improve overall structure of documentation

modules/mol/mm/doc/buildingblock.rst

@@ -14,6 +14,9 @@ Blockmodifiers come in, with the GromacsBlockModifier as a specific
 implementation. As a special case there also exist HydrogenConstructors.
 
 
+The BuildingBlock Class
+--------------------------------------------------------------------------------
+
 .. class:: BuildingBlock
 
   .. method:: Match(residue, [,match_connectivity=True])
@@ -227,7 +230,7 @@ implementation. As a special case there also exist HydrogenConstructors.
   .. method:: GetConstraints()
     :returns: :class:`list` of all constraints
 
-Automated modification of :class:`BuildingBlock` and :class:`ResidueHandle`
+Block Modifiers
 --------------------------------------------------------------------------------
 
 .. class:: GromacsBlockModifier
@@ -321,6 +324,9 @@ Automated modification of :class:`BuildingBlock` and :class:`ResidueHandle`
     :param cmap:        :class:`Interaction` cmap to be added
 
 
+Hydrogen Constructors
+--------------------------------------------------------------------------------
+
 .. class:: GromacsHydrogenConstructor
 
   The :class:`GromacsHydrogenConstructor` is the gromacs way of adding

modules/mol/mm/doc/integrators.rst

@@ -7,6 +7,11 @@ The Integrators are a wrapper around the integrators provided by OpenMM and
 have to be attached to the :class:`Settings` when setting up a simulation
 to provide a way of making the thing shake.
 
+
+
+Verlet Dynamics
+--------------------------------------------------------------------------------
+
 .. class:: VerletIntegrator(step_size)
 
   Implementation of Verlet dynamics
@@ -15,9 +20,27 @@ to provide a way of making the thing shake.
 
 
 
-.. class:: BrownianIntegrator(temperature, friction_coeff, step_size)
+.. class:: VariableVerletIntegrator(error_tol)
 
-  Implementation of Brownian dynamics
+  Implementation of Verlet dynamics with variable time steps
+
+  :param error_tol:     :class:`float` error tolerance
+
+  .. method:: GetErrorTolerance()
+
+    :returns:           :class:`float`
+
+  .. method:: SetErrorTolerance(tol)
+
+    :param tol:         :class:`float`
+
+
+Langevin Dynamics
+--------------------------------------------------------------------------------
+
+.. class:: LangevinIntegrator(temperature, friction_coeff, step_size)
+
+  Implementation of the Langevin dynamics
 
   :param temperature:   :class:`float` temperature of heat bath in K
 
@@ -28,7 +51,7 @@ to provide a way of making the thing shake.
 
   .. method:: GetTemperature()
 
-    :returns:           :class:`float`
+    :returns:         :class:`float`
 
   .. method:: SetTemperature(temperature)
 
@@ -53,16 +76,16 @@ to provide a way of making the thing shake.
 
 
 
-.. class:: LangevinIntegrator(temperature, friction_coeff, step_size)
+.. class:: VariableLangevinIntegrator(temperature, friction_coeff, error_tol)
 
-  Implementation of the Langevin dynamics
+  Implementation of Langevin dynamics with variable time steps
 
   :param temperature:   :class:`float` temperature of heat bath in K
 
   :param friction_coeff: :class:`float` friction coefficient coupling the
                          system to the heat bath in 1/ps
 
-  :param step_size:     :class:`float` defining timestep in ps.
+  :param error_tol:     :class:`float` error_tolerance.
 
   .. method:: GetTemperature()
 
@@ -88,38 +111,32 @@ to provide a way of making the thing shake.
 
     :param seed:        :class:`int`
 
-
-
-.. class:: VariableVerletIntegrator(error_tol)
-
-  Implementation of Verlet dynamics with variable time steps
-
-  :param error_tol:     :class:`float` error tolerance
-
   .. method:: GetErrorTolerance()
 
     :returns:           :class:`float`
 
-  .. method:: SetErrorTolerance(tol)
+  .. method:: SetErrorTolerance()
 
     :param tol:         :class:`float`
 
 
+Brownian Dynamics
+--------------------------------------------------------------------------------
 
-.. class:: VariableLangevinIntegrator(temperature, friction_coeff, error_tol)
+.. class:: BrownianIntegrator(temperature, friction_coeff, step_size)
 
-  Implementation of Langevin dynamics with variable time steps
+  Implementation of Brownian dynamics
 
   :param temperature:   :class:`float` temperature of heat bath in K
 
   :param friction_coeff: :class:`float` friction coefficient coupling the
                          system to the heat bath in 1/ps
 
-  :param error_tol:     :class:`float` error_tolerance.
+  :param step_size:     :class:`float` defining timestep in ps.
 
   .. method:: GetTemperature()
 
-    :returns:         :class:`float`
+    :returns:           :class:`float`
 
   .. method:: SetTemperature(temperature)
 
@@ -140,11 +157,3 @@ to provide a way of making the thing shake.
   .. method:: SetRandomNumberSeed(seed)
 
     :param seed:        :class:`int`
-
-  .. method:: GetErrorTolerance()
-
-    :returns:           :class:`float`
-
-  .. method:: SetErrorTolerance()
-
-    :param tol:         :class:`float`

modules/mol/mm/doc/interaction.rst

@@ -108,6 +108,9 @@ Interaction Parametrization
 
 
 
+The Interaction Class
+--------------------------------------------------------------------------------
+
 .. class:: Interaction(func_type)
 
   :param func_type:     :class:`FuncType` defining a particular interaction

modules/mol/mm/doc/observers.rst

@@ -7,6 +7,9 @@ Observers can be registered to a :class:`Simulation` and get called at a
 defined interval.
 
 
+Trajectory Observers
+--------------------------------------------------------------------------------
+
 .. class:: TrajObserver(rythm) 
 
   Stores and updates the MD trajectory produced by a :class:`Simulation`

modules/mol/mm/doc/simulation.rst

@@ -47,13 +47,22 @@ mapped back to the attached structure at any time.
                         in **topology**
 
 
-  .. method:: Save(filename)
+  .. method:: Save(filename, settings)
+
+    Dumps current status of the simulation with its connected **entity** onto 
+    disk. All informations from the **entity** except plain chains, residues, 
+    atoms and bonds are lost.
 
     :param filename: :class:`str`
 
   .. method:: Load(filename)
 
+    Loads dumped simulation from disk. You have to make sure, that the provided 
+    settings are consistent with those from the saved simualtion. Undefined 
+    behaviour must be expected otherwise. 
+
     :param filename: :class:`str`
+    :param settings: :class:`ost.mm.Settings`
 
   .. method:: ApplyLBFGS([tolerance=1.0,max_iterations=1000])