Merge branch 'oeps' into trunk

GNUmakefile.in

@@ -44,7 +44,7 @@ DEBUG               = @DEBUG@
 
 ifeq "$(DEBUG)" "1"
 DEFINES				+= DEBUG
-CXXFLAGS            += -g -O0
+CXXFLAGS            += -g -O0 -fstandalone-debug
 LDFLAGS				+= -g
 else
 CXXFLAGS			+= -O3

src/Secondary.cpp

@@ -1224,11 +1224,21 @@ void DSSPImpl::calculateSecondaryStructure()
 
 		auto r1 = findRes(asym1, seq1);
 		if (r1 == mResidues.end())
-			throw std::runtime_error("Invalid file, missing residue for SS bond");
+		{
+			if (cif::VERBOSE)
+				std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym1 << '/' << seq1 << std::endl;
+			continue;
+			// throw std::runtime_error("Invalid file, missing residue for SS bond");
+		}
 
 		auto r2 = findRes(asym2, seq2);
 		if (r2 == mResidues.end())
-			throw std::runtime_error("Invalid file, missing residue for SS bond");
+		{
+			if (cif::VERBOSE)
+				std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym2 << '/' << seq2 << std::endl;
+			continue;
+			// throw std::runtime_error("Invalid file, missing residue for SS bond");
+		}
 
 		mSSBonds.emplace_back(&*r1, &*r2);
 	}

src/Structure.cpp

@@ -1276,6 +1276,7 @@ bool Monomer::isComplete() const
 		else if (a.labelAtomID() == "C")		seen |= 2;
 		else if (a.labelAtomID() == "N")		seen |= 4;
 		else if (a.labelAtomID() == "O")		seen |= 8;
+		// else if (a.labelAtomID() == "OXT")		seen |= 16;
 	}
 	return seen == 15;
 }