Changeset 3054

Timestamp:

Sep 7, 2017 4:13:57 PM (6 years ago)

Author:

vondreele

Message:

fixes to MCSA gui routines; trap <3 atom RBs
fix missing AtLookup? error in LeBail? refinements

Location:

trunk

Files:

• GSASIIconstrGUI.py (modified) (7 diffs)
• GSASIIphsGUI.py (modified) (3 diffs)
• GSASIIstrIO.py (modified) (1 diff)

trunk/GSASIIconstrGUI.py

@@ -1505 +1505 @@
                 break
             items = txtStr.split()
-        rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[0])
-        data['Residue'][rbId] = {'RBname':'UNKRB','rbXYZ':rbXYZ,'rbTypes':rbTypes,
-            'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
-        data['RBIds']['Residue'].append(rbId)
-        print 'Rigid body UNKRB added'
+        if len(atNames) < 3:
+            G2G.G2MessageBox(G2frame,'Not enough atoms in rigid body; must be 3 or more')
+        else:
+            rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[0])
+            data['Residue'][rbId] = {'RBname':'UNKRB','rbXYZ':rbXYZ,'rbTypes':rbTypes,
+                'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
+            data['RBIds']['Residue'].append(rbId)
+            print 'Rigid body UNKRB added'
         text.close()
         UpdateResidueRB()
@@ -1524 +1527 @@
         IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
         for j in IndB[0]:
-            if j != Orig:
+            if j != Orig and atTypes[j] != 'H':
                 Neigh.append(atNames[j])
         return Neigh
@@ -1827 +1830 @@
                 wx.CallAfter(UpdateResidueRB)
                 
+            def OnStripH(event):
+                Obj = event.GetEventObject()
+                rbId = Indx[Obj.GetId()]
+                if rbId in data['Residue']:
+                    newNames = []
+                    newTypes = []
+                    newXYZ = []
+                    for i,atype in enumerate(rbData['rbTypes']):
+                        if atype != 'H':
+                            newNames.append(rbData['atNames'][i])
+                            newTypes.append(rbData['rbTypes'][i])
+                            newXYZ.append(rbData['rbXYZ'][i])
+                    rbData['atNames'] = newNames
+                    rbData['rbTypes'] = newTypes
+                    rbData['rbXYZ'] = newXYZ
+                wx.CallAfter(UpdateResidueRB)
+                    
             def OnPlotRB(event):
                 Obj = event.GetEventObject()
@@ -1851 +1871 @@
                 delRB.Bind(wx.EVT_CHECKBOX,OnDelRB)
                 nameSizer.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
+                if 'H'  in rbData['rbTypes']:
+                    stripH = wx.CheckBox(ResidueRBDisplay,-1,'Strip H-atoms?')
+                    Indx[stripH.GetId()] = rbId
+                    stripH.Bind(wx.EVT_CHECKBOX,OnStripH)
+                    nameSizer.Add(stripH,0,wx.ALIGN_CENTER_VERTICAL)
             return nameSizer
             
@@ -1891 +1916 @@
                 sel = Obj.GetValue()
                 ind = atNames.index(sel)
+                if rbData['rbTypes'][ind] == 'H':
+                    G2G.G2MessageBox(G2frame,'You should not select an H-atom for rigid body orientation')
                 rbData['rbRef'][iref] = ind
                 FillRefChoice(rbId,rbData)
@@ -1940 +1967 @@
             if rbData['rbRef'][3] or rbData['useCount']:
                 refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
-                    'Orientation reference atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \
+                    'Orientation reference non-H atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \
                      atNames[rbRef[1]],atNames[rbRef[2]])),0)
             else:
                 refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
-                    'Orientation reference atoms A-B-C: '),0,wx.ALIGN_CENTER_VERTICAL)
+                    'Orientation reference non-H atoms A-B-C: '),0,wx.ALIGN_CENTER_VERTICAL)
                 refObj = [0,0,0]
                 for i in range(3):
@@ -2063 +2090 @@
         for rbId in data['RBIds']['Residue']:
             rbData = data['Residue'][rbId]
+            if len(rbData['rbXYZ']) < 3:    #patch - skip around bad RBs with too few atoms
+                continue
             FillRefChoice(rbId,rbData)
             ResidueRBSizer.Add(rbNameSizer(rbId,rbData),0)

trunk/GSASIIphsGUI.py

@@ -7650 +7650 @@
             resultsSizer.Add(resultsGrid,0,wx.EXPAND)
             return resultsSizer
+
+        def OnSelect(event):
+            rbId = rbids[select.GetSelection()]
+            wx.CallLater(100,RepaintRBInfo,rbId)
+           
+        def RepaintRBInfo(rbId,Scroll=0):
+            oldFocus = wx.Window.FindFocus()
+            G2frame.bottomSizer.DeleteWindows()
+            Indx.clear()
+            rbObj = data['MCSA']['Models'][rbId]
+            G2frame.bottomSizer.Insert(0,rbSizer(rbObj))
+            mainSizer.Layout()
+            G2frame.dataWindow.Refresh()
+            G2frame.dataWindow.SendSizeEvent()
+            wx.CallAfter(oldFocus.SetFocus)
         
         # UpdateMCSA executable code starts here
@@ -7675 +7690 @@
             mainSizer.Add(wx.StaticText(G2frame.MCSA,-1,'MC/SA models:'),0,WACV)
             mainSizer.Add((5,5),0)
-            for model in data['MCSA']['Models']:
-                Xsize = 500
+            rbNames = []
+            rbids = []
+            for im,model in enumerate(data['MCSA']['Models']):
                 if model['Type'] == 'MD':
                     mainSizer.Add(MDSizer(model))
@@ -7682 +7698 @@
                     Asizer = atomSizer(model)
                     mainSizer.Add(Asizer)
-                    Xsize = max(Asizer.GetMinSize()[0],Xsize)
                 else:
-                    Rsizer = rbSizer(model)
-                    mainSizer.Add(Rsizer)
-                    Xsize = max(Rsizer.GetMinSize()[0],Xsize)
-                G2G.HorizontalLine(mainSizer,G2frame.MCSA)
+                    rbNames.append(model['name'])
+                    rbids.append(im)
+            G2G.HorizontalLine(mainSizer,G2frame.MCSA)
+            if len(rbNames):
+                rbName = rbNames[0]
+                select = wx.ListBox(G2frame.MCSA,choices=rbNames,style=wx.LB_SINGLE,size=(-1,65))
+                select.SetSelection(rbNames.index(rbName))
+                select.SetFirstItem(rbNames.index(rbName))
+                select.Bind(wx.EVT_LISTBOX,OnSelect)
+                mainSizer.Add(select,0,WACV)
+                G2frame.bottomSizer = wx.BoxSizer(wx.VERTICAL)
+                G2frame.bottomSizer.Add(rbSizer(data['MCSA']['Models'][rbids[0]]))
+                mainSizer.Add(G2frame.bottomSizer)
                 
         if not data['MCSA']['Results']:

trunk/GSASIIstrIO.py

@@ -1883 +1883 @@
         SGData = General['SGData']
         Atoms = Phase['Atoms']
+        AtLookup = []
         if Atoms and not General.get('doPawley'):
             cx,ct,cs,cia = General['AtomPtrs']