mirror of
https://github.com/PDB-REDO/dssp.git
synced 2026-06-04 13:44:21 +08:00
Removed boost dependency
This commit is contained in:
Maarten L. Hekkelman
6
.gitmodules
vendored
Normal file
6
.gitmodules
vendored
Normal file
@@ -0,0 +1,6 @@
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[submodule "libconfig"]
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path = libconfig
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url = https://github.com/mhekkel/libconfig.git
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[submodule "date"]
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path = date
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url = https://github.com/HowardHinnant/date.git
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@@ -6,10 +6,10 @@
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# modification, are permitted provided that the following conditions are met:
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# 1. Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer
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# list of conditions and the following disclaimer
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# 2. Redistributions in binary form must reproduce the above copyright notice,
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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@@ -37,6 +37,7 @@ include(CMakePackageConfigHelpers)
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include(Dart)
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include(FindFilesystem)
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include(GenerateExportHeader)
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include(AddGitSubmodule)
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set(CXX_EXTENSIONS OFF)
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set(CMAKE_CXX_STANDARD 17)
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@@ -47,24 +48,25 @@ find_package(Filesystem REQUIRED)
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if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
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elseif(MSVC)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
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endif()
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if(NOT "$ENV{CCP4}" STREQUAL "")
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set(CCP4 $ENV{CCP4})
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list(PREPEND CMAKE_MODULE_PATH "${CCP4}/Lib")
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list(APPEND CMAKE_PREFIX_PATH ${CCP4})
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if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
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set(CMAKE_INSTALL_PREFIX ${CCP4})
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endif()
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endif()
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if(MSVC)
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# make msvc standards compliant...
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add_compile_options(/permissive-)
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# make msvc standards compliant...
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add_compile_options(/permissive-)
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macro(get_WIN32_WINNT version)
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if (WIN32 AND CMAKE_SYSTEM_VERSION)
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if(WIN32 AND CMAKE_SYSTEM_VERSION)
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set(ver ${CMAKE_SYSTEM_VERSION})
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string(REPLACE "." "" ver ${ver})
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string(REGEX REPLACE "([0-9])" "0\\1" ver ${ver})
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@@ -118,14 +120,22 @@ set(CMAKE_THREAD_PREFER_PTHREAD)
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set(THREADS_PREFER_PTHREAD_FLAG)
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find_package(Threads)
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# Note: use -DBoost_USE_STATIC_LIBS=ON to use boost static libraries
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find_package(cifpp 5.0.0 REQUIRED)
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find_package(pdbxpp 5.0.0)
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find_package(Boost COMPONENTS date_time program_options)
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find_package(date)
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if(NOT date_FOUND)
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add_git_submodule(date EXCLUDE_FROM_ALL)
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endif()
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find_package(libconfig)
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if(NOT libconfig_FOUND)
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add_git_submodule(libconfig EXCLUDE_FROM_ALL)
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endif()
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# The DSSP code is in a separate library, optionally to be used by others
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add_library(dssp_library OBJECT ${PROJECT_SOURCE_DIR}/src/DSSP.cpp)
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target_link_libraries(dssp_library cifpp::cifpp pdbxpp::pdbxpp)
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@@ -136,18 +146,17 @@ add_executable(mkdssp
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$<TARGET_OBJECTS:dssp_library>)
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target_include_directories(mkdssp PRIVATE ${CMAKE_BINARY_DIR})
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target_link_libraries(mkdssp PRIVATE dssp_library cifpp::cifpp pdbxpp::pdbxpp Boost::date_time Boost::program_options)
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target_link_libraries(mkdssp PRIVATE dssp_library cifpp::cifpp pdbxpp::pdbxpp date::date libconfig::libconfig)
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if(USE_RSRC)
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mrc_target_resources(mkdssp ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
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endif()
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install(TARGETS ${PROJECT_NAME}
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RUNTIME DESTINATION ${BIN_INSTALL_DIR}
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RUNTIME DESTINATION ${BIN_INSTALL_DIR}
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)
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# manual
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if(UNIX)
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install(FILES doc/mkdssp.1
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DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
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@@ -159,38 +168,39 @@ if(EXISTS "${CCP4}/html")
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endif()
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# test
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if(ENABLE_TESTING)
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add_executable(dssp-unit-test ${PROJECT_SOURCE_DIR}/test/dssp-unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp)
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add_executable(dssp-unit-test ${PROJECT_SOURCE_DIR}/test/dssp-unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp)
