Merge branch 'cmake' into trunk

83f72395 · Maarten L. Hekkelman · 060c760c · d215fd3e · 83f72395 · 83f72395
Commit 83f72395 authored Aug 31, 2021 by Maarten L. Hekkelman
37 changed files
--- a/.gitignore
+++ b/.gitignore
 .vscode
-node_modules
 rsrc/version.txt
 version-info*.txt
-docroot/fonts
-docroot/scripts
-obj
-obj.dbg
-mini-ibs
-make.config
-docroot/css/google-font*.css
-autom4te.cache/
-GNUmakefile
-config.status
-config.log
-aclocal.m4
-dssp
-*.dssp
-src/config.hpp
-src/config.hpp.in~
-src/revision.hpp
 mkdssp
-msvc/x64/
-.vscode/
 .vs/
 build
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.15)
 # set the project name
-project(mkdssp VERSION 4.0.0)
+project(mkdssp VERSION 4.0.1 LANGUAGES CXX)
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+enable_testing()
+include(GNUInstallDirs)
+include(CheckFunctionExists)
+include(CheckIncludeFiles)
+include(CheckLibraryExists)
+include(CMakePackageConfigHelpers)
+include(Dart)
+include(GenerateExportHeader)
+set(CXX_EXTENSIONS OFF)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
-# Set bindir, if not use -DBIN_INSTALL_DIR
+if(CMAKE_COMPILER_IS_GNUCC)
-if(NOT BIN_INSTALL_DIR)
+    set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter")
-  if(CMAKE_INSTALL_BINDIR)
+endif()
-    set(BIN_INSTALL_DIR ${CMAKE_INSTALL_BINDIR})
+if(MSVC)
-  else(CMAKE_INSTALL_BINDIR)
+    set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} /W4")
-    set(BIN_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/bin")
+endif()
-  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)
+if(NOT "$ENV{CCP4}" STREQUAL "")
-# set (BOOST_ROOT ${PROJECT_SOURCE_DIR}/../boost_1_75_0)
+	set(BUILD_SHARED_LIBS ON)
-# 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(CCP4 $ENV{CCP4})
+	list(PREPEND CMAKE_MODULE_PATH "${CCP4}/Lib")
+	list(APPEND CMAKE_PREFIX_PATH ${CCP4})
+	if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+		set(CMAKE_PREFIX_PATH ${CCP4})
+	endif()
+endif()
+if(MSVC)
+    # make msvc standards compliant...
+    add_compile_options(/permissive-)
+	macro(get_WIN32_WINNT version)
+		if (WIN32 AND CMAKE_SYSTEM_VERSION)
+			set(ver ${CMAKE_SYSTEM_VERSION})
+			string(REPLACE "." "" ver ${ver})
+			string(REGEX REPLACE "([0-9])" "0\\1" ver ${ver})
+			set(${version} "0x${ver}")
+		endif()
+	endmacro()
+	get_WIN32_WINNT(ver)
+	add_definitions(-D_WIN32_WINNT=${ver})
+	# On Windows, do not install in the system location
+	if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND NOT ($ENV{LOCALAPPDATA} STREQUAL ""))
+		message(WARNING "The executable will be installed in $ENV{LOCALAPPDATA}")
+		set(CMAKE_INSTALL_PREFIX "$ENV{LOCALAPPDATA}" CACHE PATH "..." FORCE)
+	endif()
+	# Find out the processor type for the target
+	if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "AMD64")
+		set(COFF_TYPE "x64")
+	elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "i386")
+		set(COFF_TYPE "x86")
+	elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "ARM64")
+		set(COFF_TYPE "arm64")
+	else()
+		message(FATAL_ERROR "Unsupported or unknown processor type ${CMAKE_SYSTEM_PROCESSOR}")
+	endif()	
+	set(COFF_SPEC "--coff=${COFF_TYPE}")
+endif()
+if(UNIX AND NOT APPLE)
+	# On Linux, install in the $HOME/.local folder by default
+	if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+		message(WARNING "The library and auxiliary files will be installed in $ENV{HOME}/.local")
+		set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "..." FORCE)
+	endif()
+endif()
-find_package(cifpp 1.0 REQUIRED)
+# Create a revision file, containing the current git version info
+find_package(Git)
+if(GIT_FOUND AND EXISTS "${CMAKE_SOURCE_DIR}/.git")
+	include(GetGitRevisionDescription)
+    get_git_head_revision(REFSPEC COMMITHASH)
+	# Generate our own version string
+	git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty)
+else()
+    message(WARNING "Git not found, cannot set version info")
+    SET(BUILD_VERSION_STRING "unknown")
+endif()
+# generate version.h
+include_directories(${CMAKE_BINARY_DIR} PRIVATE)
+string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%d" UTC)
+configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
+# Optionally use mrc to create resources
+find_program(MRC mrc HINTS "$ENV{LOCALAPPDATA}/bin"  "$ENV{LOCALAPPDATA}/mrc" "${CMAKE_INSTALL_PREFIX}/../mrc" "/usr/local/bin")
+if(MRC)
+	option(USE_RSRC "Use mrc to create resources" ON)
+else()
+	message(WARNING "Not using resources since mrc was not found")
+endif()
+if(USE_RSRC STREQUAL "ON")
+	set(USE_RSRC 1)
+	message("Using resources compiled with ${MRC}")
+	add_compile_definitions(USE_RSRC)
+endif()
 set(CMAKE_THREAD_PREFER_PTHREAD)
 set(THREADS_PREFER_PTHREAD_FLAG)
-find_package(Threads)
+find_package(Threads REQUIRED)
+set (Boost_DETAILED_FAILURE_MSG ON)
+find_package(Boost 1.70.0 REQUIRED COMPONENTS program_options system iostreams regex date_time)
+# extra diagnostic -- helpful for problem with FindBoost.cmake
+message(STATUS "Boost headers in: ${Boost_INCLUDE_DIR}")
+message(STATUS "Boost libraries in: ${Boost_LIBRARY_DIRS}")
+find_package(ZLIB)
+find_package(BZip2)
+find_package(cifpp 1.0 REQUIRED HINTS $ENV{LOCALAPPDATA}/cifpp)
+if(CIFPP_FOUND)
+	add_compile_definitions("DATA_DIR=\"${CIFPP_SHARE_DIR}\"")
+endif()
+include_directories(${Boost_INCLUDE_DIR} cifpp::cifpp ${CMAKE_SOURCE_DIR}/include)
+link_libraries(${Boost_LIBRARIES} cifpp::cifpp ${CMAKE_THREAD_LIBS_INIT})
+if (ZLIB_FOUND)
+	link_libraries(ZLIB::ZLIB)
+endif()
+if (BZIP2_FOUND)
+	link_libraries(BZip2::BZip2)
+endif()
+if(USE_RSRC)
+	add_custom_command(OUTPUT mkdssp_rsrc.obj
+		COMMAND ${MRC} -o mkdssp_rsrc.obj ${CIFPP_SHARE_DIR}/mmcif_pdbx_v50.dic ${COFF_SPEC}
+	)
+	set(DSSP_RESOURCE mkdssp_rsrc.obj)
+endif()
 include_directories(
    ${PROJECT_SOURCE_DIR}/src
 	PUBLIC ${cifpp_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS}
 )
-add_executable(mkdssp ${PROJECT_SOURCE_DIR}/src/mkdssp.cpp)
+add_executable(mkdssp
+	${PROJECT_SOURCE_DIR}/src/dssp.cpp
+	${PROJECT_SOURCE_DIR}/src/dssp.hpp
+	${PROJECT_SOURCE_DIR}/src/mkdssp.cpp
+	${DSSP_RESOURCE})
 install(TARGETS ${PROJECT_NAME}
    RUNTIME DESTINATION ${BIN_INSTALL_DIR}
 )
-target_link_libraries(${PROJECT_NAME} CifPP::cifpp ${Boost_LIBRARIES} Threads::Threads)
+# manual
-if(MSVC)
+if(UNIX)
-    # make msvc standards compliant...
