Changeset 854

Timestamp:

Feb 20, 2013 9:51:42 AM (11 years ago)

Author:

vondreele

Message:

more rigid body stuff

Location:

trunk

Files:

• GSASIIconstrGUI.py (modified) (3 diffs)
• GSASIIphsGUI.py (modified) (6 diffs)
• GSASIIplot.py (modified) (1 diff)

trunk/GSASIIconstrGUI.py

@@ -1271 +1271 @@
             def ChangeAngle(event):
                 Obj = event.GetEventObject()
-                rbId,Seq = Indx[Obj.GetId()]
+                rbId,Seq = Indx[Obj.GetId()][:2]
                 val = Seq[2]
                 try:
@@ -1301 +1301 @@
             seqSizer.Add(bond,0,wx.ALIGN_CENTER_VERTICAL)
             Indx[radBt.GetId()] = [Seq,iSeq,ang.GetId()]
-            Indx[ang.GetId()] = [rbId,Seq]
+            Indx[ang.GetId()] = [rbId,Seq,ang]
             ang.Bind(wx.EVT_TEXT_ENTER,ChangeAngle)
             ang.Bind(wx.EVT_KILL_FOCUS,ChangeAngle)
@@ -1338 +1338 @@
             for seq in rbData['rbSeq']:
                 for i in seq[3]:
-                    choiceIds.remove(i)
+                    try:
+                        choiceIds.remove(i)
+                    except ValueError:
+                        pass
             rbRef = rbData['rbRef']
             for i in range(3):
-                choiceIds.remove(rbRef[i])
+                try:
+                    choiceIds.remove(rbRef[i])
+                except ValueError:
+                    pass
             refChoice[rbId] = [choiceIds[:],choiceIds[:],choiceIds[:]]
             for i in range(3):

trunk/GSASIIphsGUI.py

@@ -1641 +1641 @@
         rbId = ran.randint(0,sys.maxint)
         RBData['Residue'][rbId] = {'RBname':'UNKRB','rbXYZ':rbXYZ,'rbTypes':rbType,
-            'atNames':atNames,'rbRef':[0,1,2],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
+            'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
         G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
 
@@ -3187 +3187 @@
                     refName.append(reftype+' '+str(rbRef[0]))
                 atNames = [{},{},{}]
+                AtNames = {}
                 for iatm,atom in enumerate(atomData):
+                    AtNames[atom[ct-1]] = iatm
                     for i,reftype in enumerate(refType):
                         if atom[ct] == reftype:
                             atNames[i][atom[ct-1]] = iatm
                 data['testRBObj']['atNames'] = atNames
+                data['testRBObj']['AtNames'] = AtNames
                 data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],'Orient':[[0,0,0,1.],' '],
-                    'RBId':rbId,'Torsions':[],'numChain':'','RBname':rbData[rbType][rbId]['RBname']}                
+                    'RBId':rbId,'Torsions':[],'numChain':'','RBname':rbData[rbType][rbId]['RBname']}
+                data['testRBObj']['torAtms'] = []                
                 for item in rbData[rbType][rbId].get('rbSeq',[]):
-                    data['testRBObj']['rbObj']['Torsions'].append([0.0,False])
+                    data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
+                    data['testRBObj']['torAtms'].append([-1,-1,-1])
                 Draw()
                 
@@ -3273 +3278 @@
                     data['testRBObj']['rbObj']['Orig'][0] = Nxyz-Oxyz
                 Draw()
+                
+            def OnTorAngle(event):
+                Obj = event.GetEventObject()
+                tor = Indx[Obj.GetId()]
+                Tors = data['testRBObj']['rbObj']['Torsions'][tor]
+                try:
+                    value = Obj.GetValue()
+                except ValueError:
+                    value = Tors[0]
+                Tors[0] = value
+                Obj.SetValue('%8.3f'%(value))
+                G2plt.PlotStructure(G2frame,data)
+
+            def OnTorAtPick(event):
+                Obj = event.GetEventObject()
+                tor,ind = Indx[Obj.GetId()]
+                atName = Obj.GetValue()
+                data['testRBObj']['torAtms'][tor][ind] = AtNames[atName]
+                if all([i > -1 for i in data['testRBObj']['torAtms'][tor]]):
+                    rbObj = data['testRBObj']['rbObj']
+                    rbId = rbObj['RBId']
+                    rbXYZ = rbData['Residue'][rbId]['rbXYZ']
+                    Oatm,Patm,Ratm = data['testRBObj']['torAtms'][tor]
+                    Seq = rbData['Residue'][rbId]['rbSeq'][tor]
+                    Tors = data['testRBObj']['rbObj']['Torsions'][tor]
+                    VBR = rbXYZ[Oatm]-rbXYZ[Patm]
+                    VAR = rbXYZ[Ratm]-rbXYZ[Patm]
+                    VAC = np.inner(Amat,atomData[Seq[3][0]][cx:cx+3])-np.inner(Amat,atomData[Seq[1]][cx:cx+3])
+                    QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
+                    angle = 180.*D/np.pi
+                    Tors[0] = angle
+                G2plt.PlotStructure(G2frame,data)
+                Draw()
 
