hbon analysis: doc fixes

Apparently, napoleon does not like a single Notes and See Also section, need to
use reST.

Also named the 1-based indices "idx" in the docs.

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -65,12 +65,12 @@
     results = [
         [ # frame 1
            [ # hbond 1
-              <donor index (1-based)>, <acceptor index (1-based)>, <donor index (0-based)>,
+              <donor idx (1-based)>, <acceptor idx (1-based)>, <donor index (0-based)>,
               <acceptor index (0-based)>, <donor string>, <acceptor string>,
               <distance>, <angle>
            ],
            [ # hbond 2
-              <donor index (1-based)>, <acceptor index (1-based)>, <donor index (0-based)>,
+              <donor idx (1-based)>, <acceptor idx (1-based)>, <donor index (0-based)>,
               <acceptor index (0-based)>, <donor string>, <acceptor string>,
               <distance>, <angle>
            ],
@@ -286,7 +286,7 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
 
       .. Note::
 
-         The *index* is a 1-based index. To get the :attr:`Atom.index` (the
+         Each index variable named *idx* is a 1-based index. To get the :attr:`Atom.index` (the
          0-based index typically used in MDAnalysis simply subtract 1. For
          instance, to find an atom in :attr:`Universe.atoms` by *index* one
          would use ``u.atoms[idx_zero]``. The 1-based index is deprecated and
@@ -1001,12 +1001,12 @@ def timeseries(self):
           results = [
               [ # frame 1
                  [ # hbond 1
-                    <donor index (1-based)>, <acceptor index (1-based)>, <donor index (0-based)>,
+                    <donor idx (1-based)>, <acceptor idx (1-based)>, <donor index (0-based)>,
                     <acceptor index (0-based)>, <donor string>, <acceptor string>,
                     <distance>, <angle>
                  ],
                  [ # hbond 2
-                    <donor index (1-based)>, <acceptor index (1-based)>, <donor index (0-based)>,
+                    <donor idx (1-based)>, <acceptor idx (1-based)>, <donor index (0-based)>,
                     <acceptor index (0-based)>, <donor string>, <acceptor string>,
                     <distance>, <angle>
                  ],
@@ -1022,25 +1022,24 @@ def timeseries(self):
         :attr:`~HydrogenBondAnalysis.timesteps`.
 
 
-        Note
-        ----
-        The *index* is a 1-based index. To get the :attr:`Atom.index` (the
-        0-based index typically used in MDAnalysis simply subtract 1. For
-        instance, to find an atom in :attr:`Universe.atoms` by *index* one
-        would use ``u.atoms[index-1]``.
+        .. note::
+           Each index variable named *idx* is a 1-based index. To get the :attr:`Atom.index` (the
+           0-based index typically used in MDAnalysis simply subtract 1. For
+           instance, to find an atom in :attr:`Universe.atoms` by *index* one
+           would use ``u.atoms[index-1]``.
 
-        The :attr:`timeseries` is a managed attribute and it is generated from
-        the underlying data in :attr:`_timeseries` every time the attribute is
-        accessed. It is therefore costly to call and if :attr:`timeseries` is
-        needed repeatedly it is recommended that you assign to a variable::
+           The :attr:`timeseries` is a managed attribute and it is generated
+           from the underlying data in :attr:`_timeseries` every time the
+           attribute is accessed. It is therefore costly to call and if
+           :attr:`timeseries` is needed repeatedly it is recommended that you
+           assign to a variable::
 
-          h = HydrogenBondAnalysis(u)
-          h.run()
-          timeseries = h.timeseries
+             h = HydrogenBondAnalysis(u)
+             h.run()
+             timeseries = h.timeseries
 
-        See Also
-        --------
-        HydrogenBondAnalysis.table : structured array of the data
+        .. SeeAlso::
+           :attr:`table` : structured array of the data
 
 
         .. versionchanged:: 0.16.1