diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py index 19c47bedbe1..5945ee5ac32 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py @@ -65,12 +65,12 @@ results = [ [ # frame 1 [ # hbond 1 - , , , + , , , , , , , ], [ # hbond 2 - , , , + , , , , , , , ], @@ -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 - , , , + , , , , , , , ], [ # hbond 2 - , , , + , , , , , , , ], @@ -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