Updating documentation

docs/source/api.rst

@@ -2,3 +2,6 @@ API Documentation
 =================
 
 .. automodule:: helanal.helanal
+    :show-inheritance:
+    :members:
+    :inherited-members:

docs/source/conf.py

@@ -24,11 +24,11 @@
 
 project = "helanal"
 copyright = (
-    "2024, Your name (or your organization/company/team). "
+    "2024, Fiona Naughton. "
     "Project structure based on the "
     "MDAnalysis Cookiecutter version 0.1"
 )
-author = "Your name (or your organization/company/team)"
+author = "Fiona Naughton"
 
 # The short X.Y version
 version = ""
@@ -54,7 +54,6 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.extlinks",
     "mdanalysis_sphinx_theme",
-    "nbsphinx",
 ]
 
 autosummary_generate = True

docs/source/getting_started.rst

@@ -6,33 +6,93 @@ Installation
 *TBA*
 
 
-Example use
+Basic Usage
 -----------
-Import MDAnalysis and helanal::
+helanal is used to calculate helix properties for helices with at least
+9 residues.
+
+Here, we demonstrate the basic usage and options of helanal. First, import 
+MDAnalysis and helanal::
 
     import MDAnalysis as mda
-    from MDAnalysis.tests.datafiles import PSF, DCD
     import helanal
 
-You can pass in a single selection::
+For this example, we will use datafiles from the MDAnalysis tests::
 
+    from MDAnalysis.tests.datafiles import PSF, DCD
     u = mda.Universe(PSF, DCD)
-    hel = helanl.HELANAL(u, select='name CA and resnum 161-187')
+
+To analyse a single helix, pass a selection with one atom per residue 
+(normally this will be the Cα atoms)::
+
+    hel = helanal.HELANAL(u, select='name CA and resnum 161-187')
     hel.run()
 
-All computed properties are available in ``.results``::
+All computed properties for each simulation frame will be available as
+arrays in ``.results``, e.g.::
+
+    helix_tilt = hel.results.global_tilts
+
+For more details about the properties calculated and method used, 
+see :doc:`properties_computed`.
+
+
+Further Options
+---------------
+
+- The **simulation frames** over which analysis is performed can be specified 
+  using ``start``, ``stop``, and/or ``step``, or by providing a list 
+  ``frames`` with which to slice the trajectory:: 
+
+    hel.run(start=5, step=10)
 
-    print(hel.results.summary)
+- The **reference axis** to which helix tilts and screw angles are calculated 
+  can be specified using ``ref_axis``::
 
-Alternatively, you can analyse several helices at once by passing
-in multiple selection strings::
+    hel_xaxis = helanal.HELANAL(u, select='name CA and resnum 161-187',
+                                ref_axis=[1,0,0])
 
-    hel2 = helanal.HELANAL(u, select=('name CA and resnum 100-160',
-                                      'name CA and resnum 200-230'))
+- To analyse **multiple helices** at once, pass in a list of selection
+  strings::
 
-The :func:`helix_analysis` function will carry out helix analysis on
-atom positions, treating each row of coordinates as an alpha-carbon
-equivalent::
+    hel_multi = helanal.HELANAL(u, select=('name CA and resnum 100-160',
+                                           'name CA and resnum 200-230'))
+
+  Each property in ``.results`` will now be a list of arrays, one for 
+  each helix.  
+
+- By default, the results of a single-helix analysis are flattened, such
+  that each result is a single array, rather than a list-of-arrays of 
+  length 1. This behaviour can be turned off (i.e. to be consistent 
+  with the behaviour for multi-helix analysis) using 
+  ``flatten_single_helix``::
+
+    hel_noflat = helanal.HELANAL(u, select='name CA and resnum 161-187',
+                                 flatten_single_helix=False)
+
+- Analysis can be carried out directly on a single set of positions using
+  the :func:`helix_analysis` function::
 
     hel_xyz = helanal.helix_analysis(u.atoms.positions, ref_axis=[0, 0, 1])
 
+  Results are returned as a dictionary.
+
+
+
+Citations
+---------
+
+helanal is based on the `HELANAL algorithm`_ from  [Bansal2000]_, which itself
+uses the method of [Sugeta1967]_ to characterise each local axis. Please cite 
+them when using this module in published work.
+
+.. [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.
+
+.. _`HELANAL algorithm`:
+   https://web.archive.org/web/20090226192455/http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.f