With cmake file

.gitignore

@@ -24,3 +24,4 @@ msvc/x64/
 .vscode/
 .vs/
 
+build

CMakeLists.txt

+cmake_minimum_required(VERSION 3.10)
+
+include(FindPkgConfig)
+
+# set the project name
+project(mkdssp VERSION 4.0.0)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Set bindir, if not use -DBIN_INSTALL_DIR
+if(NOT BIN_INSTALL_DIR)
+  if(CMAKE_INSTALL_BINDIR)
+    set(BIN_INSTALL_DIR ${CMAKE_INSTALL_BINDIR})
+  else(CMAKE_INSTALL_BINDIR)
+    set(BIN_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/bin")
+  endif(CMAKE_INSTALL_BINDIR)
+endif(NOT BIN_INSTALL_DIR)
+
+# Set libdir, if not use -DLIB_INSTALL_DIR
+if(NOT LIB_INSTALL_DIR)
+  if(CMAKE_INSTALL_LIBDIR)
+    set(LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR})
+  else(CMAKE_INSTALL_LIBDIR)
+    set(LIB_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}")
+  endif(CMAKE_INSTALL_LIBDIR)
+endif(NOT LIB_INSTALL_DIR)
+
+# Set includedir, if not use -DINCLUDE_INSTALL_DIR
+if(NOT INCLUDE_INSTALL_DIR)
+  if(CMAKE_INSTALL_INCLUDEDIR)
+    set(INCLUDE_INSTALL_DIR ${CMAKE_INSTALL_INCLUDEDIR})
+  else(CMAKE_INSTALL_INCLUDEDIR)
+    set(INCLUDE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/include")
+  endif(CMAKE_INSTALL_INCLUDEDIR)
+endif(NOT INCLUDE_INSTALL_DIR)
+
+# Set sharedir, if not use -DSHARE_INSTALL_DIR
+if(NOT SHARE_INSTALL_DIR)
+  if(CMAKE_INSTALL_DATADIR)
+    set(SHARE_INSTALL_DIR "${CMAKE_INSTALL_DATADIR}")
+  else(CMAKE_INSTALL_DATADIR)
+    set(SHARE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/share")
+  endif(CMAKE_INSTALL_DATADIR)
+endif(NOT SHARE_INSTALL_DIR)
+
+set (Boost_DETAILED_FAILURE_MSG ON)
+# set (BOOST_ROOT ${PROJECT_SOURCE_DIR}/../boost_1_75_0)
+# set (Boost_COMPILER "-vc")
+# set (Boost_USE_STATIC_RUNTIME ON)  
+
+find_package(Boost 1.73.0 REQUIRED COMPONENTS system iostreams regex date_time program_options)
+
+set(CMAKE_THREAD_PREFER_PTHREAD)
+set(THREADS_PREFER_PTHREAD_FLAG)
+find_package(Threads)
+
+pkg_check_modules(LibcifPP libcifpp)
+
+include_directories(
+    ${PROJECT_SOURCE_DIR}/src
+)
+
+add_executable(mkdssp ${PROJECT_SOURCE_DIR}/src/mkdssp.cpp)
+
+include_directories(${PROJECT_NAME} PUBLIC ${LibcifPP_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS})
+
+install(TARGETS ${PROJECT_NAME}
+    RUNTIME DESTINATION ${BIN_INSTALL_DIR}
+)
+
+target_link_libraries(${PROJECT_NAME} ${LibcifPP_LINK_LIBRARIES} ${Boost_LIBRARIES} z bz2 Threads::Threads)
+
+if(MSVC)
+    # make msvc standards compliant...
+    target_compile_options(${PROJECT_NAME} PRIVATE /permissive-)
+    target_compile_options(unit-test PRIVATE /permissive-)
+endif()
+

src/mkdssp.cpp

@@ -475,6 +475,11 @@ int d_main(int argc, const char* argv[])
 		("xyzin,i",				po::value<std::string>(),	"coordinates file")
 		("output,o",            po::value<std::string>(),	"Output to this file")
 		("debug,d",				po::value<int>(),			"Debug level (for even more verbose output)")
+
+		("compounds",			po::value<std::string>(),	"Location of the components.cif file from CCD")
+		("components",			po::value<std::string>(),	"Location of the components.cif file from CCD, alias")
+		("extra-compounds",		po::value<std::string>(),	"File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
+		("mmcif-dictionary",	po::value<std::string>(),	"Path to the mmcif_pdbx.dic file to use instead of default")
 		;
 
 	po::options_description cmdline_options;
@@ -520,7 +525,22 @@ int d_main(int argc, const char* argv[])
 		cif::VERBOSE = vm["debug"].as<int>();
 
 	// --------------------------------------------------------------------
+
+	// Load extra CCD definitions, if any
+
+	if (vm.count("compounds"))
+		cif::addFileResource("components.cif", vm["compounds"].as<std::string>());
+	else if (vm.count("components"))
+		cif::addFileResource("components.cif", vm["components"].as<std::string>());
 	
+	if (vm.count("extra-compounds"))
+		mmcif::CompoundFactory::instance().pushDictionary(vm["extra-compounds"].as<std::string>());
+	
+	// And perhaps a private mmcif_pdbx dictionary
+
+	if (vm.count("mmcif-dictionary"))
+		cif::addFileResource("mmcif_pdbx_v50.dic", vm["mmcif-dictionary"].as<std::string>());
+
 	if (vm.count("dict"))
 	{
 		for (auto dict: vm["dict"].as<std::vector<std::string>>())