From 3c7303014f76daddcd0c000242de19df2572d1c0 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 27 Jun 2024 17:46:16 +0200
Subject: [PATCH] doc: clarify deprecation warning/notes
Now we always have a warning on the deprecated doc with a link to the
new implementation; and a note on the new implementation which starts
with "this is the new implementation" rather than "XXX is deprecated".
---
modules/mol/alg/doc/lddt_deprecated.rst | 3 ++-
modules/mol/alg/doc/stereochemistry.rst | 8 --------
modules/mol/alg/doc/stereochemistry_deprecated.rst | 5 +++++
modules/mol/alg/pymod/stereochemistry.py | 10 ++++++++++
4 files changed, 17 insertions(+), 9 deletions(-)
diff --git a/modules/mol/alg/doc/lddt_deprecated.rst b/modules/mol/alg/doc/lddt_deprecated.rst
index 433591c26..80e1b1355 100644
--- a/modules/mol/alg/doc/lddt_deprecated.rst
+++ b/modules/mol/alg/doc/lddt_deprecated.rst
@@ -6,7 +6,8 @@ lDDT (deprecated)
.. warning::
These functions in `ost.mol.alg` are deprecated. Consider using the newer
- implementation in :class:`ost.mol.alg.lDDTScorer` instead.
+ implementation in
+ :class:`ost.mol.alg.lddt.lDDTScorer <ost.mol.alg.lddt.lDDTScorer>` instead.
.. function:: LocalDistDiffTest(model, distance_list, tolerance_list, \
sequence_separation=0, \
diff --git a/modules/mol/alg/doc/stereochemistry.rst b/modules/mol/alg/doc/stereochemistry.rst
index 78ebf8b02..2b4f763eb 100644
--- a/modules/mol/alg/doc/stereochemistry.rst
+++ b/modules/mol/alg/doc/stereochemistry.rst
@@ -1,14 +1,6 @@
:mod:`~ost.mol.alg.stereochemistry` -- Stereochemistry Checks
--------------------------------------------------------------------------------------
-.. warning::
-
- Stereochemistry checks described in
- `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ are
- considered deprecated. They have been re-implemented and now support
- nucleotides. The old code is still available and documented
- :doc:`here <stereochemistry_deprecated>`.
-
.. automodule:: ost.mol.alg.stereochemistry
:members:
:member-order: bysource
diff --git a/modules/mol/alg/doc/stereochemistry_deprecated.rst b/modules/mol/alg/doc/stereochemistry_deprecated.rst
index 3a4802a7a..b9e2422a8 100644
--- a/modules/mol/alg/doc/stereochemistry_deprecated.rst
+++ b/modules/mol/alg/doc/stereochemistry_deprecated.rst
@@ -3,6 +3,11 @@
Stereochemistry (deprecated)
================================================================================
+.. warning::
+
+ These functions in `ost.mol.alg` are deprecated.
+ Consider using the newer implementation in
+ :mod:`~ost.mol.alg.stereochemistry` instead.
.. function:: CheckStructure(ent, \
bond_table, \
diff --git a/modules/mol/alg/pymod/stereochemistry.py b/modules/mol/alg/pymod/stereochemistry.py
index b6aa98a58..1a2d7fb1a 100644
--- a/modules/mol/alg/pymod/stereochemistry.py
+++ b/modules/mol/alg/pymod/stereochemistry.py
@@ -1,3 +1,13 @@
+"""
+.. note::
+
+ This is a new implementation of the stereochemistry checks, introduced in
+ OpenStructure 2.4, with support for nucleotides. The
+ :doc:`previous stereochemistry checks <stereochemistry_deprecated>` that come
+ with `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ are
+ considered deprecated.
+"""
+
import os
import json
import datetime
--
GitLab