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
+
+

docs/source/index.rst

@@ -18,6 +18,9 @@ PROPKA 3 predicts the |pKa| values of ionizable groups in proteins
 [Sondergaard2011]_ and protein-ligand complexes based on the 3D
 structure [Olsson2011]_.
 
+This package installs the :program:`propka3` command and the
+:mod:`propka` Python package.
+
    
 License and source code
 =======================
@@ -81,6 +84,7 @@ Indices and tables
 
    installation
    quickstart
+   api
    references
 
   

docs/source/installation.rst

@@ -21,7 +21,7 @@ The easiest way to install a release of PROPKA 3 is from the `PyPI archive`_ wit
 
    
 This installation will install the :mod:`propka` Python module and the
-:command:`propka3` executable script. As always, a virtual environment (e.g., via
+:program:`propka3` executable script. As always, a virtual environment (e.g., via
 `virtualenv`_) is recommended when installing packages.
 
 Source-based installation

docs/source/quickstart.rst

@@ -8,7 +8,7 @@
  Quickstart Guide
 ==================
 
-PROPKA can be used either as a module or via the installed script :command:`propka3`; i.e., either
+PROPKA can be used either as a module or via the installed script :program:`propka3`; i.e., either
 
 .. code-block:: bash
 
@@ -26,9 +26,9 @@ works for invoking PROPKA.
 Predicting protein residue |pKa| values
 =======================================
 
-Most users run PROPKA by invoking the program with a PDB file as its
-argument; e.g., for PDB 1HPX_ (HIV-1 protease complexed with the
-inhibitor KNI-272)
+Most users run PROPKA by invoking the :program:`propka3` program with
+a PDB file as its argument; e.g., for PDB 1HPX_ (HIV-1 protease
+complexed with the inhibitor KNI-272)
 
 .. code-block:: bash