From c7e1db4b44fbf1d457e00a44e0df895977adad0a Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Fri, 22 Oct 2010 15:05:34 +0200
Subject: [PATCH] added unit test for deuterium import
---
modules/conop/src/conop.cc | 1 +
modules/io/tests/test_io_pdb.cc | 16 ++++++++++++++++
.../tests/testfiles/pdb/val-with-deuterium.pdb | 16 ++++++++++++++++
3 files changed, 33 insertions(+)
create mode 100644 modules/io/tests/testfiles/pdb/val-with-deuterium.pdb
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index e21519d7c..e992fd7d5 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -55,6 +55,7 @@ Conopology::Conopology():
known_elements_.insert("BR");
known_elements_.insert("C");
known_elements_.insert("CA");
+ known_elements_.insert("D");
known_elements_.insert("CD");
known_elements_.insert("CE");
known_elements_.insert("CF");
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 1c9218aa4..fe1abe329 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -190,6 +190,20 @@ BOOST_AUTO_TEST_CASE(no_endmdl_record)
BOOST_CHECK_THROW(reader.Import(ent), IOException);
}
+BOOST_AUTO_TEST_CASE(deuterium_import)
+{
+ String fname("testfiles/pdb/val-with-deuterium.pdb");
+ PDBReader reader(fname);
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ // we use conopology to mark amino acids as peptide-linking.
+ conop::Conopology& conop_inst=conop::Conopology::Instance();
+ conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ // this check makes sure that we correctly detect deal with the deuterium
+ // atoms in the residue.
+ BOOST_CHECK(ent.FindResidue("A", 297).IsPeptideLinking());
+}
+
BOOST_AUTO_TEST_CASE(faulty_lines)
{
String fname("testfiles/pdb/faulty.pdb");
@@ -399,4 +413,6 @@ BOOST_AUTO_TEST_CASE(atom_name_too_long)
BOOST_CHECK_THROW(writer.Write(ent), IOException);
}
+
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/io/tests/testfiles/pdb/val-with-deuterium.pdb b/modules/io/tests/testfiles/pdb/val-with-deuterium.pdb
new file mode 100644
index 000000000..6c623a1ef
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/val-with-deuterium.pdb
@@ -0,0 +1,16 @@
+ATOM 4772 N VAL A 297 26.034 -2.215 17.509 1.00 14.11 N
+ATOM 4773 CA VAL A 297 25.704 -3.589 17.846 1.00 15.41 C
+ATOM 4774 C VAL A 297 24.570 -4.026 16.905 1.00 15.48 C
+ATOM 4775 O VAL A 297 24.557 -5.141 16.370 1.00 16.17 O
+ATOM 4776 CB VAL A 297 25.107 -3.702 19.323 1.00 20.96 C
+ATOM 4777 CG1 VAL A 297 24.248 -4.971 19.490 1.00 42.92 C
+ATOM 4778 CG2 VAL A 297 26.208 -3.657 20.282 1.00 32.10 C
+ATOM 4779 D VAL A 297 25.787 -1.658 18.107 1.00 15.70 D
+ATOM 4780 DA VAL A 297 26.490 -4.176 17.775 1.00 13.23 D
+ATOM 4781 DB VAL A 297 24.531 -2.950 19.540 1.00 12.82 D
+ATOM 4782 DG11 VAL A 297 23.948 -5.038 20.400 1.00 47.60 D
+ATOM 4783 DG12 VAL A 297 23.489 -4.925 18.903 1.00 46.87 D
+ATOM 4784 DG13 VAL A 297 24.779 -5.737 19.277 1.00 48.62 D
+ATOM 4785 DG21 VAL A 297 25.850 -3.693 21.173 1.00 34.84 D
+ATOM 4786 DG22 VAL A 297 26.791 -4.401 20.116 1.00 33.13 D
+ATOM 4787 DG23 VAL A 297 26.704 -2.845 20.129 1.00 28.37 D
\ No newline at end of file
--
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