From 01016615ece14df85f50158d9efd05973d763717 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Thu, 17 Oct 2024 14:15:53 +0200
Subject: [PATCH] SDF reader reads .mol files as well
---
modules/io/doc/structure_formats.rst | 9 +++++----
modules/io/src/mol/entity_io_sdf_handler.cc | 3 ++-
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/modules/io/doc/structure_formats.rst b/modules/io/doc/structure_formats.rst
index 2fe0eaf67..6903ed50f 100644
--- a/modules/io/doc/structure_formats.rst
+++ b/modules/io/doc/structure_formats.rst
@@ -51,12 +51,13 @@ radii.
SDF - Structured Data File
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Chemical table (Ctab) file format (V2000; read-only V3000 experimental support),
-aka MDL Molfile.
-The SDF format does not support residues, chains or atom names natively.
+Chemical table (Ctab) file format, aka SDF, aka MDL Molfile, originally named
+after Molecular Design Limited, Inc. Follows the "BIOVIA Databases 2020" format
+specification (V2000; read-only V3000 experimental support).
The SDF importer supports loading gzipped files, which are auto-detected by the
.gz file extension.
+The SDF format does not support residues, chains or atom names natively.
The reader assigns 1-based atom indices as atom names.
SDF files containing several molecules are loaded into distinct chains,
named after the molecule name in the MOLfile header with a numerical prefix.
@@ -66,5 +67,5 @@ Chains are written as separate molecules. If a chain contains more than one
residue, they will be merged into a single molecule.
*Recognized File Extensions*
- .sdf, .sdf.gz
+ .sdf, .sdf.gz, .mol, .mol.gz
diff --git a/modules/io/src/mol/entity_io_sdf_handler.cc b/modules/io/src/mol/entity_io_sdf_handler.cc
index cf1ff10c6..fed25f86b 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.cc
+++ b/modules/io/src/mol/entity_io_sdf_handler.cc
@@ -70,7 +70,8 @@ bool sdf_handler_is_responsible_for(const boost::filesystem::path& loc,
if(type=="auto") {
String match_suf_string=loc.string();
std::transform(match_suf_string.begin(),match_suf_string.end(),match_suf_string.begin(),tolower);
- if(detail::FilenameEndsWith(match_suf_string,".sdf") || detail::FilenameEndsWith(match_suf_string,".sdf.gz")) {
+ if(detail::FilenameEndsWith(match_suf_string,".sdf") || detail::FilenameEndsWith(match_suf_string,".sdf.gz") ||
+ detail::FilenameEndsWith(match_suf_string,".mol") || detail::FilenameEndsWith(match_suf_string,".mol.gz")) {
return true;
}
--
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