Added function for setting splines; converted an assertion into a warning when...

Added function for setting splines; converted an assertion into a warning when beads are very close; fiex crash when helices lack crossovers

segmentmodel.py

@@ -358,12 +358,16 @@ class Segment(ConnectableElement, Group):
         self.end_position = end_position
 
         ## Set up interpolation for positions
+        self._set_splines_from_ends()
+
+        self.sequence = None
+
+
+    def _set_splines_from_ends(self):
         a = np.array([self.start_position,self.end_position]).T
         tck, u = interpolate.splprep( a, u=[0,1], s=0, k=1)
         self.position_spline_params = tck
         self.quaternion_spline_params = None
-        
-        self.sequence = None
 
 
     def clear_all(self):
@@ -1284,7 +1288,7 @@ class SegmentModel(ArbdModel):
         self._clear_beads()
 
     def update(self, segment , copy=False):
-        assert( isinstance(other, SegmentModel) )
+        assert( isinstance(segment, Segment) )
         if copy:
             segment = deepcopy(segment)
         self.segments.append(segment)
@@ -1654,7 +1658,8 @@ class SegmentModel(ArbdModel):
         if self.DEBUG: print("  Adding %d bonds" % len(intra_beads))
         for b1,b2 in intra_beads:
             # assert( not np.isclose( np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()), 0 ) )
-            assert( np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()) > 1 )
+            if np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()) < 1:
+                print("WARNING: some beads are very close")
             parent = self._getParent(b1,b2)
 
             ## TODO: could be sligtly smarter about sep
@@ -1993,7 +1998,9 @@ class SegmentModel(ArbdModel):
             for s,d in SegmentModel.walk_through_helices(s0,-d0):
                 if s == s0 and len(tmp) > 0:
                     ## end of circular helix, only add first crossover
-                    tmp.append( s.get_contour_sorted_connections_and_locations("crossover")[::d][0] + [d] )
+                    cl_list = s.get_contour_sorted_connections_and_locations("crossover")
+                    if len(cl_list) > 0:
+                        tmp.append( cl_list[::d][0] + [d] )
                 else:
                     tmp.extend( [cl + [d] for cl in s.get_contour_sorted_connections_and_locations("crossover")[::d]] )
                 processed_segments.add(s)