Skip to content

D
dssp
Commit 83f72395 by Maarten L. Hekkelman
Options

Merge branch 'cmake' into trunk

parents 060c760c d215fd3e
Showing with 1454 additions and 5582 deletions
.gitignore
.vscode .vscode
node_modules
rsrc/version.txt rsrc/version.txt
version-info*.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 mkdssp
msvc/x64/
.vscode/
.vs/ .vs/
build build
CMakeLists.txt
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.15)
# set the project name # set the project name
project(mkdssp VERSION 4.0.0) project(mkdssp VERSION 4.0.1 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
enable_testing()
include(GNUInstallDirs)
include(CheckFunctionExists)
include(CheckIncludeFiles)
include(CheckLibraryExists)
include(CMakePackageConfigHelpers)
include(Dart)
include(GenerateExportHeader)
set(CXX_EXTENSIONS OFF)
set(CMAKE_CXX_STANDARD 17) set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Set bindir, if not use -DBIN_INSTALL_DIR if(CMAKE_COMPILER_IS_GNUCC)
if(NOT BIN_INSTALL_DIR) set(CMAKE_CXX_FLAGS "${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(CMAKE_THREAD_PREFER_PTHREAD)
set(THREADS_PREFER_PTHREAD_FLAG) 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( include_directories(
${PROJECT_SOURCE_DIR}/src ${PROJECT_SOURCE_DIR}/src
PUBLIC ${cifpp_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS} 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} install(TARGETS ${PROJECT_NAME}
RUNTIME DESTINATION ${BIN_INSTALL_DIR} 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() 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 ...@@ -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: 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 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/config.guess deleted 100644 → 0
#! /bin/sh
# Attempt to guess a canonical system name.
# Copyright 1992-2020 Free Software Foundation, Inc.
timestamp='2020-04-26'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <https://www.gnu.org/licenses/>.
#
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that
# program. This Exception is an additional permission under section 7
# of the GNU General Public License, version 3 ("GPLv3").
#
# Originally written by Per Bothner; maintained since 2000 by Ben Elliston.
#
# You can get the latest version of this script from:
# https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
#
# Please send patches to <config-patches@gnu.org>.
me=`echo "$0" | sed -e 's,.*/,,'`
usage="\
Usage: $0 [OPTION]
Output the configuration name of the system \`$me' is run on.
Options:
-h, --help print this help, then exit
-t, --time-stamp print date of last modification, then exit
-v, --version print version number, then exit
Report bugs and patches to <config-patches@gnu.org>."
version="\
GNU config.guess ($timestamp)
Originally written by Per Bothner.
Copyright 1992-2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
help="
Try \`$me --help' for more information."
# Parse command line
while test $# -gt 0 ; do
case $1 in
--time-stamp | --time* | -t )
echo "$timestamp" ; exit ;;
--version | -v )
echo "$version" ; exit ;;
--help | --h* | -h )
echo "$usage"; exit ;;
-- ) # Stop option processing
shift; break ;;
- ) # Use stdin as input.
break ;;
-* )
echo "$me: invalid option $1$help" >&2
exit 1 ;;
* )
break ;;
esac
done
if test $# != 0; then
echo "$me: too many arguments$help" >&2
exit 1
fi
# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
# compiler to aid in system detection is discouraged as it requires
# temporary files to be created and, as you can see below, it is a
# headache to deal with in a portable fashion.
# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
# use `HOST_CC' if defined, but it is deprecated.
# Portable tmp directory creation inspired by the Autoconf team.
tmp=
# shellcheck disable=SC2172
trap 'test -z "$tmp" || rm -fr "$tmp"' 0 1 2 13 15
set_cc_for_build() {
# prevent multiple calls if $tmp is already set
test "$tmp" && return 0
: "${TMPDIR=/tmp}"
# shellcheck disable=SC2039
{ tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
{ test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir "$tmp" 2>/dev/null) ; } ||
{ tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir "$tmp" 2>/dev/null) && echo "Warning: creating insecure temp directory" >&2 ; } ||
{ echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; }
dummy=$tmp/dummy
case ${CC_FOR_BUILD-},${HOST_CC-},${CC-} in
,,) echo "int x;" > "$dummy.c"
for driver in cc gcc c89 c99 ; do
if ($driver -c -o "$dummy.o" "$dummy.c") >/dev/null 2>&1 ; then
CC_FOR_BUILD="$driver"
break
fi
done
if test x"$CC_FOR_BUILD" = x ; then
CC_FOR_BUILD=no_compiler_found
fi
;;
,,*) CC_FOR_BUILD=$CC ;;
,*,*) CC_FOR_BUILD=$HOST_CC ;;
esac
}
# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
# (ghazi@noc.rutgers.edu 1994-08-24)
if test -f /.attbin/uname ; then
PATH=$PATH:/.attbin ; export PATH
fi
UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
case "$UNAME_SYSTEM" in
Linux|GNU|GNU/*)
# If the system lacks a compiler, then just pick glibc.
# We could probably try harder.
LIBC=gnu
set_cc_for_build
cat <<-EOF > "$dummy.c"
#include <features.h>
#if defined(__UCLIBC__)
LIBC=uclibc
#elif defined(__dietlibc__)
LIBC=dietlibc
#else
LIBC=gnu
#endif
EOF
eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`"
# If ldd exists, use it to detect musl libc.
if command -v ldd >/dev/null && \
ldd --version 2>&1 | grep -q ^musl
then
LIBC=musl
fi
;;
esac
# Note: order is significant - the case branches are not exclusive.
case "$UNAME_MACHINE:$UNAME_SYSTEM:$UNAME_RELEASE:$UNAME_VERSION" in
*:NetBSD:*:*)
# NetBSD (nbsd) targets should (where applicable) match one or
# more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*,
# *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
# switched to ELF, *-*-netbsd* would select the old
# object file format. This provides both forward
# compatibility and a consistent mechanism for selecting the
# object file format.
#
# Note: NetBSD doesn't particularly care about the vendor
# portion of the name. We always set it to "unknown".
sysctl="sysctl -n hw.machine_arch"
UNAME_MACHINE_ARCH=`(uname -p 2>/dev/null || \
"/sbin/$sysctl" 2>/dev/null || \
"/usr/sbin/$sysctl" 2>/dev/null || \
echo unknown)`
case "$UNAME_MACHINE_ARCH" in
armeb) machine=armeb-unknown ;;
arm*) machine=arm-unknown ;;
sh3el) machine=shl-unknown ;;
sh3eb) machine=sh-unknown ;;
sh5el) machine=sh5le-unknown ;;
earmv*)
arch=`echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
endian=`echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p'`
machine="${arch}${endian}"-unknown
;;
*) machine="$UNAME_MACHINE_ARCH"-unknown ;;
esac
# The Operating System including object format, if it has switched
# to ELF recently (or will in the future) and ABI.
case "$UNAME_MACHINE_ARCH" in
earm*)
os=netbsdelf
;;
arm*|i386|m68k|ns32k|sh3*|sparc|vax)
set_cc_for_build
if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ELF__
then
# Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
# Return netbsd for either. FIX?
os=netbsd
else
os=netbsdelf
fi
;;
*)
os=netbsd
;;
esac
# Determine ABI tags.
case "$UNAME_MACHINE_ARCH" in
earm*)
expr='s/^earmv[0-9]/-eabi/;s/eb$//'
abi=`echo "$UNAME_MACHINE_ARCH" | sed -e "$expr"`
;;
esac
# The OS release
# Debian GNU/NetBSD machines have a different userland, and
# thus, need a distinct triplet. However, they do not need
# kernel version information, so it can be replaced with a
# suitable tag, in the style of linux-gnu.
case "$UNAME_VERSION" in
Debian*)
release='-gnu'
;;
*)
release=`echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2`
;;
esac
# Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
# contains redundant information, the shorter form:
# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
echo "$machine-${os}${release}${abi-}"
exit ;;
*:Bitrig:*:*)
UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'`
echo "$UNAME_MACHINE_ARCH"-unknown-bitrig"$UNAME_RELEASE"
exit ;;
*:OpenBSD:*:*)
UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
echo "$UNAME_MACHINE_ARCH"-unknown-openbsd"$UNAME_RELEASE"
exit ;;
*:LibertyBSD:*:*)
UNAME_MACHINE_ARCH=`arch | sed 's/^.*BSD\.//'`
echo "$UNAME_MACHINE_ARCH"-unknown-libertybsd"$UNAME_RELEASE"
exit ;;
*:MidnightBSD:*:*)
echo "$UNAME_MACHINE"-unknown-midnightbsd"$UNAME_RELEASE"
exit ;;
*:ekkoBSD:*:*)
echo "$UNAME_MACHINE"-unknown-ekkobsd"$UNAME_RELEASE"
exit ;;
*:SolidBSD:*:*)
echo "$UNAME_MACHINE"-unknown-solidbsd"$UNAME_RELEASE"
exit ;;
*:OS108:*:*)
echo "$UNAME_MACHINE"-unknown-os108_"$UNAME_RELEASE"
exit ;;
macppc:MirBSD:*:*)
echo powerpc-unknown-mirbsd"$UNAME_RELEASE"
exit ;;
*:MirBSD:*:*)
echo "$UNAME_MACHINE"-unknown-mirbsd"$UNAME_RELEASE"
exit ;;
*:Sortix:*:*)
echo "$UNAME_MACHINE"-unknown-sortix
exit ;;
*:Twizzler:*:*)
echo "$UNAME_MACHINE"-unknown-twizzler
exit ;;
*:Redox:*:*)
echo "$UNAME_MACHINE"-unknown-redox
exit ;;
mips:OSF1:*.*)
echo mips-dec-osf1
exit ;;
alpha:OSF1:*:*)
case $UNAME_RELEASE in
*4.0)
UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
;;
*5.*)
UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
;;
esac
# According to Compaq, /usr/sbin/psrinfo has been available on
# OSF/1 and Tru64 systems produced since 1995. I hope that
# covers most systems running today. This code pipes the CPU
# types through head -n 1, so we only detect the type of CPU 0.
ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
case "$ALPHA_CPU_TYPE" in
"EV4 (21064)")
UNAME_MACHINE=alpha ;;
"EV4.5 (21064)")
UNAME_MACHINE=alpha ;;
"LCA4 (21066/21068)")
UNAME_MACHINE=alpha ;;
"EV5 (21164)")
UNAME_MACHINE=alphaev5 ;;
"EV5.6 (21164A)")
UNAME_MACHINE=alphaev56 ;;
"EV5.6 (21164PC)")
UNAME_MACHINE=alphapca56 ;;
"EV5.7 (21164PC)")
UNAME_MACHINE=alphapca57 ;;
"EV6 (21264)")
UNAME_MACHINE=alphaev6 ;;
"EV6.7 (21264A)")
UNAME_MACHINE=alphaev67 ;;
"EV6.8CB (21264C)")
UNAME_MACHINE=alphaev68 ;;
"EV6.8AL (21264B)")
UNAME_MACHINE=alphaev68 ;;
"EV6.8CX (21264D)")
UNAME_MACHINE=alphaev68 ;;
"EV6.9A (21264/EV69A)")
UNAME_MACHINE=alphaev69 ;;
"EV7 (21364)")
UNAME_MACHINE=alphaev7 ;;
"EV7.9 (21364A)")
UNAME_MACHINE=alphaev79 ;;
esac
# A Pn.n version is a patched version.
# A Vn.n version is a released version.
# A Tn.n version is a released field test version.
# A Xn.n version is an unreleased experimental baselevel.
# 1.2 uses "1.2" for uname -r.
echo "$UNAME_MACHINE"-dec-osf"`echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`"
# Reset EXIT trap before exiting to avoid spurious non-zero exit code.
exitcode=$?
trap '' 0
exit $exitcode ;;
Amiga*:UNIX_System_V:4.0:*)
echo m68k-unknown-sysv4
exit ;;
*:[Aa]miga[Oo][Ss]:*:*)
echo "$UNAME_MACHINE"-unknown-amigaos
exit ;;
*:[Mm]orph[Oo][Ss]:*:*)
echo "$UNAME_MACHINE"-unknown-morphos
exit ;;
*:OS/390:*:*)
echo i370-ibm-openedition
exit ;;
*:z/VM:*:*)
echo s390-ibm-zvmoe
exit ;;
*:OS400:*:*)
echo powerpc-ibm-os400
exit ;;
arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
echo arm-acorn-riscix"$UNAME_RELEASE"
exit ;;
arm*:riscos:*:*|arm*:RISCOS:*:*)
echo arm-unknown-riscos
exit ;;
SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
echo hppa1.1-hitachi-hiuxmpp
exit ;;
Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
# akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
if test "`(/bin/universe) 2>/dev/null`" = att ; then
echo pyramid-pyramid-sysv3
else
echo pyramid-pyramid-bsd
fi
exit ;;
NILE*:*:*:dcosx)
echo pyramid-pyramid-svr4
exit ;;
DRS?6000:unix:4.0:6*)
echo sparc-icl-nx6
exit ;;
DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
case `/usr/bin/uname -p` in
sparc) echo sparc-icl-nx7; exit ;;
esac ;;
s390x:SunOS:*:*)
echo "$UNAME_MACHINE"-ibm-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
exit ;;
sun4H:SunOS:5.*:*)
echo sparc-hal-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
exit ;;
sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
echo sparc-sun-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
exit ;;
i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
echo i386-pc-auroraux"$UNAME_RELEASE"
exit ;;
i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
set_cc_for_build
SUN_ARCH=i386
# If there is a compiler, see if it is configured for 64-bit objects.
# Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
# This test works for both compilers.
if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
(CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
grep IS_64BIT_ARCH >/dev/null
then
SUN_ARCH=x86_64
fi
fi
echo "$SUN_ARCH"-pc-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
exit ;;
sun4*:SunOS:6*:*)
# According to config.sub, this is the proper way to canonicalize
# SunOS6. Hard to guess exactly what SunOS6 will be like, but
# it's likely to be more like Solaris than SunOS4.
echo sparc-sun-solaris3"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
exit ;;
sun4*:SunOS:*:*)
case "`/usr/bin/arch -k`" in
Series*|S4*)
UNAME_RELEASE=`uname -v`
;;
esac
# Japanese Language versions have a version number like `4.1.3-JL'.
echo sparc-sun-sunos"`echo "$UNAME_RELEASE"|sed -e 's/-/_/'`"
exit ;;
sun3*:SunOS:*:*)
echo m68k-sun-sunos"$UNAME_RELEASE"
exit ;;
sun*:*:4.2BSD:*)
UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3
case "`/bin/arch`" in
sun3)
echo m68k-sun-sunos"$UNAME_RELEASE"
;;
sun4)
echo sparc-sun-sunos"$UNAME_RELEASE"
;;
esac
exit ;;
aushp:SunOS:*:*)
echo sparc-auspex-sunos"$UNAME_RELEASE"
exit ;;
