From 5747adeb3cf18030bd34e597d07972eda3475583 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 28 Apr 2015 19:49:04 +0200
Subject: [PATCH] documentation for mm observers

---
 modules/mol/mm/doc/observers.rst | 49 ++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 modules/mol/mm/doc/observers.rst

diff --git a/modules/mol/mm/doc/observers.rst b/modules/mol/mm/doc/observers.rst
new file mode 100644
index 000000000..b0a7fade2
--- /dev/null
+++ b/modules/mol/mm/doc/observers.rst
@@ -0,0 +1,49 @@
+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.
+
-- 
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