From f6aa7ec43b2d9e53c5e241858475b1886a0b5ad7 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 22 Apr 2010 07:00:05 +0000
Subject: [PATCH] unit test (and fix) for loading pdb files with only 66
columns
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2100 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/src/mol/pdb_reader.cc | 16 ++++++++++++----
modules/io/tests/test_io_pdb.cc | 8 ++++++++
modules/io/tests/testfiles/pdb/short.pdb | 2 ++
3 files changed, 22 insertions(+), 4 deletions(-)
create mode 100644 modules/io/tests/testfiles/pdb/short.pdb
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index c8e113652..8c8e7cbca 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -382,11 +382,19 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
if(is_pqr_) {
occ=std::make_pair(true, 1.0);
temp=std::make_pair(true, 0.0);
- charge=line.substr(54,6).ltrim().to_float();
- radius=line.substr(60, 6).ltrim().to_float();
+ if (line.length()>=60) {
+ charge=line.substr(54,6).ltrim().to_float();
+ }
+ if (line.length()>=66) {
+ radius=line.substr(60, 6).ltrim().to_float();
+ }
} else {
- occ=line.substr(54,6).ltrim().to_float();
- temp=line.substr(60, 6).ltrim().to_float();
+ if (line.length()>=60) {
+ occ=line.substr(54,6).ltrim().to_float();
+ }
+ if (line.length()>=66) {
+ temp=line.substr(60, 6).ltrim().to_float();
+ }
}
LOGN_TRACE( "line: [" << line << "]" );
String s_ele;
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index fe5c51f3a..f8a5d70ad 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -171,4 +171,12 @@ BOOST_AUTO_TEST_CASE(anisou_record)
}
+BOOST_AUTO_TEST_CASE(only_66_cols)
+{
+ String fname("testfiles/pdb/short.pdb");
+ PDBReader reader(fname);
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+}
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/io/tests/testfiles/pdb/short.pdb b/modules/io/tests/testfiles/pdb/short.pdb
new file mode 100644
index 000000000..316a527e8
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/short.pdb
@@ -0,0 +1,2 @@
+ATOM 1 N SER 1 -35.012 -34.611 -8.045 1.0 0.0
+ATOM 2 H1 SER 1 -34.315 -35.342 -8.037 1.0 0.0
\ No newline at end of file
--
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