             if len(data['testRBObj']):
@@ -3286 +3324 @@
                 Osizers = []
                 OriSizer = wx.FlexGridSizer(1,6,5,5)
-                Orig = data['testRBObj']['rbObj']['Orig'][0]
-                Orien = data['testRBObj']['rbObj']['Orient'][0]
+                rbObj = data['testRBObj']['rbObj']
+                rbId = rbObj['RBId']
+                Orig = rbObj['Orig'][0]
+                Orien = rbObj['Orient'][0]
                 rbRef = data['testRBObj']['rbRef']
+                Torsions = rbObj['Torsions']
                 refName = []
                 for ref in rbRef:
@@ -3333 +3374 @@
                 mainSizer.Add(OriSizer)
                 mainSizer.Add((5,5),0)
-                
+                if Torsions:
+                    AtNames = data['testRBObj']['AtNames']
+                    rbAtTypes = data['testRBObj']['rbAtTypes']
+                    TorSizer = wx.FlexGridSizer(1,9,5,5)
+                    TorAtms = data['testRBObj']['torAtms']
+                    rbSeq = rbData['Residue'][rbId]['rbSeq']
+                    for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
+                        torName = []
+                        for item in [seq[0],seq[1],seq[3][0]]:
+                            torName.append(data['testRBObj']['rbAtTypes'][item]+str(item))
+                        TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion: Select match to:'),0,wx.ALIGN_CENTER_VERTICAL)
+                        for i,item in enumerate([seq[0],seq[1],seq[3][0]]):
+                            atChoice = []
+                            for at in AtNames.keys():
+                                if rbAtTypes[item] in at:
+                                    atChoice.append(at)
+                            Value = ''
+                            if TorAtms[t][i] > -1:
+                                Value = atomData[TorAtms[t][i]][ct-1]
+                            TorSizer.Add(wx.StaticText(RigidBodies,-1,torName[i]),0,wx.ALIGN_CENTER_VERTICAL)
+                            torPick = wx.ComboBox(RigidBodies,-1,value=Value,
+                                choices=atChoice,style=wx.CB_READONLY|wx.CB_DROPDOWN)
+                            torPick.Bind(wx.EVT_COMBOBOX,OnTorAtPick)
+                            Indx[torPick.GetId()] = [t,i]
+                            TorSizer.Add(torPick,0,wx.ALIGN_CENTER_VERTICAL)
+                        TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,wx.ALIGN_CENTER_VERTICAL)
+                        ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
+                        ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
+                        ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
+                        Indx[ang.GetId()] = t
+                        TorSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
+                            
+                    mainSizer.Add(TorSizer)
+                else:
+                    mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,wx.ALIGN_CENTER_VERTICAL)
             else:
                 topSizer = wx.BoxSizer(wx.HORIZONTAL)
@@ -3354 +3429 @@
             btnSizer.Add((20,20),1)
             mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
-            RigidBodies.SetSizer(mainSizer)
             mainSizer.FitInside(RigidBodies)
             Size = mainSizer.GetMinSize()
+            RigidBodies.SetSizer(mainSizer)
             Size[0] += 40
             Size[1] = max(Size[1],290) + 35
             RigidBodies.SetSize(Size)
             RigidBodies.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
-            Size[1] = min(Size[1],450)
             G2frame.dataFrame.setSizePosLeft(Size)
-            
         Draw()
         

trunk/GSASIIplot.py

@@ -3521 +3521 @@
         for Atype in rbTypes:
             Radii.append(AtInfo[Atype][0])
+            if Atype == 'H':
+                Radii[-1] = 0.5
         Radii = np.array(Radii)
         Bonds = [[] for i in range(len(Radii))]