From ea127b5382f461b56ca82f1c562e6fcfcbac8dea Mon Sep 17 00:00:00 2001
From: juergen <juergen.haas@unibas.ch>
Date: Fri, 2 Dec 2011 15:03:11 +0100
Subject: [PATCH] BZDN-291: fixing segfault on erroneous COMPND records
---
modules/io/src/mol/pdb_reader.cc | 21 +++++++++++----
modules/io/tests/test_io_pdb.cc | 36 +++++++++++++------------
modules/io/tests/testfiles/pdb/1oax.pdb | 24 +++++++++++++++++
modules/io/tests/testfiles/pdb/2p6a.pdb | 25 +++++++++++++++++
4 files changed, 84 insertions(+), 22 deletions(-)
create mode 100644 modules/io/tests/testfiles/pdb/1oax.pdb
create mode 100644 modules/io/tests/testfiles/pdb/2p6a.pdb
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 850556679..3d7bd3756 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -150,11 +150,22 @@ void PDBReader::ParseCompndEntry (const StringRef& line, int line_num)
}
if((entry.find(':')!=entry.end())){
std::vector<StringRef> fields=entry.split(':');
- key=fields[0].trim();
- old_key_=key.str();
- data=fields[1].trim();
+ key=fields[0].trim();
+ old_key_=key.str();
+ if (fields.size()>1) {
+ data=fields[1].trim();
+ }
+
if(data.size()<1){
+ if (!(key.str()=="MOL_ID")&&!(key.str()=="CHAIN")){
+ LOG_WARNING("skipping unsupported COMPND record on line " << line_num<< ": record value"<< key.str()<<" too small");
+ if (data_continues_) {
+ skip_next_=true;
+ } else {
+ return;
+ }
+ }
ThrowFaultTolerant(str(format("invalid COMPND record on line %d, record after ':' too small")%line_num));
}
data_continues_=true;
@@ -182,7 +193,7 @@ void PDBReader::ParseCompndEntry (const StringRef& line, int line_num)
}
//currently only these are parsed
if (!(key.str()=="MOL_ID")&&!(key.str()=="CHAIN")){
- LOG_TRACE("reading COMPND record on line " << line_num<< "is not supported");
+ LOG_INFO("reading COMPND record on line " << line_num<< "is not supported");
if (data_continues_) {
skip_next_=true;
} else {
@@ -474,7 +485,7 @@ void PDBReader::AssignMolIds(mol::EntityHandle ent) {
if (chain) {
chain.SetIntProp("mol_id", compnd_iterator->mol_id);
}else{
- std::cout << "failedchain: "<<*chain_iterator <<":: "<<std::endl;
+ std::cout << "failed to assign MOL_ID to chain: "<<*chain_iterator <<std::endl;
std::stringstream ss;
ss << "could not map COMPND record MOL_ID onto chain";
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index fbf45c67a..5bbfbf699 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -139,26 +139,28 @@ BOOST_AUTO_TEST_CASE(test_parse_compnd_record5)
PDBReader reader(fname, IOProfile());
mol::EntityHandle ent=mol::CreateEntity();
- BOOST_CHECK_THROW(reader.Import(ent), IOException);
+ BOOST_CHECK_NO_THROW(reader.Import(ent));
+
+ mol::ChainHandle ch = ent.FindChain("A");
+ BOOST_CHECK(ch.HasProp("mol_id")==true);
+ BOOST_CHECK(ch.GetIntProp("mol_id")==1);
+
+ ch = ent.FindChain("B");
+ BOOST_CHECK(ch.HasProp("mol_id")==false);
}
+//chain I in MOL_ID record but no chain I
+BOOST_AUTO_TEST_CASE(test_parse_compnd_record6)
+{
+ String fname("testfiles/pdb/1oax.pdb");
