From 425e394de288477592eea0b01fc2b86d842f60de Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 17 Mar 2023 17:20:25 +0100
Subject: [PATCH] feat: SCHWED-5481 read gzipped SDF
---
modules/io/doc/structure_formats.rst | 2 +-
modules/io/src/mol/entity_io_sdf_handler.cc | 2 +-
modules/io/src/mol/sdf_reader.cc | 10 ++++++++--
modules/io/src/mol/sdf_reader.hh | 2 ++
modules/io/tests/CMakeLists.txt | 1 +
.../io/tests/testfiles/sdf/6d5w_rank1_crlf.sdf.gz | Bin 0 -> 505 bytes
6 files changed, 13 insertions(+), 4 deletions(-)
create mode 100644 modules/io/tests/testfiles/sdf/6d5w_rank1_crlf.sdf.gz
diff --git a/modules/io/doc/structure_formats.rst b/modules/io/doc/structure_formats.rst
index a80133842..42aca8826 100644
--- a/modules/io/doc/structure_formats.rst
+++ b/modules/io/doc/structure_formats.rst
@@ -54,5 +54,5 @@ SDF - Structured Data File
Chemical-data file format.
*Recognized File Extensions*
- .sdf
+ .sdf, .sdf.gz
diff --git a/modules/io/src/mol/entity_io_sdf_handler.cc b/modules/io/src/mol/entity_io_sdf_handler.cc
index a9dced835..a843d986c 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.cc
+++ b/modules/io/src/mol/entity_io_sdf_handler.cc
@@ -69,7 +69,7 @@ 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")) {
+ if(detail::FilenameEndsWith(match_suf_string,".sdf") || detail::FilenameEndsWith(match_suf_string,".sdf.gz")) {
return true;
}
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index 064c14f29..7f3a7f560 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -21,7 +21,9 @@
*/
#include <boost/algorithm/string.hpp>
+#include <boost/filesystem/convenience.hpp>
#include <boost/format.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
#include <boost/lexical_cast.hpp>
#include <ost/mol/bond_handle.hh>
#include <ost/conop/conop.hh>
@@ -58,7 +60,7 @@ void SDFReader::Import(mol::EntityHandle& ent)
{
String line;
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
- while (std::getline(instream_,line)) {
+ while (std::getline(in_,line)) {
++line_num;
// std::getline removes EOL character but may leave a DOS CR (\r) in Unix
@@ -87,7 +89,7 @@ void SDFReader::Import(mol::EntityHandle& ent)
throw IOException(str(format(msg) % line_num));
}
String data_value="";
- while(std::getline(instream_,line) && !boost::iequals(line, "")) {
+ while(std::getline(in_,line) && !boost::iequals(line, "")) {
data_value.append(line);
}
curr_chain_.SetStringProp(data_header, data_value);
@@ -103,6 +105,10 @@ void SDFReader::Import(mol::EntityHandle& ent)
void SDFReader::ClearState(const boost::filesystem::path& loc)
{
+ if (boost::iequals(".gz", boost::filesystem::extension(loc))) {
+ in_.push(boost::iostreams::gzip_decompressor());
+ }
+ in_.push(instream_);
if(!infile_) throw IOException("could not open "+loc.string());
curr_chain_=mol::ChainHandle();
curr_residue_=mol::ResidueHandle();
diff --git a/modules/io/src/mol/sdf_reader.hh b/modules/io/src/mol/sdf_reader.hh
index e7a478b7a..04d05a2d6 100644
--- a/modules/io/src/mol/sdf_reader.hh
+++ b/modules/io/src/mol/sdf_reader.hh
@@ -22,6 +22,7 @@
#ifndef OST_IO_SDF_READER_HH
#define OST_IO_SDF_READER_HH
+#include <boost/iostreams/filtering_stream.hpp>
#include <boost/filesystem/fstream.hpp>
#include <ost/mol/chain_handle.hh>
#include <ost/mol/residue_handle.hh>
@@ -61,6 +62,7 @@ private:
int line_num;
boost::filesystem::ifstream infile_;
std::istream& instream_;
+ boost::iostreams::filtering_stream<boost::iostreams::input> in_;
};
}}
diff --git a/modules/io/tests/CMakeLists.txt b/modules/io/tests/CMakeLists.txt
index 0af1dfd5b..fbfef7413 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -2,6 +2,7 @@ set(OST_IO_UNIT_TESTS
test_io_pdb.py
test_io_mmcif.py
test_io_omf.py
+ test_io_sdf.py
test_clustal.cc
test_io_pdb.cc
test_io_crd.cc
diff --git a/modules/io/tests/testfiles/sdf/6d5w_rank1_crlf.sdf.gz b/modules/io/tests/testfiles/sdf/6d5w_rank1_crlf.sdf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..658c3b9f089ef67229a54e18c766302083b22b16
GIT binary patch
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--
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