From 061412e70d898fe5bf3a65217624059d7c973e70 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 7 Jul 2023 17:31:36 +0200
Subject: [PATCH] doc: fix sphinx warnings about duplicate object description
---
modules/io/doc/io.rst | 16 +++-------------
modules/mol/base/doc/editors.rst | 23 ++++++-----------------
modules/mol/base/doc/entity.rst | 2 +-
3 files changed, 10 insertions(+), 31 deletions(-)
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 57677f7a5..30ef45bad 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -549,13 +549,7 @@ Loading Density Maps
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. function:: LoadImage(filename)
-
- Load density map from disk with the extension being guessed by the function.
-
- :param filename: The filename
- :type filename: string
-
-.. function:: LoadImage(filename, format)
+ LoadImage(filename, format)
Load density map from disk. If no format is given, the function guesses the
filetype based on the extension of the file. If the extension is unknown or not present the
@@ -589,12 +583,8 @@ Loading Density Maps
Saving Density Maps
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. function:: SaveImage(image,filename)
-
- Save density map to disk with the function guessing the
- filetype based on the file extension.
-
-.. function:: SaveImage(image,filename, format)
+.. function:: SaveImage(image, filename)
+ SaveImage(image, filename, format)
Save density map to disk. If no format is set, the function guesses the
filetype based on the file extension.
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index 2be8e65f6..24162f9fa 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -192,6 +192,7 @@ The basic functionality of editors is implemented in the EditorBase class.
:returns: :class:`AtomHandle`
.. method:: InsertAltAtom(residue, atom, alt_group)
+ :noindex:
Insert new atom with alternative position indicator
@@ -336,6 +337,7 @@ The basic functionality of editors is implemented in the EditorBase class.
:type new_numbers: :class:`ResNumList`
.. method:: RenumberChain(chain, start, keep_spacing)
+ :noindex:
Renumber residues of the given chain
@@ -409,29 +411,14 @@ Euclidian space.
atoms positions.
:param transform: The transformation to be applied
- :type transform: :class:`geom.Mat4`
-
- .. method:: ApplyTransform(transform)
-
- Apply a transformation to the entity. The transformation is applied to all
- atoms positions.
-
- :param transform: The transformation to be applied
- :type transform: :class:`Transform`
+ :type transform: :class:`geom.Mat4` or :class:`Transform`
.. method:: SetTransform(transform)
Set the entity transformation. See also :meth:`ApplyTransform`
:param transform: The transformation to be applied
- :type transform: :class:`geom.Mat4`
-
- .. method:: SetTransform(transform)
-
- Set the entity transformation. See also :meth:`ApplyTransform`
-
- :param transform: The transformation to be applied
- :type transform: :class:`Transform`
+ :type transform: :class:`geom.Mat4` or :class:`Transform`
.. method:: FixTransform()
@@ -544,6 +531,7 @@ using an :class:`ICSEditor` is undefined and vice versa.
.. method:: SetTorsionAngle(atom1, atom2, atom3, atom4, angle, update_others=True)
+ :noindex:
Set the angles of the given atoms. All connectors at the third atom (A3) will be adjusted accordingly.
If you only want to adjust the bond between A3 and A4, and leave
@@ -587,6 +575,7 @@ using an :class:`ICSEditor` is undefined and vice versa.
.. method:: RotateTorsionAngle(atom1, atom2, atom3, atom4, angle, update_others=True)
+ :noindex:
Rotate torsion angle
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index f56797a42..14e3d9fa4 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -2343,7 +2343,7 @@ Other Entity-Related Functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. function:: CreateViewFromAtoms(atom_list)
-.. function:: CreateViewFromAtomList(atom_list)
+ CreateViewFromAtomList(atom_list)
Returns a view made up of the atoms in *atom_list*. All atoms are required to
be atoms of the same entity. Duplicate atoms are only added to the view once.
--
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