fix parsing PDB files containing carriage returns

GNUmakefile.in

@@ -215,7 +215,7 @@ $(1)_OBJECTS = $$(OBJDIR)/$(1)-test.o
 
 
 test/$(1)-test: $(LIB_TARGET) $$($(1)_OBJECTS)
 test/$(1)-test: $(LIB_TARGET) $$($(1)_OBJECTS)
 	@ echo ">>> building $(1)-test"
 	@ echo ">>> building $(1)-test"
-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $$@ $$($(1)_OBJECTS) -L.libs -lcifpp $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $$@ $$($(1)_OBJECTS) -L.libs -lcifpp -lboost_program_options $(LIBS)
 
 
 .PHONY: $(1)-test
 .PHONY: $(1)-test
 $(1)-test: test/$(1)-test
 $(1)-test: test/$(1)-test
@@ -223,7 +223,7 @@ $(1)-test: test/$(1)-test
 
 
 endef
 endef
 
 
-TESTS = unit
+TESTS = unit pdb2cif
 
 
 $(foreach part,$(TESTS),$(eval $(call TEST_template,$(part))))
 $(foreach part,$(TESTS),$(eval $(call TEST_template,$(part))))
 
 

src/PDB2Cif.cpp

@@ -1124,6 +1124,9 @@ void PDBFileParser::PreParseInput(std::istream& is)
 	uint32_t lineNr = 1;
 	uint32_t lineNr = 1;
 	getline(is, lookahead);
 	getline(is, lookahead);
 
 
+	if (lookahead.back() == '\r')
+		lookahead.pop_back();
+
 //	if (ba::starts_with(lookahead, "HEADER") == false)
 //	if (ba::starts_with(lookahead, "HEADER") == false)
 //		throw std::runtime_error("This does not look like a PDB file, should start with a HEADER line");
 //		throw std::runtime_error("This does not look like a PDB file, should start with a HEADER line");
 
 
@@ -1284,7 +1287,7 @@ void PDBFileParser::PreParseInput(std::istream& is)
 						stoi(lookahead.substr(7, 3)) == compNr and
 						stoi(lookahead.substr(7, 3)) == compNr and
 						contNr(16, 2) == n)
 						contNr(16, 2) == n)
 					{
 					{
-						value += lookahead.substr(19);
+						value += ba::trim_right_copy(lookahead.substr(19));;
 						getline(is, lookahead);
 						getline(is, lookahead);
 						++lineNr;
 						++lineNr;
 						++n;
 						++n;
@@ -1308,7 +1311,7 @@ void PDBFileParser::PreParseInput(std::istream& is)
 			int n = 2;
 			int n = 2;
 			while (lookahead.substr(0, 6) == type and contNr(8, 2) == n)
 			while (lookahead.substr(0, 6) == type and contNr(8, 2) == n)
 			{
 			{
-				value += lookahead.substr(16);
+				value += ba::trim_right_copy(lookahead.substr(16));;
 				getline(is, lookahead);
 				getline(is, lookahead);
 				++lineNr;
 				++lineNr;
 				++n;
 				++n;

test/pdb2cif-test.cpp

+#include "../src/Config.hpp"
+#include "../include/cif++/Cif++.hpp"
+#include "../include/cif++/PDB2Cif.hpp"
+
+#include <iostream>
+#include <fstream>
+
+#include <boost/program_options.hpp>
+
+// #include "pdb2cif.h"
+
+namespace po = boost::program_options;
+
+int main(int argc, char* argv[])
+{
+	using namespace std::literals;
+
+	po::options_description desc("pdb2cif-test "s + PACKAGE_VERSION + " options");
+	desc.add_options()
+		("input,i",		po::value<std::string>(),	"Input file")
+		("help,h",									"Display help message")
+		("version",									"Print version")
+		("verbose,v",								"Verbose output")
+		("debug,d",		po::value<int>(),			"Debug level (for even more verbose output)");
+
+	po::positional_options_description p;
+	p.add("input", 1);
+	
+	po::variables_map vm;
+	po::store(po::command_line_parser(argc, argv).options(desc).positional(p).run(), vm);
+	po::notify(vm);
+
+	if (vm.count("version"))
+	{
+		std::cout << argv[0] << " version " PACKAGE_VERSION << std::endl;
+		exit(0);
+	}
+
+	if (vm.count("help") or vm.count("input") == 0)
+	{
+		std::cerr << desc << std::endl;
+		exit(1);
+	}
+
+	cif::VERBOSE = vm.count("verbose") != 0;
+	if (vm.count("debug"))
+		cif::VERBOSE = vm["debug"].as<int>();
+	
+	std::ifstream is(vm["input"].as<std::string>());
+	if (not is.is_open())
+		throw std::runtime_error("Could not open file " + vm["input"].as<std::string>());
+	
+	cif::File f;
+	ReadPDBFile(is, f);
+	// f.write(std::cout);
+	
+	return 0;	
+}