+	install(FILES doc/mkdssp.1
-    target_compile_options(${PROJECT_NAME} PRIVATE /permissive-)
+		DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
-else()
+elseif(MSVC AND EXISTS "${CCP4}/html")
-	find_library(Z z)
+	install(FILES doc/mkdssp.html
-	find_library(BZ2 bz2)
+		DESTINATION ${CCP4}/html)
+endif()
+# test
+add_executable(unit-test ${PROJECT_SOURCE_DIR}/test/unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp.cpp ${DSSP_RESOURCE})
+target_include_directories(unit-test PRIVATE
+	${CMAKE_CURRENT_SOURCE_DIR}/include
+)
-	target_link_libraries(${PROJECT_NAME} ${Z} ${BZ2})
+target_link_libraries(unit-test Threads::Threads ${Boost_LIBRARIES} cifpp::cifpp)
+if(${ZLIB_FOUND})
+	target_link_libraries(unit-test ZLIB::ZLIB)
+endif()
+if(${BZip2_FOUND})
+	target_link_libraries(unit-test BZip2::BZip2)
+endif()
+if(MSVC)
+	# Specify unwind semantics so that MSVC knowns how to handle exceptions
+	target_compile_options(unit-test PRIVATE /EHsc)
 endif()
+add_test(NAME unit-test
+	COMMAND $<TARGET_FILE:unit-test>
+	WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/test)
\ No newline at end of file
--- a/GNUmakefile.in
+++ b/GNUmakefile.in
-# SPDX-License-Identifier: BSD-2-Clause
-# 
-# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
-# 
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# 
-# 1. Redistributions of source code must retain the above copyright notice, this
-#    list of conditions and the following disclaimer
-# 2. Redistributions in binary form must reproduce the above copyright notice,
-#    this list of conditions and the following disclaimer in the documentation
-#    and/or other materials provided with the distribution.
-# 
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-firstTarget: all
-empty =
-space = $(empty) $(empty)
-CXX					= @CXX@
-CXXFLAGS			= @BOOST_CPPFLAGS@ \
-					  @CXXFLAGS@ \
-					  @CPPFLAGS@ \
-					  @PTHREAD_CFLAGS@ \
-					  @CIFPP_CFLAGS@
-LDFLAGS				= @BOOST_LDFLAGS@ \
-					  @LDFLAGS@ \
-					  @PTHREAD_CFLAGS@
-LIBS				= @PTHREAD_LIBS@ \
-					  @CIFPP_LIBS@ \
-					  @BOOST_PROGRAM_OPTIONS_LIB@ \
-					  @BOOST_IOSTREAMS_LIB@ \
-					  @BOOST_DATE_TIME_LIB@ \
-					  @BOOST_REGEX_LIB@ \
-					  @LIBS@
-prefix				= $(DESTDIR)@prefix@
-exec_prefix			= @exec_prefix@
-bindir				= @bindir@
-datarootdir			= @datarootdir@
-datadir				= @datadir@
-mandir				= @mandir@
-GNUmakefile: config.status GNUmakefile.in
-	$(SHELL) ./config.status
-# main build variables
-PROGRAM				= @PACKAGE_NAME@
-VERSION				= @PACKAGE_VERSION@
-SEARCH_PATHS		= src test @LIBCIFPP_DATA_DIR@
-OBJECTS				= $(PROGRAM).o
-RESOURCES			= mmcif_pdbx_v50.dic
-# Use the DEBUG flag to build debug versions of the code
-DEBUG				= @DEBUG@
-ifeq "$(DEBUG)" "1"
-DEFINES				+= DEBUG
-CXXFLAGS            += -g -O0
-LDFLAGS				+= -g
-else
-CXXFLAGS			+= -O2
-DEFINES				+= NDEBUG
-endif
-MRC					= @MRC@
-USE_RSRC			= @USE_RSRC@
-VPATH += $(subst $(space),:,$(SEARCH_PATHS))
-CXXFLAGS            += -Wall -Wno-multichar
-CXXFLAGS			+= $(DEFINES:%=-D%)
-OBJDIR = obj
-ifeq "$(DEBUG)" "1"
-	OBJDIR	:= $(OBJDIR).dbg
-endif
-$(OBJDIR):
-	mkdir -p $(OBJDIR)
-$(OBJDIR)/%.o: %.cpp | $(OBJDIR)
-	@ echo ">>" $<
-	@ $(CXX) -MD -c -o $@ $< $(CFLAGS) $(CXXFLAGS)
-# We have development releases and official releases, for each we
-# maintain different versioning schemes.
-ifneq "x@UPDATE_REVISION@" "x"
-REVISION = $(shell git log --pretty=format:%h --max-count=1)
-REVISION_FILE = version-info-$(REVISION).txt
-$(REVISION_FILE):
-	rm -f version-info-*.txt
-	@ echo $(PROGRAM)-version: $(VERSION) > $@
-	@ git describe --match=build --dirty >> $@
-	@ git log --pretty=medium --date=iso8601 -1 >> $@
-src/revision.hpp: $(REVISION_FILE)
-	@ echo 'const char kRevision[] = R"(' > $@
-	@ cat $? >> $@
-	@ echo ')";' >> $@
-else
-src/revision.hpp:
-	@ echo 'const char kRevision[] = R"(' > $@
-	@ echo $(PROGRAM)-version: $(VERSION) >> $@
-	@ echo Date:   $$(TZ=GMT date +"%Y-%m-%d") >> $@
-	@ echo ')";' >> $@
-endif
-# The program rules
-ifneq "$(USE_RSRC)" "0"
-OBJECTS += $(PROGRAM)_rsrc.o
-# dictionaries may be found compressed
-%.dic: %.dic.gz
-	gunzip -c $^ > $@
-$(OBJDIR)/$(PROGRAM)_rsrc.o: $(RESOURCES)
-	$(MRC) -o $@ $^
-endif
-$(OBJDIR)/$(PROGRAM).o: src/revision.hpp
-$(PROGRAM): $(OBJECTS:%.o=$(OBJDIR)/%.o)
-	@ echo '->' $@
-	@ $(CXX) -o $@ $^ $(CXXFLAGS) $(LDFLAGS) $(LIBS)
-$(OBJDIR)/%.d: $(OBJDIR)/%.o
-include $(OBJECTS:%.o=$(OBJDIR)/%.d)
-.PHONY: clean all
-clean:
-	rm -rf $(PROGRAM) $(OBJDIR)/* src/revision.hpp
-all: $(PROGRAM)
-.PHONY: install
-install: $(PROGRAM)
-	install -d $(bindir)
-	install $(PROGRAM) $(bindir)/$(PROGRAM)
-	install -d $(mandir)/man1
-	install -m 644 doc/$(PROGRAM).1 $(mandir)/man1/$(PROGRAM).1;
-	gzip $(mandir)/man1/$(PROGRAM).1;
-.PHONY: FORCE
-FORCE:
-.PHONY: test
-test:
-	@ echo $(OBJECTS)
--- a/README.md
+++ b/README.md
@@ -32,12 +32,20 @@ Make sure you install [libcif++](https://github.com/PDB-REDO/libcifpp) first bef
 After that, building should be as easy as typing:
 ```
-./configure
+git clone https://github.com/PBD-REDO/dssp.git
-make
+cd dssp
-sudo make install
+mkdir build
+cd build
+cmake ..
