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dssp
Commit 83f72395 by Maarten L. Hekkelman
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Merge branch 'cmake' into trunk

parents 060c760c d215fd3e
Showing with 849 additions and 1200 deletions
.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
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(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)
if(CMAKE_COMPILER_IS_GNUCC)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter")
endif()
if(MSVC)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
endif()
set (Boost_DETAILED_FAILURE_MSG ON)
# set (BOOST_ROOT ${PROJECT_SOURCE_DIR}/../boost_1_75_0)
# set (Boost_COMPILER "-vc")
# set (Boost_USE_STATIC_RUNTIME ON)
if(NOT "$ENV{CCP4}" STREQUAL "")
set(BUILD_SHARED_LIBS 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 ${Boost_LIBRARIES} Threads::Threads)
# manual
if(MSVC)
# make msvc standards compliant...
target_compile_options(${PROJECT_NAME} PRIVATE /permissive-)
else()
find_library(Z z)
find_library(BZ2 bz2)
if(UNIX)
install(FILES doc/mkdssp.1
DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
elseif(MSVC AND EXISTS "${CCP4}/html")
install(FILES doc/mkdssp.html
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
GNUmakefile.in deleted 100644 → 0
# 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 $(OBJECTS)
README.md
......@@ -32,12 +32,20 @@ Make sure you install [libcif++](https://github.com/PDB-REDO/libcifpp) first bef
After that, building should be as easy as typing:
```
./configure
make
sudo make install
git clone https://github.com/PBD-REDO/dssp.git
cd dssp
mkdir build
cd build
cmake ..
cmake --build . --config Release
ctest -C Release
cmake --install .
```
This will install the `mkdssp` program in `$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.
changelog 0 → 100644
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
cmake/GetGitRevisionDescription.cmake 0 → 100644
# - 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(${_var}
"DIRTY"
PARENT_SCOPE)
endif()
endfunction()
cmake/GetGitRevisionDescription.cmake.in 0 → 100644
#
# Internal file for GetGitRevisionDescription.cmake
#
# Requires CMake 2.6 or newer (uses the 'function' command)
#
# Original Author:
# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
# http://academic.cleardefinition.com
# Iowa State University HCI Graduate Program/VRAC
#
# Copyright 2009-2012, Iowa State University
# Copyright 2011-2015, Contributors
# Distributed under the Boost Software License, Version 1.0.
# (See accompanying file LICENSE_1_0.txt or copy at
# http://www.boost.org/LICENSE_1_0.txt)
# SPDX-License-Identifier: BSL-1.0
set(HEAD_HASH)
file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
string(STRIP "${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 "${HEAD_HASH}" HEAD_HASH)
endif()
config/m4/ax_filesystem.m4 deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Description: m4 macro to detect std::filesystem and optionally the linker flags to use it
AC_DEFUN([AX_FILESYSTEM],
[
AC_CHECK_HEADER([filesystem], [], [AC_MSG_ERROR([The file <filesystem> is missing, perhaps you should install a more recent libstdc++ implementation.])])
dnl check if we need stdc++fs as library
AC_TRY_LINK(
[#include <filesystem>],
[(void)std::filesystem::current_path();],
[],
[
LIBS="$LIBS -lstdc++fs"
AC_TRY_LINK(
[#include <filesystem>],
[(void)std::filesystem::current_path();],
[],
[
AC_MSG_ERROR([Could not link filesystem])
]
)
]
)
])
config/m4/ax_libcifpp.m4 deleted 100644 → 0
# 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
config/m4/ax_mrc.m4 deleted 100644 → 0
# 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
config/m4/ax_z_bz2.m4 deleted 100644 → 0
# 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
config/test/iostreams-bzip2-test.cpp deleted 100644 → 0
#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;
}
config/test/iostreams-zlib-test.cpp deleted 100644 → 0
#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;
}
config/tools/m4esc.sh deleted 100755 → 0
#!/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 < "$file"
echo -n "]]"
configure deleted 100755 → 0
This source diff could not be displayed because it is too large. You can view the blob instead.
configure.ac deleted 100644 → 0
AC_PREREQ([2.69])
m4_define([dssp_version_major],[4])
m4_define([dssp_version_minor],[0])
m4_define([dssp_version_micro],[0])
m4_define([dssp_version_extra],[])
m4_define([dssp_version],[dssp_version_major().dssp_version_minor().dssp_version_micro()dssp_version_extra])
AC_INIT([mkdssp], [dssp_version], [m.hekkelman@nki.nl])
dnl Switch to a decent C++ compiler, and check if it works.
AC_LANG(C++)
AX_CXX_COMPILE_STDCXX_17([noext])
AX_CHECK_COMPILE_FLAG([-fstandalone-debug],
[
CXXFLAGS="$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])
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
.SH "SEE ALSO"
\fBcif-drop\fR, \fBcif-grep\fR, \fBcif-merge\fR, \fBcif-validate\fR,
\fBcif2pdb\fR, \fBmmCQL\fR, \fBpdb2cif\fR.
Report bugs at https://github.com/PDB-REDO/dssp/issues
doc/mkdssp.html 0 → 100644
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>
doc/mkdssp.pdf 0 → 100644
File added
msvc/mkdssp.sln deleted 100644 → 0

Microsoft Visual Studio Solution File, Format Version 12.00
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msvc/mkdssp.vcxproj deleted 100644 → 0
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src/config.hpp.in deleted 100644 → 0
/* src/config.hpp.in. Generated from configure.ac by autoheader. */
/* define if the Boost library is available */
#undef HAVE_BOOST
/* define if the Boost::Date_Time library is available */
#undef HAVE_BOOST_DATE_TIME
/* define if the Boost::IOStreams library is available */
#undef HAVE_BOOST_IOSTREAMS
/* define if the Boost::PROGRAM_OPTIONS library is available */
#undef HAVE_BOOST_PROGRAM_OPTIONS
/* define if the Boost::Regex library is available */
#undef HAVE_BOOST_REGEX
/* Define to 1 if CIFPP is found */
#undef HAVE_CIFPP
/* define if the compiler supports basic C++17 syntax */
#undef HAVE_CXX17
/* Define to 1 if you have the <inttypes.h> header file. */
#undef HAVE_INTTYPES_H
/* Define to 1 if LIBBZ2 is found */
#undef HAVE_LIBBZ2
/* Define to 1 if LIBZ is found */
#undef HAVE_LIBZ
/* Define to 1 if you have the <memory.h> header file. */
#undef HAVE_MEMORY_H
/* Define if you have POSIX threads libraries and header files. */
#undef HAVE_PTHREAD
/* Have PTHREAD_PRIO_INHERIT. */
#undef HAVE_PTHREAD_PRIO_INHERIT
/* Define to 1 if you have the <stdint.h> header file. */
#undef HAVE_STDINT_H
/* Define to 1 if you have the <stdlib.h> header file. */
#undef HAVE_STDLIB_H
/* Define to 1 if you have the <strings.h> header file. */
#undef HAVE_STRINGS_H
/* Define to 1 if you have the <string.h> header file. */
#undef HAVE_STRING_H
/* Define to 1 if you have the <sys/stat.h> header file. */
#undef HAVE_SYS_STAT_H
/* Define to 1 if you have the <sys/types.h> header file. */
#undef HAVE_SYS_TYPES_H
/* Define to 1 if you have the <unistd.h> header file. */
#undef HAVE_UNISTD_H
/* Define to the address where bug reports for this package should be sent. */
#undef PACKAGE_BUGREPORT
/* Define to the full name of this package. */
#undef PACKAGE_NAME
/* Define to the full name and version of this package. */
#undef PACKAGE_STRING
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
/* Define to the home page for this package. */
#undef PACKAGE_URL
/* Define to the version of this package. */
#undef PACKAGE_VERSION
/* Define to necessary symbol if this constant uses a non-standard name on
your system. */
#undef PTHREAD_CREATE_JOINABLE
/* Define to 1 if you have the ANSI C header files. */
#undef STDC_HEADERS
/* Use mrc to store resources */
#undef USE_RSRC
src/dssp.cpp 0 → 100644
This diff is collapsed. Click to expand it.
src/dssp.hpp 0 → 100644
/*-
* 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);
src/mkdssp.hpp 0 → 100644
/*-
* 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.
*/
src/pr-main.cpp deleted 100644 → 0
/* 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;
}
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.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;
}
src/revision.hpp.in 0 → 100644
const char kRevision[] = R"(
mkdssp-version: @PROJECT_VERSION@
@BUILD_VERSION_STRING@
Date: @BUILD_DATE_TIME@
)";
test/1cbs-dssp.cif 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
test/1cbs.dssp 0 → 100644
This diff is collapsed. Click to expand it.
test/unit-test.cpp 0 → 100644
/*-
* 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());
}
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