From ec25b68e4bc25a5b6990b8a3293ab9d01ea9bc3e Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Fri, 1 Jul 2011 15:30:04 +0200
Subject: [PATCH] fixed writing TER for empty chains, added testcase
(BZDNG-276)
---
modules/io/src/mol/pdb_writer.cc | 8 +++-
modules/io/tests/test_io_pdb.cc | 42 +++++++++++++++++++
.../io/tests/testfiles/pdb/ter_emptychain.pdb | 4 ++
.../testfiles/pdb/ter_view-emptychain.pdb | 4 ++
4 files changed, 56 insertions(+), 2 deletions(-)
create mode 100644 modules/io/tests/testfiles/pdb/ter_emptychain.pdb
create mode 100644 modules/io/tests/testfiles/pdb/ter_view-emptychain.pdb
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index ffbd145fa..45115e9a7 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -233,17 +233,21 @@ public:
virtual bool VisitChain(const mol::ChainHandle& chain)
{
- if (peptide_) {
- this->WriteTer(prev_);
+ if (chain.GetResidueCount()!=0) {
+ if (peptide_) {
+ this->WriteTer(prev_);
+ }
}
return true;
}
+
virtual void OnExit()
{
if (peptide_) {
this->WriteTer(prev_);
}
}
+
void WriteTer(mol::ResidueHandle res)
{
counter_++;
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 982bd2f46..4c69702bf 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -373,6 +373,48 @@ BOOST_AUTO_TEST_CASE(write_ter3)
"testfiles/pdb/ter3-out.pdb"));
}
+BOOST_AUTO_TEST_CASE(write_ter4)
+{
+ {
+ PDBWriter writer(String("testfiles/pdb/ter_emptychain-out.pdb"), IOProfile());
+
+ mol::EntityHandle ent=mol::CreateEntity();
+ mol::XCSEditor edi=ent.EditXCS();
+ mol::ChainHandle ch=edi.InsertChain("A");
+ mol::ResidueHandle r=edi.AppendResidue(ch, "ALA");
+ mol::AtomHandle a=edi.InsertAtom(r, "N", geom::Vec3(32.0, -128.0, -2.5));
+ mol::ResidueHandle r2=edi.AppendResidue(ch, "GLY");
+ mol::AtomHandle a2=edi.InsertAtom(r2, "N", geom::Vec3(35.0, -99.0, -10.5));
+ mol::ChainHandle ch2=edi.InsertChain("B");
+ conop::Conopology& conop_inst=conop::Conopology::Instance();
+ conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ writer.Write(ent);
+ }
+ BOOST_CHECK(compare_files("testfiles/pdb/ter_emptychain.pdb",
+ "testfiles/pdb/ter_emptychain-out.pdb"));
+}
+
+BOOST_AUTO_TEST_CASE(write_ter5)
+{
+ {
+ PDBWriter writer(String("testfiles/pdb/ter_view-emptychain-out.pdb"), IOProfile());
+
+ mol::EntityHandle ent=mol::CreateEntity();
+ mol::XCSEditor edi=ent.EditXCS();
+ mol::ChainHandle ch=edi.InsertChain("A");
+ mol::ResidueHandle r=edi.AppendResidue(ch, "ALA");
+ mol::AtomHandle a=edi.InsertAtom(r, "N", geom::Vec3(32.0, -128.0, -2.5));
+ mol::ResidueHandle r2=edi.AppendResidue(ch, "GLY");
+ mol::AtomHandle a2=edi.InsertAtom(r2, "N", geom::Vec3(35.0, -99.0, -10.5));
+ mol::ChainHandle ch2=edi.InsertChain("B");
+ conop::Conopology& conop_inst=conop::Conopology::Instance();
+ conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ writer.Write(ent.Select(""));
+ }
+ BOOST_CHECK(compare_files("testfiles/pdb/ter_view-emptychain.pdb",
+ "testfiles/pdb/ter_view-emptychain-out.pdb"));
+}
+
BOOST_AUTO_TEST_CASE(write_conect)
{
// this scope is required to force the writer stream to be closed before
diff --git a/modules/io/tests/testfiles/pdb/ter_emptychain.pdb b/modules/io/tests/testfiles/pdb/ter_emptychain.pdb
new file mode 100644
index 000000000..129e5225f
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/ter_emptychain.pdb
@@ -0,0 +1,4 @@
+ATOM 1 N ALA A 1 32.000-128.000 -2.500 1.00 0.00 N
+ATOM 2 N GLY A 2 35.000 -99.000 -10.500 1.00 0.00 N
+TER 3 GLY A 2
+END
diff --git a/modules/io/tests/testfiles/pdb/ter_view-emptychain.pdb b/modules/io/tests/testfiles/pdb/ter_view-emptychain.pdb
new file mode 100644
index 000000000..129e5225f
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/ter_view-emptychain.pdb
@@ -0,0 +1,4 @@
+ATOM 1 N ALA A 1 32.000-128.000 -2.500 1.00 0.00 N
+ATOM 2 N GLY A 2 35.000 -99.000 -10.500 1.00 0.00 N
+TER 3 GLY A 2
+END
--
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