From 06358987337811d6bc8314ba635c6a7543f0b78e Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 19 Apr 2010 14:54:20 +0000
Subject: [PATCH] don't try to read PDB file past end
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2052 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/src/mol/pdb_io.hh | 4 +++-
modules/io/src/mol/pdb_reader.cc | 11 +++++++++--
modules/io/src/mol/pdb_reader.hh | 1 +
modules/io/tests/test_io_pdb.cc | 10 +++++++++-
modules/io/tests/testfiles/pdb/end.pdb | 3 +++
5 files changed, 25 insertions(+), 4 deletions(-)
create mode 100644 modules/io/tests/testfiles/pdb/end.pdb
diff --git a/modules/io/src/mol/pdb_io.hh b/modules/io/src/mol/pdb_io.hh
index 54edc8a13..140db87e3 100644
--- a/modules/io/src/mol/pdb_io.hh
+++ b/modules/io/src/mol/pdb_io.hh
@@ -64,7 +64,9 @@ struct PDB {
/// PDB::JOIN_SPREAD_ATOM_RECORDS and CoordGroups.
///
/// The atoms are accessible via PDBReader::GetSequentialAtoms()
- SEQUENTIAL_ATOM_IMPORT=32
+ SEQUENTIAL_ATOM_IMPORT=32,
+ /// \brief only import C-alpha atoms
+ CALPHA_ONLY=64
} Type;
};
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index e4a68ee11..ec0dbaccb 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -92,11 +92,15 @@ void PDBReader::Init(const boost::filesystem::path& loc)
} else {
is_pqr_=false;
}
+ hard_end_=false;
}
bool PDBReader::HasNext()
{
+ if (hard_end_) {
+ return false;
+ }
// since helix and sheet have to appear before any atom/hetatm records
// a HELIX/SHEET entry implies a next model.
while (std::getline(in_, curr_line_) && ++line_num_) {
@@ -108,7 +112,8 @@ bool PDBReader::HasNext()
IEquals(curr_line.substr(0, 6), StringRef("SHEET ", 6)) ||
IEquals(curr_line.substr(0, 6), StringRef("HELIX ", 6))) {
return true;
- } else if (IEquals(curr_line, StringRef("END", 3))) {
+ } else if (IEquals(curr_line.substr(0, 3), StringRef("END", 3))) {
+ hard_end_=true;
return false;
}
}
@@ -149,6 +154,7 @@ void PDBReader::Import(mol::EntityHandle& ent,
continue;
}
if (IEquals(curr_line.substr(0, 3), StringRef("END", 3))) {
+ hard_end_=true;
go_on=false;
break;
}
@@ -184,7 +190,7 @@ void PDBReader::Import(mol::EntityHandle& ent,
default:
break;
}
- } while (std::getline(in_, curr_line_) && ++line_num_);
+ } while (std::getline(in_, curr_line_) && ++line_num_ && go_on);
LOGN_MESSAGE("imported "
<< chain_count_ << " chains, "
<< residue_count_ << " residues, "
@@ -241,6 +247,7 @@ void PDBReader::ClearState()
chain_count_=0;
residue_count_=0;
atom_count_=0;
+ hard_end_=false;
helix_list_.clear();
strand_list_.clear();
sequential_atom_list_.clear();
diff --git a/modules/io/src/mol/pdb_reader.hh b/modules/io/src/mol/pdb_reader.hh
index 5beb44eb3..5c85e23a1 100644
--- a/modules/io/src/mol/pdb_reader.hh
+++ b/modules/io/src/mol/pdb_reader.hh
@@ -81,6 +81,7 @@ private:
int residue_count_;
int atom_count_;
int line_num_;
+ bool hard_end_;
String restrict_chains_;
HSList helix_list_;
HSList strand_list_;
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 8ae918f4f..64f46c26b 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -76,7 +76,15 @@ BOOST_AUTO_TEST_CASE(atom_record)
BOOST_CHECK_EQUAL(a2.GetProp().occupancy, 1.0);
BOOST_CHECK_EQUAL(a2.GetProp().element, "C");
BOOST_CHECK_EQUAL(a2.GetProp().is_hetatm, true);
-
+}
+
+BOOST_AUTO_TEST_CASE(end_record)
+{
+ String fname("testfiles/pdb/end.pdb");
+ PDBReader reader(fname);
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 1);
}
BOOST_AUTO_TEST_CASE(join_spread_records_on)
diff --git a/modules/io/tests/testfiles/pdb/end.pdb b/modules/io/tests/testfiles/pdb/end.pdb
new file mode 100644
index 000000000..daf824177
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/end.pdb
@@ -0,0 +1,3 @@
+ATOM 1 N MET A 1 16.000 64.000 8.000 0.50 1.00 N
+END
+ATOM 2 CA MET A 1 32.000-128.000 -2.500 1.00128.00 C
--
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