catch when another thread is still running

src/Secondary.cpp

@@ -1211,6 +1211,8 @@ DSSPImpl::DSSPImpl(const Structure& s, int min_poly_proline_stretch_length)
 
 
 	std::thread ta(std::bind(&CalculateAccessibilities, std::ref(mResidues), std::ref(mStats)));
 	std::thread ta(std::bind(&CalculateAccessibilities, std::ref(mResidues), std::ref(mStats)));
 
 
+	try
+	{
 		auto& db = s.getFile().data();
 		auto& db = s.getFile().data();
 		for (auto r: db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
 		for (auto r: db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
 		{
 		{
@@ -1279,7 +1281,11 @@ DSSPImpl::DSSPImpl(const Structure& s, int min_poly_proline_stretch_length)
 		for (const auto& [a, b]: mSSBonds)
 		for (const auto& [a, b]: mSSBonds)
 		{
 		{
 			if (a == b)
 			if (a == b)
-			throw std::runtime_error("first and second residue are the same");
+			{
+				std::cerr << "In the SS bonds list, the residue " << a->mM << " is bonded to itself" << std::endl;
+				continue;
+			}
+				// throw std::runtime_error("first and second residue are the same");
 
 
 			if (a->mM.asymID() == b->mM.asymID() and NoChainBreak(a, b))
 			if (a->mM.asymID() == b->mM.asymID() and NoChainBreak(a, b))
 				++mStats.nrOfIntraChainSSBridges;
 				++mStats.nrOfIntraChainSSBridges;
@@ -1303,6 +1309,12 @@ DSSPImpl::DSSPImpl(const Structure& s, int min_poly_proline_stretch_length)
 				}
 				}
 			}
 			}
 		}
 		}
+	}
+	catch (const std::exception& ex)
+	{
+		ta.join();
+		throw;
+	}
 
 
 	ta.join();
 	ta.join();
 }
 }