Changeset 3247

Timestamp:

Jan 29, 2018 9:34:15 AM (5 years ago)

Author:

vondreele

Message:

implement pick of protein validation bar - new view point on structure plot an N atom for selected residue
fix of non-gray modulated magnetic structures

Location:

trunk

Files:

• GSASIImath.py (modified) (7 diffs)
• GSASIIphsGUI.py (modified) (2 diffs)
• GSASIIplot.py (modified) (6 diffs)
• GSASIIspc.py (modified) (2 diffs)

trunk/GSASIImath.py

@@ -2689 +2689 @@
                 cartAtoms[-1][4] = 'O'
             cartAtoms[-1][cx:cx+3] = np.inner(Amat,cartAtoms[-1][cx:cx+3])
+            cartAtoms[-1].append(atom[cia+8])
     XYZ = np.array([atom[cx:cx+3] for atom in cartAtoms])
     xyzmin = np.array([np.min(XYZ.T[i]) for i in [0,1,2]])
@@ -2713 +2714 @@
     res = []
     resNames = []
+    resIDs = {}
     resname = []
+    resID = {}
     newChain = True
     intact = {'CC':0,'CN':0,'CO':0,'NN':0,'NO':0,'OO':0,'NC':0,'OC':0,'ON':0}
@@ -2724 +2727 @@
                 chainIntAct.append(resIntAct)
                 resNames += resname
+                resIDs.update(resID)
                 res = []
                 resname = []
+                resID = {}
                 resIntAct = []
                 intact = {'CC':0,'CN':0,'CO':0,'NN':0,'NO':0,'OO':0,'NC':0,'OC':0,'ON':0}
@@ -2738 +2743 @@
                     resIntAct.append(sumintact(intact))
             res.append(atom[0])
-            resname.append('%s-%s%s'%(atom[2],atom[0],atom[1]))
+            name = '%s-%s%s'%(atom[2],atom[0],atom[1])
+            resname.append(name)
+            resID[name] = atom[-1]
             if not newChain:
                 resIntAct.append(sumintact(intact))
@@ -2777 +2784 @@
 #        print ia,atom[0]+atom[1]+atom[3],tgts,jntact['CC'],jntact['CN']+jntact['NC'],jntact['CO']+jntact['OC'],jntact['NN'],jntact['NO']+jntact['ON']
     resNames += resname
+    resIDs.update(resID)
     resIntAct.append(sumintact(intact))
     chainIntAct.append(resIntAct)
@@ -2789 +2797 @@
                 summ = 0.
                 for j in range(i-4,i+5):
-                    summ += np.sum(np.array(IntAct[j].values()))
+                    summ += np.sum(np.array(list(IntAct[j].values())))
                     if old:
                         mtrx[0] += IntAct[j]['CC']
@@ -2815 +2823 @@
         Probs += 4*[0.,]        #skip last 4 residues in chain
         chainProb += Probs
-    return resNames,chainProb
+    return resNames,chainProb,resIDs
     
 ################################################################################

trunk/GSASIIphsGUI.py

@@ -3457 +3457 @@
                         
     def OnValidProtein(event):
-        resNames,Probs1 = G2mth.validProtein(data,True)         #old version
-        resNames,Probs2 = G2mth.validProtein(data,False)        #new version
+        
+        def pickHandler(resName):
+            drawData = data['Drawing']
+            resid = resIDs[resName]
+            drawData['viewPoint'][0] = atomData[AtLookUp[resid]][cx:cx+3]
+            UpdateDrawAtoms()
+            G2plt.PlotStructure(G2frame,data)
+        
+        atomData = data['Atoms']
+        cx,ct,cs,cia = data['General']['AtomPtrs']
+        AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8)
+        resNames,Probs1,resIDs = G2mth.validProtein(data,True)         #old version
+        resNames,Probs2,resIDs = G2mth.validProtein(data,False)        #new version
         print ('Plot 1 is Protein validation based on errat.f')
         print ('Ref: Colovos, C. & Yeates, T.O. Protein Science 2, 1511-1519 (1991).')
@@ -3468 +3479 @@
         print ('NB: this calc. gives a close approximate to original erratv2 result')
         G2plt.PlotAAProb(G2frame,resNames,Probs1,Probs2,Title='Error score for %s'%(data['General']['Name']),
-            thresh=[[8.0,6.0],[17.191,11.527]])
+            thresh=[[8.0,6.0],[17.191,11.527]],pickHandler=pickHandler)
 
