Made changes that should improve handling of connections within a segment

mrdna/segmentmodel.py

@@ -111,7 +111,8 @@ class Connection():
 
     def delete(self):
         self.A.container.connections.remove(self)
-        self.B.container.connections.remove(self)
+        if self.B.container is not self.A.container:
+            self.B.container.connections.remove(self)
         self.A.connection = None
         self.B.connection = None
 
@@ -188,7 +189,8 @@ class ConnectableElement():
             
         A.connection = B.connection = connection
         self.connections.append(connection)
-        other.connections.append(connection)
+        if other is not self:
+            other.connections.append(connection)
         l = A.container.locations
         if A not in l: l.append(A)
         l = B.container.locations
@@ -532,9 +534,11 @@ class Segment(ConnectableElement, Group):
     def clear_all(self):
         Group.clear_all(self)  # TODO: use super?
         self.beads = []
-        for c,loc,other in self.get_connections_and_locations():
-            loc.particle = None
-            other.particle = None
+        # for c,loc,other in self.get_connections_and_locations():
+        #     loc.particle = None
+        #     other.particle = None
+        for l in self.locations:
+            l.particle = None
 
     def contour_to_nt_pos(self, contour_pos, round_nt=False):
         nt = contour_pos*(self.num_nt) - 0.5