From 750146f105ef5cc1404d0c28db34155a2e4a5aa1 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Thu, 17 Oct 2024 14:01:03 +0200
Subject: [PATCH] doc: IO profiles in SDF reader
---
CHANGELOG.txt | 2 ++
modules/io/doc/io.rst | 16 ++++++----------
2 files changed, 8 insertions(+), 10 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index ade415745..f5ed1821e 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -30,6 +30,8 @@ Changes in Release 2.9.0
even though there is no experimental evidence. The approach with trimmed
models removes any model residue that cannot be mapped to the target
structure before scoring.
+ * The SDF reader is now aware of IOProfiles and can read files with invalid
+ bond types (order) from RDKit in fault tolerant mode.
* Several bug fixes and improvements.
Changes in Release 2.8.0
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index d4c364c2c..933f33cc3 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -119,22 +119,18 @@ behaviour.
:rtype: :class:`~ost.mol.EntityHandle`.
+.. autofunction:: ost.io.LoadSDF
-.. function:: LoadSDF(filename)
-
- Load an SDF file and return an entity.
-
- :param filename: File to be loaded
- :type filename: :class:`str`
-
- :rtype: :class:`~ost.mol.EntityHandle`
-
-.. function:: SDFStrToEntity(sdf_string)
+.. function:: SDFStrToEntity(sdf_string, profile=IOProfile())
Load entity from a string in SDF format.
:param pdb_string: A SDF file as a string.
+ :param profile: The IO Profile to read the entity with. For more information
+ on the IO Profiles available, see :doc:`profile`.
+ :type profile: :class:`ost.io.IOProfile`
+
:rtype: :class:`~ost.mol.EntityHandle`.
.. class:: ost.io.OMF
--
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