# The situation for MiNT is a little confusing. The machine name
# can be virtually everything (everything which is not
# "atarist" or "atariste" at least should have a processor
# > m68000). The system name ranges from "MiNT" over "FreeMiNT"
# to the lowercase version "mint" (or "freemint"). Finally
# the system name "TOS" denotes a system which is actually not
# MiNT. But MiNT is downward compatible to TOS, so this should
# be no problem.
atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
echo m68k-atari-mint"$UNAME_RELEASE"
exit ;;
atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
echo m68k-atari-mint"$UNAME_RELEASE"
exit ;;
*falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
echo m68k-atari-mint"$UNAME_RELEASE"
exit ;;
milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
echo m68k-milan-mint"$UNAME_RELEASE"
exit ;;
hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
echo m68k-hades-mint"$UNAME_RELEASE"
exit ;;
*:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
echo m68k-unknown-mint"$UNAME_RELEASE"
exit ;;
m68k:machten:*:*)
echo m68k-apple-machten"$UNAME_RELEASE"
exit ;;
powerpc:machten:*:*)
echo powerpc-apple-machten"$UNAME_RELEASE"
exit ;;
RISC*:Mach:*:*)
echo mips-dec-mach_bsd4.3
exit ;;
RISC*:ULTRIX:*:*)
echo mips-dec-ultrix"$UNAME_RELEASE"
exit ;;
VAX*:ULTRIX*:*:*)
echo vax-dec-ultrix"$UNAME_RELEASE"
exit ;;
2020:CLIX:*:* | 2430:CLIX:*:*)
echo clipper-intergraph-clix"$UNAME_RELEASE"
exit ;;
mips:*:*:UMIPS | mips:*:*:RISCos)
set_cc_for_build
sed 's/^ //' << EOF > "$dummy.c"
#ifdef __cplusplus
#include <stdio.h> /* for printf() prototype */
int main (int argc, char *argv[]) {
#else
int main (argc, argv) int argc; char *argv[]; {
#endif
#if defined (host_mips) && defined (MIPSEB)
#if defined (SYSTYPE_SYSV)
printf ("mips-mips-riscos%ssysv\\n", argv[1]); exit (0);
#endif
#if defined (SYSTYPE_SVR4)
printf ("mips-mips-riscos%ssvr4\\n", argv[1]); exit (0);
#endif
#if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
printf ("mips-mips-riscos%sbsd\\n", argv[1]); exit (0);
#endif
#endif
exit (-1);
}
EOF
$CC_FOR_BUILD -o "$dummy" "$dummy.c" &&
dummyarg=`echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p'` &&
SYSTEM_NAME=`"$dummy" "$dummyarg"` &&
{ echo "$SYSTEM_NAME"; exit; }
echo mips-mips-riscos"$UNAME_RELEASE"
exit ;;
Motorola:PowerMAX_OS:*:*)
echo powerpc-motorola-powermax
exit ;;
Motorola:*:4.3:PL8-*)
echo powerpc-harris-powermax
exit ;;
Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
echo powerpc-harris-powermax
exit ;;
Night_Hawk:Power_UNIX:*:*)
echo powerpc-harris-powerunix
exit ;;
m88k:CX/UX:7*:*)
echo m88k-harris-cxux7
exit ;;
m88k:*:4*:R4*)
echo m88k-motorola-sysv4
exit ;;
m88k:*:3*:R3*)
echo m88k-motorola-sysv3
exit ;;
AViiON:dgux:*:*)
# DG/UX returns AViiON for all architectures
UNAME_PROCESSOR=`/usr/bin/uname -p`
if [ "$UNAME_PROCESSOR" = mc88100 ] || [ "$UNAME_PROCESSOR" = mc88110 ]
then
if [ "$TARGET_BINARY_INTERFACE"x = m88kdguxelfx ] || \
[ "$TARGET_BINARY_INTERFACE"x = x ]
then
echo m88k-dg-dgux"$UNAME_RELEASE"
else
echo m88k-dg-dguxbcs"$UNAME_RELEASE"
fi
else
echo i586-dg-dgux"$UNAME_RELEASE"
fi
exit ;;
M88*:DolphinOS:*:*) # DolphinOS (SVR3)
echo m88k-dolphin-sysv3
exit ;;
M88*:*:R3*:*)
# Delta 88k system running SVR3
echo m88k-motorola-sysv3
exit ;;
XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
echo m88k-tektronix-sysv3
exit ;;
Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
echo m68k-tektronix-bsd
exit ;;
*:IRIX*:*:*)
echo mips-sgi-irix"`echo "$UNAME_RELEASE"|sed -e 's/-/_/g'`"
exit ;;
????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
exit ;; # Note that: echo "'`uname -s`'" gives 'AIX '
i*86:AIX:*:*)
echo i386-ibm-aix
exit ;;
ia64:AIX:*:*)
if [ -x /usr/bin/oslevel ] ; then
IBM_REV=`/usr/bin/oslevel`
else
IBM_REV="$UNAME_VERSION.$UNAME_RELEASE"
fi
echo "$UNAME_MACHINE"-ibm-aix"$IBM_REV"
exit ;;
*:AIX:2:3)
if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
set_cc_for_build
sed 's/^ //' << EOF > "$dummy.c"
#include <sys/systemcfg.h>
main()
{
if (!__power_pc())
exit(1);
puts("powerpc-ibm-aix3.2.5");
exit(0);
}
EOF
if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"`
then
echo "$SYSTEM_NAME"
else
echo rs6000-ibm-aix3.2.5
fi
elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
echo rs6000-ibm-aix3.2.4
else
echo rs6000-ibm-aix3.2
fi
exit ;;
*:AIX:*:[4567])
IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then
IBM_ARCH=rs6000
else
IBM_ARCH=powerpc
fi
if [ -x /usr/bin/lslpp ] ; then
IBM_REV=`/usr/bin/lslpp -Lqc bos.rte.libc |
awk -F: '{ print $3 }' | sed s/[0-9]*$/0/`
else
IBM_REV="$UNAME_VERSION.$UNAME_RELEASE"
fi
echo "$IBM_ARCH"-ibm-aix"$IBM_REV"
exit ;;
*:AIX:*:*)
echo rs6000-ibm-aix
exit ;;
ibmrt:4.4BSD:*|romp-ibm:4.4BSD:*)
echo romp-ibm-bsd4.4
exit ;;
ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
echo romp-ibm-bsd"$UNAME_RELEASE" # 4.3 with uname added to
exit ;; # report: romp-ibm BSD 4.3
*:BOSX:*:*)
echo rs6000-bull-bosx
exit ;;
DPX/2?00:B.O.S.:*:*)
echo m68k-bull-sysv3
exit ;;
9000/[34]??:4.3bsd:1.*:*)
echo m68k-hp-bsd
exit ;;
hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
echo m68k-hp-bsd4.4
exit ;;
9000/[34678]??:HP-UX:*:*)
HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
case "$UNAME_MACHINE" in
9000/31?) HP_ARCH=m68000 ;;
9000/[34]??) HP_ARCH=m68k ;;
9000/[678][0-9][0-9])
if [ -x /usr/bin/getconf ]; then
sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
case "$sc_cpu_version" in
523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0
528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1
532) # CPU_PA_RISC2_0
case "$sc_kernel_bits" in
32) HP_ARCH=hppa2.0n ;;
64) HP_ARCH=hppa2.0w ;;
'') HP_ARCH=hppa2.0 ;; # HP-UX 10.20
esac ;;
esac
fi
if [ "$HP_ARCH" = "" ]; then
set_cc_for_build
sed 's/^ //' << EOF > "$dummy.c"
#define _HPUX_SOURCE
#include <stdlib.h>
#include <unistd.h>
int main ()
{
#if defined(_SC_KERNEL_BITS)
long bits = sysconf(_SC_KERNEL_BITS);
#endif
long cpu = sysconf (_SC_CPU_VERSION);
switch (cpu)
{
case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
case CPU_PA_RISC2_0:
#if defined(_SC_KERNEL_BITS)
switch (bits)
{
case 64: puts ("hppa2.0w"); break;
case 32: puts ("hppa2.0n"); break;
default: puts ("hppa2.0"); break;
} break;
#else /* !defined(_SC_KERNEL_BITS) */
puts ("hppa2.0"); break;
#endif
default: puts ("hppa1.0"); break;
}
exit (0);
}
EOF
(CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"`
test -z "$HP_ARCH" && HP_ARCH=hppa
fi ;;
esac
if [ "$HP_ARCH" = hppa2.0w ]
then
set_cc_for_build
# hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
# 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
# generating 64-bit code. GNU and HP use different nomenclature:
#
# $ CC_FOR_BUILD=cc ./config.guess
# => hppa2.0w-hp-hpux11.23
# $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
# => hppa64-hp-hpux11.23
if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) |
grep -q __LP64__
then
HP_ARCH=hppa2.0w
else
HP_ARCH=hppa64
fi
fi
echo "$HP_ARCH"-hp-hpux"$HPUX_REV"
exit ;;
ia64:HP-UX:*:*)
HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
echo ia64-hp-hpux"$HPUX_REV"
exit ;;
3050*:HI-UX:*:*)
set_cc_for_build
sed 's/^ //' << EOF > "$dummy.c"
#include <unistd.h>
int
main ()
{
long cpu = sysconf (_SC_CPU_VERSION);
/* The order matters, because CPU_IS_HP_MC68K erroneously returns
true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
results, however. */
if (CPU_IS_PA_RISC (cpu))
{
switch (cpu)
{
case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
default: puts ("hppa-hitachi-hiuxwe2"); break;
}
}
else if (CPU_IS_HP_MC68K (cpu))
puts ("m68k-hitachi-hiuxwe2");
else puts ("unknown-hitachi-hiuxwe2");
exit (0);
}
EOF
$CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` &&
{ echo "$SYSTEM_NAME"; exit; }
echo unknown-hitachi-hiuxwe2
exit ;;
9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*)
echo hppa1.1-hp-bsd
exit ;;
9000/8??:4.3bsd:*:*)
echo hppa1.0-hp-bsd
exit ;;
*9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
echo hppa1.0-hp-mpeix
exit ;;
hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*)
echo hppa1.1-hp-osf
exit ;;
hp8??:OSF1:*:*)
echo hppa1.0-hp-osf
exit ;;
i*86:OSF1:*:*)
if [ -x /usr/sbin/sysversion ] ; then
echo "$UNAME_MACHINE"-unknown-osf1mk
else
echo "$UNAME_MACHINE"-unknown-osf1
fi
exit ;;
parisc*:Lites*:*:*)
echo hppa1.1-hp-lites
exit ;;
C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
echo c1-convex-bsd
exit ;;
C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
if getsysinfo -f scalar_acc
then echo c32-convex-bsd
else echo c2-convex-bsd
fi
exit ;;
C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
echo c34-convex-bsd
exit ;;
C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
echo c38-convex-bsd
exit ;;
C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
echo c4-convex-bsd
exit ;;
CRAY*Y-MP:*:*:*)
echo ymp-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
CRAY*[A-Z]90:*:*:*)
echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \
| sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
-e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
-e 's/\.[^.]*$/.X/'
exit ;;
CRAY*TS:*:*:*)
echo t90-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
CRAY*T3E:*:*:*)
echo alphaev5-cray-unicosmk"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
CRAY*SV1:*:*:*)
echo sv1-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
*:UNICOS/mp:*:*)
echo craynv-cray-unicosmp"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
FUJITSU_PROC=`uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'`
echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
exit ;;
5000:UNIX_System_V:4.*:*)
FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
exit ;;
i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
echo "$UNAME_MACHINE"-pc-bsdi"$UNAME_RELEASE"
exit ;;
sparc*:BSD/OS:*:*)
echo sparc-unknown-bsdi"$UNAME_RELEASE"
exit ;;
*:BSD/OS:*:*)
echo "$UNAME_MACHINE"-unknown-bsdi"$UNAME_RELEASE"
exit ;;
arm:FreeBSD:*:*)
UNAME_PROCESSOR=`uname -p`
set_cc_for_build
if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ARM_PCS_VFP
then
echo "${UNAME_PROCESSOR}"-unknown-freebsd"`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`"-gnueabi
else
echo "${UNAME_PROCESSOR}"-unknown-freebsd"`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`"-gnueabihf
fi
exit ;;
*:FreeBSD:*:*)
UNAME_PROCESSOR=`/usr/bin/uname -p`
case "$UNAME_PROCESSOR" in
amd64)
UNAME_PROCESSOR=x86_64 ;;
i386)
UNAME_PROCESSOR=i586 ;;
esac
echo "$UNAME_PROCESSOR"-unknown-freebsd"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
exit ;;
i*:CYGWIN*:*)
echo "$UNAME_MACHINE"-pc-cygwin
exit ;;
*:MINGW64*:*)
echo "$UNAME_MACHINE"-pc-mingw64
exit ;;
*:MINGW*:*)
echo "$UNAME_MACHINE"-pc-mingw32
exit ;;
*:MSYS*:*)
echo "$UNAME_MACHINE"-pc-msys
exit ;;
i*:PW*:*)
echo "$UNAME_MACHINE"-pc-pw32
exit ;;
*:Interix*:*)
case "$UNAME_MACHINE" in
x86)
echo i586-pc-interix"$UNAME_RELEASE"
exit ;;
authenticamd | genuineintel | EM64T)
echo x86_64-unknown-interix"$UNAME_RELEASE"
exit ;;
IA64)
echo ia64-unknown-interix"$UNAME_RELEASE"
exit ;;
esac ;;
i*:UWIN*:*)
echo "$UNAME_MACHINE"-pc-uwin
exit ;;
amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
echo x86_64-pc-cygwin
exit ;;
prep*:SunOS:5.*:*)
echo powerpcle-unknown-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
exit ;;
*:GNU:*:*)
# the GNU system
echo "`echo "$UNAME_MACHINE"|sed -e 's,[-/].*$,,'`-unknown-$LIBC`echo "$UNAME_RELEASE"|sed -e 's,/.*$,,'`"
exit ;;
*:GNU/*:*:*)
# other systems with GNU libc and userland
echo "$UNAME_MACHINE-unknown-`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"``echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`-$LIBC"
exit ;;
*:Minix:*:*)
echo "$UNAME_MACHINE"-unknown-minix
exit ;;
aarch64:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
aarch64_be:Linux:*:*)
UNAME_MACHINE=aarch64_be
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
alpha:Linux:*:*)
case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' /proc/cpuinfo 2>/dev/null` in
EV5) UNAME_MACHINE=alphaev5 ;;
EV56) UNAME_MACHINE=alphaev56 ;;
PCA56) UNAME_MACHINE=alphapca56 ;;
PCA57) UNAME_MACHINE=alphapca56 ;;
EV6) UNAME_MACHINE=alphaev6 ;;
EV67) UNAME_MACHINE=alphaev67 ;;
EV68*) UNAME_MACHINE=alphaev68 ;;
esac
objdump --private-headers /bin/sh | grep -q ld.so.1
if test "$?" = 0 ; then LIBC=gnulibc1 ; fi
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
arc:Linux:*:* | arceb:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
arm*:Linux:*:*)
set_cc_for_build
if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ARM_EABI__
then
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
else
if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ARM_PCS_VFP
then
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabi
else
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabihf
fi
fi
exit ;;
avr32*:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
cris:Linux:*:*)
echo "$UNAME_MACHINE"-axis-linux-"$LIBC"
exit ;;
crisv32:Linux:*:*)
echo "$UNAME_MACHINE"-axis-linux-"$LIBC"
exit ;;
e2k:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
frv:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
hexagon:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
i*86:Linux:*:*)
echo "$UNAME_MACHINE"-pc-linux-"$LIBC"
exit ;;
ia64:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
k1om:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
m32r*:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
m68*:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
mips:Linux:*:* | mips64:Linux:*:*)
set_cc_for_build
IS_GLIBC=0
test x"${LIBC}" = xgnu && IS_GLIBC=1
sed 's/^ //' << EOF > "$dummy.c"
#undef CPU
#undef mips
#undef mipsel
#undef mips64
#undef mips64el
#if ${IS_GLIBC} && defined(_ABI64)
LIBCABI=gnuabi64
#else
#if ${IS_GLIBC} && defined(_ABIN32)
LIBCABI=gnuabin32
#else
LIBCABI=${LIBC}
#endif
#endif
#if ${IS_GLIBC} && defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6
CPU=mipsisa64r6
#else
#if ${IS_GLIBC} && !defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6
CPU=mipsisa32r6
#else
#if defined(__mips64)
CPU=mips64
#else
CPU=mips
#endif
#endif
#endif
#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
MIPS_ENDIAN=el
#else
#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
MIPS_ENDIAN=
#else
MIPS_ENDIAN=
#endif
#endif
EOF
eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU\|^MIPS_ENDIAN\|^LIBCABI'`"
test "x$CPU" != x && { echo "$CPU${MIPS_ENDIAN}-unknown-linux-$LIBCABI"; exit; }
;;
mips64el:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
openrisc*:Linux:*:*)
echo or1k-unknown-linux-"$LIBC"
exit ;;
or32:Linux:*:* | or1k*:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
padre:Linux:*:*)
echo sparc-unknown-linux-"$LIBC"
exit ;;
parisc64:Linux:*:* | hppa64:Linux:*:*)
echo hppa64-unknown-linux-"$LIBC"
exit ;;
parisc:Linux:*:* | hppa:Linux:*:*)
# Look for CPU level
case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
PA7*) echo hppa1.1-unknown-linux-"$LIBC" ;;
PA8*) echo hppa2.0-unknown-linux-"$LIBC" ;;
*) echo hppa-unknown-linux-"$LIBC" ;;
esac
exit ;;
ppc64:Linux:*:*)
echo powerpc64-unknown-linux-"$LIBC"
exit ;;
ppc:Linux:*:*)
echo powerpc-unknown-linux-"$LIBC"
exit ;;
ppc64le:Linux:*:*)
echo powerpc64le-unknown-linux-"$LIBC"
exit ;;
ppcle:Linux:*:*)
echo powerpcle-unknown-linux-"$LIBC"
exit ;;
riscv32:Linux:*:* | riscv64:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
s390:Linux:*:* | s390x:Linux:*:*)
echo "$UNAME_MACHINE"-ibm-linux-"$LIBC"
exit ;;
sh64*:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
sh*:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
sparc:Linux:*:* | sparc64:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
tile*:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
vax:Linux:*:*)
echo "$UNAME_MACHINE"-dec-linux-"$LIBC"
exit ;;
x86_64:Linux:*:*)
echo "$UNAME_MACHINE"-pc-linux-"$LIBC"
exit ;;
xtensa*:Linux:*:*)
echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
i*86:DYNIX/ptx:4*:*)
# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
# earlier versions are messed up and put the nodename in both
# sysname and nodename.
echo i386-sequent-sysv4
exit ;;
i*86:UNIX_SV:4.2MP:2.*)
# Unixware is an offshoot of SVR4, but it has its own version
# number series starting with 2...
# I am not positive that other SVR4 systems won't match this,
# I just have to hope. -- rms.
# Use sysv4.2uw... so that sysv4* matches it.
echo "$UNAME_MACHINE"-pc-sysv4.2uw"$UNAME_VERSION"
exit ;;
i*86:OS/2:*:*)
# If we were able to find `uname', then EMX Unix compatibility
# is probably installed.
echo "$UNAME_MACHINE"-pc-os2-emx
exit ;;
i*86:XTS-300:*:STOP)
echo "$UNAME_MACHINE"-unknown-stop
exit ;;
i*86:atheos:*:*)
echo "$UNAME_MACHINE"-unknown-atheos
exit ;;
i*86:syllable:*:*)
echo "$UNAME_MACHINE"-pc-syllable
exit ;;
i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
echo i386-unknown-lynxos"$UNAME_RELEASE"
exit ;;
i*86:*DOS:*:*)
echo "$UNAME_MACHINE"-pc-msdosdjgpp
exit ;;
i*86:*:4.*:*)
UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'`
if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
echo "$UNAME_MACHINE"-univel-sysv"$UNAME_REL"
else
echo "$UNAME_MACHINE"-pc-sysv"$UNAME_REL"
fi
exit ;;
i*86:*:5:[678]*)
# UnixWare 7.x, OpenUNIX and OpenServer 6.
case `/bin/uname -X | grep "^Machine"` in
*486*) UNAME_MACHINE=i486 ;;
*Pentium) UNAME_MACHINE=i586 ;;
*Pent*|*Celeron) UNAME_MACHINE=i686 ;;
esac
echo "$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}"
exit ;;
i*86:*:3.2:*)
if test -f /usr/options/cb.name; then
UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
echo "$UNAME_MACHINE"-pc-isc"$UNAME_REL"
elif /bin/uname -X 2>/dev/null >/dev/null ; then
UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
(/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
(/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
&& UNAME_MACHINE=i586
(/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
&& UNAME_MACHINE=i686
(/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
&& UNAME_MACHINE=i686
echo "$UNAME_MACHINE"-pc-sco"$UNAME_REL"
else
echo "$UNAME_MACHINE"-pc-sysv32
fi
exit ;;
pc:*:*:*)
# Left here for compatibility:
# uname -m prints for DJGPP always 'pc', but it prints nothing about
# the processor, so we play safe by assuming i586.
# Note: whatever this is, it MUST be the same as what config.sub
# prints for the "djgpp" host, or else GDB configure will decide that
# this is a cross-build.
echo i586-pc-msdosdjgpp
exit ;;
Intel:Mach:3*:*)
echo i386-pc-mach3
exit ;;
paragon:*:*:*)
echo i860-intel-osf1
exit ;;
i860:*:4.*:*) # i860-SVR4
if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
echo i860-stardent-sysv"$UNAME_RELEASE" # Stardent Vistra i860-SVR4
else # Add other i860-SVR4 vendors below as they are discovered.
echo i860-unknown-sysv"$UNAME_RELEASE" # Unknown i860-SVR4
fi
exit ;;
mini*:CTIX:SYS*5:*)
# "miniframe"
echo m68010-convergent-sysv
exit ;;
mc68k:UNIX:SYSTEM5:3.51m)
echo m68k-convergent-sysv
exit ;;
M680?0:D-NIX:5.3:*)
echo m68k-diab-dnix
exit ;;
M68*:*:R3V[5678]*:*)
test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
OS_REL=''
test -r /etc/.relid \
&& OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
&& { echo i486-ncr-sysv4.3"$OS_REL"; exit; }
/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
&& { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;;
3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
&& { echo i486-ncr-sysv4; exit; } ;;
NCR*:*:4.2:* | MPRAS*:*:4.2:*)
OS_REL='.3'
test -r /etc/.relid \
&& OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
&& { echo i486-ncr-sysv4.3"$OS_REL"; exit; }
/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
&& { echo i586-ncr-sysv4.3"$OS_REL"; exit; }
/bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
&& { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;;
m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
echo m68k-unknown-lynxos"$UNAME_RELEASE"
exit ;;
mc68030:UNIX_System_V:4.*:*)
echo m68k-atari-sysv4
exit ;;
TSUNAMI:LynxOS:2.*:*)
echo sparc-unknown-lynxos"$UNAME_RELEASE"
exit ;;
rs6000:LynxOS:2.*:*)
echo rs6000-unknown-lynxos"$UNAME_RELEASE"
exit ;;
PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
echo powerpc-unknown-lynxos"$UNAME_RELEASE"
exit ;;
SM[BE]S:UNIX_SV:*:*)
echo mips-dde-sysv"$UNAME_RELEASE"
exit ;;
RM*:ReliantUNIX-*:*:*)
echo mips-sni-sysv4
exit ;;
RM*:SINIX-*:*:*)
echo mips-sni-sysv4
exit ;;
*:SINIX-*:*:*)
if uname -p 2>/dev/null >/dev/null ; then
UNAME_MACHINE=`(uname -p) 2>/dev/null`
echo "$UNAME_MACHINE"-sni-sysv4
else
echo ns32k-sni-sysv
fi
exit ;;
PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
# says <Richard.M.Bartel@ccMail.Census.GOV>
echo i586-unisys-sysv4
exit ;;
*:UNIX_System_V:4*:FTX*)
# From Gerald Hewes <hewes@openmarket.com>.
# How about differentiating between stratus architectures? -djm
echo hppa1.1-stratus-sysv4
exit ;;
*:*:*:FTX*)
# From seanf@swdc.stratus.com.
echo i860-stratus-sysv4
exit ;;
i*86:VOS:*:*)
# From Paul.Green@stratus.com.
echo "$UNAME_MACHINE"-stratus-vos
exit ;;
*:VOS:*:*)
# From Paul.Green@stratus.com.
echo hppa1.1-stratus-vos
exit ;;
mc68*:A/UX:*:*)
echo m68k-apple-aux"$UNAME_RELEASE"
exit ;;
news*:NEWS-OS:6*:*)
echo mips-sony-newsos6
exit ;;
R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
if [ -d /usr/nec ]; then
echo mips-nec-sysv"$UNAME_RELEASE"
else
echo mips-unknown-sysv"$UNAME_RELEASE"
fi
exit ;;
BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
echo powerpc-be-beos
exit ;;
BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
echo powerpc-apple-beos
exit ;;
BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
echo i586-pc-beos
exit ;;
BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
echo i586-pc-haiku
exit ;;
x86_64:Haiku:*:*)
echo x86_64-unknown-haiku
exit ;;
SX-4:SUPER-UX:*:*)
echo sx4-nec-superux"$UNAME_RELEASE"
exit ;;
SX-5:SUPER-UX:*:*)
echo sx5-nec-superux"$UNAME_RELEASE"
exit ;;
SX-6:SUPER-UX:*:*)
echo sx6-nec-superux"$UNAME_RELEASE"
exit ;;
SX-7:SUPER-UX:*:*)
echo sx7-nec-superux"$UNAME_RELEASE"
exit ;;
SX-8:SUPER-UX:*:*)
echo sx8-nec-superux"$UNAME_RELEASE"
exit ;;
SX-8R:SUPER-UX:*:*)
echo sx8r-nec-superux"$UNAME_RELEASE"
exit ;;
SX-ACE:SUPER-UX:*:*)
echo sxace-nec-superux"$UNAME_RELEASE"
exit ;;
Power*:Rhapsody:*:*)
echo powerpc-apple-rhapsody"$UNAME_RELEASE"
exit ;;
*:Rhapsody:*:*)
echo "$UNAME_MACHINE"-apple-rhapsody"$UNAME_RELEASE"
exit ;;
*:Darwin:*:*)
UNAME_PROCESSOR=`uname -p`
case $UNAME_PROCESSOR in
unknown) UNAME_PROCESSOR=powerpc ;;
