link distance calculation

GNUmakefile.in

@@ -218,7 +218,7 @@ $(1)-test: test/$(1)-test
 
 
 endef
 endef
 
 
-TESTS = unit # pdb2cif
+TESTS = unit pdb2cif
 
 
 $(foreach part,$(TESTS),$(eval $(call TEST_template,$(part))))
 $(foreach part,$(TESTS),$(eval $(call TEST_template,$(part))))
 
 

src/PDB2Cif.cpp

@@ -5797,7 +5797,7 @@ void PDBFileParser::Parse(std::istream& is, cif::File& result)
 				const auto& [x1, y1, z1] = a1.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
 				const auto& [x1, y1, z1] = a1.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
 				const auto& [x2, y2, z2] = a2.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
 				const auto& [x2, y2, z2] = a2.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
 
 
-				if (symm1 == "1_555" and symm2 == "1_555")
+				if ((symm1.empty() or symm1 == "1_555") and (symm2.empty() or symm2 == "1_555"))
 					distance = mmcif::Distance(mmcif::Point{x1, y1, z1}, mmcif::Point{x2, y2, z2});
 					distance = mmcif::Distance(mmcif::Point{x1, y1, z1}, mmcif::Point{x2, y2, z2});
 				else if (cif::VERBOSE)
 				else if (cif::VERBOSE)
 					std::cerr << "Cannot calculate distance for link since one of the atoms is in another dimension" << std::endl;
 					std::cerr << "Cannot calculate distance for link since one of the atoms is in another dimension" << std::endl;
@@ -5805,7 +5805,7 @@ void PDBFileParser::Parse(std::istream& is, cif::File& result)
 			catch (std::exception& ex)
 			catch (std::exception& ex)
 			{
 			{
 				if (cif::VERBOSE)
 				if (cif::VERBOSE)
-					std::cerr << "Error finding atom: " << ex.what() << std::endl;
+					std::cerr << "Error finding atom for LINK distance calculation: " << ex.what() << std::endl;
 			}
 			}
 
 
 			r["pdbx_dist_value"] = distance;
 			r["pdbx_dist_value"] = distance;

test/pdb2cif-test.cpp

@@ -52,7 +52,7 @@ int main(int argc, char* argv[])
 	
 	
 	cif::File f;
 	cif::File f;
 	ReadPDBFile(is, f);
 	ReadPDBFile(is, f);
-	// f.write(std::cout);
+	f.save(std::cout);
 	
 	
 	return 0;	
 	return 0;	
 }
 }