don't try to read PDB file past end

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2052 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/io/src/mol/pdb_io.hh

@@ -64,7 +64,9 @@ struct PDB {
     /// PDB::JOIN_SPREAD_ATOM_RECORDS and CoordGroups.
     /// 
     /// The atoms are accessible via PDBReader::GetSequentialAtoms()
-    SEQUENTIAL_ATOM_IMPORT=32
+    SEQUENTIAL_ATOM_IMPORT=32,
+    /// \brief only import C-alpha atoms
+    CALPHA_ONLY=64
   } Type; 
 };
 

modules/io/src/mol/pdb_reader.cc

@@ -92,11 +92,15 @@ void PDBReader::Init(const boost::filesystem::path& loc)
   } else {
     is_pqr_=false;
   }
+  hard_end_=false;
 }
 
 
 bool PDBReader::HasNext()
 {
+  if (hard_end_) {
+    return false;
+  }
   // since helix and sheet have to appear before any atom/hetatm records
   // a HELIX/SHEET entry implies a next model.
   while (std::getline(in_, curr_line_) && ++line_num_) {
@@ -108,7 +112,8 @@ bool PDBReader::HasNext()
          IEquals(curr_line.substr(0, 6), StringRef("SHEET ", 6)) ||
          IEquals(curr_line.substr(0, 6), StringRef("HELIX ", 6))) {
        return true;
-     } else if (IEquals(curr_line, StringRef("END", 3))) {
+     } else if (IEquals(curr_line.substr(0, 3), StringRef("END", 3))) {
+       hard_end_=true;
        return false;
      }
   }
@@ -149,6 +154,7 @@ void PDBReader::Import(mol::EntityHandle& ent,
           continue;
         }
         if (IEquals(curr_line.substr(0, 3), StringRef("END", 3))) {
+          hard_end_=true;
           go_on=false;
           break;
         }
@@ -184,7 +190,7 @@ void PDBReader::Import(mol::EntityHandle& ent,
       default:
         break;
     }
-  }  while (std::getline(in_, curr_line_) && ++line_num_);
+  }  while (std::getline(in_, curr_line_) && ++line_num_ && go_on);
   LOGN_MESSAGE("imported "
                << chain_count_ << " chains, "
                << residue_count_ << " residues, "
@@ -241,6 +247,7 @@ void PDBReader::ClearState()
   chain_count_=0;
   residue_count_=0;
   atom_count_=0;
+  hard_end_=false;
   helix_list_.clear();
   strand_list_.clear();
   sequential_atom_list_.clear();

modules/io/src/mol/pdb_reader.hh

@@ -81,6 +81,7 @@ private:
   int residue_count_;
   int atom_count_;
   int line_num_;
+  bool hard_end_;
   String restrict_chains_;
   HSList helix_list_;
   HSList strand_list_;

modules/io/tests/test_io_pdb.cc

@@ -76,7 +76,15 @@ BOOST_AUTO_TEST_CASE(atom_record)
   BOOST_CHECK_EQUAL(a2.GetProp().occupancy, 1.0);  
   BOOST_CHECK_EQUAL(a2.GetProp().element, "C");
   BOOST_CHECK_EQUAL(a2.GetProp().is_hetatm, true);
-  
+}
+
+BOOST_AUTO_TEST_CASE(end_record)
+{
+  String fname("testfiles/pdb/end.pdb");
+  PDBReader reader(fname); 
+  mol::EntityHandle ent=mol::CreateEntity();
+  reader.Import(ent);
+  BOOST_CHECK_EQUAL(ent.GetAtomCount(), 1);
 }
 
 BOOST_AUTO_TEST_CASE(join_spread_records_on)

modules/io/tests/testfiles/pdb/end.pdb

+ATOM      1  N   MET A   1      16.000  64.000   8.000  0.50  1.00           N  
+END
+ATOM      2  CA  MET A   1      32.000-128.000  -2.500  1.00128.00           C