From 1a1723df1940fe1ab78c621eede33183b3499984 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 27 Jun 2024 15:29:32 +0200
Subject: [PATCH] doc: clarify full module path
---
modules/mol/alg/doc/chain_mapping.rst | 2 +-
modules/mol/alg/doc/contact_score.rst | 4 ++--
modules/mol/alg/doc/dockq.rst | 2 +-
modules/mol/alg/doc/helix_kinks.rst | 2 +-
modules/mol/alg/doc/ligand_scoring.rst | 4 ++--
modules/mol/alg/doc/molalg.rst | 21 ++++++++++-----------
modules/mol/alg/doc/qsscore.rst | 2 +-
modules/mol/alg/doc/scoring.rst | 4 ++--
modules/mol/alg/doc/stereochemistry.rst | 2 +-
modules/mol/alg/doc/structure_analysis.rst | 2 +-
modules/mol/alg/doc/trajectory_analysis.rst | 2 +-
11 files changed, 23 insertions(+), 24 deletions(-)
diff --git a/modules/mol/alg/doc/chain_mapping.rst b/modules/mol/alg/doc/chain_mapping.rst
index bda91c72d..eeb69d34a 100644
--- a/modules/mol/alg/doc/chain_mapping.rst
+++ b/modules/mol/alg/doc/chain_mapping.rst
@@ -1,4 +1,4 @@
-:mod:`chain_mapping <ost.mol.alg.chain_mapping>` -- Chain Mapping
+:mod:`mol.alg.chain_mapping <ost.mol.alg.chain_mapping>` -- Chain Mapping
--------------------------------------------------------------------------------
.. automodule:: ost.mol.alg.chain_mapping
diff --git a/modules/mol/alg/doc/contact_score.rst b/modules/mol/alg/doc/contact_score.rst
index 184c2f8c5..489ff85d7 100644
--- a/modules/mol/alg/doc/contact_score.rst
+++ b/modules/mol/alg/doc/contact_score.rst
@@ -1,5 +1,5 @@
-:mod:`contact_score <ost.mol.alg.contact_score>` -- Contact based scores
---------------------------------------------------------------------------------
+:mod:`mol.alg.contact_score <ost.mol.alg.contact_score>` -- Contact based scores
+------------------------------------------------------------------------------------
.. automodule:: ost.mol.alg.contact_score
:members:
diff --git a/modules/mol/alg/doc/dockq.rst b/modules/mol/alg/doc/dockq.rst
index f0b9d52e4..82b261fa7 100644
--- a/modules/mol/alg/doc/dockq.rst
+++ b/modules/mol/alg/doc/dockq.rst
@@ -1,4 +1,4 @@
-:mod:`dockq <ost.mol.alg.dockq>` -- DockQ implementation
+:mod:`mol.alg.dockq <ost.mol.alg.dockq>` -- DockQ implementation
--------------------------------------------------------------------------------
.. module:: ost.mol.alg.dockq
diff --git a/modules/mol/alg/doc/helix_kinks.rst b/modules/mol/alg/doc/helix_kinks.rst
index b845f2ffa..d81aa79f0 100644
--- a/modules/mol/alg/doc/helix_kinks.rst
+++ b/modules/mol/alg/doc/helix_kinks.rst
@@ -1,4 +1,4 @@
-:mod:`helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks
+:mod:`mol.alg.helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks
---------------------------------------------------------------------------------------------------------------
.. automodule:: ost.mol.alg.helix_kinks
diff --git a/modules/mol/alg/doc/ligand_scoring.rst b/modules/mol/alg/doc/ligand_scoring.rst
index 5e10e873a..8f775777b 100644
--- a/modules/mol/alg/doc/ligand_scoring.rst
+++ b/modules/mol/alg/doc/ligand_scoring.rst
@@ -1,5 +1,5 @@
-:mod:`ligand_scoring <ost.mol.alg.ligand_scoring>` -- Ligand scoring functions
------------------------------------------------------------------------------------
+:mod:`mol.alg.ligand_scoring <ost.mol.alg.ligand_scoring>` -- Ligand scoring functions
+------------------------------------------------------------------------------------------
.. module:: ost.mol.alg.ligand_scoring
:synopsis: Ligand scoring functions
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index c6e676a1b..b3e773731 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -7,17 +7,16 @@
Submodules
--------------------------------------------------------------------------------
-* :doc:`chain_mapping`
-* :doc:`contact_score`
-* :doc:`dockq`