+cmake --build . --config Release
+ctest -C Release
+cmake --install .
 ```
+This will install the `mkdssp` program in `$HOME/.local/bin`. If you want to
+install elsewhere, specify the prefix with the [CMAKE_INSTALL_PREFIX](https://cmake.org/cmake/help/v3.21/variable/CMAKE_INSTALL_PREFIX.html) variable.
 Usage
 -----
-See `man mkdssp` for more info.
+See [manual page](doc/mkdssp.pdf) for more info.
--- a/changelog
+++ b/changelog
+Version 4.0.1
+- Switch from GNU configure to cmake as the build environment
+Version 4.0.0
+- Write the secondary structure information as an annotation to an mmCIF file
+  (old format is still available as an option)
+- Added the recognition of Poly-Proline helices
--- a/cmake/GetGitRevisionDescription.cmake
+++ b/cmake/GetGitRevisionDescription.cmake
+# - Returns a version string from Git
+#
+# These functions force a re-configure on each git commit so that you can
+# trust the values of the variables in your build system.
+#
+#  get_git_head_revision(<refspecvar> <hashvar> [ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR])
+#
+# Returns the refspec and sha hash of the current head revision
+#
+#  git_describe(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe on the source tree, and adjusting
+# the output so that it tests false if an error occurs.
+#
+#  git_describe_working_tree(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe on the working tree (--dirty option),
+# and adjusting the output so that it tests false if an error occurs.
+#
+#  git_get_exact_tag(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe --exact-match on the source tree,
+# and adjusting the output so that it tests false if there was no exact
+# matching tag.
+#
+#  git_local_changes(<var>)
+#
+# Returns either "CLEAN" or "DIRTY" with respect to uncommitted changes.
+# Uses the return code of "git diff-index --quiet HEAD --".
+# Does not regard untracked files.
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2020 Ryan Pavlik <ryan.pavlik@gmail.com> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+#
+# Copyright 2009-2013, Iowa State University.
+# Copyright 2013-2020, Ryan Pavlik
+# Copyright 2013-2020, Contributors
+# SPDX-License-Identifier: BSL-1.0
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+if(__get_git_revision_description)
+    return()
+endif()
+set(__get_git_revision_description YES)
+# We must run the following at "include" time, not at function call time,
+# to find the path to this module rather than the path to a calling list file
+get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
+# Function _git_find_closest_git_dir finds the next closest .git directory
+# that is part of any directory in the path defined by _start_dir.
+# The result is returned in the parent scope variable whose name is passed
+# as variable _git_dir_var. If no .git directory can be found, the
+# function returns an empty string via _git_dir_var.
+#
+# Example: Given a path C:/bla/foo/bar and assuming C:/bla/.git exists and
+# neither foo nor bar contain a file/directory .git. This wil return
+# C:/bla/.git
+#
+function(_git_find_closest_git_dir _start_dir _git_dir_var)
+    set(cur_dir "${_start_dir}")
+    set(git_dir "${_start_dir}/.git")
+    while(NOT EXISTS "${git_dir}")
+        # .git dir not found, search parent directories
+        set(git_previous_parent "${cur_dir}")
+        get_filename_component(cur_dir "${cur_dir}" DIRECTORY)
+        if(cur_dir STREQUAL git_previous_parent)
+            # We have reached the root directory, we are not in git
+            set(${_git_dir_var}
+                ""
+                PARENT_SCOPE)
+            return()
+        endif()
+        set(git_dir "${cur_dir}/.git")
+    endwhile()
+    set(${_git_dir_var}
+        "${git_dir}"
+        PARENT_SCOPE)
+endfunction()
+function(get_git_head_revision _refspecvar _hashvar)
+    _git_find_closest_git_dir("${CMAKE_CURRENT_SOURCE_DIR}" GIT_DIR)
+    if("${ARGN}" STREQUAL "ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR")
+        set(ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR TRUE)
+    else()
+        set(ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR FALSE)
+    endif()
+    if(NOT "${GIT_DIR}" STREQUAL "")
+        file(RELATIVE_PATH _relative_to_source_dir "${CMAKE_SOURCE_DIR}"
+             "${GIT_DIR}")
+        if("${_relative_to_source_dir}" MATCHES "[.][.]" AND NOT ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR)
+            # We've gone above the CMake root dir.
+            set(GIT_DIR "")
+        endif()
+    endif()
+    if("${GIT_DIR}" STREQUAL "")
+        set(${_refspecvar}
+            "GITDIR-NOTFOUND"
+            PARENT_SCOPE)
+        set(${_hashvar}
+            "GITDIR-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+    # Check if the current source dir is a git submodule or a worktree.
+    # In both cases .git is a file instead of a directory.
+    #
+    if(NOT IS_DIRECTORY ${GIT_DIR})
+        # The following git command will return a non empty string that
+        # points to the super project working tree if the current
+        # source dir is inside a git submodule.
+        # Otherwise the command will return an empty string.
+        #
+        execute_process(
+            COMMAND "${GIT_EXECUTABLE}" rev-parse
+                    --show-superproject-working-tree
+            WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+            OUTPUT_VARIABLE out
+            ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+        if(NOT "${out}" STREQUAL "")
+            # If out is empty, GIT_DIR/CMAKE_CURRENT_SOURCE_DIR is in a submodule
+            file(READ ${GIT_DIR} submodule)
+            string(REGEX REPLACE "gitdir: (.*)$" "\\1" GIT_DIR_RELATIVE
+                                 ${submodule})
+            string(STRIP ${GIT_DIR_RELATIVE} GIT_DIR_RELATIVE)
+            get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
+            get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE}
+                                   ABSOLUTE)
+            set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD")
+        else()
+            # GIT_DIR/CMAKE_CURRENT_SOURCE_DIR is in a worktree
+            file(READ ${GIT_DIR} worktree_ref)
+            # The .git directory contains a path to the worktree information directory
+            # inside the parent git repo of the worktree.
+            #
+            string(REGEX REPLACE "gitdir: (.*)$" "\\1" git_worktree_dir
+                                 ${worktree_ref})
+            string(STRIP ${git_worktree_dir} git_worktree_dir)
+            _git_find_closest_git_dir("${git_worktree_dir}" GIT_DIR)
+            set(HEAD_SOURCE_FILE "${git_worktree_dir}/HEAD")
+        endif()
+    else()
+        set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD")
+    endif()
+    set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
+    if(NOT EXISTS "${GIT_DATA}")
+        file(MAKE_DIRECTORY "${GIT_DATA}")
+    endif()
+    if(NOT EXISTS "${HEAD_SOURCE_FILE}")
+        return()
+    endif()
+    set(HEAD_FILE "${GIT_DATA}/HEAD")
+    configure_file("${HEAD_SOURCE_FILE}" "${HEAD_FILE}" COPYONLY)
+    configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
+                   "${GIT_DATA}/grabRef.cmake" @ONLY)
+    include("${GIT_DATA}/grabRef.cmake")
+    set(${_refspecvar}
+        "${HEAD_REF}"
+        PARENT_SCOPE)
+    set(${_hashvar}
+        "${HEAD_HASH}"
+        PARENT_SCOPE)
+endfunction()
+function(git_describe _var)
+    if(NOT GIT_FOUND)
+        find_package(Git QUIET)
+    endif()
+    get_git_head_revision(refspec hash)
+    if(NOT GIT_FOUND)
+        set(${_var}
+            "GIT-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+    if(NOT hash)
+        set(${_var}
+            "HEAD-HASH-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+    # TODO sanitize
+    #if((${ARGN}" MATCHES "&&") OR
+    #	(ARGN MATCHES "||") OR
+    #	(ARGN MATCHES "\\;"))
+    #	message("Please report the following error to the project!")
+    #	message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
+    #endif()
+    #message(STATUS "Arguments to execute_process: ${ARGN}")
+    execute_process(
+        COMMAND "${GIT_EXECUTABLE}" describe --tags --always ${hash} ${ARGN}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+        RESULT_VARIABLE res
+        OUTPUT_VARIABLE out
+        ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT res EQUAL 0)
+        set(out "${out}-${res}-NOTFOUND")
+    endif()
+    set(${_var}
+        "${out}"
+        PARENT_SCOPE)
+endfunction()
+function(git_describe_working_tree _var)
+    if(NOT GIT_FOUND)
+        find_package(Git QUIET)
+    endif()
+    if(NOT GIT_FOUND)
+        set(${_var}
+            "GIT-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+    execute_process(
+        COMMAND "${GIT_EXECUTABLE}" describe --dirty ${ARGN}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+        RESULT_VARIABLE res
+        OUTPUT_VARIABLE out
+        ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT res EQUAL 0)
+        set(out "${out}-${res}-NOTFOUND")
+    endif()
+    set(${_var}
+        "${out}"
+        PARENT_SCOPE)
+endfunction()
+function(git_get_exact_tag _var)
+    git_describe(out --exact-match ${ARGN})
+    set(${_var}
+        "${out}"
+        PARENT_SCOPE)
+endfunction()
+function(git_local_changes _var)
+    if(NOT GIT_FOUND)
+        find_package(Git QUIET)
+    endif()
+    get_git_head_revision(refspec hash)
+    if(NOT GIT_FOUND)
+        set(${_var}
+            "GIT-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+    if(NOT hash)
+        set(${_var}
+            "HEAD-HASH-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+    execute_process(
+        COMMAND "${GIT_EXECUTABLE}" diff-index --quiet HEAD --
+        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+        RESULT_VARIABLE res
+        OUTPUT_VARIABLE out
+        ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(res EQUAL 0)
+        set(${_var}
+            "CLEAN"
+            PARENT_SCOPE)
+    else()
+        set(${_var}
+            "DIRTY"
+            PARENT_SCOPE)
+    endif()
+endfunction()
--- a/cmake/GetGitRevisionDescription.cmake.in
+++ b/cmake/GetGitRevisionDescription.cmake.in
+#
+# Internal file for GetGitRevisionDescription.cmake
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+# Iowa State University HCI Graduate Program/VRAC
+#
+# Copyright 2009-2012, Iowa State University
+# Copyright 2011-2015, Contributors
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+# SPDX-License-Identifier: BSL-1.0
+set(HEAD_HASH)
+file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
+string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
+if(HEAD_CONTENTS MATCHES "ref")
+	# named branch
+	string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
+	if(EXISTS "@GIT_DIR@/${HEAD_REF}")
+		configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
+	else()
+		configure_file("@GIT_DIR@/packed-refs" "@GIT_DATA@/packed-refs" COPYONLY)
+		file(READ "@GIT_DATA@/packed-refs" PACKED_REFS)
+		if(${PACKED_REFS} MATCHES "([0-9a-z]*) ${HEAD_REF}")
+			set(HEAD_HASH "${CMAKE_MATCH_1}")
+		endif()
+	endif()
+else()
+	# detached HEAD
+	configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
+endif()
+if(NOT HEAD_HASH)
+	file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
+	string(STRIP "${HEAD_HASH}" HEAD_HASH)
+endif()
--- a/config/config.guess
+++ b/config/config.guess
--- a/config/config.sub
+++ b/config/config.sub
--- a/config/install-sh
+++ b/config/install-sh
--- a/config/m4/ax_filesystem.m4
+++ b/config/m4/ax_filesystem.m4
-# SPDX-License-Identifier: BSD-2-Clause
-# 
-# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
-# 
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# 
-# 1. Redistributions of source code must retain the above copyright notice, this
-#    list of conditions and the following disclaimer
-# 2. Redistributions in binary form must reproduce the above copyright notice,
-#    this list of conditions and the following disclaimer in the documentation
-#    and/or other materials provided with the distribution.
-# 
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# Description: m4 macro to detect std::filesystem and optionally the linker flags to use it
-AC_DEFUN([AX_FILESYSTEM],
-[
-	AC_CHECK_HEADER([filesystem], [], [AC_MSG_ERROR([The file <filesystem> is missing, perhaps you should install a more recent libstdc++ implementation.])])
-	dnl check if we need stdc++fs as library
-	AC_TRY_LINK(
-		[#include <filesystem>],
-		[(void)std::filesystem::current_path();],
-		[],
-		[
-			LIBS="$LIBS -lstdc++fs"
-			AC_TRY_LINK(
-				[#include <filesystem>],
-				[(void)std::filesystem::current_path();],
-				[],
-				[
-					AC_MSG_ERROR([Could not link filesystem])
-				]
-			)
-		]
-	)
-])
--- a/config/m4/ax_libcifpp.m4
+++ b/config/m4/ax_libcifpp.m4
-# SPDX-License-Identifier: BSD-2-Clause
-# 
-# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
-# 
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# 
-# 1. Redistributions of source code must retain the above copyright notice, this
-#    list of conditions and the following disclaimer
-# 2. Redistributions in binary form must reproduce the above copyright notice,
-#    this list of conditions and the following disclaimer in the documentation
-#    and/or other materials provided with the distribution.
-# 
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# Description: m4 macro to detect std::filesystem and optionally the linker flags to use it
-# 
-# Description: Check for libcifpp
-AC_DEFUN([AX_LIBCIFPP],
-[
-	AC_ARG_WITH([cif++],
-		AS_HELP_STRING([--with-cif++=@<:@location@:>@],
-			[Use the cif++ library as specified.]),
-			[
-				AS_IF([test -d ${withval}/include], [], [
-					AC_MSG_ERROR(['${withval}'' is not a valid directory for --with-cif++])
-				])
-				CIFPP_CFLAGS="-I ${withval}/include"
-				CIFPP_LIBS="-L${withval}/.libs -lcifpp"
-				LIBCIFPP_DATA_DIR="${withval}/rsrc"
-				AC_SUBST([CIFPP_CFLAGS], [$CIFPP_CFLAGS])
-				AC_SUBST([CIFPP_LIBS], [$CIFPP_LIBS])
-			])
-	AS_IF([test "x$CIFPP_LIBS" = "x"], [
-		if test -x "$PKG_CONFIG"
-		then
-			AX_PKG_CHECK_MODULES([CIFPP], [libcifpp], [], [], [AC_MSG_ERROR([the required package libcif++ is not installed])])
-			LIBCIFPP_DATA_DIR=$(pkg-config --variable=datalibdir libcifpp)
-		else
-			AC_CHECK_HEADER(
-				[cif++/Cif++.hpp],
-				[
-					dnl CIFPP_CFLAGS="-I ${withval}/include"
-				],
-				[AC_MSG_ERROR([
-	Can't find the libcif++ header, Config.hpp.  Make sure that it
-	is installed, and either use the --with-cif++ option or install
-	pkg-config.])])
-			AX_CHECK_LIBRARY([CIFPP], [cif++/Cif++.hpp], [cifpp],
-				[
-					LIBS="-lcifpp $LIBS"
-				],
-				[AC_MSG_ERROR([libcif++ not found])])
-			AS_IF([ test -f /usr/local/share/libcifpp/mmcif_pdbx_v50.dic.gz ], [LIBCIFPP_DATA_DIR=/usr/local/share/libcifpp/ ])
-			AS_IF([ test -f /var/cache/libcifpp/mmcif_pdbx_v50.dic.gz ], [LIBCIFPP_DATA_DIR=/var/cache/libcifpp ])
-		fi
-	])
-	AC_ARG_VAR([LIBCIFPP_DATA_DIR], [Directory containing mmcif_pdbx_v50.dic file])
-	AC_SUBST([LIBCIFPP_DATA_DIR], [$LIBCIFPP_DATA_DIR])
-])
\ No newline at end of file
--- a/config/m4/ax_mrc.m4
+++ b/config/m4/ax_mrc.m4
-# SPDX-License-Identifier: BSD-2-Clause
-# 
-# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
-# 
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# 
-# 1. Redistributions of source code must retain the above copyright notice, this
-#    list of conditions and the following disclaimer
-# 2. Redistributions in binary form must reproduce the above copyright notice,
-#    this list of conditions and the following disclaimer in the documentation
-#    and/or other materials provided with the distribution.
-# 
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# Description: m4 macro to detect mrc, the resource compiler
-AC_DEFUN([AX_MRC],
-[
-	AC_ARG_VAR([MRC], [Specify a location for the mrc executable])
-	dnl using resources?
-	USE_RSRC=0
-	if test "x$MRC" = "x"; then
-		AC_PATH_PROG([MRC], [mrc])
-	fi
-	if test "x$MRC" = "x"; then
-		AC_MSG_WARN([The mrc application was not found, not using resources.])
-	else
-		AC_ARG_ENABLE(
-			resources,
-			[AS_HELP_STRING([--disable-resources], [Do not use mrc to store data in resources])])
-		AS_IF([test "x$enable_resources" != "xno" ], [
-			USE_RSRC=1
-		])
-	fi
-	AC_SUBST([USE_RSRC], [$USE_RSRC])
-	AC_DEFINE_UNQUOTED([USE_RSRC], [$USE_RSRC], [Use mrc to store resources])	
-])
\ No newline at end of file
--- a/config/m4/ax_z_bz2.m4
+++ b/config/m4/ax_z_bz2.m4
-# SPDX-License-Identifier: BSD-2-Clause
-# 
-# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
-# 
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# 
-# 1. Redistributions of source code must retain the above copyright notice, this
-#    list of conditions and the following disclaimer
-# 2. Redistributions in binary form must reproduce the above copyright notice,
-#    this list of conditions and the following disclaimer in the documentation
-#    and/or other materials provided with the distribution.
-# 
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# Description: m4 macro to detect whether the z and bz2 libraries needs to be linked
-# when using boost::iostreams
-AC_DEFUN([read_test], [
-	AC_LANG_SOURCE(esyscmd(config/tools/m4esc.sh config/test/$1))])
-AC_DEFUN([AX_IOSTREAMS_Z],
-[
-	AC_MSG_CHECKING([need to link zlib])
-	save_CPPFLAGS="$CPPFLAGS"
-	CPPFLAGS="$BOOST_CPPFLAGS $CPPFLAGS "
-	save_LDFLAGS="$LDFLAGS"
-	LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
-	save_LIBS="$LIBS"
-	LIBS="$LIBS $BOOST $BOOST_IOSTREAMS_LIB"
-	NEED_ZLIB=0
-	AC_LINK_IFELSE(
-		[read_test(iostreams-zlib-test.cpp)],
-		[AC_MSG_RESULT([no])],
-		[
-			LIBS="$LIBS -lz"
-			AC_LINK_IFELSE(
-				[read_test(iostreams-zlib-test.cpp)],
-				[
-					AC_MSG_RESULT([yes])
-					NEED_ZLIB=1
-				],
-				[AC_MSG_ERROR([Could not link iostreams, even with zlib])])
-		])
-	CPPFLAGS="$save_CPPFLAGS"
-	LDFLAGS="$save_LDFLAGS"
-	LIBS="$save_LIBS"
-	if [ test "x$NEED_ZLIB" != "x" ]; then
-		LIBS="$LIBS -lz"
-	fi
-])
-AC_DEFUN([AX_IOSTREAMS_BZ2],
-[
-	AC_MSG_CHECKING([need to link bzip2])
-	save_CPPFLAGS="$CPPFLAGS"
-	CPPFLAGS="$BOOST_CPPFLAGS $CPPFLAGS "
-	save_LDFLAGS="$LDFLAGS"
-	LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
-	save_LIBS="$LIBS"
-	LIBS="$LIBS $BOOST $BOOST_IOSTREAMS_LIB"
-	NEED_BZLIB=0
-	AC_LINK_IFELSE(
-		[read_test(iostreams-bzip2-test.cpp)],
-		[AC_MSG_RESULT([no])],
-		[
-			LIBS="$LIBS -lbz2"
-			AC_LINK_IFELSE(
-				[read_test(iostreams-bzip2-test.cpp)],
-				[
-					AC_MSG_RESULT([yes])
-					NEED_BZLIB=1
-				],
-				[AC_MSG_ERROR([Could not link iostreams, even with bzip2])])
-		])
-	CPPFLAGS="$save_CPPFLAGS"
-	LDFLAGS="$save_LDFLAGS"
-	LIBS="$save_LIBS"
-	if [ test "x$NEED_BZLIB" != "x" ]; then
-		LIBS="$LIBS -lbz2"
-	fi
-])
\ No newline at end of file
--- a/config/test/iostreams-bzip2-test.cpp
+++ b/config/test/iostreams-bzip2-test.cpp
-#include <boost/iostreams/filtering_stream.hpp>
-#include <boost/iostreams/filter/bzip2.hpp>
-namespace io = boost::iostreams;
-int main()
-{
-	io::filtering_stream<io::input> in;
-	in.push(io::bzip2_decompressor());
-	return 0;
-}
--- a/config/test/iostreams-zlib-test.cpp
+++ b/config/test/iostreams-zlib-test.cpp
-#include <boost/iostreams/filtering_stream.hpp>
-#include <boost/iostreams/filter/gzip.hpp>
-namespace io = boost::iostreams;
-int main()
-{
-	io::filtering_stream<io::input> in;
-	in.push(io::gzip_decompressor());
-	return 0;
-}
--- a/config/tools/m4esc.sh
+++ b/config/tools/m4esc.sh
-#!/bin/bash
-set -e
-file="$1"
-echo -n "[["
-while IFS= read -r line; do
-	echo $line | sed -e 's/\[/@<:@/g' -e 's/\]/@:>@/g' -e 's/#/@%:@/g' -e 's/\$/@S|@/g'
-	echo
-done < "$file"
-echo -n "]]"
--- a/configure
+++ b/configure
--- a/configure.ac
+++ b/configure.ac
-AC_PREREQ([2.69])
-m4_define([dssp_version_major],[4])
-m4_define([dssp_version_minor],[0])
-m4_define([dssp_version_micro],[0])
-m4_define([dssp_version_extra],[])
-m4_define([dssp_version],[dssp_version_major().dssp_version_minor().dssp_version_micro()dssp_version_extra])
-AC_INIT([mkdssp], [dssp_version], [m.hekkelman@nki.nl])
-dnl Switch to a decent C++ compiler, and check if it works.
-AC_LANG(C++)
-AX_CXX_COMPILE_STDCXX_17([noext])
-AX_CHECK_COMPILE_FLAG([-fstandalone-debug],
-	[
-		CXXFLAGS="$CXXFLAGS -fstandalone-debug"
-	] , , [-Werror])
-AC_CONFIG_SRCDIR([src/mkdssp.cpp])
-AC_CONFIG_AUX_DIR(config)
-AC_CONFIG_MACRO_DIR([config/m4])
-AC_CONFIG_HEADERS([src/config.hpp])
-AC_PREFIX_DEFAULT(/usr/local)
-AC_PROG_INSTALL
-PKG_PROG_PKG_CONFIG
-AX_PTHREAD
-AC_ARG_VAR([DEBUG], [Build a debug version of the application])
-AX_MRC
-dnl revision numbering is something used internally at the NKI
-AC_ARG_ENABLE(
-	revision,
-	[AS_HELP_STRING([--disable-revision], [Create a build number as revision])])
-AS_IF([test "x$enable_revision" != "xno" ], [
-	UPDATE_REVISION=1
-])
-AC_SUBST([UPDATE_REVISION], [$UPDATE_REVISION])
-AX_FILESYSTEM
-AX_BOOST_BASE([1.65.1], [], [AC_MSG_ERROR([Could not find a recent version of boost])])
-AX_BOOST_IOSTREAMS
-AX_BOOST_PROGRAM_OPTIONS
-AX_BOOST_DATE_TIME
-AX_BOOST_REGEX
-AX_IOSTREAMS_Z
-AX_IOSTREAMS_BZ2
-AX_LIBCIFPP
-dnl These are still needed outside the Debian environment
-AX_CHECK_LIBRARY([LIBZ], [zlib.h], [z],
-	[ LIBS="$LIBS -lz" ],
-	[AC_MSG_ERROR([libz not found - compressed files not supported])])
-AX_CHECK_LIBRARY([LIBBZ2], [bzlib.h], [bz2],
-	[ LIBS="$LIBS -lbz2"],
-	[AC_MSG_ERROR([libbz2 not found - compressed files not supported])])
-AC_SUBST([LIBS], [$LIBS])
-dnl Process Makefile.in to create Makefile
-AC_OUTPUT([GNUmakefile])
--- a/doc/mkdssp.1
+++ b/doc/mkdssp.1
-.TH mkdssp 1 "2020-11-23" "version 1.0.0" "User Commands"
+.TH mkdssp 1 "2021-08-31" "version 4.0.1" "User Commands"
 .if n .ad l
 .nh
 .SH NAME
@@ -74,7 +74,4 @@ the author.
 .SH AUTHOR
 Written by Maarten L. Hekkelman <maarten@hekkelman.com>
 .SH "REPORTING BUGS"
-Report bugs at https://github.com/PDB-REDO/cif-tools/issues
+Report bugs at https://github.com/PDB-REDO/dssp/issues
-.SH "SEE ALSO"
-\fBcif-drop\fR, \fBcif-grep\fR, \fBcif-merge\fR, \fBcif-validate\fR, 
-\fBcif2pdb\fR, \fBmmCQL\fR, \fBpdb2cif\fR.
--- a/doc/mkdssp.html
+++ b/doc/mkdssp.html
+Content-type: text/html; charset=UTF-8
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<HTML><HEAD><TITLE>Man page of mkdssp</TITLE>
+</HEAD><BODY>
+<H1>mkdssp</H1>
+Section: User Commands (1)<BR>Updated: 2021-08-31<BR><A HREF="#index">Index</A>
+<A HREF="/cgi-bin/man/man2html">Return to Main Contents</A><HR>
+<A NAME="lbAB">&nbsp;</A>
+<H2>NAME</H2>
+mkdssp - Assign secondary structure to proteins
+<A NAME="lbAC">&nbsp;</A>
+<H2>SYNOPSIS</H2>
+mkdssp [OPTION] input [output]
+<A NAME="lbAD">&nbsp;</A>
+<H2>DESCRIPTION</H2>
+The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
+standardize secondary structure assignment. DSSP is a database of
+secondary structure assignments (and much more) for all protein entries
+in the Protein Data Bank (PDB). mkdssp is the program that calculates
+DSSP entries from PDB entries. mkdssp does <B>not</B> predict secondary structure.
+<P>
+The original DSSP program wrote output in a fixed format, this version
+by default writes annotated mmCIF files, storing the secondary structure
+information in the _struct_conf category.
+<P>
+Since version 4.0 the mkdssp program also assigns PPII helices.
+<A NAME="lbAE">&nbsp;</A>
+<H2>OPTIONS</H2>
+The input file can be either mmCIF or PDB format and the file may be
+gzip or bzip2 compressed. Note that input files must be formatted correctly.
+E.g. PDB files must have a CRYST1 record. More info:
+<A HREF="https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1">https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1</A>
+<P>
+The output is optional, if omitted the output is written to <I>stdout</I>. If
+the name of the output file ends with either <I>.gz</I> or <I>.bz2</I> the
+output is compressed accordingly.
+<DL COMPACT>
+<DT><B>--output-format</B>=[dssp|mmcif]<DD>
+If an output file is specified, the extension of the filename is used to
+choose to output format, but if it is unclear, mmcif is the default. Use
+this option to force output in either the old fixed column DSSP format or
+the new annotated mmCIF format.
+<DT><B>--min-pp-stretch</B><DD>
+This option can be used to define the minimal number of residues with PHI/PSI
+angles within the range required to assing a PP helix.
+<DT><B>--write-other</B><DD>
+By default the new format does not write the structure information for OTHER.
+Use this flag to change that.
+</DL>
+<A NAME="lbAF">&nbsp;</A>
+<H2>DETAILS</H2>
+The DSSP algorithm assings secondary structure based on the energy calculated
+for H-bonds.
+<BR>
+<B>Table&nbsp;1.&nbsp;Secondary&nbsp;Structures&nbsp;recognized</B>
+<TABLE BORDER>
+<TR VALIGN=top><TD ALIGN=center><B>DSSP Code</B></TD><TD ALIGN=center><B>mmCIF Code</B></TD><TD ALIGN=center><B>Description</B><BR></TD></TR>
+<TR VALIGN=top><TD>H</TD><TD>HELX_RH_AL_P</TD><TD>Alphahelix<BR></TD></TR>
+<TR VALIGN=top><TD>B</TD><TD>STRN</TD><TD>Betabridge<BR></TD></TR>
+<TR VALIGN=top><TD>E</TD><TD>STRN</TD><TD>Strand<BR></TD></TR>
+<TR VALIGN=top><TD>G</TD><TD>HELX_RH_3T_P</TD><TD>Helix_3<BR></TD></TR>
+<TR VALIGN=top><TD>I</TD><TD>HELX_RH_PI_P</TD><TD>Helix_5<BR></TD></TR>
+<TR VALIGN=top><TD>P</TD><TD>HELX_LH_PP_P</TD><TD>Helix_PPII<BR></TD></TR>
+<TR VALIGN=top><TD>T</TD><TD>TURN_TY1_P</TD><TD>Turn<BR></TD></TR>
+<TR VALIGN=top><TD>S</TD><TD>BEND</TD><TD>Bend<BR></TD></TR>
+<TR VALIGN=top><TD>
+' ' (space)
+</TD><TD>OTHER</TD><TD>Loop<BR></TD></TR>
+</TABLE>
+<A NAME="lbAG">&nbsp;</A>
+<H2>BUGS</H2>
+The mmCIF format currently lacks a lot of information that was available
+in the old format like information about the bridge pairs or the span
+of the various helices recognized. Also the accessibility information
+is left out.
+<P>
+If you think this information should be part of the output, please contact
+the author.
+<A NAME="lbAH">&nbsp;</A>
+<H2>AUTHOR</H2>
+Written by Maarten L. Hekkelman &lt;<A HREF="mailto:maarten@hekkelman.com">maarten@hekkelman.com</A>&gt;
+<A NAME="lbAI">&nbsp;</A>
+<H2>REPORTING BUGS</H2>
+Report bugs at <A HREF="https://github.com/PDB-REDO/dssp/issues">https://github.com/PDB-REDO/dssp/issues</A>
+<P>
+<HR>
+<A NAME="index">&nbsp;</A><H2>Index</H2>
+<DL>
+<DT><A HREF="#lbAB">NAME</A><DD>
+<DT><A HREF="#lbAC">SYNOPSIS</A><DD>
+<DT><A HREF="#lbAD">DESCRIPTION</A><DD>
+<DT><A HREF="#lbAE">OPTIONS</A><DD>
+<DT><A HREF="#lbAF">DETAILS</A><DD>
+<DT><A HREF="#lbAG">BUGS</A><DD>
+<DT><A HREF="#lbAH">AUTHOR</A><DD>
+<DT><A HREF="#lbAI">REPORTING BUGS</A><DD>
+</DL>
+<HR>
+This document was created by
+<A HREF="/cgi-bin/man/man2html">man2html</A>,
+using the manual pages.<BR>
+Time: 13:56:55 GMT, August 31, 2021
+</BODY>
+</HTML>
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--- a/src/config.hpp.in
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-/* define if the Boost library is available */
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--- a/src/dssp.cpp
+++ b/src/dssp.cpp
--- a/src/dssp.hpp
+++ b/src/dssp.hpp
+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ * 
+ * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+#pragma once
+#include <cif++/Structure.hpp>
+#include <cif++/Secondary.hpp>
+void load_version_info();
+std::string get_version_nr();
+std::string get_version_date();
+std::string get_version_string();
+void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ostream& os);
+void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, bool writeOther, std::ostream& os);
--- a/src/mkdssp.cpp
+++ b/src/mkdssp.cpp
--- a/src/mkdssp.hpp
+++ b/src/mkdssp.hpp
+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ * 
+ * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
--- a/src/pr-main.cpp
+++ b/src/pr-main.cpp
-/* include/cif++/Config.hpp.  Generated from Config.hpp.in by configure.  */
-/*-
- * SPDX-License-Identifier: BSD-2-Clause
- * 
- * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
- * 
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- * 
- * 1. Redistributions of source code must retain the above copyright notice, this
- *    list of conditions and the following disclaimer
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-#if _MSC_VER
-#include <time.h>
-#include <winsock.h>
-#else
-#include <sys/time.h>
-#include <sys/resource.h>
-#endif
-#include <stdexcept>
-#include <iostream>
-#include <iomanip>
-#include <chrono>
-#include <cmath>
-#include <regex>
-#include "cif++/Cif++.hpp"
-#include "cif++/CifUtils.hpp"
-std::string VERSION_STRING;
-int pr_main(int argc, char* argv[]);
-// --------------------------------------------------------------------
-std::ostream& operator<<(std::ostream& os, const struct timeval& t)
-{
-	uint64_t s = t.tv_sec;
-	if (s > 24 * 60 * 60)
-	{
-		uint32_t days = s / (24 * 60 * 60);
-		os << days << "d ";
-		s %= 24 * 60 * 60;
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-	if (s > 60 * 60)
-	{
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-		os << hours << "h ";
-		s %= 60 * 60;
-	}
-	if (s > 60)
-	{
-		uint32_t minutes = s / 60;
-		os << minutes << "m ";
-		s %= 60;
-	}
-	double ss = s + 1e-6 * t.tv_usec;
-	os << std::fixed << std::setprecision(1) << ss << 's';
-	return os;
-}
-std::ostream& operator<<(std::ostream& os, const std::chrono::duration<double>& t)
-{
-	uint64_t s = static_cast<uint64_t>(std::trunc(t.count()));
-	if (s > 24 * 60 * 60)
-	{
-		uint32_t days = s / (24 * 60 * 60);
-		os << days << "d ";
-		s %= 24 * 60 * 60;
-	}
-	if (s > 60 * 60)
-	{
-		uint32_t hours = s / (60 * 60);
-		os << hours << "h ";
-		s %= 60 * 60;
-	}
-	if (s > 60)
-	{
-		uint32_t minutes = s / 60;
-		os << minutes << "m ";
-		s %= 60;
-	}
-	double ss = s + 1e-6 * (t.count() - s);
-	os << std::fixed << std::setprecision(1) << ss << 's';
-	return os;
-}
-class RUsage
-{
-  public:
-	~RUsage()
-	{
-#if not _MSC_VER
-		if (cif::VERBOSE)
-		{
-			struct rusage u;
-			auto end = std::chrono::system_clock::now();
-			std::chrono::duration<double> diff = end - start;
-			if (getrusage(RUSAGE_SELF, &u) == 0)
-				std::cerr << "CPU usage: "
-					<< u.ru_utime << " user, "
-					<< u.ru_stime << " system, "
-					<< diff << " wall" << std::endl;
-			else
-				perror("Failed to get rusage");
-		}
-#endif
-	}
-	std::chrono::time_point<std::chrono::system_clock>	start = std::chrono::system_clock::now();
-};
-// --------------------------------------------------------------------
-namespace {
-	std::string gVersionNr, gVersionDate;
-}
-void load_version_info()
-{
-	const std::regex
-		rxVersionNr(R"(build-(\d+)-g[0-9a-f]{7}(-dirty)?)"),
-		rxVersionDate(R"(Date: +(\d{4}-\d{2}-\d{2}).*)");
-#if __has_include("revision.hpp")
-#include "revision.hpp"
-#else
-	const char* kRevision = "";
-#endif
-	struct membuf : public std::streambuf
-	{
-		membuf(char* data, size_t length)       { this->setg(data, data, data + length); }
-	} buffer(const_cast<char*>(kRevision), sizeof(kRevision));
-	std::istream is(&buffer);
-	std::string line;
-	while (getline(is, line))
-	{
-		std::smatch m;
-		if (std::regex_match(line, m, rxVersionNr))
-		{
-			gVersionNr = m[1];
-			if (m[2].matched)
-				gVersionNr += '*';
-			continue;
-		}
-		if (std::regex_match(line, m, rxVersionDate))
-		{
-			gVersionDate = m[1];
-			continue;
-		}
-	}
-	if (not VERSION_STRING.empty())
-		VERSION_STRING += "\n";
-	VERSION_STRING += gVersionNr + '.' + cif::get_version_nr() + " " + gVersionDate;
-}
-std::string get_version_nr()
-{
-	return gVersionNr + '/' + cif::get_version_nr();
-}
-std::string get_version_date()
-{
-	return gVersionDate;
-}
-// --------------------------------------------------------------------
-// recursively print exception whats:
-void print_what (const std::exception& e)
-{
-	std::cerr << e.what() << std::endl;
-	try
-	{
-		std::rethrow_if_nested(e);
-	}
-	catch (const std::exception& nested)
-	{
-		std::cerr << " >> ";
-		print_what(nested);
-	}
-}
-int main(int argc, char* argv[])
-{
-	int result = -1;
-	RUsage r;
-	try
-	{
-#if not _MSC_VER
-		cif::rsrc_loader::init({
-			{ cif::rsrc_loader_type::file, "." },
-#if defined DATADIR
-			{ cif::rsrc_loader_type::file, DATADIR },
-#endif
-#if USE_RSRC
-			{ cif::rsrc_loader_type::mrsrc, "", { gResourceIndex, gResourceData, gResourceName } }
-#endif
-		});
-#endif
-		load_version_info();
-		result = pr_main(argc, argv);
-	}
-	catch (std::exception& ex)
-	{
-		print_what(ex);
-		exit(1);
-	}
-	return result;
-}
--- a/src/revision.hpp.in
+++ b/src/revision.hpp.in
+const char kRevision[] = R"(
+mkdssp-version: @PROJECT_VERSION@
+@BUILD_VERSION_STRING@
+Date: @BUILD_DATE_TIME@
+)";
--- a/test/1cbs-dssp.cif
+++ b/test/1cbs-dssp.cif
--- a/test/1cbs.cif.gz
+++ b/test/1cbs.cif.gz
--- a/test/1cbs.dssp
+++ b/test/1cbs.dssp
--- a/test/unit-test.cpp
+++ b/test/unit-test.cpp
+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ * 
+ * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+#define BOOST_TEST_MODULE DSSP_Test
+#include <boost/test/included/unit_test.hpp>
+#include <boost/algorithm/string.hpp>
+#include <stdexcept>
+#include <cif++/Structure.hpp>
+#include <cif++/Secondary.hpp>
+#include <cif++/CifUtils.hpp>
+#include <cif++/Cif2PDB.hpp>
+#include "dssp.hpp"
+namespace ba = boost::algorithm;
+// --------------------------------------------------------------------
+BOOST_AUTO_TEST_CASE(ut_dssp)
+{
+	using namespace std::literals;
+	mmcif::File f("1cbs.cif.gz");
+	mmcif::Structure structure(f, 1, mmcif::StructureOpenOptions::SkipHydrogen);
+	mmcif::DSSP dssp(structure, 3, true);
+	std::stringstream test;
+	writeDSSP(structure, dssp, test);
+	std::ifstream reference("1cbs.dssp", std::ios::binary);
+	BOOST_CHECK(reference.is_open());
+	std::string line_t, line_r;
+	BOOST_CHECK(std::getline(test, line_t) and std::getline(reference, line_r));
+	const char* kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.0                           ====";
+	BOOST_CHECK(line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
+	BOOST_CHECK(line_r.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
+	for (int line_nr = 2; ; ++line_nr)
+	{
+		bool done_t = not std::getline(test, line_t);
+		bool done_r = not std::getline(reference, line_r);
+		BOOST_CHECK_EQUAL(done_r, done_t);
+		if (done_r)
+			break;
+		if (line_t != line_r)
+			std::cerr << line_nr << std::endl
+					<< line_t << std::endl
+					<< line_r << std::endl;
+		BOOST_CHECK(line_t == line_r);
+	}
+	BOOST_CHECK(test.eof());
+	BOOST_CHECK(reference.eof());
+}
+BOOST_AUTO_TEST_CASE(ut_mmcif)
+{
+	using namespace std::literals;
+	mmcif::File f("1cbs.cif.gz");
+	mmcif::Structure structure(f, 1, mmcif::StructureOpenOptions::SkipHydrogen);
+	mmcif::DSSP dssp(structure, 3, true);
+	std::stringstream test;
+	annotateDSSP(structure, dssp, true, test);
+	std::ifstream reference("1cbs-dssp.cif");
+	BOOST_ASSERT(reference.is_open());
+	std::string line_t, line_r;
+	for (int line_nr = 1; ; ++line_nr)
+	{
+		bool done_t = not std::getline(test, line_t);
+		bool done_r = not std::getline(reference, line_r);
+		BOOST_CHECK_EQUAL(done_r, done_t);
+		if (done_r)
+			break;
+		if (line_t != line_r)
+			std::cerr << line_nr << std::endl
+					<< line_t << std::endl
+					<< line_r << std::endl;
+		BOOST_CHECK(line_t == line_r);
+	}
+	BOOST_CHECK(test.eof());
+	BOOST_CHECK(reference.eof());
+}