documentation for mm observers

modules/mol/mm/doc/observers.rst

+Observers
+================================================================================
+
+.. currentmodule:: ost.mol
+
+Observers can be registered to a :class:`Simulation` and get called at a 
+defined interval.
+
+
+.. class:: TrajObserver(rythm) 
+
+  Stores and updates the MD trajectory produced by a :class:`Simulation`
+  in memory.
+
+  :param rythm:         :class:`int` rythm, at which the observer gets
+                        notified by the simulation
+
+  .. method:: GetTraj()
+
+    Get current Trajectory
+
+    :returns:           :class:`ost.mol.CoordGroupHandle`
+
+  .. method:: Rythm()
+
+    :returns:           :class:`int` calling rythm
+
+
+.. class:: TrajWriter(rythm, pdb_filename, dcd_filename)
+
+  Writes the MD trajectory produced by a :class:`Simulation` directly to
+  disk in dcd format. 
+
+  :param rythm:         :class:`int` rythm, at which the observer gets
+                        notified by the simulation
+
+  :param pdb_filename:  :class:`str` with name of produced pdb file
+
+  :param dcd_filename:  :class:`str` with name of produced dcd file
+
+  .. method:: Rythm()
+
+    :returns:           :class:`int` calling rythm
+
+  .. method:: Finalize()
+
+    Obligatory function to be called after the last simulation step to
+    write missing information into the dcd header.
+