-* :doc:`helix_kinks`
-* :doc:`ligand_scoring`
-* :doc:`qsscore`
-* :doc:`scoring`
-* :doc:`stereochemistry`
-* :doc:`structure_analysis`
-* :doc:`trajectory_analysis`
-
+* :doc:`chain_mapping – Chain Mapping <chain_mapping>`
+* :doc:`contact_score – Contact based scores<contact_score>`
+* :doc:`dockq – DockQ implementation<dockq>`
+* :doc:`helix_kinks – Algorithms to calculate Helix Kinks<helix_kinks>`
+* :doc:`ligand_scoring – Ligand scoring functions<ligand_scoring>`
+* :doc:`qsscore – New QS score implementation<qsscore>`
+* :doc:`scoring – Specialized scoring functions<scoring>`
+* :doc:`stereochemistry – Stereochemistry Checks<stereochemistry>`
+* :doc:`structure_analysis – Functions to analyze structures<structure_analysis>`
+* :doc:`trajectory_analysis – DRMSD, pairwise distances and more<trajectory_analysis>`
Local Distance Test scores (lDDT, DRMSD)
--------------------------------------------------------------------------------
diff --git a/modules/mol/alg/doc/qsscore.rst b/modules/mol/alg/doc/qsscore.rst
index 59a2f19d3..d2c2d9eeb 100644
--- a/modules/mol/alg/doc/qsscore.rst
+++ b/modules/mol/alg/doc/qsscore.rst
@@ -1,4 +1,4 @@
-:mod:`qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
+:mod:`mol.alg.qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
--------------------------------------------------------------------------------
.. note::
diff --git a/modules/mol/alg/doc/scoring.rst b/modules/mol/alg/doc/scoring.rst
index 057088560..4b0f6a7a7 100644
--- a/modules/mol/alg/doc/scoring.rst
+++ b/modules/mol/alg/doc/scoring.rst
@@ -1,5 +1,5 @@
-:mod:`scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
---------------------------------------------------------------------------------
+:mod:`mol.alg.scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
+---------------------------------------------------------------------------------
.. module:: ost.mol.alg.scoring
:synopsis: Specialized scoring functions
diff --git a/modules/mol/alg/doc/stereochemistry.rst b/modules/mol/alg/doc/stereochemistry.rst
index 1238fd74b..6c9ccee87 100644
--- a/modules/mol/alg/doc/stereochemistry.rst
+++ b/modules/mol/alg/doc/stereochemistry.rst
@@ -1,4 +1,4 @@
-:mod:`stereochemistry <ost.mol.alg.stereochemistry>` -- Stereochemistry Checks
+:mod:`mol.alg.stereochemistry <ost.mol.alg.stereochemistry>` -- Stereochemistry Checks
--------------------------------------------------------------------------------
.. warning::
diff --git a/modules/mol/alg/doc/structure_analysis.rst b/modules/mol/alg/doc/structure_analysis.rst
index caf3c51f5..681508ac8 100644
--- a/modules/mol/alg/doc/structure_analysis.rst
+++ b/modules/mol/alg/doc/structure_analysis.rst
@@ -1,4 +1,4 @@
-:mod:`structure_analysis <ost.mol.alg.structure_analysis>` -- Functions to analyze structures
+:mod:`mol.alg.structure_analysis <ost.mol.alg.structure_analysis>` -- Functions to analyze structures
---------------------------------------------------------------------------------------------------------------
.. automodule:: ost.mol.alg.structure_analysis
diff --git a/modules/mol/alg/doc/trajectory_analysis.rst b/modules/mol/alg/doc/trajectory_analysis.rst
index 296b535df..d83c0b259 100644
--- a/modules/mol/alg/doc/trajectory_analysis.rst
+++ b/modules/mol/alg/doc/trajectory_analysis.rst
@@ -1,4 +1,4 @@
-:mod:`trajectory_analysis <ost.mol.alg.trajectory_analysis>` -- DRMSD, pairwise distances and more
+:mod:`mol.alg.trajectory_analysis <ost.mol.alg.trajectory_analysis>` -- DRMSD, pairwise distances and more
---------------------------------------------------------------------------------------------------------------
.. automodule:: ost.mol.alg.trajectory_analysis
--
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