Fixed some small bugs; updated intrahelical iteration to use linked-list...

Fixed some small bugs; updated intrahelical iteration to use linked-list scheme; updated bead generation

arbdmodel.py

@@ -177,13 +177,16 @@ class Parent():
 class Child():
     def __init__(self, parent=None):
         self.parent = parent
+        if parent is not None:
+            assert( isinstance(parent, Parent) )
+            parent.children.append(self)
 
     def __getattr__(self, name):
         """
         Try to get attribute from the parent
         """
         # if self.parent is not None:
-        if "parent" not in self.__dict__ or self.__dict__["parent"] is None:
+        if "parent" not in self.__dict__ or self.__dict__["parent"] is None or name is "children":
             raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
         # if ismethod(ret):
         #     raise AttributeError("Is Method!")
@@ -245,6 +248,7 @@ class ParticleType():
 
     excludedAttributes = ("idx","type_",
                           "position",
+                          "children",
                           "parent", "excludedAttributes",
     )
 
@@ -294,7 +298,10 @@ class ParticleType():
 
 class PointParticle(Transformable, Child):
     def __init__(self, type_, position, name="A", segname="A", **kwargs):
-        Child.__init__(self, parent=None)
+        parent = None
+        if 'parent' in kwargs:
+            parent = kwargs['parent']
+        Child.__init__(self, parent=parent)
         Transformable.__init__(self,position)
 
         self.type_    = type_                
@@ -420,7 +427,7 @@ class PdbModel(Transformable, Parent):
                 data = dict(
                     idx     = idx,
                     segname = "A",
-                    resid   = "%d%c%c" % (idx," "," "), # TODO: work with large indeces
+                    resid   = "%d%c%c" % (idx," "," "), # TODO: work with large indices
                     name    = p.type_.name[:1],
                     resname = p.type_.name[:3],
                     type    = p.type_.name[:1],