From 81b1ace7c6e1087edce6dbe1ab87c027a9d772e5 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <niklaus.johner@unibas.ch>
Date: Tue, 3 Mar 2015 17:01:55 +0100
Subject: [PATCH] Reorganise the mol.alg documentation
---
modules/mol/alg/doc/molalg.rst | 97 ++++++++++++++++++----------------
1 file changed, 51 insertions(+), 46 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index d4ce787a4..fc6ac170c 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -636,6 +636,18 @@ The following function detects steric clashes in atomic structures. Two atoms ar
:returns: true if the residue names are the same, false otherwise
+.. autofunction:: ParseAtomNames
+
+.. autofunction:: MatchResidueByNum
+
+.. autofunction:: MatchResidueByIdx
+
+.. autofunction:: MatchResidueByLocalAln
+
+.. autofunction:: MatchResidueByGlobalAln
+
+.. autofunction:: Superpose
+
.. _traj-analysis:
Trajectory Analysis
@@ -651,6 +663,45 @@ All these functions have a "stride" argument that defaults to stride=1, which is
used to skip frames in the analysis.
+.. function:: SuperposeFrames(frames, sel, from=0, to=-1, ref=-1)
+
+ This function superposes the frames of the given coord group and returns them
+ as a new coord group.
+
+ :param frames: The source coord group.
+ :type frames: :class:`~ost.mol.CoordGroupHandle`
+ :param sel: An entity view containing the selection of atoms to be used for
+ superposition. If set to an invalid view, all atoms in the coord group are
+ used.
+ :type sel: :class:`ost.mol.EntityView`
+ :param from: index of the first frame
+ :param to: index of the last frame plus one. If set to -1, the value is set to
+ the number of frames in the coord group
+ :param ref: The index of the reference frame to use for superposition. If set
+ to -1, the each frame is superposed to the previous frame.
+
+ :returns: A newly created coord group containing the superposed frames.
+
+.. function:: SuperposeFrames(frames, sel, ref_view, from=0, to=-1)
+
+ Same as SuperposeFrames above, but the superposition is done on a reference
+ view and not on another frame of the trajectory.
+
+ :param frames: The source coord group.
+ :type frames: :class:`~ost.mol.CoordGroupHandle`
+ :param sel: An entity view containing the selection of atoms of the frames to be used for
+ superposition.
+ :type sel: :class:`ost.mol.EntityView`
+ :param ref_view: The reference view on which the frames will be superposed. The number
+ of atoms in this reference view should be equal to the number of atoms in sel.
+ :type ref_view: :class:`ost.mol.EntityView`
+ :param from: index of the first frame
+ :param to: index of the last frame plus one. If set to -1, the value is set to
+ the number of frames in the coord group
+
+ :returns: A newly created coord group containing the superposed frames.
+
+
.. function:: AnalyzeAtomPos(traj, atom1, stride=1)
This function extracts the position of an atom from a trajectory. It returns
@@ -808,53 +859,7 @@ used to skip frames in the analysis.
:param stride: Size of the increment of the frame's index between two
consecutive frames analyzed.
-.. function:: SuperposeFrames(frames, sel, from=0, to=-1, ref=-1)
-
- This function superposes the frames of the given coord group and returns them
- as a new coord group.
-
- :param frames: The source coord group.
- :type frames: :class:`~ost.mol.CoordGroupHandle`
- :param sel: An entity view containing the selection of atoms to be used for
- superposition. If set to an invalid view, all atoms in the coord group are
- used.
- :type sel: :class:`ost.mol.EntityView`
- :param from: index of the first frame
- :param to: index of the last frame plus one. If set to -1, the value is set to
- the number of frames in the coord group
- :param ref: The index of the reference frame to use for superposition. If set
- to -1, the each frame is superposed to the previous frame.
-
- :returns: A newly created coord group containing the superposed frames.
-
-.. function:: SuperposeFrames(frames, sel, ref_view, from=0, to=-1)
-
- Same as SuperposeFrames above, but the superposition is done on a reference
- view and not on another frame of the trajectory.
-
- :param frames: The source coord group.
- :type frames: :class:`~ost.mol.CoordGroupHandle`
- :param sel: An entity view containing the selection of atoms of the frames to be used for
- superposition.
- :type sel: :class:`ost.mol.EntityView`
- :param ref_view: The reference view on which the frames will be superposed. The number
- of atoms in this reference view should be equal to the number of atoms in sel.
- :type ref_view: :class:`ost.mol.EntityView`
- :param from: index of the first frame
- :param to: index of the last frame plus one. If set to -1, the value is set to
- the number of frames in the coord group
-
- :returns: A newly created coord group containing the superposed frames.
-
-.. autofunction:: ParseAtomNames
-
-.. autofunction:: MatchResidueByNum
-
-.. autofunction:: MatchResidueByIdx
-.. autofunction:: MatchResidueByLocalAln
-.. autofunction:: MatchResidueByGlobalAln
-.. autofunction:: Superpose
--
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