don't throw but warn in case of microheterogeneity

modules/io/src/mol/pdb_reader.cc

@@ -609,15 +609,22 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
   LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
   mol::AtomHandle ah;
   if (curr_residue_.GetName()!=res_name.str()) {
-    if (!profile_.fault_tolerant) {
+    if (!profile_.fault_tolerant && alt_loc==' ') {
       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");      
+      if (alt_loc==' ') {
+        LOG_WARNING("Residue with number " << res_num << " has more than one name."
+                    "Ignoring atoms for everything but the first");        
+      } else {
+        LOG_WARNING("Residue with number " << res_num 
+                    << " contains a microheterogeneity. Everything but atoms for "
+                    << "the residue '" << curr_residue_.GetName() 
+                    << "' will be ignored");
+      }
     }
     warned_name_mismatch_=true;
     return;

modules/io/tests/test_io_pdb.cc

@@ -429,7 +429,7 @@ BOOST_AUTO_TEST_CASE(res_name_too_long)
 }
 
 
-BOOST_AUTO_TEST_CASE(res_name_mismatch_tolerant)
+BOOST_AUTO_TEST_CASE(res_name_mismatch_alt_loc)
 {
   String fname("testfiles/pdb/arg-glu-gln.pdb");
   IOProfile profile;
@@ -442,15 +442,40 @@ BOOST_AUTO_TEST_CASE(res_name_mismatch_tolerant)
   BOOST_CHECK_EQUAL(ent.GetAtomCount(), 11);
 }
 
-BOOST_AUTO_TEST_CASE(res_name_mismatch_pedantic)
+BOOST_AUTO_TEST_CASE(res_name_mismatch_alt_loc_pedantic)
 {
   String fname("testfiles/pdb/arg-glu-gln.pdb");
   IOProfile profile;
   PDBReader reader(fname, profile);
   mol::EntityHandle ent=mol::CreateEntity();
+  BOOST_CHECK_NO_THROW(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/more-than-one-name.pdb");
+  IOProfile profile;
+  PDBReader reader(fname, profile);
+  mol::EntityHandle ent=mol::CreateEntity();
   BOOST_CHECK_THROW(reader.Import(ent), IOException);
 }
 
+BOOST_AUTO_TEST_CASE(res_name_mismatch_tolerant)
+{
+  String fname("testfiles/pdb/more-than-one-name.pdb");
+  IOProfile profile;
+  profile.fault_tolerant=true;
+  PDBReader reader(fname, profile);
+  mol::EntityHandle ent=mol::CreateEntity();
+  BOOST_CHECK_NO_THROW(reader.Import(ent));
+  BOOST_CHECK_EQUAL(ent.GetChainCount(), 1);
+  BOOST_CHECK_EQUAL(ent.GetResidueCount(), 1);  
+  BOOST_CHECK_EQUAL(ent.GetAtomCount(), 4);
+}
+
 BOOST_AUTO_TEST_CASE(seqres_import)
 {
   SetPrefixPath(getenv("OST_ROOT"));

modules/io/tests/testfiles/pdb/more-than-one-name.pdb

+ATOM     25  N   TRP A  14       6.698 -48.684  24.846  1.00 52.82           N  
+ATOM     26  CA  TRP A  14       6.905 -49.681  23.809  1.00 51.62           C  
+ATOM     27  C   TRP A  14       8.347 -49.671  23.315  1.00 52.83           C  
+ATOM     28  O   TRP A  14       8.982 -50.733  23.187  1.00 52.24           O  
+ATOM     29  N   LYS A  14       8.863 -48.472  23.046  1.00 53.47           N  
+ATOM     30  CA  LYS A  14      10.228 -48.320  22.537  1.00 54.31           C  
+ATOM     31  C   LYS A  14      11.280 -48.867  23.508  1.00 54.74           C  
+ATOM     32  O   LYS A  14      12.215 -49.573  23.109  1.00 52.47           O  
+END
\ No newline at end of file