From 7032dc3328f45a4e2f6f8100e0b4c2600ccff152 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <niklaus.johner@unibas.ch>
Date: Wed, 13 Aug 2014 09:40:14 +0200
Subject: [PATCH] Some cleaning in the helix_kink functions
---
modules/mol/alg/pymod/helix_kinks.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/helix_kinks.py b/modules/mol/alg/pymod/helix_kinks.py
index d57196bc5..46b9dbdfb 100644
--- a/modules/mol/alg/pymod/helix_kinks.py
+++ b/modules/mol/alg/pymod/helix_kinks.py
@@ -77,14 +77,14 @@ def AnalyzeHelixKink(t,sele,proline=False):
"""
This function calculates the bend,wobble and face-shift angles
in an alpha-helix over a trajectory. The determination is more stable if
- there are at least 4 residues on each side (8 is even better) of the prolin around which
+ there are at least 4 residues on each side (8 is even better) of the proline 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
+ helix is kinked. If False, the proline will be searched for automatically
Output:
(bend_angle,face_shift,wobble_angle) : a tuple of FloatLists
"""
@@ -104,9 +104,9 @@ def AnalyzeHelixKink(t,sele,proline=False):
ca3_pos=ost.mol.alg.AnalyzeAtomPos(t,ca_3.GetHandle())
ca4_pos=ost.mol.alg.AnalyzeAtomPos(t,ca_4.GetHandle())
#Now we calculate the bend angle
- bend_angle=[]
- face_shift=[]
- wobble_angle=[]
+ bend_angle=ost.FloatList()
+ face_shift=ost.FloatList()
+ wobble_angle=ost.FloatList()
for i in range(n_frames):
bend_angle.append(__CalculateBendAngle(pre_proline_axis[i],post_proline_axis[i]))
face_shift.append(__CalculateFaceShift(pre_proline_axis[i],post_proline_axis[i],pre_proline_centers[i],post_proline_centers[i],proline_pos[i],ca3_pos[i],ca4_pos[i],bend_angle[i]))
--
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