add(ResrbSizer(RBObj))
3696	if 'Vector' in data['RBModels']:
3697	mainSizer.Add((5,5),0)
3698	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,WACV)
3699	mainSizer.Add((5,5),0)
3700	for RBObj in data['RBModels']['Vector']:
3701	mainSizer.Add(VecrbSizer(RBObj))
3702
3703	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3704
3705	def OnRBCopyParms(event):
3706	RBObjs = []
3707	for rbType in ['Vector','Residue']:
3708	RBObjs += data['RBModels'].get(rbType,[])
3709	if not len(RBObjs):
3710	print '** ERROR - no rigid bodies defined **'
3711	return
3712	if len(RBObjs) == 1:
3713	print '** INFO - only one rigid body defined; nothing to copy to **'
3714	return
3715	Source = []
3716	sourceRB = {}
3717	for RBObj in RBObjs:
3718	Source.append(RBObj['RBname'])
3719	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3720	if dlg.ShowModal() == wx.ID_OK:
3721	sel = dlg.GetSelection()
3722	name = Source[sel]
3723	for item in ['Orig','Orient','ThermalMotion']:
3724	sourceRB.update({item:RBObjs[sel][item],})
3725	dlg.Destroy()
3726	if not sourceRB:
3727	return
3728	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3729	if dlg.ShowModal() == wx.ID_OK:
3730	sel = dlg.GetSelections()
3731	for x in sel:
3732	RBObjs[x].update(copy.copy(sourceRB))
3733	G2plt.PlotStructure(G2frame,data)
3734	wx.CallAfter(FillRigidBodyGrid(True))
3735
3736	def OnRBAssign(event):
3737
3738	G2frame.dataFrame.SetStatusText('')
3739	RBData = G2frame.PatternTree.GetItemPyData(
3740	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3741	rbNames = {}
3742	for rbVec in RBData['Vector']:
3743	if rbVec != 'AtInfo':
3744	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3745	for rbRes in RBData['Residue']:
3746	if rbRes != 'AtInfo':
3747	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3748	if not rbNames:
3749	print '** ERROR - no rigid bodies defined **'
3750	return
3751	general = data['General']
3752	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3753	cx,ct = general['AtomPtrs'][:2]
3754	atomData = data['Atoms']
3755	Indx = {}
3756	atInd = [-1,-1,-1]
3757	data['testRBObj'] = {}
3758
3759	def Draw():
3760
3761	def OnOk(event):
3762	rbType = data['testRBObj']['rbType']
3763	RBObjs = data['RBModels'].get(rbType,[])
3764	rbObj = data['testRBObj']['rbObj']
3765	rbId = rbObj['RBId']
3766	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3767	Ids = []
3768	dmax = 0.0
3769	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3770	for xyz in newXYZ:
3771	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3772	dmax = max(dmax,np.min(dist))
3773	id = np.argmin(dist)
3774	Ids.append(atomData[id][-1])
3775	atomData[id][cx:cx+3] = xyz
3776	if dmax > 1.0:
3777	print '** WARNING - some atoms not found or misidentified **'
3778	print '** check torsion angles & try again **'
3779	OkBtn.SetLabel('Not Ready')
3780	OkBtn.Enable(False)
3781	return
3782	rbObj['Ids'] = Ids
3783	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3784	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3785	RBObjs.append(rbObj)
3786	data['RBModels'][rbType] = RBObjs
3787	RBData[rbType][rbId]['useCount'] += 1
3788	del data['testRBObj']
3789	G2plt.PlotStructure(G2frame,data)
3790	FillRigidBodyGrid(True)
3791
3792	def OnCancel(event):
3793	del data['testRBObj']
3794	FillRigidBodyGrid(True)
3795
3796	def OnRBSel(event):
3797	selection = rbSel.GetValue()
3798	rbType,rbId = rbNames[selection]
3799	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3800	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3801	data['testRBObj']['rbType'] = rbType
3802	data['testRBObj']['rbData'] = RBData
3803	data['testRBObj']['Sizers'] = {}
3804	rbRef = RBData[rbType][rbId]['rbRef']
3805	data['testRBObj']['rbRef'] = rbRef
3806	refType = []
3807	refName = []
3808	for ref in rbRef[:3]:
3809	reftype = data['testRBObj']['rbAtTypes'][ref]
3810	refType.append(reftype)
3811	refName.append(reftype+' '+str(rbRef[0]))
