Changeset 4113

Timestamp:

Aug 26, 2019 9:37:54 AM (4 years ago)

Author:

vondreele

Message:

add save SHAPES bead models as pdb files from plot - remove option to make SHAPES make pdb files since no longer needed.

Location:

trunk

Files:

• GSASIIplot.py (modified) (3 diffs)
• GSASIIpwdGUI.py (modified) (3 diffs)

trunk/GSASIIplot.py

@@ -9151 +9151 @@
 ################################################################################
 
-def PlotBeadModel(G2frame,Atoms,defaults):
+def PlotBeadModel(G2frame,Atoms,defaults,PDBtext):
     '''Bead modelplotting package. For bead models from SHAPES
     '''
@@ -9349 +9349 @@
             cb.SetValue(' save as/key:')
             G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
-
+        elif mode == 'pdb':
+            Fname = os.path.join(Mydir,Page.name+'.'+mode)
+            PDB = open(Fname,'w')
+            PDB.write('REMARK    '+PDBtext+'\n')
+            for iatm,xyz in enumerate(XYZ):
+                PDB.write('ATOM   %4d  CA  ALA A%4d    %8.3f%8.3f%8.3f  1.00  0.00\n'%(iatm+1,iatm+1,xyz[0],xyz[1],xyz[2]))
+            PDB.close()
     # PlotRigidBody execution starts here (N.B. initialization above)
     new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Bead model','ogl')
@@ -9356 +9362 @@
     Page.name = Atoms[0]
     Page.Choice = None
-    choice = [' save as:','jpeg','tiff','bmp',]
+    choice = [' save as:','jpeg','tiff','bmp','pdb',]
     cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN|wx.CB_READONLY,choices=choice)
     cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)

trunk/GSASIIpwdGUI.py

@@ -5676 +5676 @@
     def ShapesSizer():
         
-        def OnPDBout(event):
-            data['Shapes']['pdbOut'] = not data['Shapes']['pdbOut']
+#        def OnPDBout(event):
+#            data['Shapes']['pdbOut'] = not data['Shapes']['pdbOut']
             
         def OnShapeSelect(event):
@@ -5701 +5701 @@
             print('%s %.3f'%('selected r value',pattern[-1]))
             print('%s %.3f'%('selected Delta P(r)',PRcalc[r][-1]))
+            PDBtext = 'P(R) dif: %.3f r-value: %.3f Nbeads: %d'%(PRcalc[r][-1],pattern[-1],len(selAtoms[1]))
 #            RefreshPlots(True)
             G2plt.PlotPatterns(G2frame,plotType='SASD',newPlot=True)
             G2plt.PlotSASDPairDist(G2frame)
-            G2plt.PlotBeadModel(G2frame,selAtoms,plotDefaults)
+            G2plt.PlotBeadModel(G2frame,selAtoms,plotDefaults,PDBtext)
         
         shapeSizer = wx.BoxSizer(wx.VERTICAL)
@@ -5741 +5742 @@
         beadsep = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'boxStep',min=3.5,max=5,nDig=(10,1))
         parmSizer.Add(beadsep,0,WACV)        
-        pdb = wx.CheckBox(G2frame.dataWindow,label=' Save as pdb files?: ')
-        pdb.SetValue(data['Shapes']['pdbOut'])
-        pdb.Bind(wx.EVT_CHECKBOX, OnPDBout)       
-        parmSizer.Add(pdb,0,WACV)
+#        pdb = wx.CheckBox(G2frame.dataWindow,label=' Save as pdb files?: ')
+#        pdb.SetValue(data['Shapes']['pdbOut'])
+#        pdb.Bind(wx.EVT_CHECKBOX, OnPDBout)       
+#        parmSizer.Add(pdb,0,WACV)
         
         shapeSizer.Add(parmSizer)