Improved placement of beads

Code now always places a ssDNA bead when an ssDNA segment is between two dsDNA segments.

Code now more robustly places a bead and intrahelical junctions

dnarbd/segmentmodel.py

@@ -756,6 +756,12 @@ class Segment(ConnectableElement, Group):
             # print(" %s working on %d to %d" % (self.name, eb1.position[2], eb2.position[2]))
             e_ds = eb2.get_contour_position(self) - eb1.get_contour_position(self)
             num_beads = self._get_num_beads( e_ds, max_basepairs_per_bead, max_nucleotides_per_bead )
+
+            ## Ensure there is a ssDNA bead between dsDNA beads
+            if num_beads == 0 and isinstance(self,SingleStrandedSegment) and isinstance(eb1.parent,DoubleStrandedSegment) and isinstance(eb2.parent,DoubleStrandedSegment):
+                num_beads = 1
+            ## TODO similarly ensure there is a dsDNA bead between ssDNA beads
+
             ds = e_ds / (num_beads+1)
             nts = ds*self.num_nt
             eb1.num_nt += 0.5*nts
@@ -1595,22 +1601,22 @@ class SegmentModel(ArbdModel):
             
             ## TODO improve this for combinations of ssDNA and dsDNA (maybe a1/a2 should be calculated differently)
 
+            b = None
             if isinstance(s1,DoubleStrandedSegment):
                 b = s1.get_nearest_bead(a1)
                 if b is not None:
                     if np.abs(b.get_nt_position(s1) - s1.contour_to_nt_pos(a1)) > 0.5:
                         b = None
-            elif isinstance(s2,DoubleStrandedSegment):
+            if b is None and isinstance(s2,DoubleStrandedSegment):
                 b = s2.get_nearest_bead(a2)
                 if b is not None:
                     if np.abs(b.get_nt_position(s2) - s2.contour_to_nt_pos(a2)) > 0.5:
                         b = None
-            else:
-                b = None
+
 
             if b is not None and b.parent not in (s1,s2):
                 b = None
-                
+
             if b is None:
                 ## need to generate a bead
                 if isinstance(s2,DoubleStrandedSegment):