added unit test for deuterium import

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");

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()

modules/io/tests/testfiles/pdb/val-with-deuterium.pdb

+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