3812	atNames,AtNames = fillAtNames(refType,atomData,ct)
3813	data['testRBObj']['atNames'] = atNames
3814	data['testRBObj']['AtNames'] = AtNames
3815	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3816	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3817	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3818	data['testRBObj']['torAtms'] = []
3819	for item in RBData[rbType][rbId].get('rbSeq',[]):
3820	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3821	data['testRBObj']['torAtms'].append([-1,-1,-1])
3822	Draw()
3823
3824	def fillAtNames(refType,atomData,ct):
3825	atNames = [{},{},{}]
3826	AtNames = {}
3827	for iatm,atom in enumerate(atomData):
3828	AtNames[atom[ct-1]] = iatm
3829	for i,reftype in enumerate(refType):
3830	if atom[ct] == reftype:
3831	atNames[i][atom[ct-1]] = iatm
3832	return atNames,AtNames
3833
3834	def OnAtOrigPick(event):
3835	Obj = event.GetEventObject()
3836	item = Indx[Obj.GetId()]
3837	atName = Obj.GetValue()
3838	rbType = data['testRBObj']['rbType']
3839	atInd[0] = atNames[item][atName]
3840	if 'Vector' in rbType:
3841	rbObj = data['testRBObj']['rbObj']
3842	rbId = rbObj['RBId']
3843	rbRef = data['testRBObj']['rbRef']
3844	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3845	nref = atNames[item][atName]
3846	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3847	Nxyz = np.array(atomData[nref][cx:cx+3])
3848	Orig = Nxyz-Oxyz
3849	data['testRBObj']['rbObj']['Orig'][0] = Orig
3850	else:
3851	Orig = atomData[atNames[item][atName]][cx:cx+3]
3852	data['testRBObj']['rbObj']['Orig'][0] = Orig
3853	for x,item in zip(Orig,Xsizers):
3854	item.SetLabel('%10.5f'%(x))
3855	G2plt.PlotStructure(G2frame,data)
3856
3857	def OnAtQPick(event):
3858	Obj = event.GetEventObject()
3859	item = Indx[Obj.GetId()]
3860	atName = Obj.GetValue()
3861	atInd[item] = atNames[item][atName]
3862	if any([x<0 for x in atInd]):
3863	return
3864	OkBtn.SetLabel('OK')
3865	OkBtn.Enable(True)
3866	rbType = data['testRBObj']['rbType']
3867	rbObj = data['testRBObj']['rbObj']
3868	rbId = rbObj['RBId']
3869	rbRef = data['testRBObj']['rbRef']
3870	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3871	rbOrig = rbXYZ[rbRef[0]]
3872	VAR = rbXYZ[rbRef[1]]-rbOrig
3873	VBR = rbXYZ[rbRef[2]]-rbOrig
3874	if rbType == 'Vector':
3875	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3876	else:
3877	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3878	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3879	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3880	VCC = np.cross(VAR,VAC)
3881	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3882	VAR = G2mth.prodQVQ(QuatA,VAR)
3883	VBR = G2mth.prodQVQ(QuatA,VBR)
3884	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3885	QuatC = G2mth.prodQQ(QuatB,QuatA)
3886	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3887	for x,item in zip(QuatC,Osizers):
3888	item.SetLabel('%10.4f'%(x))
3889	if rbType == 'Vector':
3890	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3891	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3892	Orig = Nxyz-Oxyz
3893	data['testRBObj']['rbObj']['Orig'][0] = Orig
3894	for x,item in zip(Orig,Xsizers):
3895	item.SetLabel('%10.5f'%(x))
3896	G2plt.PlotStructure(G2frame,data)
3897
3898	def OnTorAngle(event):
3899	OkBtn.SetLabel('OK')
3900	OkBtn.Enable(True)
3901	Obj = event.GetEventObject()
3902	[tor,torSlide] = Indx[Obj.GetId()]
3903	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3904	try:
3905	value = float(Obj.GetValue())
3906	except ValueError:
3907	value = Tors[0]
3908	Tors[0] = value
3909	Obj.SetValue('%8.3f'%(value))
3910	torSlide.SetValue(int(value*10))
3911	G2plt.PlotStructure(G2frame,data)
3912
3913	def OnTorSlide(event):
3914	OkBtn.SetLabel('OK')
3915	OkBtn.Enable(True)
3916	Obj = event.GetEventObject()
3917	tor,ang = Indx[Obj.GetId()]
3918	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3919	val = float(Obj.GetValue())/10.
