API docs for propka

- use autosummary (with custom module template)
- updated module docs for all modules so that they are included
  with sphinx autodocs

docs/source/api.rst

@@ -0,0 +1,78 @@
+.. -*- coding: utf-8 -*-
+
+===============
+ API Reference
+===============
+
+The :program:`propka3` command provides a command-line interface to
+PROPKA 3's functionality. It is built on classes and functions in the
+:mod:`propka` module. The API of :mod:`propka` is documented here for
+developers who might want to directly use the PROPKA 3 code.
+
+.. Note::
+
+   The API is still changing and there is currently no guarantee that
+   it will remain stable between minor releases.
+
+
+
+.. currentmodule:: propka
+
+.. module:: propka		   
+
+
+Data structures
+===============
+
+.. autosummary::
+   :toctree: api
+      
+   atom
+   bonds
+   group   
+   conformation_container
+   molecular_container
+
+   
+I/O
+===
+
+.. autosummary::
+   :toctree: api
+
+   input
+   lib
+   output
+   parameters
+   hybrid36
+   ligand_pka_values
+   run
+   version
+   
+   
+Structure processing
+====================
+
+.. autosummary::
+   :toctree: api
+
+   protonate
+   hydrogens	     
+   ligand
+
+	     
+Calculations
+============
+
+.. autosummary::
+   :toctree: api
+
+   calculations
+   coupled_groups
+   determinant
+   determinants
+   energy
+   iterative
+   vector_algebra
+
+