Merge branch 'trunk' of github.com:PDB-REDO/libcifpp into trunk

CMakeLists.txt

@@ -44,10 +44,10 @@ 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_COMPILER "-vc")
 # set (Boost_USE_STATIC_RUNTIME ON)  
 
-find_package(Boost 1.73.0 REQUIRED COMPONENTS system iostreams)
+find_package(Boost 1.73.0 REQUIRED COMPONENTS system iostreams regex date_time)
 
 set(CMAKE_THREAD_PREFER_PTHREAD)
 set(THREADS_PREFER_PTHREAD_FLAG)
@@ -93,9 +93,10 @@ set(project_headers
 include_directories(
     ${PROJECT_SOURCE_DIR}/include
     ${PROJECT_SOURCE_DIR}/src
-    )
+)
 
 add_library(${PROJECT_NAME} ${project_sources} ${project_headers})
+add_executable(unit-test ${PROJECT_SOURCE_DIR}/test/unit-test.cpp)
 
 configure_file(libcifpp.pc.in ${CMAKE_BINARY_DIR}/libcifpp.pc IMMEDIATE @ONLY)
 install(FILES ${CMAKE_BINARY_DIR}/libcifpp.pc DESTINATION ${LIB_INSTALL_DIR}/pkgconfig)
@@ -105,20 +106,35 @@ target_include_directories(${PROJECT_NAME} PUBLIC "${PROJECT_BINARY_DIR}")
 # install(FILES ${CMAKE_BINARY_DIR}/Config.hpp DESTINATION ${INCLUDE_INSTALL_DIR}/${PROJECT_NAME})
 
 if(Boost_FOUND)
-    target_include_directories(${PROJECT_NAME} PUBLIC ${Boost_INCLUDE_DIRS})
-    target_link_libraries(${PROJECT_NAME} ${Boost_LIBRARIES})
+    include_directories(${PROJECT_NAME} PUBLIC ${Boost_INCLUDE_DIRS})
+    link_libraries(${PROJECT_NAME} ${Boost_LIBRARIES})
 endif()
 
 install(DIRECTORY include/cif++ DESTINATION ${INCLUDE_INSTALL_DIR})
 
+install(FILES
+	${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
+	${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic
+	DESTINATION ${SHARE_INSTALL_DIR}/libcifpp/
+)
+
 install(TARGETS ${PROJECT_NAME}
     LIBRARY DESTINATION ${LIB_INSTALL_DIR}
     ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
     RUNTIME DESTINATION ${BIN_INSTALL_DIR}
 )
 
+target_compile_definitions(${PROJECT_NAME}
+	PUBLIC "" CACHE_DIR="${SHARE_INSTALL_DIR}/libcifpp" DATA_DIR="${SHARE_INSTALL_DIR}/libcifpp" )
+
+target_compile_definitions(unit-test
+	PUBLIC "" CACHE_DIR="${SHARE_INSTALL_DIR}/libcifpp" DATA_DIR="${SHARE_INSTALL_DIR}/libcifpp" )
+
+target_link_libraries(unit-test ${PROJECT_NAME} ${Boost_LIBRARIES})
+
 if(MSVC)
-    # Disable a MSVC warning type.
-    target_compile_options(cifpp PRIVATE /permissive-)
+    # make msvc standards compliant...
+    target_compile_options(${PROJECT_NAME} PRIVATE /permissive-)
+    target_compile_options(unit-test PRIVATE /permissive-)
 endif()
 

GNUmakefile.in

@@ -282,8 +282,6 @@ install: install-lib
 	install -d $(libdir)
 	$(LIBTOOL) --mode=install install $(LIB_TARGET) $(libdir)
 	install -d $(datadir)/libcifpp
-	install -m644 rsrc/isomers.txt $(datadir)/libcifpp;
-	gzip -f $(datadir)/libcifpp/isomers.txt
 	for d in mmcif_ddl.dic mmcif_pdbx_v50.dic; do \
 		install -m644 rsrc/$$d $(datadir)/libcifpp; \
 		gzip -f $(datadir)/libcifpp/$$d; \

src/Compound.cpp

@@ -540,7 +540,7 @@ class CCP4CompoundFactoryImpl : public CompoundFactoryImpl
 
 CCP4CompoundFactoryImpl::CCP4CompoundFactoryImpl(const fs::path &clibd_mon, CompoundFactoryImpl *next)
 	: CompoundFactoryImpl(next)
-	, mFile(clibd_mon / "list" / "mon_lib_list.cif")
+	, mFile((clibd_mon / "list" / "mon_lib_list.cif").string())
 	, mCLIBD_MON(clibd_mon)
 {
 	const std::regex peptideRx("(?:[lmp]-)?peptide", std::regex::icase);
@@ -580,7 +580,7 @@ Compound *CCP4CompoundFactoryImpl::create(const std::string &id)
 
 		if (fs::exists(resFile))
 		{
-			cif::File cf(resFile);
+			cif::File cf(resFile.string());
 
 			// locate the datablock
 			auto &db = cf["comp_" + id];

src/Secondary.cpp

@@ -182,8 +182,8 @@ struct Res
 		, mChainBreak(brk)
 	{
 		// update the box containing all atoms
-		mBox[0].mX = mBox[0].mY = mBox[0].mZ =  std::numeric_limits<double>::max();
-		mBox[1].mX = mBox[1].mY = mBox[1].mZ = -std::numeric_limits<double>::max();
+		mBox[0].mX = mBox[0].mY = mBox[0].mZ =  std::numeric_limits<float>::max();
+		mBox[1].mX = mBox[1].mY = mBox[1].mZ = -std::numeric_limits<float>::max();
 
 		mH = mmcif::Point{ std::numeric_limits<float>::max(), std::numeric_limits<float>::max(), std::numeric_limits<float>::max() };