add docs

docs/source/api.rst

@@ -1,8 +1,4 @@
 API Documentation
 =================
 
-.. autosummary::
-   :toctree: autosummary
-   :recursive:
-
-   helanal
+.. automodule:: helanal.helanal

docs/source/getting_started.rst

@@ -1,4 +1,38 @@
 Getting Started
 ===============
 
-This page details how to get started with helanal. 
+Installation
+------------
+*TBA*
+
+
+Example use
+-----------
+Import MDAnalysis and helanal::
+
+    import MDAnalysis as mda
+    from MDAnalysis.tests.datafiles import PSF, DCD
+    import helanal
+
+You can pass in a single selection::
+
+    u = mda.Universe(PSF, DCD)
+    hel = helanl.HELANAL(u, select='name CA and resnum 161-187')
+    hel.run()
+
+All computed properties are available in ``.results``::
+
+    print(hel.results.summary)
+
+Alternatively, you can analyse several helices at once by passing
+in multiple selection strings::
+
+    hel2 = helanal.HELANAL(u, select=('name CA and resnum 100-160',
+                                      'name CA and resnum 200-230'))
+
+The :func:`helix_analysis` function will carry out helix analysis on
+atom positions, treating each row of coordinates as an alpha-carbon
+equivalent::
+
+    hel_xyz = helanal.helix_analysis(u.atoms.positions, ref_axis=[0, 0, 1])
+

docs/source/index.rst

@@ -6,6 +6,26 @@
 Welcome to helanal's documentation!
 =========================================================
 
+This module contains code to analyse protein helices using the
+HELANAL_ algorithm
+([Bansal2000]_ , [Sugeta1967]_ ).
+
+HELANAL_ quantifies the geometry of helices in proteins on the basis of their
+Cα atoms. It can determine local structural features such as the local
+helical twist and rise, virtual torsion angle, local helix origins and
+bending angles between successive local helix axes.
+
+.. _HELANAL: https://pubmed.ncbi.nlm.nih.gov/10798526/
+
+.. [Sugeta1967] Sugeta, H. and Miyazawa, T. 1967. General method for
+   calculating helical parameters of polymer chains from bond lengths, bond
+   angles and internal rotation angles. *Biopolymers* 5 673 - 679
+
+.. [Bansal2000] Bansal M, Kumar S, Velavan R. 2000.
+   HELANAL - A program to characterise helix geometry in proteins.
+   *J Biomol Struct Dyn.*  17(5):811-819.
+
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:

helanal/helanal.py

@@ -1,3 +1,27 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+#
+# MDAnalysis --- https://www.mdanalysis.org
+# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
 """
 HELANAL --- analysis of protein helices
 =======================================
@@ -21,6 +45,22 @@
    HELANAL - A program to characterise helix geometry in proteins.
    *J Biomol Struct Dyn.*  17(5):811-819.
 
+
+Classes
+-------
+
+.. autoclass:: HELANAL
+
+
+Functions
+---------
+
+.. autofunction:: helix_analysis
+
+.. autofunction:: vector_of_best_fit
+
+.. autofunction:: local_screw_angles
+
 """
 
 import warnings