From b5ddb1e5d3e44f4f930e7286e6980d822a9f5872 Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Fri, 14 Jan 2011 14:47:17 +0100
Subject: [PATCH] sdf reader complains if file cannot be opened
---
modules/io/src/mol/sdf_reader.cc | 20 ++++++++++++--------
modules/io/src/mol/sdf_reader.hh | 2 +-
modules/io/tests/test_io_sdf.cc | 7 +++++++
3 files changed, 20 insertions(+), 9 deletions(-)
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index 09dea4696..347da9930 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -36,18 +36,21 @@ namespace ost { namespace io {
using boost::format;
SDFReader::SDFReader(const String& filename)
- : infile_(filename), instream_(infile_) {
- this->ClearState();
+ : infile_(filename), instream_(infile_)
+{
+ this->ClearState(boost::filesystem::path(filename));
}
SDFReader::SDFReader(const boost::filesystem::path& loc)
- : infile_(loc), instream_(infile_) {
- this->ClearState();
+ : infile_(loc), instream_(infile_)
+{
+ this->ClearState(loc);
}
SDFReader::SDFReader(std::istream& instream)
- : infile_(), instream_(instream) {
- this->ClearState();
+ : infile_(), instream_(instream)
+{
+ this->ClearState(boost::filesystem::path(""));
}
// import data from provided stream
@@ -82,7 +85,7 @@ void SDFReader::Import(mol::EntityHandle& ent)
}
curr_chain_.SetStringProp(data_header, data_value);
} else if (boost::iequals(line, "$$$$")) {
- LOG_INFO("MOLECULE " << curr_chain_.GetName() << " (" << chain_count_ << ") added.")
+ LOG_VERBOSE("MOLECULE " << curr_chain_.GetName() << " (" << chain_count_ << ") added.")
NextMolecule();
}
}
@@ -91,8 +94,9 @@ void SDFReader::Import(mol::EntityHandle& ent)
<< " residues, " << atom_count_ << " atoms");
}
-void SDFReader::ClearState()
+void SDFReader::ClearState(const boost::filesystem::path& loc)
{
+ if(!infile_) throw IOException("could not open "+loc.string());
curr_chain_=mol::ChainHandle();
curr_residue_=mol::ResidueHandle();
chain_count_=0;
diff --git a/modules/io/src/mol/sdf_reader.hh b/modules/io/src/mol/sdf_reader.hh
index 0401e6ab7..3beacc031 100644
--- a/modules/io/src/mol/sdf_reader.hh
+++ b/modules/io/src/mol/sdf_reader.hh
@@ -39,7 +39,7 @@ public:
void Import(mol::EntityHandle& ent);
private:
- void ClearState();
+ void ClearState(const boost::filesystem::path& loc);
void NextMolecule();
void ParseAndAddHeader(const String& line, int line_num, mol::EntityHandle& ent,
diff --git a/modules/io/tests/test_io_sdf.cc b/modules/io/tests/test_io_sdf.cc
index db108e4c5..08ae8d80c 100644
--- a/modules/io/tests/test_io_sdf.cc
+++ b/modules/io/tests/test_io_sdf.cc
@@ -151,6 +151,13 @@ BOOST_AUTO_TEST_CASE(write_sdf)
"testfiles/sdf/compound-out.sdf"));
}
+BOOST_AUTO_TEST_CASE(nonexisting_file)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ BOOST_CHECK_THROW(sdfh.Import(eh,"non-existing-file.sdf"), IOException);
+}
+
BOOST_AUTO_TEST_CASE(wrong_atomcount_error_sdf)
{
mol::EntityHandle eh=mol::CreateEntity();
--
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