Changeset 485

Timestamp:

Feb 16, 2012 10:56:42 AM (12 years ago)

Author:

vondreele

Message:

 

Location:

trunk

Files:

• G2importphase.py (modified) (2 diffs)
• GSASIIIO.py (modified) (3 diffs)
• GSASIImath.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (1 diff)

trunk/G2importphase.py

@@ -18 +18 @@
             extensionlist=('.pdb','.ent','.PDB','.ENT'),
             strictExtension=True,
-            formatName = 'PDF',
+            formatName = 'PDB',
             longFormatName = 'Original Protein Data Bank (.pdb file) import'
             )
@@ -32 +32 @@
         except Exception as detail:
             print 'PDB read error:',detail # for testing
+            traceback.print_exc(file=sys.stdout)
             return False
 

trunk/GSASIIIO.py

@@ -1128 +1128 @@
             if 'AT' in key[6:8]:
                 S = EXPphase[key]
-                Atom = [int(S[56:60]),S[50:54].strip().upper(),S[54:56],
+                Atom = [S[56:60],S[50:54].strip().upper(),S[54:56],
                     S[46:51].strip(),S[:8].strip(),'',
                     float(S[16:24]),float(S[24:32]),float(S[32:40]),
@@ -1193 +1193 @@
             SpGrp = S[55:65]
             E,SGData = G2spc.SpcGroup(SpGrp)
-            if E: 
-                print ' ERROR in space group symbol ',SpGrp,' in file ',filename
-                print ' N.B.: make sure spaces separate axial fields in symbol' 
+            while E:
                 print G2spc.SGErrors(E)
-                return None
+                dlg = wx.TextEntryDialog(None,
+                    SpGrp[:-1]+' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
+                    'ERROR in space group symbol','',style=wx.OK)
+                if dlg.ShowModal() == wx.ID_OK:
+                    SpGrp = dlg.GetValue()
+                    E,SGData = G2spc.SpcGroup(SpGrp)
+                else:
+                    return None
+                dlg.Destroy()                
             SGlines = G2spc.SGPrint(SGData)
             for line in SGlines: print line
@@ -1208 +1214 @@
             XYZ = [float(S[31:39]),float(S[39:47]),float(S[47:55])]
             XYZ = np.inner(AB,XYZ)
+            XYZ = np.where(abs(XYZ)<0.00001,0,XYZ)
             SytSym,Mult = G2spc.SytSym(XYZ,SGData)
             Uiso = float(S[61:67])/EightPiSq

trunk/GSASIImath.py

@@ -457 +457 @@
     
     sigVals = [-0.001,-0.01,-0.01]
+    sig = sigVals[M-3]
     if 'covMatrix' in covData:
         parmNames = []
         dx = .00001
         N = M*3
-        sig = sigVals[M-3]
         dadx = np.zeros(N)
         for i in range(N):

trunk/GSASIIphsGUI.py

@@ -1893 +1893 @@
         SetupDrawingData()
         drawingData = data['Drawing']
-        print 'Rotation:',drawingData['Rotation']
         if generalData['Type'] == 'nuclear':
             pickChoice = ['Atoms','Bonds','Torsions','Planes']