From 412a98d3a6e26db026f868c28f2cdd0591489157 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <niklaus.johner@unibas.ch>
Date: Tue, 3 Mar 2015 18:47:37 +0100
Subject: [PATCH] Added documentation for the mol.alg.helix_kink module
---
modules/mol/alg/doc/molalg.rst | 5 +++++
modules/mol/alg/pymod/helix_kinks.py | 33 +++++++++++++++++-----------
2 files changed, 25 insertions(+), 13 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index fc6ac170c..2292b7720 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -860,6 +860,11 @@ used to skip frames in the analysis.
consecutive frames analyzed.
+:mod:`mol.alg.helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks
+================================================================================================
+.. autofunction:: ost.mol.alg.helix_kinks.CalculateHelixKink
+
+.. autofunction:: ost.mol.alg.helix_kinks.AnalyzeHelixKink
diff --git a/modules/mol/alg/pymod/helix_kinks.py b/modules/mol/alg/pymod/helix_kinks.py
index d57196bc5..eac71f477 100644
--- a/modules/mol/alg/pymod/helix_kinks.py
+++ b/modules/mol/alg/pymod/helix_kinks.py
@@ -80,13 +80,17 @@ def AnalyzeHelixKink(t,sele,proline=False):
there are at least 4 residues on each side (8 is even better) of the prolin around which
the helix is kinked. The selection should contain all residues in the correct
order and with no gaps and no missing C-alphas.
- Input:
- t : The trajectory to be analyzed (CoordGroup)
- sele : A selection containing the alpha helix to be analyzed (EntityView)
- proline=False : An EntityView containing only the proline (or another residue) around which the
- helix is kinked. If False, the proline will be serached for automatically
- Output:
- (bend_angle,face_shift,wobble_angle) : a tuple of FloatLists
+
+ :param t: The trajectory to be analyzed
+ :type t: `~ost.mol.CoordGroup`
+ :param sele: A selection containing the alpha helix to be analyzed
+ :type sele: :class:`~ost.mol.EntityView`
+ :param proline=False: A selection containing only the proline (or another residue) around
+ which the helix is kinked. If False, the proline will be serached for automatically
+ :type proline: :class:`ost.mol.EntityView`
+
+ :return: A tuple (bend_angle, face_shift, wobble_angle).
+ :rtype: (FloatList, FLoatList, FloatList)
"""
n_frames=t.GetFrameCount()
(proline,proline_ca)=__FindProline(sele,proline)
@@ -121,12 +125,15 @@ def CalculateHelixKink(sele,proline=False):
there are at least 4 residues on each side (8 is even better) of the prolin around which
the helix is kinked. The selection should contain all residues in the correct
order and with no gaps and no missing C-alphas.
- Input:
- sele : A selection containing the alpha helix to be analyzed (EntityView)
- proline=False : An EntityView containing only the proline (or another residue) around which the
- helix is kinked. If False, the proline will be serached for automatically
- Output:
- (bend_angle,face_shift,wobble_angle) : a tuple of Floats
+
+ :param sele: A selection containing the alpha helix to be analyzed
+ :type sele: :class:`~ost.mol.EntityView`
+ :param proline=False: A selection containing only the proline (or another residue) around
+ which the helix is kinked. If False, the proline will be serached for automatically
+ :type proline: :class:`ost.mol.EntityView`
+
+ :return: A tuple (bend_angle, face_shift, wobble_angle).
+ :rtype: (float, float, float)
"""
(proline,proline_ca)=__FindProline(sele,proline)
proline_num=proline.GetNumber().num
--
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