     def OnIsoDistortCalc(event):

trunk/GSASIIplot.py

@@ -3232 +3232 @@
 ##### PlotHist
 ################################################################################
-def PlotAAProb(G2frame,resNames,Probs1,Probs2,Title='',thresh=None):
+def PlotAAProb(G2frame,resNames,Probs1,Probs2,Title='',thresh=None,pickHandler=None):
 
     def OnMotion(event):
@@ -3256 +3256 @@
             except TypeError:
                 G2frame.G2plotNB.status.SetStatusText('Select AA error plot first',1)
+                
+    def OnPick(event):
+        xpos = event.mouseevent.xdata
+        if xpos and pickHandler:
+            xpos = int(xpos+.5)
+            if 0 <= xpos < len(resNames):
+                resName = resNames[xpos]
+            else:
+                resName = ''
+            pickHandler(resName)
     
     def Draw():
@@ -3267 +3277 @@
         colors = list(np.where(np.array(Probs1)>thresh[0][1],'r','b'))
         resNums = np.arange(len(resNames))
-        Plot1.bar(resNums,Probs1,color=colors,linewidth=0)
+        Plot1.bar(resNums,Probs1,color=colors,linewidth=0,picker=1)
         if thresh is not None:
             for item in thresh[0]:
@@ -3275 +3285 @@
         Plot2.set_xlabel(r'Residue',fontsize=14)        
         colors = list(np.where(np.array(Probs2)>thresh[1][1],'r','b'))
-        Plot2.bar(resNums,Probs2,color=colors,linewidth=0)
+        Plot2.bar(resNums,Probs2,color=colors,linewidth=0,picker=1)
         if thresh is not None:
             for item in thresh[1]:
@@ -3283 +3293 @@
     
     new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(Title,'mpl')
-#        Page.canvas.mpl_connect('key_press_event', OnKeyPress)
+    Page.canvas.mpl_connect('pick_event', OnPick)
     Page.canvas.mpl_connect('motion_notify_event', OnMotion)
     Draw()
@@ -6812 +6822 @@
             elif atom[cs+1] == 'number':
                 RenderLabel(x,y,z,'  '+str(iat),radius,wxGreen,matRot)
-            elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
+            elif atom[cs+1] == 'residue' and atom[ct-1] in ['CA','CA  A']:
                 RenderLabel(x,y,z,'  '+atom[ct-4],radius,wxGreen,matRot)
-            elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
+            elif atom[cs+1] == '1-letter' and atom[ct-1] in ['CA','CA  A']:
                 RenderLabel(x,y,z,'  '+atom[ct-3],radius,wxGreen,matRot)
-            elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
+            elif atom[cs+1] == 'chain' and atom[ct-1] in ['CA','CA  A']:
                 RenderLabel(x,y,z,'  '+atom[ct-2],radius,wxGreen,matRot)
 #        glDisable(GL_BLEND)

trunk/GSASIIspc.py

@@ -1450 +1450 @@
     SSGData = {'SSpGrp':SGData['SpGrp']+SSymbol,'modQ':modQ,'modSymb':modsym,'SSGKl':SSGKl}
     SSCen = np.zeros((len(SGData['SGCen']),4))
-#    if SGData['SGFixed']:
-#        for icen,cen in enumerate(SGData['SGCen']):
-#            SSCen[icen] = cen
-#    else:
-    if True:
-        for icen,cen in enumerate(SGData['SGCen']):
-            SSCen[icen,0:3] = cen
-        SSCen[0] = np.zeros(4)
+    for icen,cen in enumerate(SGData['SGCen']):
+        SSCen[icen,0:3] = cen
+    SSCen[0] = np.zeros(4)
     SSGData['SSGCen'] = SSCen
     SSGData['SSGOps'] = []
@@ -1463 +1458 @@
         T = np.zeros(4)
         ssop = np.zeros((4,4))
-#        if SGData['SGFixed']:
-#            ssop = op[0]
-#            T = op[1]
-#        else:
-        if True:
-            ssop[:3,:3] = op[0]
-            T[:3] = op[1]
+        ssop[:3,:3] = op[0]
+        T[:3] = op[1]
         SSGData['SSGOps'].append([ssop,T])
     E,Result = genSSGOps()