+ PDBReader reader(fname, IOProfile());
+ mol::EntityHandle ent=mol::CreateEntity();
+
+ BOOST_CHECK_THROW(reader.Import(ent), IOException);
+
+}
-//~ BOOST_AUTO_TEST_CASE(test_parse_compnd_record6)
-//~ {
- //~ String fname("testfiles/pdb/1oax.pdb");
- //~ PDBReader reader(fname, IOProfile());
- //~ mol::EntityHandle ent=mol::CreateEntity();
- //~
- //~ reader.Import(ent);
- //~ mol::ChainHandle ch = ent.FindChain("I");
- //~ BOOST_CHECK(ch.HasProp("mol_id")==true);
- //~ BOOST_CHECK(ch.GetIntProp("mol_id")==1);
-//~
- //~ ch = ent.FindChain("L");
- //~ BOOST_CHECK(ch.HasProp("mol_id")==true);
- //~ BOOST_CHECK(ch.GetIntProp("mol_id")==2);
-//~ }
-
+// has an empy MOLECULE record (unsupported ATM anyway, but crashed ost)
BOOST_AUTO_TEST_CASE(test_parse_compnd_record7)
{
String fname("testfiles/pdb/2p6a.pdb");
diff --git a/modules/io/tests/testfiles/pdb/1oax.pdb b/modules/io/tests/testfiles/pdb/1oax.pdb
new file mode 100644
index 000000000..8a61950e8
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/1oax.pdb
@@ -0,0 +1,24 @@
+
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: IMMUNOGLOBULIN E;
+COMPND 3 CHAIN: H, I, J, K;
+COMPND 4 FRAGMENT: FV REGION, RESIDUES 1-122;
+COMPND 5 ENGINEERED: YES;
+COMPND 6 MOL_ID: 2;
+COMPND 7 MOLECULE: IMMUNOGLOBULIN E;
+COMPND 8 CHAIN: L, M, N, O;
+COMPND 9 FRAGMENT: FV REGION, RESIDUES 1-110;
+COMPND 10 ENGINEERED: YES
+
+ATOM 961 CB ALA H 122 24.405 78.113 110.762 1.00 46.85 C
+TER 962 ALA H 122
+ATOM 1923 CB ALA J 122 -18.810 34.607 14.909 1.00 46.23 C
+TER 1924 ALA J 122
+ATOM 2722 CD2 LEU L 109 61.832 51.079 106.030 1.00 43.23 C
+TER 2723 LEU L 109
+ATOM 3521 CD2 LEU M 109 2.184 -0.589 68.108 1.00 43.23 C
+TER 3522 LEU M 109
+ATOM 4320 CD2 LEU N 109 7.889 -2.865 19.656 1.00 43.22 C
+TER 4321 LEU N 109
+ATOM 5113 CD2 LEU O 109 59.692 56.678 57.399 1.00 43.23 C
+TER 5114 LEU O 109
diff --git a/modules/io/tests/testfiles/pdb/2p6a.pdb b/modules/io/tests/testfiles/pdb/2p6a.pdb
new file mode 100644
index 000000000..19935ba86
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/2p6a.pdb
@@ -0,0 +1,25 @@
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: INHIBIN BETA A CHAIN;
+COMPND 3 CHAIN: A, B;
+COMPND 4 SYNONYM: ACTIVIN BETA-A CHAIN, ERYTHROID DIFFERENTIATION
+COMPND 5 PROTEIN, EDF;
+COMPND 6 ENGINEERED: YES;
+COMPND 7 MOL_ID: 2;
+COMPND 8 MOLECULE: FOLLISTATIN;
+COMPND 9 CHAIN: D, C;
+COMPND 10 SYNONYM: FS, ACTIVIN-BINDING PROTEIN;
+COMPND 11 ENGINEERED: YES;
+COMPND 12 MOL_ID: 3;
+COMPND 13 MOLECULE:;
+COMPND 14 CHAIN: E;
+COMPND 15 ENGINEERED: YES
+ATOM 882 OXT SER A 116 15.399 37.353 44.611 1.00 73.37 O
+TER 883 SER A 116
+ATOM 3870 OXT SER B 116 13.780 40.357 30.274 1.00 27.95 O
+TER 3871 SER B 116
+ATOM 2987 OE2 GLU D 299 33.348 36.499 4.332 1.00 81.88 O
+TER 2988 GLU D 299
+ATOM 5905 CB ILE C 290 46.026 -9.354 55.435 1.00233.79 C
+TER 5906 ILE C 290
+ATOM 5956 CB ALA E 10 30.651 13.129 53.296 1.00191.07 C
+TER 5957 ALA E 10
--
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