Add public versions of _generate_atomic_model and _generate_bead_model; moved...

Add public versions of _generate_atomic_model and _generate_bead_model; moved generation of strands in __init__ to precede generation of beads comands,

mrdna/segmentmodel.py

@@ -1333,12 +1333,11 @@ class SegmentModel(ArbdModel):
         self.children = self.segments = segments
 
         self._bonded_potential = dict() # cache for bonded potentials
-
+        self._generate_strands()
         self._generate_bead_model( max_basepairs_per_bead, max_nucleotides_per_bead, local_twist, escapable_twist)
 
         self.useNonbondedScheme( nbDnaScheme )
         self.useTclForces = False
-        self._generate_strands()
 
     def get_connections(self,type_=None,exclude=()):
         """ Find all connections in model, without double-counting """
@@ -1467,6 +1466,7 @@ class SegmentModel(ArbdModel):
         return self._clear_beads()
 
     def _clear_beads(self):
+        ## TODO: deprecate
         for s in self.segments:
             s.clear_all()
         self.clear_all(keep_children=True)
@@ -1641,7 +1641,20 @@ class SegmentModel(ArbdModel):
                              max_nucleotides_per_bead = 4,
                              local_twist=False,
                              escapable_twist=True):
+        ## TODO: deprecate
+        self.generate_bead_model( max_basepairs_per_bead = max_basepairs_per_bead,
+                                  max_nucleotides_per_bead = max_nucleotides_per_bead,
+                                  local_twist=local_twist,
+                                  escapable_twist=escapable_twist)
 
+    def generate_bead_model(self,
+                             max_basepairs_per_bead = 7,
+                             max_nucleotides_per_bead = 4,
+                             local_twist=False,
+                             escapable_twist=True):
+
+        self.children = self.segments # is this okay?
+        self.clear_beads()
 
         segments = self.segments
         for s in segments:
@@ -2649,7 +2662,12 @@ proc calcforces {} {
         self.dimensions = [dx,dy,dz]
 
     def _generate_atomic_model(self, scale=1):
-        self.children = self.strands
+        ## TODO: deprecate
+        self.generate_atomic_model(scale=scale)
+
+    def generate_atomic_model(self, scale=1):
+        self.clear_beads()
+        self.children = self.strands # TODO: is this going to be okay? probably
         first_atomic_index = 0
         for s in self.strands:
             first_atomic_index = s.generate_atomic_model(scale,first_atomic_index)