Changeset 839

Timestamp:

Jan 23, 2013 12:02:59 PM (10 years ago)

Author:

vondreele

Message:

draw bonds between map peaks

File:

• trunk/GSASIIplot.py (modified) (5 diffs)

trunk/GSASIIplot.py

@@ -2585 +2585 @@
     thermal motion ellipsoids and polyhedra
     '''
+
     ForthirdPI = 4.0*math.pi/3.0
     generalData = data['General']
@@ -2633 +2634 @@
     ctrlDown = False
     
+    def FindPeaksBonds(XYZ):
+        Bonds = [[] for x in XYZ]
+        for i,xyz in enumerate(XYZ):
+            Dx = XYZ-xyz
+            dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
+            IndB = ma.nonzero(ma.masked_greater(dist,2.1))
+            for j in IndB[0]:
+                Bonds[i].append(Dx[j]/2.)
+                Bonds[j].append(-Dx[j]/2.)
+        return Bonds
+
     def OnKeyBox(event):
         import Image
@@ -3327 +3339 @@
             RenderMap(rho,rhoXYZ,indx,Rok)
         if len(mapPeaks):
+            XYZ = mapPeaks.T[1:4].T
+            mapBonds = FindPeaksBonds(XYZ)
             for ind,[mag,x,y,z,d] in enumerate(mapPeaks):
                 if ind in Ind and pageName == 'Map peaks':
@@ -3332 +3346 @@
                 else:
                     RenderMapPeak(x,y,z,Wt,mag/peakMax)
+                RenderLines(x,y,z,mapBonds[ind],Wt)
         if Backbones:
             for chain in Backbones:
@@ -3386 +3401 @@
     '''
 
-    def FindBonds(XYZ):                    #uses numpy & masks - very fast even for proteins!
-        import numpy.ma as ma
+    def FindBonds(XYZ):
         rbTypes = rbData['rbTypes']
         Radii = []