esac
if command -v xcode-select > /dev/null 2> /dev/null && \
! xcode-select --print-path > /dev/null 2> /dev/null ; then
# Avoid executing cc if there is no toolchain installed as
# cc will be a stub that puts up a graphical alert
# prompting the user to install developer tools.
CC_FOR_BUILD=no_compiler_found
else
set_cc_for_build
fi
if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
(CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
grep IS_64BIT_ARCH >/dev/null
then
case $UNAME_PROCESSOR in
i386) UNAME_PROCESSOR=x86_64 ;;
powerpc) UNAME_PROCESSOR=powerpc64 ;;
esac
fi
# On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc
if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \
(CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
grep IS_PPC >/dev/null
then
UNAME_PROCESSOR=powerpc
fi
elif test "$UNAME_PROCESSOR" = i386 ; then
# uname -m returns i386 or x86_64
UNAME_PROCESSOR=$UNAME_MACHINE
fi
echo "$UNAME_PROCESSOR"-apple-darwin"$UNAME_RELEASE"
exit ;;
*:procnto*:*:* | *:QNX:[0123456789]*:*)
UNAME_PROCESSOR=`uname -p`
if test "$UNAME_PROCESSOR" = x86; then
UNAME_PROCESSOR=i386
UNAME_MACHINE=pc
fi
echo "$UNAME_PROCESSOR"-"$UNAME_MACHINE"-nto-qnx"$UNAME_RELEASE"
exit ;;
*:QNX:*:4*)
echo i386-pc-qnx
exit ;;
NEO-*:NONSTOP_KERNEL:*:*)
echo neo-tandem-nsk"$UNAME_RELEASE"
exit ;;
NSE-*:NONSTOP_KERNEL:*:*)
echo nse-tandem-nsk"$UNAME_RELEASE"
exit ;;
NSR-*:NONSTOP_KERNEL:*:*)
echo nsr-tandem-nsk"$UNAME_RELEASE"
exit ;;
NSV-*:NONSTOP_KERNEL:*:*)
echo nsv-tandem-nsk"$UNAME_RELEASE"
exit ;;
NSX-*:NONSTOP_KERNEL:*:*)
echo nsx-tandem-nsk"$UNAME_RELEASE"
exit ;;
*:NonStop-UX:*:*)
echo mips-compaq-nonstopux
exit ;;
BS2000:POSIX*:*:*)
echo bs2000-siemens-sysv
exit ;;
DS/*:UNIX_System_V:*:*)
echo "$UNAME_MACHINE"-"$UNAME_SYSTEM"-"$UNAME_RELEASE"
exit ;;
*:Plan9:*:*)
# "uname -m" is not consistent, so use $cputype instead. 386
# is converted to i386 for consistency with other x86
# operating systems.
# shellcheck disable=SC2154
if test "$cputype" = 386; then
UNAME_MACHINE=i386
else
UNAME_MACHINE="$cputype"
fi
echo "$UNAME_MACHINE"-unknown-plan9
exit ;;
*:TOPS-10:*:*)
echo pdp10-unknown-tops10
exit ;;
*:TENEX:*:*)
echo pdp10-unknown-tenex
exit ;;
KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
echo pdp10-dec-tops20
exit ;;
XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
echo pdp10-xkl-tops20
exit ;;
*:TOPS-20:*:*)
echo pdp10-unknown-tops20
exit ;;
*:ITS:*:*)
echo pdp10-unknown-its
exit ;;
SEI:*:*:SEIUX)
echo mips-sei-seiux"$UNAME_RELEASE"
exit ;;
*:DragonFly:*:*)
echo "$UNAME_MACHINE"-unknown-dragonfly"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
exit ;;
*:*VMS:*:*)
UNAME_MACHINE=`(uname -p) 2>/dev/null`
case "$UNAME_MACHINE" in
A*) echo alpha-dec-vms ; exit ;;
I*) echo ia64-dec-vms ; exit ;;
V*) echo vax-dec-vms ; exit ;;
esac ;;
*:XENIX:*:SysV)
echo i386-pc-xenix
exit ;;
i*86:skyos:*:*)
echo "$UNAME_MACHINE"-pc-skyos"`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'`"
exit ;;
i*86:rdos:*:*)
echo "$UNAME_MACHINE"-pc-rdos
exit ;;
i*86:AROS:*:*)
echo "$UNAME_MACHINE"-pc-aros
exit ;;
x86_64:VMkernel:*:*)
echo "$UNAME_MACHINE"-unknown-esx
exit ;;
amd64:Isilon\ OneFS:*:*)
echo x86_64-unknown-onefs
exit ;;
*:Unleashed:*:*)
echo "$UNAME_MACHINE"-unknown-unleashed"$UNAME_RELEASE"
exit ;;
esac
# No uname command or uname output not recognized.
set_cc_for_build
cat > "$dummy.c" <<EOF
#ifdef _SEQUENT_
#include <sys/types.h>
#include <sys/utsname.h>
#endif
#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__)
#if defined (vax) || defined (__vax) || defined (__vax__) || defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__)
#include <signal.h>
#if defined(_SIZE_T_) || defined(SIGLOST)
#include <sys/utsname.h>
#endif
#endif
#endif
main ()
{
#if defined (sony)
#if defined (MIPSEB)
/* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
I don't know.... */
printf ("mips-sony-bsd\n"); exit (0);
#else
#include <sys/param.h>
printf ("m68k-sony-newsos%s\n",
#ifdef NEWSOS4
"4"
#else
""
#endif
); exit (0);
#endif
#endif
#if defined (NeXT)
#if !defined (__ARCHITECTURE__)
#define __ARCHITECTURE__ "m68k"
#endif
int version;
version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
if (version < 4)
printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
else
printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
exit (0);
#endif
#if defined (MULTIMAX) || defined (n16)
#if defined (UMAXV)
printf ("ns32k-encore-sysv\n"); exit (0);
#else
#if defined (CMU)
printf ("ns32k-encore-mach\n"); exit (0);
#else
printf ("ns32k-encore-bsd\n"); exit (0);
#endif
#endif
#endif
#if defined (__386BSD__)
printf ("i386-pc-bsd\n"); exit (0);
#endif
#if defined (sequent)
#if defined (i386)
printf ("i386-sequent-dynix\n"); exit (0);
#endif
#if defined (ns32000)
printf ("ns32k-sequent-dynix\n"); exit (0);
#endif
#endif
#if defined (_SEQUENT_)
struct utsname un;
uname(&un);
if (strncmp(un.version, "V2", 2) == 0) {
printf ("i386-sequent-ptx2\n"); exit (0);
}
if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
printf ("i386-sequent-ptx1\n"); exit (0);
}
printf ("i386-sequent-ptx\n"); exit (0);
#endif
#if defined (vax)
#if !defined (ultrix)
#include <sys/param.h>
#if defined (BSD)
#if BSD == 43
printf ("vax-dec-bsd4.3\n"); exit (0);
#else
#if BSD == 199006
printf ("vax-dec-bsd4.3reno\n"); exit (0);
#else
printf ("vax-dec-bsd\n"); exit (0);
#endif
#endif
#else
printf ("vax-dec-bsd\n"); exit (0);
#endif
#else
#if defined(_SIZE_T_) || defined(SIGLOST)
struct utsname un;
uname (&un);
printf ("vax-dec-ultrix%s\n", un.release); exit (0);
#else
printf ("vax-dec-ultrix\n"); exit (0);
#endif
#endif
#endif
#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__)
#if defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__)
#if defined(_SIZE_T_) || defined(SIGLOST)
struct utsname *un;
uname (&un);
printf ("mips-dec-ultrix%s\n", un.release); exit (0);
#else
printf ("mips-dec-ultrix\n"); exit (0);
#endif
#endif
#endif
#if defined (alliant) && defined (i860)
printf ("i860-alliant-bsd\n"); exit (0);
#endif
exit (1);
}
EOF
$CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null && SYSTEM_NAME=`$dummy` &&
{ echo "$SYSTEM_NAME"; exit; }
# Apollos put the system type in the environment.
test -d /usr/apollo && { echo "$ISP-apollo-$SYSTYPE"; exit; }
echo "$0: unable to guess system type" >&2
case "$UNAME_MACHINE:$UNAME_SYSTEM" in
mips:Linux | mips64:Linux)
# If we got here on MIPS GNU/Linux, output extra information.
cat >&2 <<EOF
NOTE: MIPS GNU/Linux systems require a C compiler to fully recognize
the system type. Please install a C compiler and try again.
EOF
;;
esac
cat >&2 <<EOF
This script (version $timestamp), has failed to recognize the
operating system you are using. If your script is old, overwrite *all*
copies of config.guess and config.sub with the latest versions from:
https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
and
https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
EOF
year=`echo $timestamp | sed 's,-.*,,'`
# shellcheck disable=SC2003
if test "`expr "\`date +%Y\`" - "$year"`" -lt 3 ; then
cat >&2 <<EOF
If $0 has already been updated, send the following data and any
information you think might be pertinent to config-patches@gnu.org to
provide the necessary information to handle your system.
config.guess timestamp = $timestamp
uname -m = `(uname -m) 2>/dev/null || echo unknown`
uname -r = `(uname -r) 2>/dev/null || echo unknown`
uname -s = `(uname -s) 2>/dev/null || echo unknown`
uname -v = `(uname -v) 2>/dev/null || echo unknown`
/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
hostinfo = `(hostinfo) 2>/dev/null`
/bin/universe = `(/bin/universe) 2>/dev/null`
/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
/bin/arch = `(/bin/arch) 2>/dev/null`
/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
UNAME_MACHINE = "$UNAME_MACHINE"
UNAME_RELEASE = "$UNAME_RELEASE"
UNAME_SYSTEM = "$UNAME_SYSTEM"
UNAME_VERSION = "$UNAME_VERSION"
EOF
fi
exit 1
# Local variables:
# eval: (add-hook 'before-save-hook 'time-stamp)
# time-stamp-start: "timestamp='"
# time-stamp-format: "%:y-%02m-%02d"
# time-stamp-end: "'"
# End:
config/config.sub deleted 100644 → 0
#! /bin/sh
# Configuration validation subroutine script.
# Copyright 1992-2020 Free Software Foundation, Inc.
timestamp='2020-05-04'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <https://www.gnu.org/licenses/>.
#
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that
# program. This Exception is an additional permission under section 7
# of the GNU General Public License, version 3 ("GPLv3").
# Please send patches to <config-patches@gnu.org>.
#
# Configuration subroutine to validate and canonicalize a configuration type.
# Supply the specified configuration type as an argument.
# If it is invalid, we print an error message on stderr and exit with code 1.
# Otherwise, we print the canonical config type on stdout and succeed.
# You can get the latest version of this script from:
# https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
# This file is supposed to be the same for all GNU packages
# and recognize all the CPU types, system types and aliases
# that are meaningful with *any* GNU software.
# Each package is responsible for reporting which valid configurations
# it does not support. The user should be able to distinguish
# a failure to support a valid configuration from a meaningless
# configuration.
# The goal of this file is to map all the various variations of a given
# machine specification into a single specification in the form:
# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
# or in some cases, the newer four-part form:
# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
# It is wrong to echo any other type of specification.
me=`echo "$0" | sed -e 's,.*/,,'`
usage="\
Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS
Canonicalize a configuration name.
Options:
-h, --help print this help, then exit
-t, --time-stamp print date of last modification, then exit
-v, --version print version number, then exit
Report bugs and patches to <config-patches@gnu.org>."
version="\
GNU config.sub ($timestamp)
Copyright 1992-2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
help="
Try \`$me --help' for more information."
# Parse command line
while test $# -gt 0 ; do
case $1 in
--time-stamp | --time* | -t )
echo "$timestamp" ; exit ;;
--version | -v )
echo "$version" ; exit ;;
--help | --h* | -h )
echo "$usage"; exit ;;
-- ) # Stop option processing
shift; break ;;
- ) # Use stdin as input.
break ;;
-* )
echo "$me: invalid option $1$help" >&2
exit 1 ;;
*local*)
# First pass through any local machine types.
echo "$1"
exit ;;
* )
break ;;
esac
done
case $# in
0) echo "$me: missing argument$help" >&2
exit 1;;
1) ;;
*) echo "$me: too many arguments$help" >&2
exit 1;;
esac
# Split fields of configuration type
# shellcheck disable=SC2162
IFS="-" read field1 field2 field3 field4 <<EOF
$1
EOF
# Separate into logical components for further validation
case $1 in
*-*-*-*-*)
echo Invalid configuration \`"$1"\': more than four components >&2
exit 1
;;
*-*-*-*)
basic_machine=$field1-$field2
os=$field3-$field4
;;
*-*-*)
# Ambiguous whether COMPANY is present, or skipped and KERNEL-OS is two
# parts
maybe_os=$field2-$field3
case $maybe_os in
nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc \
| linux-newlib* | linux-musl* | linux-uclibc* | uclinux-uclibc* \
| uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* \
| netbsd*-eabi* | kopensolaris*-gnu* | cloudabi*-eabi* \
| storm-chaos* | os2-emx* | rtmk-nova*)
basic_machine=$field1
os=$maybe_os
;;
android-linux)
basic_machine=$field1-unknown
os=linux-android
;;
*)
basic_machine=$field1-$field2
os=$field3
;;
esac
;;
*-*)
# A lone config we happen to match not fitting any pattern
case $field1-$field2 in
decstation-3100)
basic_machine=mips-dec
os=
;;
*-*)
# Second component is usually, but not always the OS
case $field2 in
# Prevent following clause from handling this valid os
sun*os*)
basic_machine=$field1
os=$field2
;;
# Manufacturers
dec* | mips* | sequent* | encore* | pc533* | sgi* | sony* \
| att* | 7300* | 3300* | delta* | motorola* | sun[234]* \
| unicom* | ibm* | next | hp | isi* | apollo | altos* \
| convergent* | ncr* | news | 32* | 3600* | 3100* \
| hitachi* | c[123]* | convex* | sun | crds | omron* | dg \
| ultra | tti* | harris | dolphin | highlevel | gould \
| cbm | ns | masscomp | apple | axis | knuth | cray \
| microblaze* | sim | cisco \
| oki | wec | wrs | winbond)
basic_machine=$field1-$field2
os=
;;
*)
basic_machine=$field1
os=$field2
;;
esac
;;
esac
;;
*)
# Convert single-component short-hands not valid as part of
# multi-component configurations.
case $field1 in
386bsd)
basic_machine=i386-pc
os=bsd
;;
a29khif)
basic_machine=a29k-amd
os=udi
;;
adobe68k)
basic_machine=m68010-adobe
os=scout
;;
alliant)
basic_machine=fx80-alliant
os=
;;
altos | altos3068)
basic_machine=m68k-altos
os=
;;
am29k)
basic_machine=a29k-none
os=bsd
;;
amdahl)
basic_machine=580-amdahl
os=sysv
;;
amiga)
basic_machine=m68k-unknown
os=
;;
amigaos | amigados)
basic_machine=m68k-unknown
os=amigaos
;;
amigaunix | amix)
basic_machine=m68k-unknown
os=sysv4
;;
apollo68)
basic_machine=m68k-apollo
os=sysv
;;
apollo68bsd)
basic_machine=m68k-apollo
os=bsd
;;
aros)
basic_machine=i386-pc
os=aros
;;
aux)
basic_machine=m68k-apple
os=aux
;;
balance)
basic_machine=ns32k-sequent
os=dynix
;;
blackfin)
basic_machine=bfin-unknown
os=linux
;;
cegcc)
basic_machine=arm-unknown
os=cegcc
;;
convex-c1)
basic_machine=c1-convex
os=bsd
;;
convex-c2)
basic_machine=c2-convex
os=bsd
;;
convex-c32)
basic_machine=c32-convex
os=bsd
;;
convex-c34)
basic_machine=c34-convex
os=bsd
;;
convex-c38)
basic_machine=c38-convex
os=bsd
;;
cray)
basic_machine=j90-cray
os=unicos
;;
crds | unos)
basic_machine=m68k-crds
os=
;;
da30)
basic_machine=m68k-da30
os=
;;
decstation | pmax | pmin | dec3100 | decstatn)
basic_machine=mips-dec
os=
;;
delta88)
basic_machine=m88k-motorola
os=sysv3
;;
dicos)
basic_machine=i686-pc
os=dicos
;;
djgpp)
basic_machine=i586-pc
os=msdosdjgpp
;;
ebmon29k)
basic_machine=a29k-amd
os=ebmon
;;
es1800 | OSE68k | ose68k | ose | OSE)
basic_machine=m68k-ericsson
os=ose
;;
gmicro)
basic_machine=tron-gmicro
os=sysv
;;
go32)
basic_machine=i386-pc
os=go32
;;
h8300hms)
basic_machine=h8300-hitachi
os=hms
;;
h8300xray)
basic_machine=h8300-hitachi
os=xray
;;
h8500hms)
basic_machine=h8500-hitachi
os=hms
;;
harris)
basic_machine=m88k-harris
os=sysv3
;;
hp300 | hp300hpux)
basic_machine=m68k-hp
os=hpux
;;
hp300bsd)
basic_machine=m68k-hp
os=bsd
;;
hppaosf)
basic_machine=hppa1.1-hp
os=osf
;;
hppro)
basic_machine=hppa1.1-hp
os=proelf
;;
i386mach)
basic_machine=i386-mach
os=mach
;;
isi68 | isi)
basic_machine=m68k-isi
os=sysv
;;
m68knommu)
basic_machine=m68k-unknown
os=linux
;;
magnum | m3230)
basic_machine=mips-mips
os=sysv
;;
merlin)
basic_machine=ns32k-utek
os=sysv
;;
mingw64)
basic_machine=x86_64-pc
os=mingw64
;;
mingw32)
basic_machine=i686-pc
os=mingw32
;;
mingw32ce)
basic_machine=arm-unknown
os=mingw32ce
;;
monitor)
basic_machine=m68k-rom68k
os=coff
;;
morphos)
basic_machine=powerpc-unknown
os=morphos
;;
moxiebox)
basic_machine=moxie-unknown
os=moxiebox
;;
msdos)
basic_machine=i386-pc
os=msdos
;;
msys)
basic_machine=i686-pc
os=msys
;;
mvs)
basic_machine=i370-ibm
os=mvs
;;
nacl)
basic_machine=le32-unknown
os=nacl
;;
ncr3000)
basic_machine=i486-ncr
os=sysv4
;;
netbsd386)
basic_machine=i386-pc
os=netbsd
;;
netwinder)
basic_machine=armv4l-rebel
os=linux
;;
news | news700 | news800 | news900)
basic_machine=m68k-sony
os=newsos
;;
news1000)
basic_machine=m68030-sony
os=newsos
;;
necv70)
basic_machine=v70-nec
os=sysv
;;
nh3000)
basic_machine=m68k-harris
os=cxux
;;
nh[45]000)
basic_machine=m88k-harris
os=cxux
;;
nindy960)
basic_machine=i960-intel
os=nindy
;;
mon960)
basic_machine=i960-intel
os=mon960
;;
nonstopux)
basic_machine=mips-compaq
os=nonstopux
;;
os400)
basic_machine=powerpc-ibm
os=os400
;;
OSE68000 | ose68000)
basic_machine=m68000-ericsson
os=ose
;;
os68k)
basic_machine=m68k-none
os=os68k
;;
paragon)
basic_machine=i860-intel
os=osf
;;
parisc)
basic_machine=hppa-unknown
os=linux
;;
pw32)
basic_machine=i586-unknown
os=pw32
;;
rdos | rdos64)
basic_machine=x86_64-pc
os=rdos
;;
rdos32)
basic_machine=i386-pc
os=rdos
;;
rom68k)
basic_machine=m68k-rom68k
os=coff
;;
sa29200)
basic_machine=a29k-amd
os=udi
;;
sei)
basic_machine=mips-sei
os=seiux
;;
sequent)
basic_machine=i386-sequent
os=
;;
sps7)
basic_machine=m68k-bull
os=sysv2
;;
st2000)
basic_machine=m68k-tandem
os=
;;
stratus)
basic_machine=i860-stratus
os=sysv4
;;
sun2)
basic_machine=m68000-sun
os=
;;
sun2os3)
basic_machine=m68000-sun
os=sunos3
;;
sun2os4)
basic_machine=m68000-sun
os=sunos4
;;
sun3)
basic_machine=m68k-sun
os=
;;
sun3os3)
basic_machine=m68k-sun
os=sunos3
;;
sun3os4)
basic_machine=m68k-sun
os=sunos4
;;
sun4)
basic_machine=sparc-sun
os=
;;
sun4os3)
basic_machine=sparc-sun
os=sunos3
;;
sun4os4)
basic_machine=sparc-sun
os=sunos4
;;
sun4sol2)
basic_machine=sparc-sun
os=solaris2
;;
sun386 | sun386i | roadrunner)
basic_machine=i386-sun
os=
;;
sv1)
basic_machine=sv1-cray
os=unicos
;;
symmetry)
basic_machine=i386-sequent
os=dynix
;;
t3e)
basic_machine=alphaev5-cray
os=unicos
;;
t90)
basic_machine=t90-cray
os=unicos
;;
toad1)
basic_machine=pdp10-xkl
os=tops20
;;
tpf)
basic_machine=s390x-ibm
os=tpf
;;
udi29k)
basic_machine=a29k-amd
os=udi
;;
ultra3)
basic_machine=a29k-nyu
os=sym1
;;
v810 | necv810)
basic_machine=v810-nec
os=none
;;
vaxv)
basic_machine=vax-dec
os=sysv
;;
vms)
basic_machine=vax-dec
os=vms
;;
vsta)
basic_machine=i386-pc
os=vsta
;;
vxworks960)
basic_machine=i960-wrs
os=vxworks
;;
vxworks68)
basic_machine=m68k-wrs
os=vxworks
;;
vxworks29k)
basic_machine=a29k-wrs
os=vxworks
;;
xbox)
basic_machine=i686-pc
os=mingw32
;;
ymp)
basic_machine=ymp-cray
os=unicos
;;
*)
basic_machine=$1
os=
;;
esac
;;
esac
# Decode 1-component or ad-hoc basic machines
case $basic_machine in
# Here we handle the default manufacturer of certain CPU types. It is in
# some cases the only manufacturer, in others, it is the most popular.
w89k)
cpu=hppa1.1
vendor=winbond
;;
op50n)
cpu=hppa1.1
vendor=oki
;;
op60c)
cpu=hppa1.1
vendor=oki
;;
ibm*)
cpu=i370
vendor=ibm
;;
orion105)
cpu=clipper
vendor=highlevel
;;
mac | mpw | mac-mpw)
cpu=m68k
vendor=apple
;;
pmac | pmac-mpw)
cpu=powerpc
vendor=apple
;;
# Recognize the various machine names and aliases which stand
# for a CPU type and a company and sometimes even an OS.
3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
cpu=m68000
vendor=att
;;
3b*)
cpu=we32k
vendor=att
;;
bluegene*)
cpu=powerpc
vendor=ibm
os=cnk
;;
decsystem10* | dec10*)
cpu=pdp10
vendor=dec
os=tops10
;;
decsystem20* | dec20*)
cpu=pdp10
vendor=dec
os=tops20
;;
delta | 3300 | motorola-3300 | motorola-delta \
| 3300-motorola | delta-motorola)
cpu=m68k
vendor=motorola
;;
dpx2*)
cpu=m68k
vendor=bull
os=sysv3
;;
encore | umax | mmax)
cpu=ns32k
vendor=encore
;;
elxsi)
cpu=elxsi
vendor=elxsi
os=${os:-bsd}
;;
fx2800)
cpu=i860
vendor=alliant
;;
genix)
cpu=ns32k
vendor=ns
;;
h3050r* | hiux*)
cpu=hppa1.1
vendor=hitachi
os=hiuxwe2
;;
hp3k9[0-9][0-9] | hp9[0-9][0-9])
cpu=hppa1.0
vendor=hp
;;
hp9k2[0-9][0-9] | hp9k31[0-9])
cpu=m68000
vendor=hp
;;
hp9k3[2-9][0-9])
cpu=m68k
vendor=hp
;;
hp9k6[0-9][0-9] | hp6[0-9][0-9])
cpu=hppa1.0
vendor=hp
;;
hp9k7[0-79][0-9] | hp7[0-79][0-9])
cpu=hppa1.1
vendor=hp
;;
hp9k78[0-9] | hp78[0-9])
# FIXME: really hppa2.0-hp
cpu=hppa1.1
vendor=hp
;;
hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
# FIXME: really hppa2.0-hp
cpu=hppa1.1
vendor=hp
;;
hp9k8[0-9][13679] | hp8[0-9][13679])
cpu=hppa1.1
vendor=hp
;;
hp9k8[0-9][0-9] | hp8[0-9][0-9])
cpu=hppa1.0
vendor=hp
;;
i*86v32)
cpu=`echo "$1" | sed -e 's/86.*/86/'`
vendor=pc
os=sysv32
;;
i*86v4*)
cpu=`echo "$1" | sed -e 's/86.*/86/'`
vendor=pc
os=sysv4
;;
i*86v)
cpu=`echo "$1" | sed -e 's/86.*/86/'`
vendor=pc
os=sysv
;;
i*86sol2)
cpu=`echo "$1" | sed -e 's/86.*/86/'`
vendor=pc
os=solaris2
;;
j90 | j90-cray)
cpu=j90
vendor=cray
os=${os:-unicos}
;;
iris | iris4d)
cpu=mips
vendor=sgi
case $os in
irix*)
;;
*)
os=irix4
;;
esac
;;
miniframe)
cpu=m68000
vendor=convergent
;;
*mint | mint[0-9]* | *MiNT | *MiNT[0-9]*)
cpu=m68k
vendor=atari
os=mint
;;
news-3600 | risc-news)
cpu=mips
vendor=sony
os=newsos
;;
next | m*-next)
cpu=m68k
vendor=next
case $os in
openstep*)
;;
nextstep*)
;;
ns2*)
os=nextstep2
;;
*)
os=nextstep3
;;
esac
;;
np1)
cpu=np1
vendor=gould
;;
op50n-* | op60c-*)
cpu=hppa1.1
vendor=oki
os=proelf
;;
pa-hitachi)
cpu=hppa1.1
vendor=hitachi
os=hiuxwe2
;;
pbd)
cpu=sparc
vendor=tti
;;
pbb)
cpu=m68k
vendor=tti
;;
pc532)
cpu=ns32k
vendor=pc532
;;
pn)
cpu=pn
vendor=gould
;;
power)
cpu=power
vendor=ibm
;;
ps2)
cpu=i386
vendor=ibm
;;
rm[46]00)
cpu=mips
vendor=siemens
;;
rtpc | rtpc-*)
cpu=romp
vendor=ibm
;;
sde)
cpu=mipsisa32
vendor=sde
os=${os:-elf}
;;
simso-wrs)
cpu=sparclite
vendor=wrs
os=vxworks
;;
tower | tower-32)
cpu=m68k
vendor=ncr
;;
vpp*|vx|vx-*)
cpu=f301
vendor=fujitsu
;;
w65)
cpu=w65
vendor=wdc
;;
w89k-*)
cpu=hppa1.1
vendor=winbond
os=proelf
;;
none)
cpu=none
vendor=none
;;
leon|leon[3-9])
cpu=sparc
vendor=$basic_machine
;;
leon-*|leon[3-9]-*)
cpu=sparc
vendor=`echo "$basic_machine" | sed 's/-.*//'`
;;
*-*)
# shellcheck disable=SC2162
IFS="-" read cpu vendor <<EOF
$basic_machine
EOF
;;
# We use `pc' rather than `unknown'
# because (1) that's what they normally are, and
# (2) the word "unknown" tends to confuse beginning users.
i*86 | x86_64)
cpu=$basic_machine
vendor=pc
;;
# These rules are duplicated from below for sake of the special case above;
# i.e. things that normalized to x86 arches should also default to "pc"
pc98)
cpu=i386
vendor=pc
;;
x64 | amd64)
cpu=x86_64
vendor=pc
;;
# Recognize the basic CPU types without company name.
*)
cpu=$basic_machine
vendor=unknown
;;
esac
unset -v basic_machine
# Decode basic machines in the full and proper CPU-Company form.
case $cpu-$vendor in
# Here we handle the default manufacturer of certain CPU types in canonical form. It is in
# some cases the only manufacturer, in others, it is the most popular.
craynv-unknown)
vendor=cray
os=${os:-unicosmp}
;;
c90-unknown | c90-cray)
vendor=cray
os=${os:-unicos}
;;
fx80-unknown)
vendor=alliant
;;
romp-unknown)
vendor=ibm
;;
mmix-unknown)
vendor=knuth
;;
microblaze-unknown | microblazeel-unknown)
vendor=xilinx
;;
rs6000-unknown)
vendor=ibm
;;
vax-unknown)
vendor=dec
;;
pdp11-unknown)
vendor=dec
;;
we32k-unknown)
vendor=att
;;
cydra-unknown)
vendor=cydrome
;;
i370-ibm*)
vendor=ibm
;;
orion-unknown)
vendor=highlevel
;;
xps-unknown | xps100-unknown)
cpu=xps100
vendor=honeywell
;;
# Here we normalize CPU types with a missing or matching vendor
dpx20-unknown | dpx20-bull)
cpu=rs6000
vendor=bull
os=${os:-bosx}
;;
# Here we normalize CPU types irrespective of the vendor
amd64-*)
cpu=x86_64
;;
blackfin-*)
cpu=bfin
os=linux
;;
c54x-*)
cpu=tic54x
;;
c55x-*)
cpu=tic55x
;;
c6x-*)
cpu=tic6x
;;
e500v[12]-*)
cpu=powerpc
os=$os"spe"
;;
mips3*-*)
cpu=mips64
;;
ms1-*)
cpu=mt
;;
m68knommu-*)
cpu=m68k
os=linux
;;
m9s12z-* | m68hcs12z-* | hcs12z-* | s12z-*)
cpu=s12z
;;
openrisc-*)
cpu=or32
;;
parisc-*)
cpu=hppa
os=linux
;;
pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
cpu=i586
;;
pentiumpro-* | p6-* | 6x86-* | athlon-* | athalon_*-*)
cpu=i686
;;
pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
cpu=i686
;;
pentium4-*)
cpu=i786
;;
pc98-*)
cpu=i386
;;
ppc-* | ppcbe-*)
cpu=powerpc
;;
ppcle-* | powerpclittle-*)
cpu=powerpcle
;;
ppc64-*)
cpu=powerpc64
;;
ppc64le-* | powerpc64little-*)
cpu=powerpc64le
;;
sb1-*)
cpu=mipsisa64sb1
;;
sb1el-*)
cpu=mipsisa64sb1el
;;
sh5e[lb]-*)
cpu=`echo "$cpu" | sed 's/^\(sh.\)e\(.\)$/\1\2e/'`
;;
spur-*)
cpu=spur
;;
strongarm-* | thumb-*)
cpu=arm
;;
tx39-*)
cpu=mipstx39
;;
tx39el-*)
cpu=mipstx39el
;;
x64-*)
cpu=x86_64
;;
xscale-* | xscalee[bl]-*)
cpu=`echo "$cpu" | sed 's/^xscale/arm/'`
;;
# Recognize the canonical CPU Types that limit and/or modify the
# company names they are paired with.
cr16-*)
os=${os:-elf}
;;
crisv32-* | etraxfs*-*)
cpu=crisv32
vendor=axis
;;
cris-* | etrax*-*)
cpu=cris
vendor=axis
;;
crx-*)
os=${os:-elf}
;;
neo-tandem)
cpu=neo
vendor=tandem
;;
nse-tandem)
cpu=nse
vendor=tandem
;;
nsr-tandem)
cpu=nsr
vendor=tandem
;;
nsv-tandem)
cpu=nsv
vendor=tandem
;;
nsx-tandem)
cpu=nsx
vendor=tandem
;;
s390-*)
cpu=s390
vendor=ibm
;;
s390x-*)
cpu=s390x
vendor=ibm
;;
tile*-*)
os=${os:-linux-gnu}
;;
*)
# Recognize the canonical CPU types that are allowed with any
# company name.
case $cpu in
1750a | 580 \
| a29k \
| aarch64 | aarch64_be \
| abacus \
| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] \
| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] \
| alphapca5[67] | alpha64pca5[67] \
| am33_2.0 \
| amdgcn \
| arc | arceb \
| arm | arm[lb]e | arme[lb] | armv* \
| avr | avr32 \
| asmjs \
| ba \
| be32 | be64 \
| bfin | bpf | bs2000 \
| c[123]* | c30 | [cjt]90 | c4x \
| c8051 | clipper | craynv | csky | cydra \
| d10v | d30v | dlx | dsp16xx \
| e2k | elxsi | epiphany \
| f30[01] | f700 | fido | fr30 | frv | ft32 | fx80 \
| h8300 | h8500 \
| hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
| hexagon \
| i370 | i*86 | i860 | i960 | ia16 | ia64 \
| ip2k | iq2000 \
| k1om \
| le32 | le64 \
| lm32 \
| m32c | m32r | m32rle \
| m5200 | m68000 | m680[012346]0 | m68360 | m683?2 | m68k \
| m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x \
| m88110 | m88k | maxq | mb | mcore | mep | metag \
| microblaze | microblazeel \
| mips | mipsbe | mipseb | mipsel | mipsle \
| mips16 \
| mips64 | mips64eb | mips64el \
| mips64octeon | mips64octeonel \
| mips64orion | mips64orionel \
| mips64r5900 | mips64r5900el \
| mips64vr | mips64vrel \
| mips64vr4100 | mips64vr4100el \
| mips64vr4300 | mips64vr4300el \
| mips64vr5000 | mips64vr5000el \
| mips64vr5900 | mips64vr5900el \
| mipsisa32 | mipsisa32el \
| mipsisa32r2 | mipsisa32r2el \
| mipsisa32r6 | mipsisa32r6el \
| mipsisa64 | mipsisa64el \
| mipsisa64r2 | mipsisa64r2el \
| mipsisa64r6 | mipsisa64r6el \
| mipsisa64sb1 | mipsisa64sb1el \
| mipsisa64sr71k | mipsisa64sr71kel \
| mipsr5900 | mipsr5900el \
| mipstx39 | mipstx39el \
| mmix \
| mn10200 | mn10300 \
| moxie \
| mt \
| msp430 \
| nds32 | nds32le | nds32be \
| nfp \
| nios | nios2 | nios2eb | nios2el \
| none | np1 | ns16k | ns32k | nvptx \
| open8 \
| or1k* \
| or32 \
| orion \
| picochip \
| pdp10 | pdp11 | pj | pjl | pn | power \
| powerpc | powerpc64 | powerpc64le | powerpcle | powerpcspe \
| pru \
| pyramid \
| riscv | riscv32 | riscv64 \
| rl78 | romp | rs6000 | rx \
| score \
| sh | shl \
| sh[1234] | sh[24]a | sh[24]ae[lb] | sh[23]e | she[lb] | sh[lb]e \
| sh[1234]e[lb] | sh[12345][lb]e | sh[23]ele | sh64 | sh64le \
| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet \
| sparclite \
| sparcv8 | sparcv9 | sparcv9b | sparcv9v | sv1 | sx* \
| spu \
| tahoe \
| tic30 | tic4x | tic54x | tic55x | tic6x | tic80 \
| tron \
| ubicom32 \
| v70 | v850 | v850e | v850e1 | v850es | v850e2 | v850e2v3 \
| vax \
| visium \
| w65 \
| wasm32 | wasm64 \
| we32k \
| x86 | x86_64 | xc16x | xgate | xps100 \
| xstormy16 | xtensa* \
| ymp \
| z8k | z80)
;;
*)
echo Invalid configuration \`"$1"\': machine \`"$cpu-$vendor"\' not recognized 1>&2
exit 1
;;
esac
;;
esac
# Here we canonicalize certain aliases for manufacturers.
case $vendor in
digital*)
vendor=dec
;;
commodore*)
vendor=cbm
;;
*)
;;
esac
# Decode manufacturer-specific aliases for certain operating systems.
if [ x$os != x ]
then
case $os in
# First match some system type aliases that might get confused
# with valid system types.
# solaris* is a basic system type, with this one exception.
auroraux)
os=auroraux
;;
bluegene*)
os=cnk
;;
solaris1 | solaris1.*)
os=`echo $os | sed -e 's|solaris1|sunos4|'`
;;
solaris)
os=solaris2
;;
unixware*)
os=sysv4.2uw
;;
gnu/linux*)
os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
;;
# es1800 is here to avoid being matched by es* (a different OS)
es1800*)
os=ose
;;
# Some version numbers need modification
chorusos*)
os=chorusos
;;
isc)
os=isc2.2
;;
sco6)
os=sco5v6
;;
sco5)
os=sco3.2v5
;;
sco4)
os=sco3.2v4
;;
sco3.2.[4-9]*)
os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
;;
sco3.2v[4-9]* | sco5v6*)
# Don't forget version if it is 3.2v4 or newer.
;;
scout)
# Don't match below
;;
sco*)
os=sco3.2v2
;;
psos*)
os=psos
;;
# Now accept the basic system types.
# The portable systems comes first.
# Each alternative MUST end in a * to match a version number.
# sysv* is not here because it comes later, after sysvr4.
gnu* | bsd* | mach* | minix* | genix* | ultrix* | irix* \
| *vms* | esix* | aix* | cnk* | sunos | sunos[34]*\
| hpux* | unos* | osf* | luna* | dgux* | auroraux* | solaris* \
| sym* | kopensolaris* | plan9* \
| amigaos* | amigados* | msdos* | newsos* | unicos* | aof* \
| aos* | aros* | cloudabi* | sortix* | twizzler* \
| nindy* | vxsim* | vxworks* | ebmon* | hms* | mvs* \
| clix* | riscos* | uniplus* | iris* | isc* | rtu* | xenix* \
| knetbsd* | mirbsd* | netbsd* \
| bitrig* | openbsd* | solidbsd* | libertybsd* | os108* \
| ekkobsd* | kfreebsd* | freebsd* | riscix* | lynxos* \
| bosx* | nextstep* | cxux* | aout* | elf* | oabi* \
| ptx* | coff* | ecoff* | winnt* | domain* | vsta* \
| udi* | eabi* | lites* | ieee* | go32* | aux* | hcos* \
| chorusrdb* | cegcc* | glidix* \
| cygwin* | msys* | pe* | moss* | proelf* | rtems* \
| midipix* | mingw32* | mingw64* | linux-gnu* | linux-android* \
| linux-newlib* | linux-musl* | linux-uclibc* \
| uxpv* | beos* | mpeix* | udk* | moxiebox* \
| interix* | uwin* | mks* | rhapsody* | darwin* \
| openstep* | oskit* | conix* | pw32* | nonstopux* \
| storm-chaos* | tops10* | tenex* | tops20* | its* \
| os2* | vos* | palmos* | uclinux* | nucleus* \
| morphos* | superux* | rtmk* | windiss* \
| powermax* | dnix* | nx6 | nx7 | sei* | dragonfly* \
| skyos* | haiku* | rdos* | toppers* | drops* | es* \
| onefs* | tirtos* | phoenix* | fuchsia* | redox* | bme* \
| midnightbsd* | amdhsa* | unleashed* | emscripten* | wasi* \
| nsk* | powerunix* | genode*)
# Remember, each alternative MUST END IN *, to match a version number.
;;
qnx*)
case $cpu in
x86 | i*86)
;;
*)
os=nto-$os
;;
esac
;;
hiux*)
os=hiuxwe2
;;
nto-qnx*)
;;
nto*)
os=`echo $os | sed -e 's|nto|nto-qnx|'`
;;
sim | xray | os68k* | v88r* \
| windows* | osx | abug | netware* | os9* \
| macos* | mpw* | magic* | mmixware* | mon960* | lnews*)
;;
linux-dietlibc)
os=linux-dietlibc
;;
linux*)
os=`echo $os | sed -e 's|linux|linux-gnu|'`
;;
lynx*178)
os=lynxos178
;;
lynx*5)
os=lynxos5
;;
lynx*)
os=lynxos
;;
mac*)
os=`echo "$os" | sed -e 's|mac|macos|'`
;;
opened*)
os=openedition
;;
os400*)
os=os400
;;
sunos5*)
os=`echo "$os" | sed -e 's|sunos5|solaris2|'`
;;
sunos6*)
os=`echo "$os" | sed -e 's|sunos6|solaris3|'`
;;
wince*)
os=wince
;;
utek*)
os=bsd
;;
dynix*)
os=bsd
;;
acis*)
os=aos
;;
atheos*)
os=atheos
;;
syllable*)
os=syllable
;;
386bsd)
os=bsd
;;
ctix* | uts*)
os=sysv
;;
nova*)
os=rtmk-nova
;;
ns2)
os=nextstep2
;;
# Preserve the version number of sinix5.
sinix5.*)
os=`echo $os | sed -e 's|sinix|sysv|'`
;;
sinix*)
os=sysv4
;;
tpf*)
os=tpf
;;
triton*)
os=sysv3
;;
oss*)
os=sysv3
;;
svr4*)
os=sysv4
;;
svr3)
os=sysv3
;;
sysvr4)
os=sysv4
;;
# This must come after sysvr4.
sysv*)
;;
ose*)
os=ose
;;
*mint | mint[0-9]* | *MiNT | MiNT[0-9]*)
os=mint
;;
zvmoe)
os=zvmoe
;;
dicos*)
os=dicos
;;
pikeos*)
# Until real need of OS specific support for
# particular features comes up, bare metal
# configurations are quite functional.
case $cpu in
arm*)
os=eabi
;;
*)
os=elf
;;
esac
;;
nacl*)
;;
ios)
;;
none)
;;
*-eabi)
;;
*)
echo Invalid configuration \`"$1"\': system \`"$os"\' not recognized 1>&2
exit 1
;;
esac
else
# Here we handle the default operating systems that come with various machines.
# The value should be what the vendor currently ships out the door with their
# machine or put another way, the most popular os provided with the machine.
# Note that if you're going to try to match "-MANUFACTURER" here (say,
# "-sun"), then you have to tell the case statement up towards the top
# that MANUFACTURER isn't an operating system. Otherwise, code above
# will signal an error saying that MANUFACTURER isn't an operating
# system, and we'll never get to this point.
case $cpu-$vendor in
score-*)
os=elf
;;
spu-*)
os=elf
;;
*-acorn)
os=riscix1.2
;;
arm*-rebel)
os=linux
;;
arm*-semi)
os=aout
;;
c4x-* | tic4x-*)
os=coff
;;
c8051-*)
os=elf
;;
clipper-intergraph)
os=clix
;;
hexagon-*)
os=elf
;;
tic54x-*)
os=coff
;;
tic55x-*)
os=coff
;;
tic6x-*)
os=coff
;;
# This must come before the *-dec entry.
pdp10-*)
os=tops20
;;
pdp11-*)
os=none
;;
*-dec | vax-*)
os=ultrix4.2
;;
m68*-apollo)
os=domain
;;
i386-sun)
os=sunos4.0.2
;;
m68000-sun)
os=sunos3
;;
m68*-cisco)
os=aout
;;
mep-*)
os=elf
;;
mips*-cisco)
os=elf
;;
mips*-*)
os=elf
;;
or32-*)
os=coff
;;
*-tti) # must be before sparc entry or we get the wrong os.
os=sysv3
;;
sparc-* | *-sun)
os=sunos4.1.1
;;
pru-*)
os=elf
;;
*-be)
os=beos
;;
*-ibm)
os=aix
;;
*-knuth)
os=mmixware
;;
*-wec)
os=proelf
;;
*-winbond)
os=proelf
;;
*-oki)
os=proelf
;;
*-hp)
os=hpux
;;
*-hitachi)
os=hiux
;;
i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
os=sysv
;;
*-cbm)
os=amigaos
;;
*-dg)
os=dgux
;;
*-dolphin)
os=sysv3
;;
m68k-ccur)
os=rtu
;;
m88k-omron*)
os=luna
;;
*-next)
os=nextstep
;;
*-sequent)
os=ptx
;;
*-crds)
os=unos
;;
*-ns)
os=genix
;;
i370-*)
os=mvs
;;
*-gould)
os=sysv
;;
*-highlevel)
os=bsd
;;
*-encore)
os=bsd
;;
*-sgi)
os=irix
;;
*-siemens)
os=sysv4
;;
*-masscomp)
os=rtu
;;
f30[01]-fujitsu | f700-fujitsu)
os=uxpv
;;
*-rom68k)
os=coff
;;
*-*bug)
os=coff
;;
*-apple)
os=macos
;;
*-atari*)
os=mint
;;
*-wrs)
os=vxworks
;;
*)
os=none
;;
esac
fi
# Here we handle the case where we know the os, and the CPU type, but not the
# manufacturer. We pick the logical manufacturer.
case $vendor in
unknown)
case $os in
riscix*)
vendor=acorn
;;
sunos*)
vendor=sun
;;
cnk*|-aix*)
vendor=ibm
;;
beos*)
vendor=be
;;
hpux*)
vendor=hp
;;
mpeix*)
vendor=hp
;;
hiux*)
vendor=hitachi
;;
unos*)
vendor=crds
;;
dgux*)
vendor=dg
;;
luna*)
vendor=omron
;;
genix*)
vendor=ns
;;
clix*)
vendor=intergraph
;;
mvs* | opened*)
vendor=ibm
;;
os400*)
vendor=ibm
;;
ptx*)
vendor=sequent
;;
tpf*)
vendor=ibm
;;
vxsim* | vxworks* | windiss*)
vendor=wrs
;;
aux*)
vendor=apple
;;
hms*)
vendor=hitachi
;;
mpw* | macos*)
vendor=apple
;;
*mint | mint[0-9]* | *MiNT | MiNT[0-9]*)
vendor=atari
;;
vos*)
vendor=stratus
;;
esac
;;
esac
echo "$cpu-$vendor-$os"
exit
# Local variables:
# eval: (add-hook 'before-save-hook 'time-stamp)
# time-stamp-start: "timestamp='"
# time-stamp-format: "%:y-%02m-%02d"
# time-stamp-end: "'"
# End:
config/install-sh deleted 100755 → 0
#!/bin/sh
# install - install a program, script, or datafile
scriptversion=2009-04-28.21; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
# following copyright and license.
#
# Copyright (C) 1994 X Consortium
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
# sell copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Except as contained in this notice, the name of the X Consortium shall not
# be used in advertising or otherwise to promote the sale, use or other deal-
# ings in this Software without prior written authorization from the X Consor-
# tium.
#
#
# FSF changes to this file are in the public domain.
#
# Calling this script install-sh is preferred over install.sh, to prevent
# `make' implicit rules from creating a file called install from it
# when there is no Makefile.
#
# This script is compatible with the BSD install script, but was written
# from scratch.
nl='
'
IFS=" "" $nl"
# set DOITPROG to echo to test this script
# Don't use :- since 4.3BSD and earlier shells don't like it.
doit=${DOITPROG-}
if test -z "$doit"; then
doit_exec=exec
else
doit_exec=$doit
fi
# Put in absolute file names if you don't have them in your path;
# or use environment vars.
chgrpprog=${CHGRPPROG-chgrp}
chmodprog=${CHMODPROG-chmod}
chownprog=${CHOWNPROG-chown}
cmpprog=${CMPPROG-cmp}
cpprog=${CPPROG-cp}
mkdirprog=${MKDIRPROG-mkdir}
mvprog=${MVPROG-mv}
rmprog=${RMPROG-rm}
stripprog=${STRIPPROG-strip}
posix_glob='?'
initialize_posix_glob='
test "$posix_glob" != "?" || {
if (set -f) 2>/dev/null; then
posix_glob=
else
posix_glob=:
fi
}
'
posix_mkdir=
# Desired mode of installed file.
mode=0755
chgrpcmd=
chmodcmd=$chmodprog
chowncmd=
mvcmd=$mvprog
rmcmd="$rmprog -f"
stripcmd=
src=
dst=
dir_arg=
dst_arg=
copy_on_change=false
no_target_directory=
usage="\
Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
or: $0 [OPTION]... SRCFILES... DIRECTORY
or: $0 [OPTION]... -t DIRECTORY SRCFILES...
or: $0 [OPTION]... -d DIRECTORIES...
In the 1st form, copy SRCFILE to DSTFILE.
In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
In the 4th, create DIRECTORIES.
Options:
--help display this help and exit.
--version display version info and exit.
-c (ignored)
-C install only if different (preserve the last data modification time)
-d create directories instead of installing files.
-g GROUP $chgrpprog installed files to GROUP.
-m MODE $chmodprog installed files to MODE.
-o USER $chownprog installed files to USER.
-s $stripprog installed files.
-t DIRECTORY install into DIRECTORY.
-T report an error if DSTFILE is a directory.
Environment variables override the default commands:
CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
RMPROG STRIPPROG
"
while test $# -ne 0; do
case $1 in
-c) ;;
-C) copy_on_change=true;;
-d) dir_arg=true;;
-g) chgrpcmd="$chgrpprog $2"
shift;;
--help) echo "$usage"; exit $?;;
-m) mode=$2
case $mode in
*' '* | *' '* | *'
'* | *'*'* | *'?'* | *'['*)
echo "$0: invalid mode: $mode" >&2
exit 1;;
esac
shift;;
-o) chowncmd="$chownprog $2"
shift;;
-s) stripcmd=$stripprog;;
-t) dst_arg=$2
shift;;
-T) no_target_directory=true;;
--version) echo "$0 $scriptversion"; exit $?;;
--) shift
break;;
-*) echo "$0: invalid option: $1" >&2
exit 1;;
*) break;;
esac
shift
done
if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
# When -d is used, all remaining arguments are directories to create.
# When -t is used, the destination is already specified.
# Otherwise, the last argument is the destination. Remove it from $@.
for arg
do
if test -n "$dst_arg"; then
# $@ is not empty: it contains at least $arg.
set fnord "$@" "$dst_arg"
shift # fnord
fi
shift # arg
dst_arg=$arg
done
fi
if test $# -eq 0; then
if test -z "$dir_arg"; then
echo "$0: no input file specified." >&2
exit 1
fi
# It's OK to call `install-sh -d' without argument.
# This can happen when creating conditional directories.
exit 0
fi
if test -z "$dir_arg"; then
trap '(exit $?); exit' 1 2 13 15
# Set umask so as not to create temps with too-generous modes.
# However, 'strip' requires both read and write access to temps.
case $mode in
# Optimize common cases.
*644) cp_umask=133;;
*755) cp_umask=22;;
*[0-7])
if test -z "$stripcmd"; then
u_plus_rw=
else
u_plus_rw='% 200'
fi
cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
*)
if test -z "$stripcmd"; then
u_plus_rw=
else
u_plus_rw=,u+rw
fi
cp_umask=$mode$u_plus_rw;;
esac
fi
for src
do
# Protect names starting with `-'.
case $src in
-*) src=./$src;;
esac
if test -n "$dir_arg"; then
dst=$src
dstdir=$dst
test -d "$dstdir"
dstdir_status=$?
else
# Waiting for this to be detected by the "$cpprog $src $dsttmp" command
# might cause directories to be created, which would be especially bad
# if $src (and thus $dsttmp) contains '*'.
if test ! -f "$src" && test ! -d "$src"; then
echo "$0: $src does not exist." >&2
exit 1
fi
if test -z "$dst_arg"; then
echo "$0: no destination specified." >&2
exit 1
fi
dst=$dst_arg
# Protect names starting with `-'.
case $dst in
-*) dst=./$dst;;
esac
# If destination is a directory, append the input filename; won't work
# if double slashes aren't ignored.
if test -d "$dst"; then
if test -n "$no_target_directory"; then
echo "$0: $dst_arg: Is a directory" >&2
exit 1
fi
dstdir=$dst
dst=$dstdir/`basename "$src"`
dstdir_status=0
else
# Prefer dirname, but fall back on a substitute if dirname fails.
dstdir=`
(dirname "$dst") 2>/dev/null ||
expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$dst" : 'X\(//\)[^/]' \| \
X"$dst" : 'X\(//\)$' \| \
X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$dst" |
sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
s//\1/
q
}
/^X\(\/\/\)[^/].*/{
s//\1/
q
}
/^X\(\/\/\)$/{
s//\1/
q
}
/^X\(\/\).*/{
s//\1/
q
}
s/.*/./; q'
`
test -d "$dstdir"
dstdir_status=$?
fi
fi
obsolete_mkdir_used=false
if test $dstdir_status != 0; then
case $posix_mkdir in
'')
# Create intermediate dirs using mode 755 as modified by the umask.
# This is like FreeBSD 'install' as of 1997-10-28.
umask=`umask`
case $stripcmd.$umask in
# Optimize common cases.
*[2367][2367]) mkdir_umask=$umask;;
.*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
*[0-7])
mkdir_umask=`expr $umask + 22 \
- $umask % 100 % 40 + $umask % 20 \
- $umask % 10 % 4 + $umask % 2
`;;
*) mkdir_umask=$umask,go-w;;
esac
# With -d, create the new directory with the user-specified mode.
# Otherwise, rely on $mkdir_umask.
if test -n "$dir_arg"; then
mkdir_mode=-m$mode
else
mkdir_mode=
fi
posix_mkdir=false
case $umask in
*[123567][0-7][0-7])
# POSIX mkdir -p sets u+wx bits regardless of umask, which
# is incompatible with FreeBSD 'install' when (umask & 300) != 0.
;;
*)
tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
if (umask $mkdir_umask &&
exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
then
if test -z "$dir_arg" || {
# Check for POSIX incompatibilities with -m.
# HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
# other-writeable bit of parent directory when it shouldn't.
# FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
ls_ld_tmpdir=`ls -ld "$tmpdir"`
case $ls_ld_tmpdir in
d????-?r-*) different_mode=700;;
d????-?--*) different_mode=755;;
*) false;;
esac &&
$mkdirprog -m$different_mode -p -- "$tmpdir" && {
ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
}
}
then posix_mkdir=:
fi
rmdir "$tmpdir/d" "$tmpdir"
else
# Remove any dirs left behind by ancient mkdir implementations.
rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
fi
trap '' 0;;
esac;;
esac
if
$posix_mkdir && (
umask $mkdir_umask &&
$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
)
then :
else
# The umask is ridiculous, or mkdir does not conform to POSIX,
# or it failed possibly due to a race condition. Create the
# directory the slow way, step by step, checking for races as we go.
case $dstdir in
/*) prefix='/';;
-*) prefix='./';;
*) prefix='';;
esac
eval "$initialize_posix_glob"
oIFS=$IFS
IFS=/
$posix_glob set -f
set fnord $dstdir
shift
$posix_glob set +f
IFS=$oIFS
prefixes=
for d
do
test -z "$d" && continue
prefix=$prefix$d
if test -d "$prefix"; then
prefixes=
else
if $posix_mkdir; then
(umask=$mkdir_umask &&
$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
# Don't fail if two instances are running concurrently.
test -d "$prefix" || exit 1
else
case $prefix in
*\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
*) qprefix=$prefix;;
esac
prefixes="$prefixes '$qprefix'"
fi
fi
prefix=$prefix/
done
if test -n "$prefixes"; then
# Don't fail if two instances are running concurrently.
(umask $mkdir_umask &&
eval "\$doit_exec \$mkdirprog $prefixes") ||
test -d "$dstdir" || exit 1
obsolete_mkdir_used=true
fi
fi
fi
if test -n "$dir_arg"; then
{ test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
{ test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
{ test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
else
# Make a couple of temp file names in the proper directory.
dsttmp=$dstdir/_inst.$$_
rmtmp=$dstdir/_rm.$$_
# Trap to clean up those temp files at exit.
trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
# Copy the file name to the temp name.
(umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
# and set any options; do chmod last to preserve setuid bits.
#
# If any of these fail, we abort the whole thing. If we want to
# ignore errors from any of these, just make sure not to ignore
# errors from the above "$doit $cpprog $src $dsttmp" command.
#
{ test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
{ test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
{ test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
{ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
# If -C, don't bother to copy if it wouldn't change the file.
if $copy_on_change &&
old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
eval "$initialize_posix_glob" &&
$posix_glob set -f &&
set X $old && old=:$2:$4:$5:$6 &&
set X $new && new=:$2:$4:$5:$6 &&
$posix_glob set +f &&
test "$old" = "$new" &&
$cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
then
rm -f "$dsttmp"
else
# Rename the file to the real destination.
$doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
# The rename failed, perhaps because mv can't rename something else
# to itself, or perhaps because mv is so ancient that it does not
# support -f.
{
# Now remove or move aside any old file at destination location.
# We try this two ways since rm can't unlink itself on some
# systems and the destination file might be busy for other
# reasons. In this case, the final cleanup might fail but the new
# file should still install successfully.
{
test ! -f "$dst" ||
$doit $rmcmd -f "$dst" 2>/dev/null ||
{ $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
{ $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
} ||
{ echo "$0: cannot unlink or rename $dst" >&2
(exit 1); exit 1
}
} &&
# Now rename the file to the real destination.
$doit $mvcmd "$dsttmp" "$dst"
}
fi || exit 1
trap '' 0
fi
done
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
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 .if n .ad l
.nh .nh
.SH NAME .SH NAME
...@@ -74,7 +74,4 @@ the author. ...@@ -74,7 +74,4 @@ the author.
.SH AUTHOR .SH AUTHOR
Written by Maarten L. Hekkelman <maarten@hekkelman.com> Written by Maarten L. Hekkelman <maarten@hekkelman.com>
.SH "REPORTING BUGS" .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.
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
# Visual Studio Version 16
VisualStudioVersion = 16.0.31025.194
MinimumVisualStudioVersion = 10.0.40219.1
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "mkdssp", "mkdssp.vcxproj", "{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
Debug|x64 = Debug|x64
Release|x64 = Release|x64
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}.Debug|x64.ActiveCfg = Debug|x64
{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}.Debug|x64.Build.0 = Debug|x64
{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}.Release|x64.ActiveCfg = Release|x64
{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}.Release|x64.Build.0 = Release|x64
EndGlobalSection
GlobalSection(SolutionProperties) = preSolution
HideSolutionNode = FALSE
EndGlobalSection
GlobalSection(ExtensibilityGlobals) = postSolution
SolutionGuid = {15535352-DFF9-46BB-A6F8-9E3E2B54024F}
EndGlobalSection
EndGlobal
msvc/mkdssp.vcxproj deleted 100644 → 0
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup Label="ProjectConfigurations">
<ProjectConfiguration Include="Debug|Win32">
<Configuration>Debug</Configuration>
<Platform>Win32</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Release|Win32">
<Configuration>Release</Configuration>
<Platform>Win32</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Debug|x64">
<Configuration>Debug</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Release|x64">
<Configuration>Release</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
</ItemGroup>
<PropertyGroup Label="Globals">
<VCProjectVersion>16.0</VCProjectVersion>
<ProjectGuid>{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}</ProjectGuid>
<Keyword>Win32Proj</Keyword>
<WindowsTargetPlatformVersion>10.0</WindowsTargetPlatformVersion>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
<ConfigurationType>Application</ConfigurationType>
<UseDebugLibraries>true</UseDebugLibraries>
<PlatformToolset>v142</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
<ConfigurationType>Application</ConfigurationType>
<UseDebugLibraries>false</UseDebugLibraries>
<PlatformToolset>v142</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
<ConfigurationType>Application</ConfigurationType>
<UseDebugLibraries>true</UseDebugLibraries>
<PlatformToolset>v142</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
<ConfigurationType>Application</ConfigurationType>
<UseDebugLibraries>false</UseDebugLibraries>
<PlatformToolset>v142</PlatformToolset>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
<ImportGroup Label="ExtensionSettings">
</ImportGroup>
<ImportGroup Label="Shared">
</ImportGroup>
<ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
<ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
<ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
<ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
<PropertyGroup Label="UserMacros" />
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
<LinkIncremental>true</LinkIncremental>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
<LinkIncremental>true</LinkIncremental>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<IncludePath>$(VC_IncludePath);$(WindowsSDK_IncludePath);$(SolutionDir)\..\..\boost_1_75_0;$(SolutionDir)\..\..\libcifpp\include</IncludePath>
<LibraryPath>$(VC_LibraryPath_x64);$(WindowsSDK_LibraryPath_x64);$(SolutionDir)\..\..\boost_1_75_0\stage\lib;$(SolutionDir)\..\..\libcifpp\msvc\$(Platform)\$(Configuration)</LibraryPath>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
<IncludePath>$(VC_IncludePath);$(WindowsSDK_IncludePath);$(SolutionDir)\..\..\boost_1_75_0;$(SolutionDir)\..\..\libcifpp\include</IncludePath>
<LibraryPath>$(VC_LibraryPath_x64);$(WindowsSDK_LibraryPath_x64);$(SolutionDir)\..\..\boost_1_75_0\stage\lib;$(SolutionDir)\..\..\libcifpp\msvc\$(Platform)\$(Configuration)</LibraryPath>
</PropertyGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
<ClCompile>
<PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
<RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
<WarningLevel>Level3</WarningLevel>
<DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
<Optimization>Disabled</Optimization>
</ClCompile>
<Link>
<TargetMachine>MachineX86</TargetMachine>
<GenerateDebugInformation>true</GenerateDebugInformation>
<SubSystem>Windows</SubSystem>
</Link>
</ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
<ClCompile>
<PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
<RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
<WarningLevel>Level3</WarningLevel>
<DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
</ClCompile>
<Link>
<TargetMachine>MachineX86</TargetMachine>
<GenerateDebugInformation>true</GenerateDebugInformation>
<SubSystem>Windows</SubSystem>
<EnableCOMDATFolding>true</EnableCOMDATFolding>
<OptimizeReferences>true</OptimizeReferences>
</Link>
</ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
<ClCompile>
<LanguageStandard>stdcpp17</LanguageStandard>
<RuntimeLibrary>MultiThreaded</RuntimeLibrary>
<ConformanceMode>true</ConformanceMode>
<EnableModules>true</EnableModules>
<AdditionalIncludeDirectories>$(SolutionDir)\..\src</AdditionalIncludeDirectories>
</ClCompile>
<Link>
<AdditionalDependencies>kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;libcifpp.lib;%(AdditionalDependencies)</AdditionalDependencies>
</Link>
</ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<ClCompile>
<RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
<LanguageStandard>stdcpp17</LanguageStandard>
<ConformanceMode>true</ConformanceMode>
<EnableModules>true</EnableModules>
<AdditionalIncludeDirectories>$(SolutionDir)\..\src</AdditionalIncludeDirectories>
</ClCompile>
<Link>
<AdditionalDependencies>kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;libcifpp.lib;%(AdditionalDependencies)</AdditionalDependencies>
</Link>
</ItemDefinitionGroup>
<ItemGroup>
<ClCompile Include="..\src\mkdssp.cpp" />
</ItemGroup>
<ItemGroup>
<Object Include="..\mkdssp_rsrc.obj" />
</ItemGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
<ImportGroup Label="ExtensionTargets">
</ImportGroup>
</Project>
\ No newline at end of file
msvc/mkdssp.vcxproj.filters deleted 100644 → 0
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup>
<Filter Include="Source Files">
<UniqueIdentifier>{4FC737F1-C7A5-4376-A066-2A32D752A2FF}</UniqueIdentifier>
<Extensions>cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx</Extensions>
</Filter>
<Filter Include="Header Files">
<UniqueIdentifier>{93995380-89BD-4b04-88EB-625FBE52EBFB}</UniqueIdentifier>
<Extensions>h;hh;hpp;hxx;hm;inl;inc;xsd</Extensions>
</Filter>
<Filter Include="Resource Files">
<UniqueIdentifier>{67DA6AB6-F800-4c08-8B7A-83BB121AAD01}</UniqueIdentifier>
<Extensions>rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav</Extensions>
</Filter>
</ItemGroup>
<ItemGroup>
<ClCompile Include="..\src\mkdssp.cpp">
<Filter>Source Files</Filter>
</ClCompile>
</ItemGroup>
<ItemGroup>
<Object Include="..\mkdssp_rsrc.obj">
<Filter>Source Files</Filter>
</Object>
</ItemGroup>
</Project>
\ No newline at end of file
msvc/mkdssp.vcxproj.user deleted 100644 → 0
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="Current" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<LocalDebuggerCommandArguments>../libcifpp/examples/1cbs.cif.gz</LocalDebuggerCommandArguments>
<LocalDebuggerWorkingDirectory>$(SolutionDir)\..\</LocalDebuggerWorkingDirectory>
<DebuggerFlavor>WindowsLocalDebugger</DebuggerFlavor>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
<LocalDebuggerCommandArguments>../libcifpp/examples/1cbs.cif.gz</LocalDebuggerCommandArguments>
<LocalDebuggerWorkingDirectory>$(SolutionDir)\..\</LocalDebuggerWorkingDirectory>
<DebuggerFlavor>WindowsLocalDebugger</DebuggerFlavor>
</PropertyGroup>
</Project>
\ No newline at end of file
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
/*-
* 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 __has_include("config.hpp")
#include "config.hpp"
#endif
#include <exception>
#include <iostream>
#include <filesystem>
#include <fstream>
#include <boost/format.hpp>
#include <boost/date_time/gregorian/formatters.hpp>
#include <cif++/CifUtils.hpp>
#include <cif++/Cif2PDB.hpp>
#include "dssp.hpp"
// --------------------------------------------------------------------
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}).*)"),
rxVersionNr2(R"(mkdssp-version: (\d+(?:\.\d+)+))");
#include "revision.hpp"
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;
}
// always the first, replace with more specific if followed by the other info
if (std::regex_match(line, m, rxVersionNr2))
{
gVersionNr = m[1];
continue;
}
}
}
std::string get_version_nr()
{
return gVersionNr/* + '/' + cif::get_version_nr()*/;
}
std::string get_version_date()
{
return gVersionDate;
}
std::string get_version_string()
{
return gVersionNr + " " + gVersionDate;
}
// --------------------------------------------------------------------
std::string ResidueToDSSPLine(const mmcif::DSSP::ResidueInfo& info)
{
/*
This is the header line for the residue lines in a DSSP file:
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
*/
boost::format kDSSPResidueLine(
"%5.5d%5.5d%1.1s%1.1s %c %c%c%c%c%c%c%c%c%c%4.4d%4.4d%c%4.4d %11s%11s%11s%11s %6.3f%6.1f%6.1f%6.1f%6.1f %6.1f %6.1f %6.1f");
auto& residue = info.residue();
if (residue.asymID().length() > 1)
throw std::runtime_error("This file contains data that won't fit in the original DSSP format");
char code = 'X';
if (mmcif::kAAMap.find(residue.compoundID()) != mmcif::kAAMap.end())
code = mmcif::kAAMap.at(residue.compoundID());
if (code == 'C') // a cysteine
{
auto ssbridgenr = info.ssBridgeNr();
if (ssbridgenr)
code = 'a' + ((ssbridgenr - 1) % 26);
}
char ss;
switch (info.ss())
{
case mmcif::ssAlphahelix: ss = 'H'; break;
case mmcif::ssBetabridge: ss = 'B'; break;
case mmcif::ssStrand: ss = 'E'; break;
case mmcif::ssHelix_3: ss = 'G'; break;
case mmcif::ssHelix_5: ss = 'I'; break;
case mmcif::ssHelix_PPII: ss = 'P'; break;
case mmcif::ssTurn: ss = 'T'; break;
case mmcif::ssBend: ss = 'S'; break;
case mmcif::ssLoop: ss = ' '; break;
}
char helix[4] = { ' ', ' ', ' ', ' ' };
for (mmcif::HelixType helixType: { mmcif::HelixType::rh_3_10, mmcif::HelixType::rh_alpha, mmcif::HelixType::rh_pi, mmcif::HelixType::rh_pp })
{
switch (info.helix(helixType))
{
case mmcif::Helix::None: helix[static_cast<int>(helixType)] = ' '; break;
case mmcif::Helix::Start: helix[static_cast<int>(helixType)] = '>'; break;
case mmcif::Helix::End: helix[static_cast<int>(helixType)] = '<'; break;
case mmcif::Helix::StartAndEnd: helix[static_cast<int>(helixType)] = 'X'; break;
case mmcif::Helix::Middle: helix[static_cast<int>(helixType)] = (helixType == mmcif::HelixType::rh_pp ? 'P' : static_cast<char>('3' + static_cast<int>(helixType))); break;
}
}
char bend = ' ';
if (info.bend())
bend = 'S';
double alpha = residue.alpha();
char chirality = alpha == 360 ? ' ' : (alpha < 0 ? '-' : '+');
uint32_t bp[2] = {};
char bridgelabel[2] = { ' ', ' ' };
for (uint32_t i: { 0, 1 })
{
const auto& [p, ladder, parallel] = info.bridgePartner(i);
if (not p)
continue;
bp[i] = p.nr() % 10000; // won't fit otherwise...
bridgelabel[i] = (parallel ? 'a' : 'A') + ladder % 26;
}
char sheet = ' ';
if (info.sheet() != 0)
sheet = 'A' + (info.sheet() - 1) % 26;
std::string NHO[2], ONH[2];
for (int i: { 0, 1 })
{
const auto& [donor, donorE] = info.donor(i);
const auto& [acceptor, acceptorE] = info.acceptor(i);
NHO[i] = ONH[i] = "0, 0.0";
if (acceptor)
{
auto d = acceptor.nr() - info.nr();
NHO[i] = (boost::format("%d,%3.1f") % d % acceptorE).str();
}
if (donor)
{
auto d = donor.nr() - info.nr();
ONH[i] = (boost::format("%d,%3.1f") % d % donorE).str();
}
}
auto ca = residue.atomByID("CA");
auto const& [cax, cay, caz] = ca.location();
return (kDSSPResidueLine % info.nr() % ca.authSeqID() % ca.pdbxAuthInsCode() % ca.authAsymID() % code %
ss % helix[3] % helix[0] % helix[1] % helix[2] % bend % chirality % bridgelabel[0] % bridgelabel[1] %
bp[0] % bp[1] % sheet % floor(info.accessibility() + 0.5) %
NHO[0] % ONH[0] % NHO[1] % ONH[1] %
residue.tco() % residue.kappa() % alpha % residue.phi() % residue.psi() %
cax % cay % caz).str();
}
void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ostream& os)
{
const std::string kFirstLine("==== Secondary Structure Definition by the program DSSP, NKI version 4.0 ==== ");
boost::format kHeaderLine("%1% %|127t|%2%");
using namespace boost::gregorian;
auto stats = dssp.GetStatistics();
date today = day_clock::local_day();
auto& cf = structure.getFile().file();
os << kHeaderLine % (kFirstLine + "DATE=" + to_iso_extended_string(today)) % '.' << std::endl
<< kHeaderLine % "REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637" % '.' << std::endl
<< GetPDBHEADERLine(cf, 127) << '.' << std::endl
<< GetPDBCOMPNDLine(cf, 127) << '.' << std::endl
<< GetPDBSOURCELine(cf, 127) << '.' << std::endl
<< GetPDBAUTHORLine(cf, 127) << '.' << std::endl;
os << boost::format("%5.5d%3.3d%3.3d%3.3d%3.3d TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) %|127t|%c") %
stats.nrOfResidues % stats.nrOfChains % stats.nrOfSSBridges % stats.nrOfIntraChainSSBridges % (stats.nrOfSSBridges - stats.nrOfIntraChainSSBridges) % '.' << std::endl;
os << kHeaderLine % (boost::format("%8.1f ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)") % stats.accessibleSurface) % '.' << std::endl;
// hydrogenbond summary
os << kHeaderLine % (
boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES")
% stats.nrOfHBonds % (stats.nrOfHBonds * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
os << kHeaderLine % (
boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES")
% stats.nrOfHBondsInParallelBridges % (stats.nrOfHBondsInParallelBridges * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
os << kHeaderLine % (
boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES")
% stats.nrOfHBondsInAntiparallelBridges % (stats.nrOfHBondsInAntiparallelBridges * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
boost::format kHBondsLine("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I%c%1.1d), SAME NUMBER PER 100 RESIDUES");
for (int k = 0; k < 11; ++k)
os << kHeaderLine % (kHBondsLine % stats.nrOfHBondsPerDistance[k] % (stats.nrOfHBondsPerDistance[k] * 100.0 / stats.nrOfResidues) % (k - 5 < 0 ? '-' : '+') % abs(k - 5)) % '.' << std::endl;
// histograms...
os << " 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** ." << std::endl;
for (auto hi: stats.residuesPerAlphaHelixHistogram)
os << boost::format("%3.3d") % hi;
os << " RESIDUES PER ALPHA HELIX ." << std::endl;
for (auto hi: stats.parallelBridgesPerLadderHistogram)
os << boost::format("%3.3d") % hi;
os << " PARALLEL BRIDGES PER LADDER ." << std::endl;
for (auto hi: stats.antiparallelBridgesPerLadderHistogram)
os << boost::format("%3.3d") % hi;
os << " ANTIPARALLEL BRIDGES PER LADDER ." << std::endl;
for (auto hi: stats.laddersPerSheetHistogram)
os << boost::format("%3.3d") % hi;
os << " LADDERS PER SHEET ." << std::endl;
// per residue information
os << " # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA" << std::endl;
boost::format kDSSPResidueLine(
"%5.5d !%c 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0");
int last = 0;
for (auto ri: dssp)
{
// insert a break line whenever we detect missing residues
// can be the transition to a different chain, or missing residues in the current chain
if (ri.nr() != last + 1)
os << (kDSSPResidueLine % (last + 1) % (ri.chainBreak() == mmcif::ChainBreak::NewChain ? '*' : ' ')) << std::endl;
os << ResidueToDSSPLine(ri) << std::endl;
last = ri.nr();
}
}
void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, bool writeOther, std::ostream& os)
{
auto& db = structure.getFile().data();
if (dssp.empty())
{
if (cif::VERBOSE)
std::cout << "No secondary structure information found" << std::endl;
}
else
{
// replace all struct_conf and struct_conf_type records
auto& structConfType = db["struct_conf_type"];
structConfType.clear();
auto& structConf = db["struct_conf"];
structConf.clear();
std::map<std::string,int> foundTypes;
auto st = dssp.begin(), lt = st;
auto lastSS = st->ss();
for (auto t = dssp.begin(); ; lt = t, ++t)
{
bool stop = t == dssp.end();
bool flush = (stop or t->ss() != lastSS);
if (flush and (writeOther or lastSS != mmcif::SecondaryStructureType::ssLoop))
{
auto& rb = st->residue();
auto& re = lt->residue();
std::string id;
switch (lastSS)
{
case mmcif::SecondaryStructureType::ssHelix_3:
id = "HELX_RH_3T_P";
break;
case mmcif::SecondaryStructureType::ssAlphahelix:
id = "HELX_RH_AL_P";
break;
case mmcif::SecondaryStructureType::ssHelix_5:
id = "HELX_RH_PI_P";
break;
case mmcif::SecondaryStructureType::ssHelix_PPII:
id = "HELX_LH_PP_P";
break;
case mmcif::SecondaryStructureType::ssTurn:
id = "TURN_TY1_P";
break;
case mmcif::SecondaryStructureType::ssBend:
id = "BEND";
break;
case mmcif::SecondaryStructureType::ssBetabridge:
case mmcif::SecondaryStructureType::ssStrand:
id = "STRN";
break;
case mmcif::SecondaryStructureType::ssLoop:
id = "OTHER";
break;
}
if (foundTypes.count(id) == 0)
{
structConfType.emplace({
{ "id", id },
{ "criteria", "DSSP" }
});
foundTypes[id] = 1;
}
structConf.emplace({
{ "conf_type_id", id },
{ "id", id + std::to_string(foundTypes[id]++) },
// { "pdbx_PDB_helix_id", vS(12, 14) },
{ "beg_label_comp_id", rb.compoundID() },
{ "beg_label_asym_id", rb.asymID() },
{ "beg_label_seq_id", rb.seqID() },
{ "pdbx_beg_PDB_ins_code", rb.authInsCode() },
{ "end_label_comp_id", re.compoundID() },
{ "end_label_asym_id", re.asymID() },
{ "end_label_seq_id", re.seqID() },
{ "pdbx_end_PDB_ins_code", re.authInsCode() },
{ "beg_auth_comp_id", rb.compoundID() },
{ "beg_auth_asym_id", rb.authAsymID() },
{ "beg_auth_seq_id", rb.authSeqID() },
{ "end_auth_comp_id", re.compoundID() },
{ "end_auth_asym_id", re.authAsymID() },
{ "end_auth_seq_id", re.authSeqID() }
// { "pdbx_PDB_helix_class", vS(39, 40) },
// { "details", vS(41, 70) },
// { "pdbx_PDB_helix_length", vI(72, 76) }
});
st = t;
}
if (lastSS != t->ss())
{
st = t;
lastSS = t->ss();
}
if (stop)
break;
}
}
db.add_software("dssp", "other", get_version_nr(), get_version_date());
db.write(os);
}
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.cpp
...@@ -46,6 +46,8 @@ ...@@ -46,6 +46,8 @@
#include <boost/iostreams/filter/bzip2.hpp> #include <boost/iostreams/filter/bzip2.hpp>
#include <boost/iostreams/filtering_stream.hpp> #include <boost/iostreams/filtering_stream.hpp>
#include "dssp.hpp"
namespace fs = std::filesystem; namespace fs = std::filesystem;
namespace io = boost::iostreams; namespace io = boost::iostreams;
namespace po = boost::program_options; namespace po = boost::program_options;
...@@ -69,390 +71,6 @@ void print_what (const std::exception& e) ...@@ -69,390 +71,6 @@ void print_what (const std::exception& e)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
namespace {
std::string gVersionNr, gVersionDate, VERSION_STRING;
}
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}).*)"),
rxVersionNr2(R"(mkdssp-version: (\d+(?:\.\d+)+))");
#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;
}
// always the first, replace with more specific if followed by the other info
if (std::regex_match(line, m, rxVersionNr2))
{
gVersionNr = m[1];
continue;
}
}
if (not VERSION_STRING.empty())
VERSION_STRING += "\n";
VERSION_STRING += gVersionNr + " " + gVersionDate;
}
std::string get_version_nr()
{
return gVersionNr/* + '/' + cif::get_version_nr()*/;
}
std::string get_version_date()
{
return gVersionDate;
}
// --------------------------------------------------------------------
std::string ResidueToDSSPLine(const mmcif::DSSP::ResidueInfo& info)
{
/*
This is the header line for the residue lines in a DSSP file:
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
*/
boost::format kDSSPResidueLine(
"%5.5d%5.5d%1.1s%1.1s %c %c%c%c%c%c%c%c%c%c%4.4d%4.4d%c%4.4d %11s%11s%11s%11s %6.3f%6.1f%6.1f%6.1f%6.1f %6.1f %6.1f %6.1f");
auto& residue = info.residue();
if (residue.asymID().length() > 1)
throw std::runtime_error("This file contains data that won't fit in the original DSSP format");
char code = 'X';
if (mmcif::kAAMap.find(residue.compoundID()) != mmcif::kAAMap.end())
code = mmcif::kAAMap.at(residue.compoundID());
if (code == 'C') // a cysteine
{
auto ssbridgenr = info.ssBridgeNr();
if (ssbridgenr)
code = 'a' + ((ssbridgenr - 1) % 26);
}
char ss;
switch (info.ss())
{
case mmcif::ssAlphahelix: ss = 'H'; break;
case mmcif::ssBetabridge: ss = 'B'; break;
case mmcif::ssStrand: ss = 'E'; break;
case mmcif::ssHelix_3: ss = 'G'; break;
case mmcif::ssHelix_5: ss = 'I'; break;
case mmcif::ssHelix_PPII: ss = 'P'; break;
case mmcif::ssTurn: ss = 'T'; break;
case mmcif::ssBend: ss = 'S'; break;
case mmcif::ssLoop: ss = ' '; break;
}
char helix[4] = { ' ', ' ', ' ', ' ' };
for (mmcif::HelixType helixType: { mmcif::HelixType::rh_3_10, mmcif::HelixType::rh_alpha, mmcif::HelixType::rh_pi, mmcif::HelixType::rh_pp })
{
switch (info.helix(helixType))
{
case mmcif::Helix::None: helix[static_cast<int>(helixType)] = ' '; break;
case mmcif::Helix::Start: helix[static_cast<int>(helixType)] = '>'; break;
case mmcif::Helix::End: helix[static_cast<int>(helixType)] = '<'; break;
case mmcif::Helix::StartAndEnd: helix[static_cast<int>(helixType)] = 'X'; break;
case mmcif::Helix::Middle: helix[static_cast<int>(helixType)] = (helixType == mmcif::HelixType::rh_pp ? 'P' : ('3' + static_cast<int>(helixType))); break;
}
}
char bend = ' ';
if (info.bend())
bend = 'S';
double alpha = residue.alpha();
char chirality = alpha == 360 ? ' ' : (alpha < 0 ? '-' : '+');
uint32_t bp[2] = {};
char bridgelabel[2] = { ' ', ' ' };
for (uint32_t i: { 0, 1 })
{
const auto& [p, ladder, parallel] = info.bridgePartner(i);
if (not p)
continue;
bp[i] = p.nr() % 10000; // won't fit otherwise...
bridgelabel[i] = (parallel ? 'a' : 'A') + ladder % 26;
}
char sheet = ' ';
if (info.sheet() != 0)
sheet = 'A' + (info.sheet() - 1) % 26;
std::string NHO[2], ONH[2];
for (int i: { 0, 1 })
{
const auto& [donor, donorE] = info.donor(i);
const auto& [acceptor, acceptorE] = info.acceptor(i);
NHO[i] = ONH[i] = "0, 0.0";
if (acceptor)
{
auto d = acceptor.nr() - info.nr();
NHO[i] = (boost::format("%d,%3.1f") % d % acceptorE).str();
}
if (donor)
{
auto d = donor.nr() - info.nr();
ONH[i] = (boost::format("%d,%3.1f") % d % donorE).str();
}
}
auto ca = residue.atomByID("CA");
auto const& [cax, cay, caz] = ca.location();
return (kDSSPResidueLine % info.nr() % ca.authSeqID() % ca.pdbxAuthInsCode() % ca.authAsymID() % code %
ss % helix[3] % helix[0] % helix[1] % helix[2] % bend % chirality % bridgelabel[0] % bridgelabel[1] %
bp[0] % bp[1] % sheet % floor(info.accessibility() + 0.5) %
NHO[0] % ONH[0] % NHO[1] % ONH[1] %
residue.tco() % residue.kappa() % alpha % residue.phi() % residue.psi() %
cax % cay % caz).str();
}
void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ostream& os)
{
const std::string kFirstLine("==== Secondary Structure Definition by the program DSSP, NKI version 3.0 ==== ");
boost::format kHeaderLine("%1% %|127t|%2%");
using namespace boost::gregorian;
auto stats = dssp.GetStatistics();
date today = day_clock::local_day();
auto& cf = structure.getFile().file();
os << kHeaderLine % (kFirstLine + "DATE=" + to_iso_extended_string(today)) % '.' << std::endl
<< kHeaderLine % "REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637" % '.' << std::endl
<< GetPDBHEADERLine(cf, 127) << '.' << std::endl
<< GetPDBCOMPNDLine(cf, 127) << '.' << std::endl
<< GetPDBSOURCELine(cf, 127) << '.' << std::endl
<< GetPDBAUTHORLine(cf, 127) << '.' << std::endl;
os << boost::format("%5.5d%3.3d%3.3d%3.3d%3.3d TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) %|127t|%c") %
stats.nrOfResidues % stats.nrOfChains % stats.nrOfSSBridges % stats.nrOfIntraChainSSBridges % (stats.nrOfSSBridges - stats.nrOfIntraChainSSBridges) % '.' << std::endl;
os << kHeaderLine % (boost::format("%8.1f ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)") % stats.accessibleSurface) % '.' << std::endl;
// hydrogenbond summary
os << kHeaderLine % (
boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES")
% stats.nrOfHBonds % (stats.nrOfHBonds * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
os << kHeaderLine % (
boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES")
% stats.nrOfHBondsInParallelBridges % (stats.nrOfHBondsInParallelBridges * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
os << kHeaderLine % (
boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES")
% stats.nrOfHBondsInAntiparallelBridges % (stats.nrOfHBondsInAntiparallelBridges * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
boost::format kHBondsLine("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I%c%1.1d), SAME NUMBER PER 100 RESIDUES");
for (int k = 0; k < 11; ++k)
os << kHeaderLine % (kHBondsLine % stats.nrOfHBondsPerDistance[k] % (stats.nrOfHBondsPerDistance[k] * 100.0 / stats.nrOfResidues) % (k - 5 < 0 ? '-' : '+') % abs(k - 5)) % '.' << std::endl;
// histograms...
os << " 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** ." << std::endl;
for (auto hi: stats.residuesPerAlphaHelixHistogram)
os << boost::format("%3.3d") % hi;
os << " RESIDUES PER ALPHA HELIX ." << std::endl;
for (auto hi: stats.parallelBridgesPerLadderHistogram)
os << boost::format("%3.3d") % hi;
os << " PARALLEL BRIDGES PER LADDER ." << std::endl;
for (auto hi: stats.antiparallelBridgesPerLadderHistogram)
os << boost::format("%3.3d") % hi;
os << " ANTIPARALLEL BRIDGES PER LADDER ." << std::endl;
for (auto hi: stats.laddersPerSheetHistogram)
os << boost::format("%3.3d") % hi;
os << " LADDERS PER SHEET ." << std::endl;
// per residue information
os << " # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA" << std::endl;
boost::format kDSSPResidueLine(
"%5.5d !%c 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0");
int last = 0;
for (auto ri: dssp)
{
// insert a break line whenever we detect missing residues
// can be the transition to a different chain, or missing residues in the current chain
if (ri.nr() != last + 1)
os << (kDSSPResidueLine % (last + 1) % (ri.chainBreak() == mmcif::ChainBreak::NewChain ? '*' : ' ')) << std::endl;
os << ResidueToDSSPLine(ri) << std::endl;
last = ri.nr();
}
}
void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, bool writeOther, std::ostream& os)
{
auto& db = structure.getFile().data();
if (dssp.empty())
{
if (cif::VERBOSE)
std::cout << "No secondary structure information found" << std::endl;
}
else
{
// replace all struct_conf and struct_conf_type records
auto& structConfType = db["struct_conf_type"];
structConfType.clear();
auto& structConf = db["struct_conf"];
structConf.clear();
std::map<std::string,int> foundTypes;
auto st = dssp.begin(), lt = st;
auto lastSS = st->ss();
for (auto t = dssp.begin(); ; lt = t, ++t)
{
bool stop = t == dssp.end();
bool flush = (stop or t->ss() != lastSS);
if (flush and (writeOther or lastSS != mmcif::SecondaryStructureType::ssLoop))
{
auto& rb = st->residue();
auto& re = lt->residue();
std::string id;
switch (lastSS)
{
case mmcif::SecondaryStructureType::ssHelix_3:
id = "HELX_RH_3T_P";
break;
case mmcif::SecondaryStructureType::ssAlphahelix:
id = "HELX_RH_AL_P";
break;
case mmcif::SecondaryStructureType::ssHelix_5:
id = "HELX_RH_PI_P";
break;
case mmcif::SecondaryStructureType::ssHelix_PPII:
id = "HELX_LH_PP_P";
break;
case mmcif::SecondaryStructureType::ssTurn:
id = "TURN_TY1_P";
break;
case mmcif::SecondaryStructureType::ssBend:
id = "BEND";
break;
case mmcif::SecondaryStructureType::ssBetabridge:
case mmcif::SecondaryStructureType::ssStrand:
id = "STRN";
break;
case mmcif::SecondaryStructureType::ssLoop:
id = "OTHER";
break;
}
if (foundTypes.count(id) == 0)
{
structConfType.emplace({
{ "id", id },
{ "criteria", "DSSP" }
});
foundTypes[id] = 1;
}
structConf.emplace({
{ "conf_type_id", id },
{ "id", id + std::to_string(foundTypes[id]++) },
// { "pdbx_PDB_helix_id", vS(12, 14) },
{ "beg_label_comp_id", rb.compoundID() },
{ "beg_label_asym_id", rb.asymID() },
{ "beg_label_seq_id", rb.seqID() },
{ "pdbx_beg_PDB_ins_code", rb.authInsCode() },
{ "end_label_comp_id", re.compoundID() },
{ "end_label_asym_id", re.asymID() },
{ "end_label_seq_id", re.seqID() },
{ "pdbx_end_PDB_ins_code", re.authInsCode() },
{ "beg_auth_comp_id", rb.compoundID() },
{ "beg_auth_asym_id", rb.authAsymID() },
{ "beg_auth_seq_id", rb.authSeqID() },
{ "end_auth_comp_id", re.compoundID() },
{ "end_auth_asym_id", re.authAsymID() },
{ "end_auth_seq_id", re.authSeqID() }
// { "pdbx_PDB_helix_class", vS(39, 40) },
// { "details", vS(41, 70) },
// { "pdbx_PDB_helix_length", vI(72, 76) }
});
st = t;
}
if (lastSS != t->ss())
{
st = t;
lastSS = t->ss();
}
if (stop)
break;
}
}
db.add_software("dssp", "other", get_version_nr(), get_version_date());
db.write(os);
}
// --------------------------------------------------------------------
int d_main(int argc, const char* argv[]) int d_main(int argc, const char* argv[])
{ {
using namespace std::literals; using namespace std::literals;
...@@ -498,7 +116,7 @@ int d_main(int argc, const char* argv[]) ...@@ -498,7 +116,7 @@ int d_main(int argc, const char* argv[])
if (vm.count("version")) if (vm.count("version"))
{ {
std::cout << argv[0] << " version " << VERSION_STRING << std::endl; std::cout << argv[0] << " version " << get_version_string() << std::endl;
exit(0); exit(0);
} }
...@@ -564,14 +182,14 @@ int d_main(int argc, const char* argv[]) ...@@ -564,14 +182,14 @@ int d_main(int argc, const char* argv[])
if (fmt.empty() and vm.count("output")) if (fmt.empty() and vm.count("output"))
{ {
fs::path p = vm["output"].as<std::string>(); fs::path output = vm["output"].as<std::string>();
if (p.extension() == ".gz") if (output.extension() == ".gz")
p = p.stem(); output = output.stem();
else if (p.extension() == ".bz2") else if (output.extension() == ".bz2")
p = p.stem(); output = output.stem();
if (p.extension() == ".dssp") if (output.extension() == ".dssp")
fmt = "dssp"; fmt = "dssp";
else else
fmt = "cif"; fmt = "cif";
...@@ -582,8 +200,8 @@ int d_main(int argc, const char* argv[]) ...@@ -582,8 +200,8 @@ int d_main(int argc, const char* argv[])
if (vm.count("output")) if (vm.count("output"))
{ {
fs::path p = vm["output"].as<std::string>(); fs::path output = vm["output"].as<std::string>();
std::ofstream of(p, std::ios_base::out | std::ios_base::binary); std::ofstream of(output, std::ios_base::out | std::ios_base::binary);
if (not of.is_open()) if (not of.is_open())
{ {
...@@ -593,9 +211,9 @@ int d_main(int argc, const char* argv[]) ...@@ -593,9 +211,9 @@ int d_main(int argc, const char* argv[])
io::filtering_stream<io::output> out; io::filtering_stream<io::output> out;
if (p.extension() == ".gz") if (output.extension() == ".gz")
out.push(io::gzip_compressor()); out.push(io::gzip_compressor());
else if (p.extension() == ".bz2") else if (output.extension() == ".bz2")
out.push(io::bzip2_compressor()); out.push(io::bzip2_compressor());
out.push(of); out.push(of);
...@@ -624,6 +242,9 @@ int main(int argc, const char* argv[]) ...@@ -624,6 +242,9 @@ int main(int argc, const char* argv[])
try try
{ {
#if defined(DATA_DIR)
cif::addDataDirectory(DATA_DIR);
#endif
load_version_info(); load_version_info();
result = d_main(argc, argv); result = d_main(argc, argv);
......
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
==== Secondary Structure Definition by the program DSSP, NKI version 4.0 ==== DATE=2021-08-25 .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 .
HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS .
COMPND MOL_ID: 1; MOLECULE: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II; CHAIN: A; ENGINEERED: YES .
SOURCE MOL_ID: 1; ORGANISM_COMMON: human; GENE: HUMAN CRABP-II; CELL_LINE: BL21; ORGANISM_SCIENTIFIC: Homo sapiens; ORGA... .
AUTHOR G.J.Kleywegt; T.Bergfors; T.A.Jones .
137 1 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .
7905.0 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .
94 68.6 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
65 47.4 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES .
3 2.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES .
4 2.9 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES .
7 5.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES .
9 6.6 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES .
14 10.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES .
1 0.7 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES .
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** .
0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 RESIDUES PER ALPHA HELIX .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER .
0 0 1 1 1 1 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER .
0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET .
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
1 1 A P 0 0 64 0, 0.0 2,-0.5 0, 0.0 91,-0.0 0.000 360.0 360.0 360.0 151.2 18.1 13.5 43.7
2 2 A N + 0 0 89 1,-0.1 89,-0.0 2,-0.1 44,-0.0 -0.903 360.0 172.5-124.5 100.5 20.6 16.5 43.6
3 3 A F + 0 0 1 -2,-0.5 40,-0.2 110,-0.0 -1,-0.1 0.524 40.0 127.0 -80.0 -9.9 21.1 17.8 40.1
4 4 A S + 0 0 28 41,-0.1 2,-0.3 38,-0.1 40,-0.2 -0.158 37.2 69.9 -55.6 140.2 23.2 20.8 41.5
5 5 A G E S-A 43 0A 19 38,-2.5 38,-2.6 2,-0.1 2,-0.6 -0.868 82.5 -67.6 145.0 177.2 26.6 21.5 40.1
6 6 A N E -A 42 0A 78 -2,-0.3 131,-2.8 36,-0.2 2,-0.4 -0.958 54.1-159.8-104.9 115.8 28.8 22.7 37.2
7 7 A W E -AB 41 136A 1 34,-2.8 34,-1.4 -2,-0.6 2,-0.4 -0.824 13.0-164.1-107.0 141.0 28.5 20.1 34.4
8 8 A K E - B 0 135A 92 127,-3.0 127,-2.3 -2,-0.4 2,-0.1 -0.933 28.2-112.8-119.6 141.9 30.8 19.4 31.5
9 9 A I E + B 0 134A 26 30,-0.4 125,-0.3 -2,-0.4 3,-0.1 -0.449 32.7 170.7 -78.1 144.9 29.7 17.4 28.4
10 10 A I E + 0 0A 86 123,-3.1 2,-0.3 1,-0.4 124,-0.2 0.456 69.4 21.2-126.0 -12.2 31.3 14.0 27.7
11 11 A R E - B 0 133A 141 122,-1.3 122,-2.5 2,-0.0 -1,-0.4 -0.954 53.6-178.8-159.0 138.7 29.0 12.7 24.9
12 12 A S E - B 0 132A 48 -2,-0.3 2,-0.4 120,-0.2 120,-0.2 -0.982 9.1-177.7-140.7 127.1 26.6 14.2 22.3
13 13 A E E - B 0 131A 95 118,-2.5 118,-1.5 -2,-0.4 -2,-0.0 -0.986 62.7 -1.8-128.8 138.0 24.6 12.3 19.8
14 14 A N S > S+ 0 0 64 -2,-0.4 4,-1.6 116,-0.2 5,-0.1 0.655 75.6 137.6 65.5 22.9 22.2 13.4 17.0
15 15 A F H > S+ 0 0 23 2,-0.2 4,-1.9 1,-0.2 5,-0.1 0.940 73.9 44.8 -66.9 -48.6 22.4 17.2 17.7
16 16 A E H > S+ 0 0 67 1,-0.2 4,-2.0 2,-0.2 -1,-0.2 0.902 111.2 55.1 -61.6 -39.6 22.6 18.3 14.1
17 17 A E H > S+ 0 0 91 1,-0.2 4,-1.8 2,-0.2 -1,-0.2 0.857 106.0 52.0 -60.9 -36.1 19.8 15.9 13.1
18 18 A L H X S+ 0 0 1 -4,-1.6 4,-1.7 1,-0.2 -1,-0.2 0.921 109.6 49.8 -65.5 -43.2 17.5 17.5 15.8
19 19 A L H <>S+ 0 0 5 -4,-1.9 5,-2.4 1,-0.2 -2,-0.2 0.852 106.3 56.4 -65.4 -32.2 18.3 20.9 14.3
20 20 A K H ><5S+ 0 0 103 -4,-2.0 3,-1.5 1,-0.2 -1,-0.2 0.929 106.5 48.6 -65.1 -45.5 17.4 19.6 10.8
21 21 A V H 3<5S+ 0 0 53 -4,-1.8 -1,-0.2 1,-0.3 -2,-0.2 0.860 107.3 56.5 -62.3 -36.0 14.0 18.5 11.9
22 22 A L T 3<5S- 0 0 10 -4,-1.7 -1,-0.3 -5,-0.1 -2,-0.2 0.481 120.3-112.1 -75.2 -4.6 13.4 21.9 13.6
23 23 A G T < 5 + 0 0 63 -3,-1.5 2,-0.4 1,-0.2 -3,-0.2 0.696 58.8 158.5 84.0 20.3 14.1 23.5 10.2
24 24 A V < - 0 0 28 -5,-2.4 -1,-0.2 1,-0.1 -2,-0.1 -0.661 41.2-117.3 -79.6 130.0 17.4 25.2 10.9
25 25 A N > - 0 0 92 -2,-0.4 4,-2.5 1,-0.1 3,-0.2 -0.143 25.5-100.1 -67.0 161.3 19.4 25.9 7.6
26 26 A V H > S+ 0 0 97 1,-0.2 4,-1.9 2,-0.2 5,-0.1 0.835 117.9 43.9 -47.2 -52.0 22.8 24.4 6.7
27 27 A M H > S+ 0 0 148 2,-0.2 4,-1.7 1,-0.2 -1,-0.2 0.862 114.2 48.8 -67.6 -38.7 24.9 27.4 7.6
28 28 A L H > S+ 0 0 97 -3,-0.2 4,-2.6 2,-0.2 -1,-0.2 0.872 110.3 54.0 -68.8 -34.0 23.2 28.2 10.9
29 29 A R H X S+ 0 0 26 -4,-2.5 4,-3.0 2,-0.2 5,-0.3 0.924 104.0 54.4 -63.4 -44.3 23.5 24.5 11.8
30 30 A K H X S+ 0 0 164 -4,-1.9 4,-1.6 1,-0.2 -1,-0.2 0.928 111.7 44.7 -54.8 -47.3 27.2 24.6 11.2
31 31 A I H X S+ 0 0 93 -4,-1.7 4,-1.9 1,-0.2 -2,-0.2 0.935 114.7 48.3 -62.9 -48.6 27.6 27.5 13.7
32 32 A A H X S+ 0 0 28 -4,-2.6 4,-2.6 1,-0.2 -2,-0.2 0.914 109.1 51.5 -61.0 -48.3 25.3 25.9 16.3
33 33 A V H X S+ 0 0 49 -4,-3.0 4,-0.5 1,-0.2 -1,-0.2 0.880 110.3 48.7 -59.1 -41.5 26.9 22.5 16.3
34 34 A A H >< S+ 0 0 61 -4,-1.6 3,-0.8 -5,-0.3 4,-0.2 0.933 115.2 43.9 -65.9 -45.8 30.4 23.9 16.8
35 35 A A H >< S+ 0 0 4 -4,-1.9 3,-1.2 1,-0.2 22,-0.2 0.878 110.0 56.3 -68.1 -36.3 29.4 26.1 19.7
36 36 A A H 3< S+ 0 0 10 -4,-2.6 -1,-0.2 1,-0.2 -2,-0.2 0.552 88.7 76.5 -73.9 -8.6 27.3 23.4 21.3
37 37 A S T << S+ 0 0 74 -3,-0.8 -1,-0.2 -4,-0.5 -2,-0.1 0.667 103.3 35.9 -76.7 -14.7 30.2 21.0 21.5
38 38 A K S < S+ 0 0 129 -3,-1.2 -1,-0.2 -4,-0.2 19,-0.1 -0.500 80.2 163.6-135.8 65.0 31.7 22.9 24.5
39 39 A P - 0 0 13 0, 0.0 2,-0.5 0, 0.0 -30,-0.4 -0.429 32.9-139.6 -84.3 157.8 28.9 24.2 26.7
40 40 A A E - C 0 55A 56 15,-2.1 15,-3.0 -2,-0.1 2,-0.5 -0.988 25.8-169.0-111.4 121.5 29.2 25.4 30.3
41 41 A V E -AC 7 54A 7 -34,-1.4 -34,-2.8 -2,-0.5 2,-0.5 -0.976 9.8-176.7-119.1 128.1 26.2 24.2 32.3
42 42 A E E -AC 6 53A 56 11,-2.5 11,-2.6 -2,-0.5 2,-0.4 -0.984 2.8-175.2-124.9 124.3 25.3 25.3 35.8
43 43 A I E -AC 5 52A 3 -38,-2.6 -38,-2.5 -2,-0.5 2,-0.4 -0.963 6.0-174.1-121.0 134.3 22.4 23.9 37.8
44 44 A K E - C 0 51A 114 7,-2.2 7,-1.8 -2,-0.4 2,-0.4 -0.998 10.8-174.0-126.7 121.9 21.1 25.1 41.2
45 45 A Q E + C 0 50A 29 -2,-0.4 2,-0.4 5,-0.2 5,-0.2 -0.969 17.1 177.2-122.2 135.7 18.4 23.0 42.9
46 46 A E E > S- C 0 49A 166 3,-2.5 3,-1.7 -2,-0.4 2,-0.5 -0.849 71.6 -60.6-134.0 90.9 16.4 23.7 46.1
47 47 A G T 3 S- 0 0 51 -2,-0.4 -1,-0.0 1,-0.3 19,-0.0 -0.529 121.1 -13.7 71.2-119.2 13.9 21.0 46.5
48 48 A D T 3 S+ 0 0 67 -2,-0.5 19,-2.4 -3,-0.1 2,-0.5 0.233 116.9 99.1-101.2 12.8 11.6 21.1 43.4
49 49 A T E < -CD 46 66A 69 -3,-1.7 -3,-2.5 17,-0.2 2,-0.3 -0.888 54.3-172.5-104.0 129.6 12.9 24.6 42.3
50 50 A F E -CD 45 65A 2 15,-3.0 15,-2.1 -2,-0.5 2,-0.4 -0.901 22.3-170.5-127.8 149.5 15.5 24.7 39.6
51 51 A Y E -CD 44 64A 41 -7,-1.8 -7,-2.2 -2,-0.3 2,-0.4 -0.995 16.4-175.9-132.3 124.9 17.7 27.3 37.9
52 52 A I E -CD 43 63A 2 11,-2.3 11,-2.5 -2,-0.4 2,-0.5 -0.980 5.8-174.6-131.1 119.3 19.5 26.0 34.8
53 53 A K E -CD 42 62A 71 -11,-2.6 -11,-2.5 -2,-0.4 2,-0.5 -0.967 0.6-175.0-115.1 121.8 22.0 28.1 32.9
54 54 A T E -CD 41 61A 32 7,-2.5 7,-2.3 -2,-0.5 2,-0.4 -0.969 11.8-170.1-118.9 119.0 23.5 26.7 29.6
55 55 A S E +CD 40 60A 40 -15,-3.0 -15,-2.1 -2,-0.5 2,-0.3 -0.888 16.2 157.5-120.5 137.5 26.2 28.9 28.0
56 56 A T - 0 0 29 3,-0.9 3,-0.3 -2,-0.4 -20,-0.1 -0.899 55.0 -98.1-140.6 168.5 28.0 28.8 24.7
57 57 A T S S+ 0 0 113 -2,-0.3 3,-0.1 -22,-0.2 -21,-0.0 0.701 122.9 34.9 -62.8 -20.9 29.9 31.5 22.6
58 58 A V S S+ 0 0 85 1,-0.3 2,-0.3 -26,-0.1 -1,-0.2 0.543 126.6 14.3-112.4 -10.4 26.7 32.1 20.5
59 59 A R - 0 0 97 -3,-0.3 -3,-0.9 -24,-0.1 2,-0.4 -0.899 52.0-169.3-169.0 135.3 23.8 31.7 22.9
60 60 A T E -D 55 0A 67 -2,-0.3 2,-0.4 -5,-0.2 -5,-0.2 -0.986 9.4-169.0-129.9 134.7 23.1 31.5 26.6
61 61 A T E -D 54 0A 51 -7,-2.3 -7,-2.5 -2,-0.4 2,-0.4 -0.957 4.9-170.6-124.3 144.3 19.8 30.4 28.2
62 62 A E E -D 53 0A 112 -2,-0.4 2,-0.3 -9,-0.2 -9,-0.2 -0.978 10.4-175.8-133.9 117.2 18.7 30.7 31.8
63 63 A I E -D 52 0A 20 -11,-2.5 -11,-2.3 -2,-0.4 2,-0.4 -0.892 10.3-166.6-118.8 147.4 15.5 29.0 32.9
64 64 A N E +D 51 0A 109 -2,-0.3 2,-0.3 -13,-0.2 -13,-0.2 -0.987 23.9 152.5-130.4 122.4 13.8 29.1 36.3
65 65 A F E -D 50 0A 10 -15,-2.1 -15,-3.0 -2,-0.4 2,-0.4 -0.977 38.3-140.1-149.7 160.9 11.1 26.6 37.1
66 66 A K E > -D 49 0A 82 3,-0.4 3,-2.0 -2,-0.3 19,-0.3 -0.972 44.0-104.7-117.8 132.7 9.3 24.7 39.8
67 67 A V T 3 S+ 0 0 16 -19,-2.4 19,-0.2 -2,-0.4 3,-0.1 -0.410 107.2 20.4 -59.2 130.3 8.3 21.1 39.0
68 68 A G T 3 S+ 0 0 48 17,-2.7 2,-0.5 1,-0.2 -1,-0.3 0.378 103.5 101.8 91.4 -2.6 4.6 21.0 38.3
69 69 A E S < S- 0 0 111 -3,-2.0 -3,-0.4 16,-0.1 16,-0.4 -0.957 74.5-116.4-119.7 127.6 4.2 24.7 37.6
70 70 A E + 0 0 126 -2,-0.5 2,-0.3 14,-0.1 14,-0.2 -0.295 39.9 168.6 -62.3 140.7 3.9 26.1 34.1
71 71 A F E -E 83 0A 25 12,-2.4 12,-3.2 -6,-0.1 2,-0.4 -0.902 30.8-112.1-143.5 174.1 6.6 28.4 32.8
72 72 A E E +E 82 0A 112 -2,-0.3 10,-0.2 10,-0.2 2,-0.2 -0.936 45.1 135.3-119.4 132.7 7.8 30.1 29.6
73 73 A E E -E 81 0A 25 8,-2.1 8,-2.4 -2,-0.4 2,-0.3 -0.644 46.1 -93.1-144.9-154.3 11.1 29.3 27.8
74 74 A Q E -E 80 0A 83 6,-0.3 25,-0.0 -2,-0.2 2,-0.0 -0.963 28.5-111.5-135.1 153.8 12.2 28.7 24.2
75 75 A T > - 0 0 1 4,-2.6 3,-2.1 -2,-0.3 6,-0.0 -0.283 47.6 -93.9 -71.7 171.4 12.7 25.7 22.1
76 76 A V T 3 S+ 0 0 54 1,-0.3 -1,-0.1 2,-0.1 -57,-0.0 0.849 128.4 51.8 -56.9 -37.1 16.3 24.8 21.0
77 77 A D T 3 S- 0 0 49 2,-0.1 -1,-0.3 1,-0.0 -2,-0.0 0.327 127.9 -97.4 -83.5 6.0 15.9 26.7 17.8
78 78 A G S < S+ 0 0 23 -3,-2.1 -2,-0.1 1,-0.2 -1,-0.0 0.611 72.7 141.1 93.1 16.9 14.7 29.8 19.7
79 79 A R - 0 0 64 1,-0.1 -4,-2.6 21,-0.0 -1,-0.2 -0.765 54.5-109.8 -96.9 133.7 10.9 29.8 19.6
80 80 A P E +E 74 0A 50 0, 0.0 20,-1.6 0, 0.0 21,-0.5 -0.292 46.8 167.2 -58.4 138.3 8.8 30.9 22.7
81 81 A C E -EF 73 99A 1 -8,-2.4 -8,-2.1 18,-0.2 2,-0.5 -0.957 38.3-118.4-150.0 160.5 6.9 28.1 24.3
82 82 A K E -EF 72 98A 60 16,-2.5 16,-2.1 -2,-0.3 2,-0.3 -0.910 38.2-165.0-100.8 129.3 5.0 27.2 27.5
83 83 A S E -EF 71 97A 1 -12,-3.2 -12,-2.4 -2,-0.5 2,-0.4 -0.889 17.2-169.4-121.5 152.9 6.6 24.4 29.4
84 84 A L E - F 0 96A 43 12,-1.4 12,-2.0 -2,-0.3 2,-0.4 -0.956 10.3-159.2-142.2 117.6 5.6 22.0 32.2
85 85 A V E + F 0 95A 0 -16,-0.4 -17,-2.7 -2,-0.4 2,-0.3 -0.800 14.0 174.8-100.5 138.7 8.0 19.7 34.0
86 86 A K E - F 0 94A 129 8,-2.4 8,-2.6 -2,-0.4 2,-0.8 -0.944 39.0-104.1-136.9 158.9 6.9 16.6 35.9
87 87 A W E - F 0 93A 77 -2,-0.3 6,-0.2 6,-0.2 3,-0.1 -0.765 29.3-178.2 -84.3 111.9 8.8 13.8 37.7
88 88 A E E S- 0 0A 121 4,-2.5 2,-0.3 -2,-0.8 -1,-0.2 0.875 78.2 -15.4 -73.2 -40.5 8.5 10.8 35.4
89 89 A S E > S- F 0 92A 60 3,-1.7 3,-1.2 -3,-0.2 -1,-0.3 -0.870 89.8 -77.8-147.6 178.8 10.4 9.0 38.2
90 90 A E T 3 S+ 0 0 148 -2,-0.3 3,-0.0 1,-0.2 -3,-0.0 0.832 129.7 27.0 -53.9 -37.5 12.4 9.8 41.3
91 91 A N T 3 S+ 0 0 59 1,-0.1 22,-2.1 22,-0.0 2,-0.4 0.218 112.5 75.7-112.6 15.7 15.6 10.8 39.3
92 92 A K E < -FG 89 112A 38 -3,-1.2 -4,-2.5 20,-0.2 -3,-1.7 -0.974 53.0-169.2-137.7 122.3 14.0 11.8 36.0
93 93 A M E -FG 87 111A 0 18,-2.6 18,-2.0 -2,-0.4 2,-0.4 -0.837 8.1-161.9-106.2 143.0 12.2 15.0 35.0
94 94 A V E -FG 86 110A 39 -8,-2.6 -8,-2.4 -2,-0.4 2,-0.5 -0.986 1.9-157.3-125.6 138.7 10.3 15.3 31.7
95 95 A C E -FG 85 109A 0 14,-3.1 14,-1.5 -2,-0.4 2,-0.4 -0.966 1.7-159.1-122.0 124.5 9.2 18.6 30.1
96 96 A E E -FG 84 108A 123 -12,-2.0 -12,-1.4 -2,-0.5 2,-0.4 -0.855 15.7-156.1 -99.8 132.1 6.3 19.0 27.6
97 97 A Q E -F 83 0A 12 10,-1.5 10,-0.4 -2,-0.4 2,-0.4 -0.895 10.9-169.7-114.4 144.9 6.5 22.1 25.4
98 98 A K E -F 82 0A 131 -16,-2.1 -16,-2.5 -2,-0.4 2,-0.1 -0.988 28.2-118.8-134.2 119.6 3.7 24.0 23.6
99 99 A L E -F 81 0A 37 -2,-0.4 -18,-0.2 -18,-0.2 3,-0.1 -0.354 11.5-147.7 -60.2 132.2 4.4 26.7 21.0
100 100 A L S S+ 0 0 52 -20,-1.6 2,-0.3 1,-0.2 -1,-0.1 0.859 84.4 11.3 -67.3 -37.4 2.9 30.1 22.1
101 101 A K S S+ 0 0 148 -21,-0.5 -1,-0.2 2,-0.0 2,-0.1 -0.997 113.0 4.8-144.1 142.6 2.3 31.0 18.4
102 102 A G S S- 0 0 59 -2,-0.3 2,-0.3 -3,-0.1 -3,-0.1 -0.340 76.5 -76.8 87.0-168.2 2.4 29.0 15.2
103 103 A E + 0 0 184 -2,-0.1 -2,-0.0 3,-0.0 3,-0.0 -0.879 52.2 128.8-132.0 164.5 3.0 25.3 14.4
104 104 A G - 0 0 44 -2,-0.3 -5,-0.1 -5,-0.0 -82,-0.1 -0.963 58.5 -33.3 169.2-177.6 6.0 23.0 14.2
105 105 A P - 0 0 23 0, 0.0 2,-0.4 0, 0.0 -83,-0.0 -0.225 67.0-102.9 -59.3 151.2 7.3 19.6 15.4
106 106 A K - 0 0 96 -8,-0.1 20,-2.7 -3,-0.0 2,-0.3 -0.674 48.7-165.6 -76.9 125.9 6.3 18.5 18.9
107 107 A T E + H 0 125A 11 -2,-0.4 -10,-1.5 -10,-0.4 2,-0.3 -0.856 18.9 154.7-118.8 155.7 9.2 19.1 21.2
108 108 A S E -GH 96 124A 32 16,-1.4 16,-2.7 -2,-0.3 2,-0.3 -0.947 19.8-150.9-161.2 170.5 10.2 18.0 24.7
109 109 A W E -GH 95 123A 14 -14,-1.5 -14,-3.1 -2,-0.3 2,-0.3 -0.975 4.3-163.0-149.0 154.2 13.2 17.4 26.9
110 110 A T E -GH 94 122A 13 12,-2.0 12,-2.3 -2,-0.3 2,-0.4 -0.971 1.6-163.6-137.0 150.2 14.2 15.2 29.8
111 111 A R E +GH 93 121A 25 -18,-2.0 -18,-2.6 -2,-0.3 2,-0.3 -0.997 16.0 174.7-134.8 130.2 17.0 15.4 32.4
112 112 A E E -GH 92 120A 52 8,-2.0 8,-2.7 -2,-0.4 2,-0.6 -1.000 28.6-136.1-142.5 143.9 18.0 12.4 34.5
113 113 A L E - H 0 119A 28 -22,-2.1 6,-0.2 -2,-0.3 2,-0.1 -0.866 30.0-148.1 -95.8 122.9 20.6 11.5 37.1
114 114 A T > - 0 0 40 4,-2.4 3,-1.7 -2,-0.6 -22,-0.0 -0.402 26.2-103.8 -89.5 168.1 22.1 8.1 36.5
115 115 A N T 3 S+ 0 0 179 1,-0.3 -1,-0.1 2,-0.1 -2,-0.0 0.705 117.8 58.2 -62.1 -23.8 23.4 5.5 39.0
116 116 A D T 3 S- 0 0 108 2,-0.0 -1,-0.3 0, 0.0 -3,-0.0 0.354 122.5-100.0 -88.4 4.3 27.1 6.4 38.1
117 117 A G S < S+ 0 0 37 -3,-1.7 19,-0.3 1,-0.3 -2,-0.1 0.513 82.4 124.3 91.4 6.2 26.7 10.0 39.0
118 118 A E - 0 0 53 17,-0.1 -4,-2.4 15,-0.0 2,-0.4 -0.405 55.4-126.8 -95.6 171.5 26.2 11.4 35.5
119 119 A L E -HI 113 134A 2 15,-2.3 15,-2.7 -6,-0.2 2,-0.5 -0.980 15.1-160.0-121.9 126.8 23.5 13.5 33.9
120 120 A I E -HI 112 133A 38 -8,-2.7 -8,-2.0 -2,-0.4 2,-0.4 -0.956 6.4-170.8-109.9 123.8 21.6 12.5 30.7
121 121 A L E -HI 111 132A 10 11,-3.1 11,-2.7 -2,-0.5 2,-0.4 -0.932 3.2-171.6-108.9 129.8 19.8 15.2 28.8
122 122 A T E -HI 110 131A 22 -12,-2.3 -12,-2.0 -2,-0.4 2,-0.4 -0.970 3.8-167.5-121.6 141.7 17.5 14.2 25.9
123 123 A M E -HI 109 130A 24 7,-2.0 7,-3.1 -2,-0.4 2,-0.4 -0.998 9.6-161.5-125.0 135.5 15.9 16.6 23.5
124 124 A T E +HI 108 129A 30 -16,-2.7 -16,-1.4 -2,-0.4 2,-0.4 -0.935 19.0 178.7-124.9 143.7 13.1 15.5 21.1
125 125 A A E > S-HI 107 128A 0 3,-2.1 3,-2.5 -2,-0.4 -18,-0.2 -0.925 73.9 -54.0-140.0 107.7 11.6 17.0 17.9
126 126 A D T 3 S- 0 0 88 -20,-2.7 -18,-0.0 -2,-0.4 -1,-0.0 -0.384 123.7 -18.3 55.7-116.0 8.9 14.7 16.5
127 127 A D T 3 S+ 0 0 160 -2,-0.2 2,-0.5 -3,-0.1 -1,-0.3 0.444 114.9 98.5-100.3 2.3 10.7 11.3 16.3
128 128 A V E < - I 0 125A 37 -3,-2.5 -3,-2.1 -110,-0.1 2,-0.4 -0.776 54.5-163.7 -93.6 129.4 14.3 12.5 16.4
129 129 A V E - I 0 124A 65 -2,-0.5 2,-0.5 -5,-0.2 -5,-0.2 -0.950 7.7-158.5-118.4 128.4 16.1 12.3 19.8
130 130 A C E - I 0 123A 0 -7,-3.1 -7,-2.0 -2,-0.4 2,-0.5 -0.908 11.2-160.7-103.2 129.9 19.3 14.0 20.8
131 131 A T E +BI 13 122A 49 -118,-1.5 -118,-2.5 -2,-0.5 2,-0.4 -0.947 11.6 176.6-116.6 123.9 21.2 12.5 23.7
132 132 A R E -BI 12 121A 14 -11,-2.7 -11,-3.1 -2,-0.5 2,-0.4 -0.990 10.2-160.7-128.1 136.6 23.9 14.4 25.7
133 133 A V E -BI 11 120A 16 -122,-2.5 -123,-3.1 -2,-0.4 -122,-1.3 -0.947 10.3-175.8-120.4 137.5 25.7 13.1 28.7
134 134 A Y E -BI 9 119A 11 -15,-2.7 -15,-2.3 -2,-0.4 2,-0.3 -0.896 12.9-164.0-131.0 162.0 27.5 15.2 31.3
135 135 A V E -B 8 0A 51 -127,-2.3 -127,-3.0 -2,-0.3 -17,-0.1 -0.938 40.8 -90.9-137.8 151.6 29.7 14.8 34.4
136 136 A R E B 7 0A 96 -19,-0.3 -129,-0.3 -2,-0.3 -131,-0.0 -0.432 360.0 360.0 -67.1 146.1 30.5 17.4 37.0
137 137 A E 0 0 182 -131,-2.8 -131,-0.2 -2,-0.1 -1,-0.1 -0.363 360.0 360.0 -61.5 360.0 33.6 19.4 36.4
\ No newline at end of file
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());
}
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment