Added documentation

core/doc/CMakeLists.txt

 set(CORE_RST
 index.rst
 argcheck.rst
+pm3argparse.rst
 helper.rst
 setcompoundschemlib.rst
 )

core/doc/index.rst

@@ -9,7 +9,9 @@ modeling per se but cover standard programming issues.
 
 .. toctree:: 
   :maxdepth: 2
-  
+
+  pm3argparse
+
   argcheck
 
   helper

core/doc/pm3argparse.rst

+:mod:`~promod3.core.pm3argparse` - Parsing Command Lines
+================================================================================
+
+.. currentmodule:: promod3.core.pm3argparse
+
+Introduction
+--------------------------------------------------------------------------------
+
+A lot of the actions in |project| have a bunch of command line parameters/
+arguments in common. For example we need an input alignment quite often and
+usually for an alignment we need information on what is the target sequence,
+what identifies a template sequence and eventually a hint on the format. That
+means we need the same functionality on the command line in several actions.
+There :class:`pm3argparse.PM3ArgumentParser` serves as a simplification. It
+provides a set of standard arguments you just need to activate for your action
+plus it comes with some verification functionality for input.
+
+.. synopsis/ example
+
+Argument Parser
+--------------------------------------------------------------------------------
+
+.. autoclass:: PM3ArgumentParser
+  :members:
+
+  .. automethod:: __init__
+
+.. |descattr| replace:: :attr:`description`
+.. |argpinit| replace:: :meth:`ArgumentParser.__init__`
+.. |progattr| replace:: :attr:`prog`
+
+..  LocalWords:  currentmodule argparse ArgumentParser autoclass automethod
+..  LocalWords:  init descattr attr argpinit meth progattr prog

doc/conf.py.in

@@ -286,6 +286,9 @@ rst_epilog = """
 .. _ost_s: http://www.OpenStructure.org
 .. _nameattr: @PYTHON_DOC_URL@/library/__main__.html
 .. _mainattr: @PYTHON_DOC_URL@/library/__main__.html
+.. _descattr: @PYTHON_DOC_URL@/library/argparse.html#description
+.. _progattr: @PYTHON_DOC_URL@/library/argparse.html#prog
+.. _argpinit: @PYTHON_DOC_URL@/library/argparse.html#argparse.ArgumentParser
 .. |pep8| replace:: PEP 8
 .. _pep8: https://www.python.org/dev/peps/pep-0008/
 """ % project