3920	Tors[0] = val
3921	ang.SetValue('%8.3f'%(val))
3922	G2plt.PlotStructure(G2frame,data)
3923
3924	if len(data['testRBObj']):
3925	G2plt.PlotStructure(G2frame,data)
3926
3927	RigidBodies.DestroyChildren()
3928	mainSizer = wx.BoxSizer(wx.VERTICAL)
3929	mainSizer.Add((5,5),0)
3930	if data['testRBObj']:
3931	Xsizers = []
3932	Osizers = []
3933	rbObj = data['testRBObj']['rbObj']
3934	rbName = rbObj['RBname']
3935	rbId = rbObj['RBId']
3936	Orig = rbObj['Orig'][0]
3937	Orien = rbObj['Orient'][0]
3938	rbRef = data['testRBObj']['rbRef']
3939	Torsions = rbObj['Torsions']
3940	refName = []
3941	for ref in rbRef:
3942	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3943	atNames = data['testRBObj']['atNames']
3944	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3945	0,WACV)
3946	mainSizer.Add((5,5),0)
3947	OriSizer = wx.FlexGridSizer(1,5,5,5)
3948	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,WACV)
3949	for ix,x in enumerate(Orig):
3950	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3951	OriSizer.Add(origX,0,WACV)
3952	Xsizers.append(origX)
3953	OriSizer.Add((5,0),)
3954	if len(atomData):
3955	choice = atNames[0].keys()
3956	choice.sort()
3957	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3958	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,WACV)
3959	for ix,x in enumerate(Orien):
3960	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3961	OriSizer.Add(orien,0,WACV)
3962	Osizers.append(orien)
3963	data['testRBObj']['Sizers']['Osizers'] = Osizers
3964	mainSizer.Add(OriSizer)
3965	mainSizer.Add((5,5),0)
3966	RefSizer = wx.FlexGridSizer(1,7,5,5)
3967	if len(atomData):
3968	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,WACV)
3969	for i in [0,1,2]:
3970	choice = ['',]+atNames[i].keys()
3971	choice.sort()
3972	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,WACV)
3973	atPick = wx.ComboBox(RigidBodies,-1,value='',
3974	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3975	if i:
3976	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3977	else:
3978	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3979	Indx[atPick.GetId()] = i
3980	RefSizer.Add(atPick,0,WACV)
3981	mainSizer.Add(RefSizer)
3982	mainSizer.Add((5,5),0)
3983	if Torsions:
3984	AtNames = data['testRBObj']['AtNames']
3985	rbAtTypes = data['testRBObj']['rbAtTypes']
3986	rbSeq = RBData['Residue'][rbId]['rbSeq']
3987	TorSizer = wx.FlexGridSizer(1,4)
3988	TorSizer.AddGrowableCol(1,1)
3989	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3990	torName = ''
3991	for item in [seq[0],seq[1],seq[3][0]]:
3992	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3993	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,WACV)
3994	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3995	torSlide.SetRange(0,3600)
3996	torSlide.SetValue(int(torsion[0]*10.))
3997	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3998	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3999	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,WACV)
4000	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
4001	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
4002	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
4003	Indx[torSlide.GetId()] = [t,ang]
4004	Indx[ang.GetId()] = [t,torSlide]
4005	TorSizer.Add(ang,0,WACV)
4006	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
4007	else:
4008	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,WACV)
4009	else:
4010	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,WACV)
4011	mainSizer.Add((5,5),0)
4012	topSizer = wx.BoxSizer(wx.HORIZONTAL)
4013	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,WACV)
4014	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
4015	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
4016	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
4017	topSizer.Add((5,5),0)
4018	topSizer.Add(rbSel,0,WACV)
4019	mainSizer.Add(topSizer)
4020
4021	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
4022	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
4023	OkBtn.Enable(False)
4024	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
4025	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
4026	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
4027	btnSizer.Add((20,20),1)
4028	btnSizer.Add(OkBtn)
4029	btnSizer.Add(CancelBtn)
4030	btnSizer.Add((20,20),1)
4031	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
4032	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
4033	Draw()
4034
4035	def OnAutoFindResRB(event):
4036	RBData = G2frame.PatternTree.GetItemPyData(
4037	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4038	rbKeys = RBData['Residue'].keys()
4039	rbKeys.remove('AtInfo')
4040	if not len(rbKeys):
4041	print '** ERROR - no residue rigid bodies are defined **'
4042	return
4043	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
4044	RBIds = dict(zip(RBNames,rbKeys))
4045	general = data['General']
4046	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
4047	Atoms = data['Atoms']
4048	AtLookUp = G2mth.FillAtomLookUp(Atoms)
4049	if 'macro' not in general['Type']:
4050	print '** ERROR - this phase is not a macromolecule **'
4051	return
4052	if not len(Atoms):
4053	print '** ERROR - this phase has no atoms **'
4054	return
4055	RBObjs = []
4056	cx,ct = general['AtomPtrs'][:2]
4057	iatm = 0
4058	wx.BeginBusyCursor()
4059	try:
4060	while iatm < len(Atoms):
4061	atom = Atoms[iatm]
4062	res = atom[1].strip()
4063	numChain = ' %s %s'%(atom[0],atom[2])
4064	if res not in RBIds or atom[ct-1] == 'OXT':
4065	iatm += 1
4066	continue #skip for OXT, water molecules, etc.
