From f221d10ec880e5dbedf0dffbfea9708957ca9d0e Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Fri, 8 Apr 2011 11:29:16 +0200
Subject: [PATCH] don't throw but warn in case of microheterogeneity
---
modules/io/src/mol/pdb_reader.cc | 13 +++++++--
modules/io/tests/test_io_pdb.cc | 29 +++++++++++++++++--
.../testfiles/pdb/more-than-one-name.pdb | 9 ++++++
3 files changed, 46 insertions(+), 5 deletions(-)
create mode 100644 modules/io/tests/testfiles/pdb/more-than-one-name.pdb
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 1ea2c56b8..7bafa40a0 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -609,15 +609,22 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
mol::AtomHandle ah;
if (curr_residue_.GetName()!=res_name.str()) {
- if (!profile_.fault_tolerant) {
+ if (!profile_.fault_tolerant && alt_loc==' ') {
std::stringstream ss;
ss << "error on line " << line_num << ": "
<< "residue with number " << res_num << " has more than one name.";
throw IOException(ss.str());
}
if (!warned_name_mismatch_) {
- LOG_INFO("Residue with number " << res_num << " has more than one name."
- "Ignoring atoms for everything but the first");
+ if (alt_loc==' ') {
+ LOG_WARNING("Residue with number " << res_num << " has more than one name."
+ "Ignoring atoms for everything but the first");
+ } else {
+ LOG_WARNING("Residue with number " << res_num
+ << " contains a microheterogeneity. Everything but atoms for "
+ << "the residue '" << curr_residue_.GetName()
+ << "' will be ignored");
+ }
}
warned_name_mismatch_=true;
return;
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index e890a5b6c..878a645d3 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -429,7 +429,7 @@ BOOST_AUTO_TEST_CASE(res_name_too_long)
}
-BOOST_AUTO_TEST_CASE(res_name_mismatch_tolerant)
+BOOST_AUTO_TEST_CASE(res_name_mismatch_alt_loc)
{
String fname("testfiles/pdb/arg-glu-gln.pdb");
IOProfile profile;
@@ -442,15 +442,40 @@ BOOST_AUTO_TEST_CASE(res_name_mismatch_tolerant)
BOOST_CHECK_EQUAL(ent.GetAtomCount(), 11);
}
-BOOST_AUTO_TEST_CASE(res_name_mismatch_pedantic)
+BOOST_AUTO_TEST_CASE(res_name_mismatch_alt_loc_pedantic)
{
String fname("testfiles/pdb/arg-glu-gln.pdb");
IOProfile profile;
PDBReader reader(fname, profile);
mol::EntityHandle ent=mol::CreateEntity();
+ BOOST_CHECK_NO_THROW(reader.Import(ent));
+ BOOST_CHECK_EQUAL(ent.GetChainCount(), 1);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 1);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 11);
+}
+
+BOOST_AUTO_TEST_CASE(res_name_mismatch_pedantic)
+{
+ String fname("testfiles/pdb/more-than-one-name.pdb");
+ IOProfile profile;
+ PDBReader reader(fname, profile);
+ mol::EntityHandle ent=mol::CreateEntity();
BOOST_CHECK_THROW(reader.Import(ent), IOException);
}
+BOOST_AUTO_TEST_CASE(res_name_mismatch_tolerant)
+{
+ String fname("testfiles/pdb/more-than-one-name.pdb");
+ IOProfile profile;
+ profile.fault_tolerant=true;
+ PDBReader reader(fname, profile);
+ mol::EntityHandle ent=mol::CreateEntity();
+ BOOST_CHECK_NO_THROW(reader.Import(ent));
+ BOOST_CHECK_EQUAL(ent.GetChainCount(), 1);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 1);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 4);
+}
+
BOOST_AUTO_TEST_CASE(seqres_import)
{
SetPrefixPath(getenv("OST_ROOT"));
diff --git a/modules/io/tests/testfiles/pdb/more-than-one-name.pdb b/modules/io/tests/testfiles/pdb/more-than-one-name.pdb
new file mode 100644
index 000000000..905b4c766
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/more-than-one-name.pdb
@@ -0,0 +1,9 @@
+ATOM 25 N TRP A 14 6.698 -48.684 24.846 1.00 52.82 N
+ATOM 26 CA TRP A 14 6.905 -49.681 23.809 1.00 51.62 C
+ATOM 27 C TRP A 14 8.347 -49.671 23.315 1.00 52.83 C
+ATOM 28 O TRP A 14 8.982 -50.733 23.187 1.00 52.24 O
+ATOM 29 N LYS A 14 8.863 -48.472 23.046 1.00 53.47 N
+ATOM 30 CA LYS A 14 10.228 -48.320 22.537 1.00 54.31 C
+ATOM 31 C LYS A 14 11.280 -48.867 23.508 1.00 54.74 C
+ATOM 32 O LYS A 14 12.215 -49.573 23.109 1.00 52.47 O
+END
\ No newline at end of file
--
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