Changeset 3030

Timestamp:

Aug 28, 2017 3:29:45 PM (6 years ago)

Author:

vondreele

Message:

make protein validation work with old (works) and new (doesn't work) errat versions via config control
add reference text to console out put for protein validation
contour plots for PWDR q-plots & d-plots - now not allowed as X-axes not linear as required for contour plots.

Location:

trunk

Files:

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

trunk/GSASIImath.py

@@ -2565 +2565 @@
 ###############################################################################
 
-def validProtein(Phase):
+def validProtein(Phase,old):
     
     def sumintact(intact):
@@ -2574 +2574 @@
     resNames = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
         'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE']
-    old = True          #use errat version 1 math
 # data from errat.f
     b1_old = np.array([ 
@@ -2660 +2659 @@
                 tgts += list(Boxes[jbox[0],jbox[1],jbox[2]])
         tgts = list(set(tgts))
-        tgts = [tgt for tgt in tgts if np.sum((XYZ[ia]-XYZ[tgt])**2) <= dsmax]
+        tgts = [tgt for tgt in tgts if np.sum((XYZ[ia]-XYZ[tgt])**2) < dsmax]
         tgts = [tgt for tgt in tgts if atom[:3] != cartAtoms[tgt][:3]]    #exclude same residue
         ires = int(atom[0])

trunk/GSASIIphsGUI.py

@@ -3291 +3291 @@
         
     def OnValidProtein(event):
-        resNames,Probs = G2mth.validProtein(data)
-        G2plt.PlotAAProb(G2frame,resNames,Probs,Title='Error score for %s'%(data['General']['Name']),
-            thresh=[8.0,6.0])
-#            thresh=[17.190823041860433,11.526684477428809])
+        old = GSASIIpath.GetConfigValue('Old protein validator',True)
+        resNames,Probs = G2mth.validProtein(data,old)
+        if old:             #duplicate errat.f  
+            print 'Protein validation based on errat.f'
+            print 'Ref: Colovos, C. & Yeates, T.O. Protein Science 2, 1511-1519 (1991).'
+            print 'Residue error scores >6 for 5% & >8 for 1% likelihood of being correct'
+            G2plt.PlotAAProb(G2frame,resNames,Probs,Title='Error score for %s'%(data['General']['Name']),
+                thresh=[8.0,6.0])
+        else:
+            print 'Protein validation based on erratv2.cpp; by D. Obukhov & T. Yeates'
+            print 'Ref: Colovos, C. & Yates, T.O. Protein Science 2, 1511-1519 (1991).'
+            print 'Residue error scores >11.5 for 5% & >17.2 for 1% likelihood of being correct'
+            G2plt.PlotAAProb(G2frame,resNames,Probs,Title='Error score for %s'%(data['General']['Name']),
+                thresh=[17.191,11.527])
 
     def OnSetAll(event):

trunk/GSASIIplot.py

@@ -1365 +1365 @@
                 G2frame.SinglePlot = True                
             G2frame.Contour = not G2frame.Contour
+            if G2frame.Contour:
+                G2frame.plotStyle['qPlot'] = False
+                G2frame.plotStyle['dPlot'] = False
         elif event.key == 'q': 
             if 'PWDR' in plottype:
                 newPlot = True
                 G2frame.plotStyle['qPlot'] = not G2frame.plotStyle['qPlot']
+                if G2frame.plotStyle['qPlot']:
+                    G2frame.Contour = False
                 G2frame.plotStyle['dPlot'] = False
             elif plottype in ['SASD','REFD']:
@@ -1375 +1380 @@
         elif event.key == 't' and 'PWDR' in plottype:
             G2frame.plotStyle['dPlot'] = not G2frame.plotStyle['dPlot']
+            if G2frame.plotStyle['dPlot']:
+                G2frame.Contour = False                
             G2frame.plotStyle['qPlot'] = False
             newPlot = True