improve writing of TER records

Fixes BZDNG-147

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2641 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/io/src/mol/pdb_writer.cc

@@ -200,6 +200,19 @@ public:
     return true;
   }
   
+  virtual bool VisitChain(const mol::ChainHandle& chain)
+  {
+    if (peptide_) {
+      this->WriteTer(prev_);
+    }
+    return true;
+  }
+  virtual void OnExit()
+  {
+    if (peptide_) {
+      this->WriteTer(prev_);
+    }
+  }
   void WriteTer(mol::ResidueHandle res)
   {
     counter_++;

modules/io/tests/test_io_pdb.cc

@@ -305,6 +305,48 @@ BOOST_AUTO_TEST_CASE(write_ter)
                             "testfiles/pdb/ter-out.pdb"));
 }
 
+BOOST_AUTO_TEST_CASE(write_ter2)
+{
+  String fname("testfiles/pdb/ter2.pdb");  
+  // this scope is required to force the writer stream to be closed before 
+  // opening the file again in compare_files. Avoids a race condition.
+  {
+    PDBReader reader(fname);
+    PDBWriter writer(String("testfiles/pdb/ter2-out.pdb"));
+    
+    mol::EntityHandle ent=mol::CreateEntity();
+    reader.Import(ent);
+    // we use conopology to mark amino acids as peptide-linking. this is 
+    // require for proper TER output
+    conop::Conopology& conop_inst=conop::Conopology::Instance();
+    conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+    writer.Write(ent);
+  }
+  BOOST_CHECK(compare_files("testfiles/pdb/ter2.pdb", 
+                            "testfiles/pdb/ter2-out.pdb"));
+}
+
+BOOST_AUTO_TEST_CASE(write_ter3)
+{
+  String fname("testfiles/pdb/ter3.pdb");  
+  // this scope is required to force the writer stream to be closed before 
+  // opening the file again in compare_files. Avoids a race condition.
+  {
+    PDBReader reader(fname);
+    PDBWriter writer(String("testfiles/pdb/ter3-out.pdb"));
+    
+    mol::EntityHandle ent=mol::CreateEntity();
+    reader.Import(ent);
+    // we use conopology to mark amino acids as peptide-linking. this is 
+    // require for proper TER output
+    conop::Conopology& conop_inst=conop::Conopology::Instance();
+    conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+    writer.Write(ent);
+  }
+  BOOST_CHECK(compare_files("testfiles/pdb/ter3.pdb", 
+                            "testfiles/pdb/ter3-out.pdb"));
+}
+
 BOOST_AUTO_TEST_CASE(write_conect)
 {
   // this scope is required to force the writer stream to be closed before

modules/io/tests/testfiles/pdb/ter2.pdb

+ATOM      1  N   GLN A 153      27.125  29.174  32.121  1.00 27.40           N  
+ATOM      2  CA  GLN A 153      28.561  29.394  32.241  1.00 30.81           C  
+ATOM      3  C   GLN A 153      29.250  29.251  30.888  1.00 35.59           C  
+ATOM      4  O   GLN A 153      28.979  28.314  30.130  1.00 33.20           O  
+ATOM      5  CB  GLN A 153      29.210  28.461  33.272  1.00 30.18           C  
+ATOM      6  CG  GLN A 153      30.694  28.783  33.468  1.00 34.18           C  
+ATOM      7  CD  GLN A 153      31.213  28.442  34.849  1.00 34.20           C  
+ATOM      8  OE1 GLN A 153      31.095  27.308  35.304  1.00 34.26           O  
+ATOM      9  NE2 GLN A 153      31.808  29.430  35.522  1.00 40.83           N  
+ATOM     10  OXT GLN A 153      30.094  30.079  30.532  1.00 45.02           O  
+TER      11      GLN A 153                                                      
+ATOM     12  N   ALA B   1      13.054  45.273  35.363  1.00 44.31           N  
+ATOM     13  CA  ALA B   1      12.088  44.308  35.884  1.00 39.90           C  
+ATOM     14  C   ALA B   1      11.751  44.590  37.349  1.00 35.09           C  
+ATOM     15  O   ALA B   1      12.633  44.881  38.156  1.00 39.85           O  
+ATOM     16  CB  ALA B   1      12.616  42.890  35.717  1.00 36.61           C  
+TER      17      ALA B   1                                                      
+TER      18      ALA B   1                                                      
+HETATM   19  S   SO4 z   1      25.896  25.925  48.976  0.60 29.86           S  
+HETATM   20  O1  SO4 z   1      25.480  27.268  48.589  0.60 30.25           O  
+HETATM   21  O2  SO4 z   1      25.611  24.961  47.915  0.60 34.83           O  
+HETATM   22  O3  SO4 z   1      27.332  25.943  49.244  0.60 34.94           O  
+HETATM   23  O4  SO4 z   1      25.183  25.525  50.189  0.60 32.47           O  
+HETATM   24 ZN    ZN z   2      23.332  26.722  48.256  0.66 22.52          ZN  
+HETATM   25 ZN    ZN z   3       4.294  31.320  20.337  0.28 33.21          ZN  
+HETATM   26  S   SO4 z   4       0.081  30.633  21.315  0.63 40.84           S  
+HETATM   27  O1  SO4 z   4      -1.116  31.446  21.507  0.63 45.94           O  
+HETATM   28  O2  SO4 z   4       1.268  31.440  21.578  0.63 33.61           O  
+HETATM   29  O3  SO4 z   4       0.032  29.503  22.239  0.63 29.10           O  
+HETATM   30  O4  SO4 z   4       0.115  30.163  19.934  0.63 40.96           O  
+CONECT   19   20   21   22   23
+CONECT   20   19
+CONECT   21   19
+CONECT   22   19
+CONECT   23   19
+CONECT   26   27   28   29   30
+CONECT   27   26
+CONECT   28   26
+CONECT   29   26
+CONECT   30   26
+END   
\ No newline at end of file

modules/io/tests/testfiles/pdb/ter3.pdb

+ATOM      1  N   GLN A 153      27.125  29.174  32.121  1.00 27.40           N  
+ATOM      2  CA  GLN A 153      28.561  29.394  32.241  1.00 30.81           C  
+ATOM      3  C   GLN A 153      29.250  29.251  30.888  1.00 35.59           C  
+ATOM      4  O   GLN A 153      28.979  28.314  30.130  1.00 33.20           O  
+ATOM      5  CB  GLN A 153      29.210  28.461  33.272  1.00 30.18           C  
+ATOM      6  CG  GLN A 153      30.694  28.783  33.468  1.00 34.18           C  
+ATOM      7  CD  GLN A 153      31.213  28.442  34.849  1.00 34.20           C  
+ATOM      8  OE1 GLN A 153      31.095  27.308  35.304  1.00 34.26           O  
+ATOM      9  NE2 GLN A 153      31.808  29.430  35.522  1.00 40.83           N  
+ATOM     10  OXT GLN A 153      30.094  30.079  30.532  1.00 45.02           O  
+TER      11      GLN A 153                                                      
+END   
\ No newline at end of file