Changeset 3033

Timestamp:

Aug 30, 2017 3:09:56 PM (5 years ago)

Author:

vondreele

Message:

fixes to protein validate, "old" works; not "old" close but not perfect

Location:

trunk

Files:

• . (modified) (1 prop)
• GSASIImath.py (modified) (2 diffs)
• GSASIIphsGUI.py (modified) (1 diff)
• config_example.py (modified) (1 diff)

trunk/GSASIImath.py

@@ -2602 +2602 @@
         if atom[1] in resNames:
             if atom[4].strip() in ['S','Se']:
+                if not old:
+                    continue        #S,Se skipped for erratv2?
                 atom[3] = 'Os'
                 atom[4] = 'O'
             cartAtoms.append(atom[:cx+3])
             cartAtoms[-1][cx:cx+3] = np.inner(Amat,cartAtoms[-1][cx:cx+3])
-            if atom[3] in ['N','CA','C','O']:
-                cartAtoms[-1].append('B')
-            else:
-                cartAtoms[-1].append('S')
     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]])
@@ -2662 +2660 @@
         tgts = [tgt for tgt in tgts if atom[:3] != cartAtoms[tgt][:3]]    #exclude same residue
         ires = int(atom[0])
-        if atom[3].strip() == 'C':
-            tgts = [tgt for tgt in tgts if not (cartAtoms[tgt][3].strip() == 'N' and int(cartAtoms[tgt][0]) in [ires-1,ires+1])]
-        elif atom[3].strip() == 'N':
-            tgts = [tgt for tgt in tgts if not (cartAtoms[tgt][3].strip() in ['C','CA'] and int(cartAtoms[tgt][0]) in [ires-1,ires+1])]
-        elif atom[3].strip() == 'CA':
-            tgts = [tgt for tgt in tgts if not (cartAtoms[tgt][3].strip() == 'N' and int(cartAtoms[tgt][0]) in [ires-1,ires+1])]
+        if old:
+            if atom[3].strip() == 'C':
+                tgts = [tgt for tgt in tgts if not (cartAtoms[tgt][3].strip() == 'N' and int(cartAtoms[tgt][0]) in [ires-1,ires+1])]
+            elif atom[3].strip() == 'N':
+                tgts = [tgt for tgt in tgts if not (cartAtoms[tgt][3].strip() in ['C','CA'] and int(cartAtoms[tgt][0]) in [ires-1,ires+1])]
+            elif atom[3].strip() == 'CA':
+                tgts = [tgt for tgt in tgts if not (cartAtoms[tgt][3].strip() == 'N' and int(cartAtoms[tgt][0]) in [ires-1,ires+1])]
+        else:
+            if atom[3].strip() == 'C':
+                tgts = [tgt for tgt in tgts if not (cartAtoms[tgt][3].strip() == 'N' and int(cartAtoms[tgt][0]) == ires+1)]
+            elif atom[3].strip() == 'N':
+                tgts = [tgt for tgt in tgts if not (cartAtoms[tgt][3].strip() == 'C' and int(cartAtoms[tgt][0]) == ires-1)]
         for tgt in tgts:
             dsqt = np.sqrt(np.sum((XYZ[ia]-XYZ[tgt])**2))

trunk/GSASIIphsGUI.py

@@ -3291 +3291 @@
         
     def OnValidProtein(event):
-        old = GSASIIpath.GetConfigValue('Old protein validator',True)
+        old = GSASIIpath.GetConfigValue('Old_protein_validator',True)
         resNames,Probs = G2mth.validProtein(data,old)
         if old:             #duplicate errat.f  

trunk/config_example.py

@@ -159 +159 @@
 computations are performed in-line. 
 '''
+
+Old_protein_validator = True
+''' When True (default) select the old protein validator of Colovos & Yeates (errat) or
+if False use that (erratv2) of Obukhov & Yeates.
+'''