Added some code for debugging

dnarbd/segmentmodel.py

@@ -317,6 +317,9 @@ class SegmentParticle(PointParticle):
                 orientation = np.eye(3)
             o.position = self.position + orientation.dot( np.array((Segment.orientation_bond.r0,0,0)) )
             
+    def __repr__(self):
+        return "<SegmentParticle {} on {}[{:.2f}]>".format( self.name, self.parent, self.contour_position)
+
 
 ## TODO break this class into smaller, better encapsulated pieces
 class Segment(ConnectableElement, Group):
@@ -724,14 +727,12 @@ class Segment(ConnectableElement, Group):
         # conn_locs = self.get_contour_sorted_connections_and_locations()
         # locs = [A for c,A,B in conn_locs]
         # existing_beads = [l.particle for l in locs if l.particle is not None]
-        # if self.name == "31-2":
-            # pdb.set_trace()
+        # if self.name == "S001":
+        #     pdb.set_trace()
 
-        existing_beads = {l.particle for l in self.locations if l.particle is not None}
-        existing_beads = sorted( list(existing_beads), key=lambda b: b.get_contour_position(self) )
+        existing_beads0 = {l.particle for l in self.locations if l.particle is not None}
+        existing_beads = sorted( list(existing_beads0), key=lambda b: b.get_contour_position(self) )
         
-        if len(existing_beads) != len(set(existing_beads)):
-            pdb.set_trace()
         for b in existing_beads:
             assert(b.parent is not None)
 
@@ -1329,6 +1330,7 @@ class SegmentModel(ArbdModel):
     def _get_potential(self, type_, kSpring, d, max_potential = None):
         key = (type_, kSpring, d, max_potential)
         if key not in self._bonded_potential:
+            assert( kSpring >= 0 )
             if type_ == "bond":
                 self._bonded_potential[key] = HarmonicBond(kSpring,d, rRange=(0,1200), max_potential=max_potential)
             elif type_ == "angle":
@@ -1484,9 +1486,15 @@ class SegmentModel(ArbdModel):
             if len(beads) <= 1:
                 pdb.set_trace()
 
+
             """ Get positions """
             positions = bead_coordinates[ids,:].T
 
+            # print("BEADS NOT IN {}:".format(s))
+            # for b,c in filter(lambda z: z[0] not in s.beads, zip(beads,contours)):
+            #     print("  {}[{:03f}]: {:0.3f}".format(b.parent.name, b.contour_position, c) )
+
+
             ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
             tck = ret[0][0]