From 4b8c54e72b1a8da654a14aeb0e86a6519250093b Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Fri, 8 Apr 2011 11:37:41 +0200
Subject: [PATCH] check for duplicate atoms when importing PDB files
It's intentional to only check for duplicate atoms during PDB import an not directly in InsertAtom, since it is completely valid for a few fileformats to have more than one atom with the same name.
---
modules/io/src/mol/pdb_reader.cc | 10 +++++++++
modules/io/tests/test_io_pdb.cc | 22 +++++++++++++++++++
.../io/tests/testfiles/pdb/duplicate-atom.pdb | 4 ++++
3 files changed, 36 insertions(+)
create mode 100644 modules/io/tests/testfiles/pdb/duplicate-atom.pdb
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 7bafa40a0..a1e1b0718 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -647,6 +647,16 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
++atom_count_;
}
} else {
+ mol::AtomHandle atom=curr_residue_.FindAtom(aname);
+ if (atom.IsValid()) {
+ if (profile_.fault_tolerant) {
+ LOG_WARNING("duplicate atom '" << aname << "' in residue "
+ << curr_residue_);
+ return;
+ }
+ throw IOException("duplicate atom '"+aname+"' in residue "+
+ curr_residue_.GetQualifiedName());
+ }
ah=editor.InsertAtom(curr_residue_, aname, apos, s_ele);
++atom_count_;
}
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 878a645d3..3b5335eef 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -463,6 +463,28 @@ BOOST_AUTO_TEST_CASE(res_name_mismatch_pedantic)
BOOST_CHECK_THROW(reader.Import(ent), IOException);
}
+BOOST_AUTO_TEST_CASE(duplicate_atom_strict)
+{
+ 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(duplicate_atom_tolerant)
+{
+ String fname("testfiles/pdb/duplicate-atom.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(), 2);
+}
+
BOOST_AUTO_TEST_CASE(res_name_mismatch_tolerant)
{
String fname("testfiles/pdb/more-than-one-name.pdb");
diff --git a/modules/io/tests/testfiles/pdb/duplicate-atom.pdb b/modules/io/tests/testfiles/pdb/duplicate-atom.pdb
new file mode 100644
index 000000000..0cc10b3c8
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/duplicate-atom.pdb
@@ -0,0 +1,4 @@
+ATOM 1 N GLU A 7 6.454 -37.820 25.751 1.00 96.94 N
+ATOM 2 CA GLU A 7 5.179 -37.470 26.444 1.00 97.55 C
+ATOM 2 CA GLU A 7 5.179 -37.470 26.444 1.00 97.55 C
+END
\ No newline at end of file
--
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