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if(USE_RSRC)
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mrc_target_resources(dssp-unit-test ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
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endif()
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if(USE_RSRC)
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mrc_target_resources(dssp-unit-test ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
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target_include_directories(dssp-unit-test PRIVATE
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${CMAKE_CURRENT_SOURCE_DIR}/src
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${CMAKE_CURRENT_SOURCE_DIR}/include
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)
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target_link_libraries(dssp-unit-test dssp_library cifpp::cifpp pdbxpp::pdbxpp date::date)
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if(MSVC)
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# Specify unwind semantics so that MSVC knowns how to handle exceptions
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target_compile_options(dssp-unit-test PRIVATE /EHsc)
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endif()
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enable_testing()
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add_test(NAME dssp-unit-test COMMAND $<TARGET_FILE:dssp-unit-test> -- ${PROJECT_SOURCE_DIR}/test)
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endif()
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target_include_directories(dssp-unit-test PRIVATE
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${CMAKE_CURRENT_SOURCE_DIR}/src
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${CMAKE_CURRENT_SOURCE_DIR}/include
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)
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target_link_libraries(dssp-unit-test dssp_library cifpp::cifpp pdbxpp::pdbxpp Boost::date_time)
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if(MSVC)
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# Specify unwind semantics so that MSVC knowns how to handle exceptions
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target_compile_options(dssp-unit-test PRIVATE /EHsc)
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endif()
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enable_testing()
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add_test(NAME dssp-unit-test COMMAND $<TARGET_FILE:dssp-unit-test> -- ${PROJECT_SOURCE_DIR}/test)
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option(DSSP_BUILD_INSTALLER "Build an installer" OFF)
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if(DSSP_BUILD_INSTALLER)
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include(InstallRequiredSystemLibraries)
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set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
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# NSIS options
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set(CPACK_NSIS_MODIFY_PATH ON)
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# configuration done, include CPack
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include(CPack)
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endif()
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20
cmake/AddGitSubmodule.cmake
Normal file
20
cmake/AddGitSubmodule.cmake
Normal file
@@ -0,0 +1,20 @@
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cmake_minimum_required(VERSION 3.19)
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function(add_git_submodule dir)
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# add a Git submodule directory to CMake, assuming the
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# Git submodule directory is a CMake project.
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#
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# Usage: in CMakeLists.txt
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#
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# include(AddGitSubmodule.cmake)
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# add_git_submodule(mysubmod_dir)
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find_package(Git REQUIRED)
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if(NOT EXISTS ${dir}/CMakeLists.txt)
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execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive -- ${dir}
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WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
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COMMAND_ERROR_IS_FATAL ANY)
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endif()
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add_subdirectory(${dir} ${ARGV})
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endfunction(add_git_submodule)
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1
date
Submodule
1
date
Submodule
Submodule date added at 22ceabf205
1
libconfig
Submodule
1
libconfig
Submodule
Submodule libconfig added at 606fd039f2
@@ -33,11 +33,9 @@
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#include <fstream>
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#include <iostream>
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#include <boost/date_time/gregorian/formatters.hpp>
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#include <boost/format.hpp>
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// #include <cif++/structure/Compound.hpp>
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#include <cif++.hpp>
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#include <date/date.h>
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#include <pdbx++.hpp>
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#include "dssp_wrapper.hpp"
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#include "revision.hpp"
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@@ -51,8 +49,6 @@ std::string ResidueToDSSPLine(const dssp::DSSP::residue_info &info)
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# 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
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*/
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boost::format kDSSPResidueLine(
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"%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");
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// auto& residue = info.residue();
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auto &residue = info;
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@@ -130,87 +126,84 @@ std::string ResidueToDSSPLine(const dssp::DSSP::residue_info &info)
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if (acceptor)
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{
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auto d = acceptor.nr() - info.nr();
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NHO[i] = (boost::format("%d,%3.1f") % d % acceptorE).str();
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NHO[i] = pdbx::format("%d,%3.1f", d, acceptorE).str();
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}
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if (donor)
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{
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auto d = donor.nr() - info.nr();
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ONH[i] = (boost::format("%d,%3.1f") % d % donorE).str();
