Fixed issue with quaternion orientations in segmentmodel_from_lists

mrdna/readers/segmentmodel_from_lists.py

@@ -88,11 +88,15 @@ def set_splines(seg, coordinates, hid, hmap, hrank, fwd, orientation=None):
         for rank in range(int(maxrank)+1):
             ids = np.where((hmap == hid) * (hrank == rank))[0]
             coords.append(np.mean( [coordinates[r,:] for r in ids ], axis=0 ))
-            contours.append( float(rank)/maxrank )
+            contours.append( float(rank+0.5)/(maxrank+1) )
+            last_q = None
             if orientation is not None:
                 ids = np.where((hmap == hid) * (hrank == rank) * fwd)[0]
                 assert(len(ids) == 1)
-                quats.append( quaternion_from_matrix( orientation[ids[0]] ) )
+                q = quaternion_from_matrix( orientation[ids[0]] )
+                if last_q is not None and last_q[1:].dot(q[1:]) < 0:
+                    q = -1*q
+                quats.append(q)
                 ## TODO: average quaterion with reverse direction
 
     coords = np.array(coords)
@@ -153,7 +157,7 @@ def model_from_basepair_stack_3prime(coordinates, basepair, stack, three_prime,
     hmap,hrank,fwd = basepairs_and_stacks_to_helixmap(bps,stack)
     double_stranded_helices = np.unique(hmap[hmap >= 0])    
     strands = _three_prime_list_to_strands(three_prime)
-    
+
     """ Add ssDNA to hmap """
     hid = double_stranded_helices[-1]+1
     ss_residues = hmap < 0

mrdna/readers/segmentmodel_from_pdb.py

@@ -258,8 +258,6 @@ def SegmentModelFromPdb(*args,**kwargs):
     bps = find_basepairs(u, centers, transforms)
     stacks = find_stacks(u, centers, transforms)
 
-    # pdb.set_trace()
-
     ## Find three-prime ends
     three_prime = -np.ones(bps.shape, dtype=np.int)
     for s in u.segments: