From 8061a66c25eef889229b6d4184a411d03a688d72 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Tue, 30 Apr 2024 14:55:38 +0200
Subject: [PATCH] doc: remove warnings about duplicate object description
---
modules/bindings/doc/tmtools.rst | 1 +
modules/db/doc/db.rst | 1 +
modules/gui/doc/layout.rst | 2 ++
modules/mol/alg/doc/lddt_deprecated.rst | 3 +++
modules/mol/mm/doc/simulation.rst | 1 +
modules/mol/mm/doc/topology.rst | 6 ++++++
modules/seq/alg/doc/seqalg.rst | 2 +-
modules/seq/base/doc/seq.rst | 1 +
8 files changed, 16 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/doc/tmtools.rst b/modules/bindings/doc/tmtools.rst
index cc08e010d..2243170b4 100644
--- a/modules/bindings/doc/tmtools.rst
+++ b/modules/bindings/doc/tmtools.rst
@@ -154,6 +154,7 @@ The advantage is that no intermediate files need to be generated.
.. method:: WrappedTMAlign(pos1, pos2, seq1, seq2 [fast=False, rna=False])
+ :noindex:
Similar as described above, but directly feeding in raw data.
diff --git a/modules/db/doc/db.rst b/modules/db/doc/db.rst
index a296c1ec6..a9f2cb59f 100644
--- a/modules/db/doc/db.rst
+++ b/modules/db/doc/db.rst
@@ -115,6 +115,7 @@ use an indexer to keep track of where to find data for a certain entry.
.. method:: GetDataRange(name, chain_name)
+ :noindex:
Get the range for a chain of an assembly
diff --git a/modules/gui/doc/layout.rst b/modules/gui/doc/layout.rst
index 5906dd964..8fcdcf45b 100644
--- a/modules/gui/doc/layout.rst
+++ b/modules/gui/doc/layout.rst
@@ -112,6 +112,7 @@ how to add a widget to the MDI area:
:type name: :class:`QWindowState`
.. method:: AddPersistentWidget(title, name, widget, width, height, x, y)
+ :noindex:
Add a widget whose geometry is preserved across application relaunches
For widgets that are volatile, use #AddWidget()
@@ -258,6 +259,7 @@ and finally display it in the right side bar:
:type limit: :class:`int`
.. method:: AddWidgetToPool(name, widget)
+ :noindex:
Add a widget to the widget pool. Same as :meth:`AddWidgetToPool`
diff --git a/modules/mol/alg/doc/lddt_deprecated.rst b/modules/mol/alg/doc/lddt_deprecated.rst
index 173bcb5ed..433591c26 100644
--- a/modules/mol/alg/doc/lddt_deprecated.rst
+++ b/modules/mol/alg/doc/lddt_deprecated.rst
@@ -61,6 +61,7 @@ lDDT (deprecated)
model and of all the checked distances
.. function:: LocalDistDiffTest(model, reference_list, distance_list, settings)
+ :noindex:
Wrapper around :func:`LocalDistDiffTest` above.
@@ -80,6 +81,7 @@ lDDT (deprecated)
.. function:: LocalDistDiffTest(model, target, cutoff, max_dist, \
local_lddt_property_string="")
+ :noindex:
Wrapper around :func:`LocalDistDiffTest` above using:
*distance_list* = :func:`CreateDistanceList` with *target* and *max_dist* as
@@ -104,6 +106,7 @@ lDDT (deprecated)
.. function:: LocalDistDiffTest(alignment, tolerance, radius, ref_index=0, \
mdl_index=1)
+ :noindex:
Calculates the Local Distance Difference Test score (see previous function)
starting from an alignment between a reference structure and a model. The
diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst
index 3fd443aea..c06b20a8e 100644
--- a/modules/mol/mm/doc/simulation.rst
+++ b/modules/mol/mm/doc/simulation.rst
@@ -32,6 +32,7 @@ mapped back to the attached structure at any time.
:class:`Topology` fails
.. class:: Simulation(topology,entity,settings)
+ :noindex:
Second constructor that takes a :class:`Topology`, a consistent
:class:`ost.mol.EntityHandle` and a :class:`Settings` as input.
diff --git a/modules/mol/mm/doc/topology.rst b/modules/mol/mm/doc/topology.rst
index 19760508c..0cd857444 100644
--- a/modules/mol/mm/doc/topology.rst
+++ b/modules/mol/mm/doc/topology.rst
@@ -130,6 +130,7 @@ The Topology Class
contains OBC scalings but the **other** not
.. method:: Merge(ent, other, other_ent)
+ :noindex:
Merges in another :class:`Topology` and adds all their particles and
interactions. Assuming the actual :class:`Topology` contains n particles,
@@ -1191,6 +1192,7 @@ The Topology Class
.. method:: GetHarmonicBondIndices(index)
+ :noindex:
:param index: Index of particle
:type index: :class:`int`
@@ -1203,6 +1205,7 @@ The Topology Class
.. method:: GetHarmonicAngleIndices(index)
+ :noindex:
:param index: Index of particle
:type index: :class:`int`
@@ -1215,6 +1218,7 @@ The Topology Class
.. method:: GetUreyBradleyAngleIndices(index)
+ :noindex:
:param index: Index of particle
:type index: :class:`int`
@@ -1228,6 +1232,7 @@ The Topology Class
.. method:: GetPeriodicDihedralIndices(index)
+ :noindex:
:param index: Index of particle
:type index: :class:`int`
@@ -1263,6 +1268,7 @@ The Topology Class
.. method:: GetCMapIndices(index)
+ :noindex:
:param index: Index of particle
:type index: :class:`int`
diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index 75593e9f2..c0f9b885b 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -941,8 +941,8 @@ etc.) to be set, which is the case if you load a file in hhm format.
:param filename: Filename of db
:type filename: :class:`str`
-
.. method:: AddAAPseudoCounts(profile, db, a=0.9, b=4.0, c=1.0)
+ :noindex:
Adds pseudo counts to the emission probabilities in *profile* by utilizing
context profiles as described in
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index a5ea7ec66..012e31305 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -526,6 +526,7 @@ an alignment:
:rtype: :class:`AlignedColumn`
.. method:: __getitem__(slice)
+ :noindex:
:return: Columns defined by by pythonic slicing.
:rtype: :class:`AlignedRegion`
--
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