some documentation pimps

modules/mol/mm/doc/forcefield.rst

@@ -127,6 +127,8 @@ as they are used in GROMACS.
     ff = new_reader.GetForcefield()
     ff.Save("charmm_forcefield.dat")
 
+The Forcefield Class
+--------------------------------------------------------------------------------
 
 .. class:: Forcefield
 

modules/mol/mm/doc/molmm.rst

@@ -78,3 +78,16 @@ You want to create your own :class:`BuildingBlock` to parametrize custom
 residues? Or even generate your custom :class:`Forcefield`? 
 Check out the mm dir in the examples/code_fragments directory. 
 
+Documentation
+--------------------------------------------------------------------------------
+
+.. toctree::
+  interaction
+  buildingblock
+  forcefield
+  settings
+  topology
+  observers
+  integrators
+  simulation
+

modules/mol/mm/doc/topology.rst

@@ -13,6 +13,9 @@ as soon as a :class:`Simulation` is set up. To make setting up a
 to create a :class:`Topology` based on an mm :class:`Settings` object, 
 that should suffice most needs.
 
+Automatically Create Topologies
+--------------------------------------------------------------------------------
+
 .. class:: TopologyCreator
 
   .. method:: Create(entity, settings)
@@ -41,8 +44,10 @@ that should suffice most needs.
     #. Check, whether the residues match with the building blocks
     
     #. Extract bonds/angles etc. based on the flags in the **settings**
+
+    #. Impropers and CMaps get only extracted when they are defined in the :class:`BuildingBlock`
     
-    #. Add Parametrization from forcefield to the Topology
+    #. Add Parametrization from :class:`Forcefield` to the :class:`Topology`. Note, that you can override the :class:`Forcefield` parametrization if you add this particular :class:`Interaction` in a parametrized form in the :class:`Buildingblock`!!!
     
     #. Rename entity back to PDB naming if according flag is set in **settings**
 
@@ -67,6 +72,10 @@ that should suffice most needs.
                         :class:`RuntimeError` can be supressed by the 
                         according flag in the :class:`Settings` object.
 
+
+The Topology Class
+--------------------------------------------------------------------------------
+
 .. class:: Topology(masses)
 
   :param masses:        :class:`list` of the particles masses