Changeset 3048

Timestamp:

Sep 5, 2017 4:00:51 PM (6 years ago)

Author:

vondreele

Message:

remove item from config_example.py
fix bug in FindAtomsDraw?
implement multiprocessing for refinement - seems ok

Location:

trunk

Files:

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

trunk/GSASIImath.py

@@ -2657 +2657 @@
                 tgts += list(Boxes[jbox[0],jbox[1],jbox[2]])
         tgts = list(set(tgts))
+        tgts = [tgt for tgt in tgts if atom[:3] != cartAtoms[tgt][:3]]    #exclude same residue
         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])
         if old:
@@ -2686 +2686 @@
         IntAct = chainIntAct[ich]
         nRes = len(IntAct)
-        Probs = [0.,0.,0.,0.]
+        Probs = [0.,0.,0.,0.]   #skip 1st 4 residues in chain
         for i in range(4,nRes-4):
             mtrx = np.zeros(5)
@@ -2712 +2712 @@
                 prob = np.inner(np.inner(mtrx,b1),mtrx)
             Probs.append(prob)
-        Probs += 4*[0.,]
+        Probs += 4*[0.,]        #skip last 4 residues in chain
         chainProb += Probs
     return resNames,chainProb

trunk/GSASIIphsGUI.py

@@ -1003 +1003 @@
     Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
     radii = generalData['BondRadii']
-    if generalData.get('DisAglCtls',{}):
-        radii = generalData['DisAglCtls']['BondRadii']
+#    if generalData.get('DisAglCtls',{}):
+#        radii = generalData['DisAglCtls']['BondRadii']
     atomTypes = generalData['AtomTypes']
     try:
@@ -3291 +3291 @@
         
     def OnValidProtein(event):
-        resNames,Probs1 = G2mth.validProtein(data,True)
-        resNames,Probs2 = G2mth.validProtein(data,False)
+        resNames,Probs1 = G2mth.validProtein(data,True)         #old version
+        resNames,Probs2 = 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).'

trunk/GSASIIstrMath.py

@@ -28 +28 @@
 import GSASIIobj as G2obj
 import GSASIImpsubs as G2mp
-G2mp.InitMP(False)  # This disables multiprocessing 
+#G2mp.InitMP(False)  # This disables multiprocessing 
 
 sind = lambda x: np.sin(x*np.pi/180.)

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.
-'''