From 7c3137b9a89f9dec7e32a5d423f42b7197111d18 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Mon, 12 Jun 2023 14:47:32 +0200
Subject: [PATCH] doc: clarify what is deprecated/what replaces lDDT and
qsscoring
---
modules/mol/alg/doc/lddt_deprecated.rst | 5 +++++
modules/mol/alg/doc/molalg.rst | 24 ++++++++++++------------
modules/mol/alg/pymod/qsscoring.py | 5 +++++
3 files changed, 22 insertions(+), 12 deletions(-)
diff --git a/modules/mol/alg/doc/lddt_deprecated.rst b/modules/mol/alg/doc/lddt_deprecated.rst
index 4293046fd..173bcb5ed 100644
--- a/modules/mol/alg/doc/lddt_deprecated.rst
+++ b/modules/mol/alg/doc/lddt_deprecated.rst
@@ -3,6 +3,11 @@
lDDT (deprecated)
================================================================================
+.. warning::
+
+ These functions in `ost.mol.alg` are deprecated. Consider using the newer
+ implementation in :class:`ost.mol.alg.lDDTScorer` instead.
+
.. function:: LocalDistDiffTest(model, distance_list, tolerance_list, \
sequence_separation=0, \
local_lddt_property_string="")
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index bf451df52..3a43ea5de 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -7,14 +7,14 @@
Local Distance Test scores (lDDT, DRMSD)
--------------------------------------------------------------------------------
-.. warning::
+.. note::
- The code that comes with
+ This is a new implementation of lDDT, introduced in OpenStructure 2.4 with
+ focus on supporting quaternary structure and compounds beyond the 20
+ standard proteinogenic amino acids.
+ The :doc:`previous lDDT code <lddt_deprecated>` that comes with
`Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ is
- considered deprecated. lDDT has been re-implemented with a focus on
- supporting quaternary structure and compounds beyond the 20 standard
- proteinogenic amino acids. The old code is still available and documented
- :doc:`here <lddt_deprecated>`.
+ considered deprecated.
.. note::
@@ -135,16 +135,16 @@ Local Distance Test scores (lDDT, DRMSD)
.. currentmodule:: ost.mol.alg
-:mod:`qsscoring <ost.mol.alg.qsscore>` -- QS score implementation
+:mod:`qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
--------------------------------------------------------------------------------
-.. warning::
+.. note::
- The code that comes with
+ This is a new implementation of QS Score, introduced in OpenStructure 2.4 and
+ tightly integrated with the chain mapping algorithms.
+ The :doc:`previous qsscoring code <qsscoring_deprecated>` that comes with
`Bertoni et al. <https://www.nature.com/articles/s41598-017-09654-8>`_ is
- considered deprecated. QS score has been re-implemented to be tightly
- integrated with the chain mapping algorithms. The old code is still available
- and documented :doc:`here <qsscoring_deprecated>`.
+ considered deprecated.
.. automodule:: ost.mol.alg.qsscore
:members:
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index b47aa4e76..8928646b9 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -2,6 +2,11 @@
Scoring of quaternary structures (QS). The QS scoring is according to the paper
by `Bertoni et al. <https://dx.doi.org/10.1038/s41598-017-09654-8>`_.
+.. warning::
+
+ The `qsscoring` module is deprecated. Consider using the newer implementation
+ in :mod:`~ost.mol.alg.qsscore` instead.
+
.. note ::
Requirements for use:
--
GitLab