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ONH[i] = pdbx::format("%d,%3.1f", d, donorE).str();
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}
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}
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// auto ca = residue.atomByID("CA");
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auto const &[cax, cay, caz] = residue.ca_location();
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return (kDSSPResidueLine % info.nr() % residue.pdb_seq_num() % residue.pdb_ins_code() % residue.pdb_strand_id() % code %
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ss % helix[3] % helix[0] % helix[1] % helix[2] % bend % chirality % bridgelabel[0] % bridgelabel[1] %
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bp[0] % bp[1] % sheet % floor(info.accessibility() + 0.5) %
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NHO[0] % ONH[0] % NHO[1] % ONH[1] %
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residue.tco() % residue.kappa() % alpha % residue.phi() % residue.psi() %
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cax % cay % caz)
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return pdbx::format("%5d%5d%1.1s%1.1s %c %c%c%c%c%c%c%c%c%c%4d%4d%c%4.0f %11s%11s%11s%11s %6.3f%6.1f%6.1f%6.1f%6.1f %6.1f %6.1f %6.1f",
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info.nr(), residue.pdb_seq_num(), residue.pdb_ins_code(), residue.pdb_strand_id(), code,
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ss, helix[3], helix[0], helix[1], helix[2], bend, chirality, bridgelabel[0], bridgelabel[1],
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bp[0], bp[1], sheet, floor(info.accessibility() + 0.5),
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NHO[0], ONH[0], NHO[1], ONH[1],
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residue.tco(), residue.kappa(), alpha, residue.phi(), residue.psi(),
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cax, cay, caz)
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.str();
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}
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void writeDSSP(const dssp::DSSP &dssp, std::ostream &os)
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{
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const std::string kFirstLine("==== Secondary Structure Definition by the program DSSP, NKI version 4.0 ==== ");
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boost::format kHeaderLine("%1% %|127t|%2%");
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using namespace boost::gregorian;
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using namespace date;
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using namespace std::chrono;
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auto stats = dssp.get_statistics();
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date today = day_clock::local_day();
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auto today = system_clock::now();
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os << kHeaderLine % (kFirstLine + "DATE=" + to_iso_extended_string(today)) % '.' << std::endl
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<< kHeaderLine % "REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637" % '.' << std::endl
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os << "==== Secondary Structure Definition by the program DSSP, NKI version 4.0 ==== DATE=" << format("%F", today) << " ." << std::endl
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<< "REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 ." << std::endl
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<< dssp.get_pdb_header_line(dssp::DSSP::pdb_record_type::HEADER) << '.' << std::endl
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<< dssp.get_pdb_header_line(dssp::DSSP::pdb_record_type::COMPND) << '.' << std::endl
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<< dssp.get_pdb_header_line(dssp::DSSP::pdb_record_type::SOURCE) << '.' << std::endl
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<< dssp.get_pdb_header_line(dssp::DSSP::pdb_record_type::AUTHOR) << '.' << std::endl;
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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") %
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stats.count.residues % stats.count.chains % stats.count.SS_bridges % stats.count.intra_chain_SS_bridges % (stats.count.SS_bridges - stats.count.intra_chain_SS_bridges) % '.'
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os << pdbx::format("%5d%3d%3d%3d%3d TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .",
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stats.count.residues, stats.count.chains, stats.count.SS_bridges, stats.count.intra_chain_SS_bridges, (stats.count.SS_bridges - stats.count.intra_chain_SS_bridges))
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<< std::endl;
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os << kHeaderLine % (boost::format("%8.1f ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)") % stats.accessible_surface) % '.' << std::endl;
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os << pdbx::format("%8.1f ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .", stats.accessible_surface) << std::endl;
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// hydrogenbond summary
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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.count.H_bonds % (stats.count.H_bonds * 100.0 / stats.count.residues)) % '.' << std::endl;
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os << pdbx::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds, (stats.count.H_bonds * 100.0 / stats.count.residues)) << std::endl;
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os << kHeaderLine % (boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES") % stats.count.H_bonds_in_parallel_bridges % (stats.count.H_bonds_in_parallel_bridges * 100.0 / stats.count.residues)) % '.' << std::endl;
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os << pdbx::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds_in_parallel_bridges, (stats.count.H_bonds_in_parallel_bridges * 100.0 / stats.count.residues)) << std::endl;
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os << kHeaderLine % (boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES") % stats.count.H_bonds_in_antiparallel_bridges % (stats.count.H_bonds_in_antiparallel_bridges * 100.0 / stats.count.residues)) % '.' << std::endl;
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os << pdbx::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds_in_antiparallel_bridges, (stats.count.H_bonds_in_antiparallel_bridges * 100.0 / stats.count.residues)) << std::endl;
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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");
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for (int k = 0; k < 11; ++k)
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os << kHeaderLine % (kHBondsLine % stats.count.H_Bonds_per_distance[k] % (stats.count.H_Bonds_per_distance[k] * 100.0 / stats.count.residues) % (k - 5 < 0 ? '-' : '+') % abs(k - 5)) % '.' << std::endl;
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os << pdbx::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I%c%1d), SAME NUMBER PER 100 RESIDUES .", stats.count.H_Bonds_per_distance[k], (stats.count.H_Bonds_per_distance[k] * 100.0 / stats.count.residues), (k - 5 < 0 ? '-' : '+'), abs(k - 5)) << std::endl;
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// histograms...
