update notes to include path finding

docs/source/getting_started.rst

@@ -2,7 +2,7 @@ Getting Started
 ===============
 
 This page details how to get started with ``mdahole2``.
-Note that ``mdahole2`` is only supported on Linux or macOS.
+Note that ``mdahole2`` is currently only supported on Linux or macOS.
 
 Documentation
 ~~~~~~~~~~~~~

docs/source/usage.rst

@@ -6,15 +6,35 @@ This toolkit contains the tools to interface with HOLE_
 :cite:p:`Smart1993,Smart1996` to analyse an ion channel pore or transporter
 pathway :cite:p:`Stelzl2014`.
 
+Finding your hole executable
+----------------------------
+
+The first step is to find your HOLE executable. If you have installed HOLE
+through ``conda-forge``, then you can find the executable path by searching
+``which hole``, e.g.:
+
+.. code-block:: bash
+
+    $ which hole
+    /home/username/miniforge3/envs/mdahole2/bin/hole
+
+If you have installed HOLE from the original source, the executable
+may be in your home directory instead, e.g. a path such as ``~/hole2/exe/hole``.
+
+Throughout the rest of this documentation, we will assume that your executable
+is at ``~/miniforge3/envs/mdahole2/bin/hole``.
+
+
 Using HOLE on a PDB file
 ------------------------
 
 Use the ``hole`` function to run `HOLE`_ on a single PDB file. For example,
-the code below runs the `HOLE`_ program installed at `~/hole2/exe/hole`::
+the code below runs the `HOLE`_ program installed at `~/miniforge3/envs/mdahole2/bin/hole`::
 
     from MDAnalysis.tests.datafiles import PDB_HOLE
-    from MDAnalysis.analysis import hole2
-    profiles = hole2.hole(PDB_HOLE, executable='~/hole2/exe/hole')
+    from mdahole2.analysis import hole
+
+    profiles = hole(PDB_HOLE, executable='~/miniforge3/envs/mdahole2/bin/hole')
     # to create a VMD surface of the pore
     hole2.create_vmd_surface(filename='hole.vmd')
 
@@ -55,11 +75,11 @@ The class can be set-up and run like a normal MDAnalysis analysis class::
 
     import MDAnalysis as mda
     from MDAnalysis.tests.datafiles import MULTIPDB_HOLE
-    from MDAnalysis.analysis import hole2
+    from mdahole2.analysis import HoleAnalysis
 
     u = mda.Universe(MULTIPDB_HOLE)
 
-    ha = hole2.HoleAnalysis(u, executable='~/hole2/exe/hole') as h2:
+    ha = HoleAnalysis(u, executable='~/miniforge3/envs/mdahole2/bin/hole') as h2:
     ha.run()
     ha.create_vmd_surface(filename='hole.vmd')
 
@@ -80,7 +100,7 @@ call :meth:`~HoleAnalysis.delete_temporary_files`::
 Alternatively, you can use HoleAnalysis as a context manager that deletes
 temporary files when you are finished with the context manager::
 
-    with hole2.HoleAnalysis(u, executable='~/hole2/exe/hole') as h2:
+    with HoleAnalysis(u, executable='~/miniforge3/envs/mdahole2/bin/hole') as h2:
         h2.run()
         h2.create_vmd_surface()
 
@@ -104,14 +124,14 @@ To analyze a full trajectory and write pore surfaces for all frames to file
 :file:`hole_surface.vmd`, use ::
 
     import MDAnalysis as mda
-    from MDAnalysis.analysis import hole2
+    from mdahole2.analysis import HoleAnalysis
 
     # load example trajectory MULTIPDB_HOLE
     from MDAnalysis.tests.datafiles import MULTIPDB_HOLE
 
     u = mda.Universe(MULTIPDB_HOLE)
 
-    with hole2.HoleAnalysis(u, executable='~/hole2/exe/hole') as h2:
+    with HoleAnalysis(u, executable='~/miniforge3/envs/mdahole2/bin/hole') as h2:
         h2.run()
         h2.create_vmd_surface(filename="hole_surface.vmd")
 
@@ -135,7 +155,7 @@ For example, if we want to start displaying at frame 1 (i.e., skip frame
 0), stop at frame 7, and only show every other frame (step 2) then the HOLE
 analysis will be ::
 
-    with hole2.HoleAnalysis(u, executable='~/hole2/exe/hole') as h2:
+    with HoleAnalysis(u, executable='~/miniforge3/envs/mdahole2/bin/hole') as h2:
         h2.run(start=1, stop=9, step=2)
         h2.create_vmd_surface(filename="hole_surface_subsampled.vmd")
 
@@ -238,7 +258,7 @@ You can now animate your molecule together with the surface and render it.
 
 .. [#create_vmd_surface_function] If you use the :class:`hole` class to run
               :program:`hole` on a single PDB file then you can use
-              :func:`MDAnalysis.analysis.hole2.utils.create_vmd_surface`
+              :func:`mdahole2.analysis.utils.create_vmd_surface`
               function to manually run :program:`sph_process` and
               :program:`sos_triangle` on the output files andcr eate a surface
               file.