4067	rbRes = RBData['Residue'][RBIds[res]]
4068	rbRef = rbRes['rbRef']
4069	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
4070	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
4071	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
4072	rbAtoms = []
4073	rbIds = []
4074	for iratm in range(len(rbRes['atNames'])):
4075	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
4076	rbIds.append(Atoms[iatm][20])
4077	iatm += 1 #puts this at beginning of next residue?
4078	Orig = rbAtoms[rbRef[0]]
4079	rbObj['RBId'] = RBIds[res]
4080	rbObj['Ids'] = rbIds
4081	rbObj['Orig'] = [Orig,False]
4082	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
4083	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
4084	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
4085	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
4086	VCC = np.cross(VAR,VAC)
4087	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
4088	VAR = G2mth.prodQVQ(QuatA,VAR)
4089	VBR = G2mth.prodQVQ(QuatA,VBR)
4090	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
4091	QuatC = G2mth.prodQQ(QuatB,QuatA)
4092	rbObj['Orient'] = [QuatC,' ']
4093	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
4094	SXYZ = []
4095	TXYZ = []
4096	rbObj['Torsions'] = []
4097	for i,xyz in enumerate(rbRes['rbXYZ']):
4098	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
4099	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
4100	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
4101	VBR = SXYZ[Oatm]-SXYZ[Patm]
4102	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
4103	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
4104	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
4105	ang = 180.*D/np.pi
4106	rbObj['Torsions'].append([ang,False])
4107	for ride in Riders:
4108	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
4109	rbRes['useCount'] += 1
4110	RBObjs.append(rbObj)
4111	data['RBModels']['Residue'] = RBObjs
4112	for RBObj in RBObjs:
4113	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
4114	for i,id in enumerate(RBObj['Ids']):
4115	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
4116	finally:
4117	wx.EndBusyCursor()
4118	wx.CallAfter(FillRigidBodyGrid,True)
4119
4120	def OnRBRemoveAll(event):
4121	data['RBModels']['Residue'] = []
4122	data['RBModels']['Vector'] = []
4123	RBData = G2frame.PatternTree.GetItemPyData(
4124	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4125	for RBType in ['Vector','Residue']:
4126	for rbId in RBData[RBType]:
4127	RBData[RBType][rbId]['useCount'] = 0
4128	FillRigidBodyGrid(True)
4129
4130	def OnGlobalResRBTherm(event):
4131	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
4132	RBObjs = data['RBModels']['Residue']
4133	names = ['None','Uiso','T','TL','TLS']
4134	cia = data['General']['AtomPtrs'][3]
4135	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
4136	if dlg.ShowModal() == wx.ID_OK:
4137	sel = dlg.GetSelection()
4138	parm = names[sel]
4139	Ttype = 'A'
4140	if parm == 'Uiso':
4141	Ttype = 'I'
4142	for rbObj in RBObjs:
4143	rbObj['ThermalMotion'][0] = parm
4144	if parm != 'None':
4145	for i,id in enumerate(rbObj['Ids']):
4146	data['Atoms'][AtLookUp[id]][cia] = Ttype
4147	dlg.Destroy()
4148	wx.CallAfter(FillRigidBodyGrid,True)
4149
4150	def OnGlobalResRBRef(event):
4151	RBObjs = data['RBModels']['Residue']
4152	names = ['Origin','Orient. angle','Full Orient.']
4153	nTor = 0
4154	for rbObj in RBObjs:
4155	nTor = max(nTor,len(rbObj['Torsions']))
4156	names += ['Torsion '+str(i) for i in range(nTor)]
4157	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
4158	names += ['Uiso',]
4159	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
4160	names += ['Tii','Tij','Lii','Lij','Sij']
4161	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
4162	names += ['Tii','Tij','Lii','Lij']
4163	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
4164	names += ['Tii','Tij']
4165
4166	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
4167	if dlg.ShowModal() == wx.ID_OK: