create symop table

CMakeLists.txt

@@ -30,6 +30,26 @@ endif()
 option(BUILD_SHARED_LIBS "Build a shared library instead of a static one" OFF)
 set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
 
+# Only try to recreate SymOpTable_data.hpp if CCP4 is known
+option(CCP4 "The location where ccp4 is installed" "")
+if(DEFINED CCP4 AND EXISTS ${CCP4})
+	set(CCP4 $ENV{CCP4})
+	set(CLIBD ${CCP4}/lib/data)
+elseif(NOT DEFINED CCP4 AND DEFINED $ENV{CCP4} AND EXISTS $ENV{CCP4})
+	set(CCP4 $ENV{CCP4})
+	set(CLIBD ${CCP4}/lib/data)
+endif()
+
+if(EXISTS "${CCP4}")
+	option(RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
+
+	if(RECREATE_SYMOP_DATA AND NOT EXISTS "${CLIBD}/syminfo.lib")
+		message(FATAL_ERROR "Symop data table recreation requested, but file syminfo.lib was not found in ${CLIBD}")
+	endif()
+else()
+	message("Not trying to recreate SymOpTable_data.hpp since CCP4 is not defined")
+endif()
+
 # set(CMAKE_DEBUG_POSTFIX d)
 
 if(MSVC)
@@ -128,6 +148,27 @@ include_directories(${CMAKE_BINARY_DIR} PRIVATE)
 string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
 configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
 
+# SymOp data table
+if(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 ${Boost_LIBRARIES})
+
+	set($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
+		)
+	
+	add_custom_target(
+		OUTPUT ${CMAKE_SOURCE_DIR}/src/SymOpTable_data.hpp
+		DEPENDS symop-map-generator "$ENV{CLIBD}/syminfo.lib"
+	)
+endif()
+
 # Sources
 
 set(project_sources 
@@ -166,7 +207,7 @@ set(project_headers
 	${PROJECT_SOURCE_DIR}/include/cif++/TlsParser.hpp
 )
 
-add_library(cifpp ${project_sources} ${project_headers})
+add_library(cifpp ${project_sources} ${project_headers} ${PROJECT_SOURCE_DIR}/src/SymOpTable_data.hpp)
 set_target_properties(cifpp PROPERTIES POSITION_INDEPENDENT_CODE ON)
 
 target_include_directories(cifpp
@@ -352,11 +393,11 @@ if(CIFPP_BUILD_TESTS)
 		add_custom_command(
 			OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch
 			COMMAND $<TARGET_FILE:${CIFPP_TEST}>
-			WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/test)
+			WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test)
 
 		add_test(NAME ${CIFPP_TEST}
 			COMMAND $<TARGET_FILE:${CIFPP_TEST}>
-			WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/test)
+			WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/test)
 
 	endforeach()
 endif()

include/cif++/CifUtils.hpp

@@ -48,13 +48,11 @@
 #include "cif++/Cif++Export.hpp"
 
 #if _MSC_VER
-#	pragma warning (disable : 4355)	// this is used in Base Initializer list
-#	pragma warning (disable : 4996)	// unsafe function or variable
+#	pragma warning (disable : 4996)	// unsafe function or variable	(strcpy e.g.)
 #	pragma warning (disable : 4068)	// unknown pragma
-#	pragma warning (disable : 4996)	// stl copy()
-#	pragma warning (disable : 4800)	// BOOL conversion
 #	pragma warning (disable : 4100) // unreferenced formal parameter
 #	pragma warning (disable : 4101) // unreferenced local variable
+#	define _SILENCE_CXX17_CODECVT_HEADER_DEPRECATION_WARNING 1
 #endif
 
 namespace cif

src/Symmetry.cpp

@@ -30,7 +30,7 @@
 #include "cif++/Symmetry.hpp"
 #include "cif++/CifUtils.hpp"
 
-#include "SymOpTable_data.cpp"
+#include "SymOpTable_data.hpp"
 
 namespace mmcif
 {

test/rename-compound-test.cpp

@@ -12,18 +12,29 @@ namespace po = boost::program_options;
 int main(int argc, char* argv[])
 {
 	cif::VERBOSE = 3;
-	
-	mmcif::CompoundFactory::instance().pushDictionary("RXA.cif");
 
-	mmcif::File f("../examples/1cbs.cif.gz");
-	mmcif::Structure structure(f);
+	try
+	{
+		if (std::filesystem::exists("../data/components.cif"))
+			cif::addFileResource("components.cif", "../data/components.cif");
+
+		mmcif::CompoundFactory::instance().pushDictionary("RXA.cif");
+
+		mmcif::File f("../examples/1cbs.cif.gz");
+		mmcif::Structure structure(f);
 
-	auto &res = structure.getResidue("B", "REA");
-	structure.changeResidue(res, "RXA", {});
+		auto &res = structure.getResidue("B", "REA");
+		structure.changeResidue(res, "RXA", {});
 
-	structure.cleanupEmptyCategories();
+		structure.cleanupEmptyCategories();
 
-	f.file().save(std::cout);
+		f.file().save(std::cout);
+	}
+	catch (const std::exception& e)
+	{
+		std::cerr << e.what() << std::endl;
+		exit(1);
+	}
 	
 	return 0;	
 }

tools/symop-map-generator.cpp

@@ -26,6 +26,7 @@
 
 #include <cassert>
 
+#include <array>
 #include <iostream>
 #include <iomanip>
 #include <fstream>
@@ -33,9 +34,12 @@
 #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+) +'([^']+)'( +'([^']+)')?(?: +!.+)?$)");
 
@@ -185,18 +189,42 @@ int main(int argc, char* const argv[])
 
 	try
 	{
-		if (argc != 2)
-			throw std::runtime_error("Usage: symom-map-generator <outputfile>");
+		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"))
+		{
+			std::cerr << visible_options << std::endl;
+			exit(vm.count("help") == 0);
+		}
+
+		fs::path input(vm["input"].as<std::string>());
+		fs::path output(vm["output"].as<std::string>());
+		
+		tmpFile = output.parent_path() / (output.filename().string() + ".tmp");
 
-		tmpFile = argv[1] + ".tmp"s;
 		std::ofstream out(tmpFile);
 		if (not out.is_open())
 			throw std::runtime_error("Failed to open output file");
 
-		const char* CLIBD = getenv("CLIBD");
-		
-		if (CLIBD == nullptr)
-			throw std::runtime_error("CCP4 not sourced");
 
 		// --------------------------------------------------------------------
 
@@ -216,15 +244,13 @@ int main(int argc, char* const argv[])
 		std::map<int,SymInfoBlock> symInfo;
 		int symopnr, mysymnr = 10000;
 
-		std::ifstream file(CLIBD + "/syminfo.lib"s);
+		std::ifstream file(input);
 		if (not file.is_open())
 			throw std::runtime_error("Could not open syminfo.lib file");
 
 		enum class State { skip, spacegroup } state = State::skip;
 
 		std::string line;
-		std::string Hall;
-		std::vector<std::string> old;
 
 		const std::regex rx(R"(^symbol +(Hall|xHM|old) +'(.+?)'(?: +'(.+?)')?$)"),
 			rx2(R"(symbol ccp4 (\d+))");;
@@ -383,7 +409,7 @@ const size_t kSymopNrTableSize = sizeof(kSymopNrTable) / sizeof(SymopDataBlock);
 )" << std::endl;
 
 		out.close();
-		fs::rename(tmpFile, argv[1]);
+		fs::rename(tmpFile, output);
 	}
 	catch (const std::exception& ex)
 	{