remove dependency on boost::program_options

CMakeLists.txt

@@ -184,18 +184,17 @@ if(CIFPP_RECREATE_SYMOP_DATA)
 	# The tool to create the table
 	add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp")
 
-	target_link_libraries(symop-map-generator Threads::Threads
-		Boost::regex Boost::program_options ${CIFPP_REQUIRED_LIBRARIES})
+	target_link_libraries(symop-map-generator Threads::Threads ${CIFPP_REQUIRED_LIBRARIES})
 
 	set($ENV{CLIBD} ${CLIBD})
 
 	add_custom_command(
-		OUTPUT ${CMAKE_SOURCE_DIR}/src/SymOpTable_data.hpp
-		COMMAND $<TARGET_FILE:symop-map-generator> ${CLIBD}/syminfo.lib ${CMAKE_SOURCE_DIR}/src/SymOpTable_data.hpp
+		OUTPUT ${CMAKE_SOURCE_DIR}/src/structure/SymOpTable_data.hpp
+		COMMAND $<TARGET_FILE:symop-map-generator> ${CLIBD}/syminfo.lib ${CMAKE_SOURCE_DIR}/src/structure/SymOpTable_data.hpp
 	)
 
 	add_custom_target(
-		OUTPUT ${CMAKE_SOURCE_DIR}/src/SymOpTable_data.hpp
+		OUTPUT ${CMAKE_SOURCE_DIR}/src/structure/SymOpTable_data.hpp
 		DEPENDS symop-map-generator "$ENV{CLIBD}/syminfo.lib"
 	)
 endif()
@@ -418,7 +417,7 @@ if(CIFPP_BUILD_TESTS)
 
 	list(APPEND CIFPP_tests
 
-		# pdb2cif
+		pdb2cif
 		# rename-compound
 		# structure
 		# sugar

test/pdb2cif-test.cpp

-#include "../include/cif++/Cif++.hpp"
-#include "../include/cif++/PDB2Cif.hpp"
+#include "../include/cif++/cif.hpp"
+#include "../include/cif++/pdb/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 options");
-	desc.add_options()
-		("input,i",		po::value<std::string>(),	"Input file")
-		("help,h",									"Display help message")
-		("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("help") or vm.count("input") == 0)
+	if (argc != 2)
 	{
-		std::cerr << desc << std::endl;
+		std::cerr << "Usage: pdb2cif-test <input-file>" << 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>());
+	std::ifstream is(argv[1]);
 	if (not is.is_open())
-		throw std::runtime_error("Could not open file " + vm["input"].as<std::string>());
+		throw std::runtime_error("Could not open file "s + argv[1]);
 	
 	cif::File f;
 	ReadPDBFile(is, f);

test/rename-compound-test.cpp

@@ -5,10 +5,6 @@
 #include <iostream>
 #include <fstream>
 
-#include <boost/program_options.hpp>
-
-namespace po = boost::program_options;
-
 int main(int argc, char* argv[])
 {
 	cif::VERBOSE = 3;

tools/symop-map-generator.cpp

@@ -34,12 +34,9 @@
 #include <map>
 #include <filesystem>
 
-#include <boost/program_options.hpp>
-
 #include <cstdlib>
 
 namespace fs = std::filesystem;
-namespace po = boost::program_options;
 
 std::regex kNameRx(R"(^(\d+) +(\d+) +(\d+) +(\S+) +(\S+) +(\S+) +'([^']+)'( +'([^']+)')?(?: +!.+)?$)");
 
@@ -233,35 +230,14 @@ int main(int argc, char* const argv[])
 
 	try
 	{
-		po::options_description visible_options("symop-map-generator symlib-file output-file");
-		visible_options.add_options()
-			( "help,h",							"Display help message" )
-			( "verbose,v",						"Verbose output") ;
-
-		po::options_description hidden_options("hidden options");
-		hidden_options.add_options()
-			( "input,i", po::value<std::string>(), "Input file")
-			( "output,o", po::value<std::string>(), "Output file");
-
-		po::options_description cmdline_options;
-		cmdline_options.add(visible_options).add(hidden_options);
-
-		po::positional_options_description p;
-		p.add("input", 1);
-		p.add("output", 1);
-
-		po::variables_map vm;
-		po::store(po::command_line_parser(argc, argv).options(cmdline_options).positional(p).run(), vm);
-		po::notify(vm);
-		
-		if (vm.count("input") == 0 or vm.count("output") == 0 or vm.count("help"))
+		if (argc != 3)
 		{
-			std::cerr << visible_options << std::endl;
-			exit(vm.count("help") == 0);
+			std::cerr << "Usage symop-map-generator <input-file> <output-file>" << std::endl;
+			exit(1);
 		}
 
-		fs::path input(vm["input"].as<std::string>());
-		fs::path output(vm["output"].as<std::string>());
+		fs::path input(argv[1]);
+		fs::path output(argv[2]);
 		
 		tmpFile = output.parent_path() / (output.filename().string() + ".tmp");
 

tools/update-dictionary-script

@@ -45,3 +45,7 @@ fetch_dictionary () {
 
 fetch_dictionary "/var/cache/libcifpp/mmcif_pdbx_v50.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
 fetch_dictionary "/var/cache/libcifpp/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
+
+# this one is not compressed
+
+wget -O/var/cache/libcifpp/mmcif_ma.dic "https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic"