fixed BZDNG-183

modules/io/src/mol/pdb_reader.cc

@@ -82,6 +82,7 @@ PDBReader::PDBReader(const boost::filesystem::path& loc,
 
 void PDBReader::Init(const boost::filesystem::path& loc)
 {
+  warned_name_mismatch_=false;
   charmm_style_=profile_.dialect=="CHARMM";
   num_model_records_=0;
   if (boost::iequals(".gz", boost::filesystem::extension(loc))) {
@@ -531,6 +532,7 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
     if (!curr_residue_.IsValid()) {
       LOG_DEBUG("new residue " << res_name << " " << res_num);
       curr_residue_=editor.AppendResidue(curr_chain_, res_name.str(), res_num);
+      warned_name_mismatch_=false;
       ++residue_count_; 
     }
     assert(curr_residue_.IsValid());
@@ -538,6 +540,20 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
   // finally add atom
   LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
   mol::AtomHandle ah;
+  if (curr_residue_.GetName()!=res_name.str()) {
+    if (!profile_.fault_tolerant) {
+      std::stringstream ss;
+      ss << "error on line " << line_num << ": "
+         << "residue with number " << res_num << " has more than one name.";
+      throw IOException(ss.str());
+    }
+    if (!warned_name_mismatch_) {
+      LOG_INFO("Residue with number " << res_num << " has more than one name."
+               "Ignoring atoms for everything but the first");      
+    }
+    warned_name_mismatch_=true;
+    return;
+  }
   if (alt_loc!=' ') {
     // Check if there is already a atom with the same name.
     mol::AtomHandle me=curr_residue_.FindAtom(aname);

modules/io/src/mol/pdb_reader.hh

@@ -93,6 +93,7 @@ private:
   bool is_pqr_;
   IOProfile profile_;
   bool charmm_style_;
+  bool warned_name_mismatch_;
 };
 
 }}

modules/io/tests/test_io_pdb.cc

@@ -423,6 +423,30 @@ BOOST_AUTO_TEST_CASE(res_name_too_long)
   BOOST_CHECK_THROW(writer.Write(ent), IOException);
 }
 
+
+BOOST_AUTO_TEST_CASE(res_name_mismatch_tolerant)
+{
+  String fname("testfiles/pdb/arg-glu-gln.pdb");
+  IOProfile profile;
+  profile.fault_tolerant=true;
+  PDBReader reader(fname, profile);
+  mol::EntityHandle ent=mol::CreateEntity();
+  reader.Import(ent);
+  BOOST_CHECK_EQUAL(ent.GetChainCount(), 1);
+  BOOST_CHECK_EQUAL(ent.GetResidueCount(), 1);  
+  BOOST_CHECK_EQUAL(ent.GetAtomCount(), 11);
+}
+
+BOOST_AUTO_TEST_CASE(res_name_mismatch_pedantic)
+{
+  String fname("testfiles/pdb/arg-glu-gln.pdb");
+  IOProfile profile;
+  PDBReader reader(fname, profile);
+  mol::EntityHandle ent=mol::CreateEntity();
+  BOOST_CHECK_THROW(reader.Import(ent), IOException);
+}
+
+
 BOOST_AUTO_TEST_CASE(chain_name_too_long)
 {
   std::stringstream out;

modules/io/tests/testfiles/pdb/arg-glu-gln.pdb

+ATOM    134  N  AARG A  15       8.286  13.769  40.774  0.50 60.53           N  
+ATOM    135  CA AARG A  15       8.903  14.440  41.922  0.50 64.64           C  
+ATOM    136  C  AARG A  15       7.867  15.000  42.911  0.50 65.25           C  
+ATOM    137  O  AARG A  15       8.174  15.244  44.080  0.50 60.65           O  
+ATOM    138  CB AARG A  15       9.857  15.549  41.457  0.50 65.83           C  
+ATOM    139  CG AARG A  15      10.863  15.121  40.391  0.50 64.71           C  
+ATOM    140  CD AARG A  15      11.814  16.270  40.051  0.50 69.97           C  
+ATOM    141  NE AARG A  15      12.505  16.084  38.775  0.50 69.52           N  
+ATOM    142  CZ AARG A  15      12.236  16.774  37.670  0.50 69.32           C  
+ATOM    143  NH1AARG A  15      11.291  17.706  37.674  0.50 55.65           N  
+ATOM    144  NH2AARG A  15      12.919  16.538  36.559  0.50 76.31           N  
+ATOM    145  N  CGLU A  15       8.306  13.754  40.761  0.17 60.57           N  
+ATOM    146  CA CGLU A  15       8.887  14.450  41.904  0.17 64.60           C  
+ATOM    147  C  CGLU A  15       7.813  14.816  42.928  0.17 64.89           C  
+ATOM    148  O  CGLU A  15       8.037  14.735  44.137  0.17 61.75           O  
+ATOM    149  CB CGLU A  15       9.635  15.707  41.448  0.17 65.94           C  
+ATOM    150  CG CGLU A  15      10.877  15.425  40.613  0.17 65.71           C  
+ATOM    151  CD CGLU A  15      11.545  16.692  40.105  0.17 68.96           C  
+ATOM    152  OE1CGLU A  15      10.877  17.748  40.063  0.17 67.85           O  
+ATOM    153  OE2CGLU A  15      12.740  16.631  39.744  0.17 68.13           O  
+ATOM    154  N  BGLN A  15       8.327  13.744  40.756  0.33 60.56           N  
+ATOM    155  CA BGLN A  15       8.877  14.452  41.907  0.33 64.61           C  
+ATOM    156  C  BGLN A  15       7.769  14.698  42.924  0.33 64.96           C  
+ATOM    157  O  BGLN A  15       7.924  14.416  44.116  0.33 61.27           O  
+ATOM    158  CB BGLN A  15       9.492  15.793  41.487  0.33 66.08           C  
+ATOM    159  CG BGLN A  15      10.726  15.695  40.597  0.33 65.69           C  
+ATOM    160  CD BGLN A  15      11.327  17.061  40.276  0.33 69.35           C  
+ATOM    161  OE1BGLN A  15      11.616  17.369  39.119  0.33 66.62           O  
+ATOM    162  NE2BGLN A  15      11.511  17.885  41.303  0.33 67.16           N
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