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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;
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for (auto hi : stats.histogram.residues_per_alpha_helix)
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os << boost::format("%3.3d") % hi;
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os << pdbx::format("%3d", hi);
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os << " RESIDUES PER ALPHA HELIX ." << std::endl;
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for (auto hi : stats.histogram.parallel_bridges_per_ladder)
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os << boost::format("%3.3d") % hi;
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os << pdbx::format("%3d", hi);
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os << " PARALLEL BRIDGES PER LADDER ." << std::endl;
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for (auto hi : stats.histogram.antiparallel_bridges_per_ladder)
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os << boost::format("%3.3d") % hi;
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os << pdbx::format("%3d", hi);
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os << " ANTIPARALLEL BRIDGES PER LADDER ." << std::endl;
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for (auto hi : stats.histogram.ladders_per_sheet)
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os << boost::format("%3.3d") % hi;
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os << pdbx::format("%3d", hi);
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os << " LADDERS PER SHEET ." << std::endl;
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// per residue information
|
||||
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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;
|
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boost::format kDSSPResidueLine(
|
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"%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;
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for (auto ri : dssp)
|
||||
@@ -219,7 +212,8 @@ void writeDSSP(const dssp::DSSP &dssp, std::ostream &os)
|
||||
// can be the transition to a different chain, or missing residues in the current chain
|
||||
|
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if (ri.nr() != last + 1)
|
||||
os << (kDSSPResidueLine % (last + 1) % (ri.chain_break() == dssp::chain_break_type::NewChain ? '*' : ' ')) << std::endl;
|
||||
os << pdbx::format("%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",
|
||||
(last + 1), (ri.chain_break() == dssp::chain_break_type::NewChain ? '*' : ' ')) << std::endl;
|
||||
|
||||
os << ResidueToDSSPLine(ri) << std::endl;
|
||||
last = ri.nr();
|
||||
@@ -297,30 +291,30 @@ void annotateDSSP(cif::datablock &db, const dssp::DSSP &dssp, bool writeOther, s
|
||||
|
||||
if (foundTypes.count(id) == 0)
|
||||
{
|
||||
structConfType.emplace({{"id", id},
|
||||
{"criteria", "DSSP"}});
|
||||
structConfType.emplace({ { "id", id },
|
||||
{ "criteria", "DSSP" } });
|
||||
foundTypes[id] = 1;
|
||||
}
|
||||
|
||||
structConf.emplace({
|
||||
{"conf_type_id", id},
|
||||
{"id", id + std::to_string(foundTypes[id]++)},
|
||||
{ "conf_type_id", id },
|
||||
{ "id", id + std::to_string(foundTypes[id]++) },
|
||||
// { "pdbx_PDB_helix_id", vS(12, 14) },
|
||||
{"beg_label_comp_id", rb.compound_id()},
|
||||
{"beg_label_asym_id", rb.asym_id()},
|
||||
{"beg_label_seq_id", rb.seq_id()},
|
||||
{"pdbx_beg_PDB_ins_code", rb.pdb_ins_code()},
|
||||
{"end_label_comp_id", re.compound_id()},
|
||||
{"end_label_asym_id", re.asym_id()},
|
||||
{"end_label_seq_id", re.seq_id()},
|
||||
{"pdbx_end_PDB_ins_code", re.pdb_ins_code()},
|
||||
{ "beg_label_comp_id", rb.compound_id() },
|
||||
{ "beg_label_asym_id", rb.asym_id() },
|
||||
{ "beg_label_seq_id", rb.seq_id() },
|
||||
{ "pdbx_beg_PDB_ins_code", rb.pdb_ins_code() },
|
||||
{ "end_label_comp_id", re.compound_id() },
|
||||
{ "end_label_asym_id", re.asym_id() },
|
||||
{ "end_label_seq_id", re.seq_id() },
|
||||
{ "pdbx_end_PDB_ins_code", re.pdb_ins_code() },
|
||||
|
||||
{"beg_auth_comp_id", rb.compound_id()},
|
||||
{"beg_auth_asym_id", rb.auth_asym_id()},
|
||||
{"beg_auth_seq_id", rb.auth_seq_id()},
|
||||
{"end_auth_comp_id", re.compound_id()},
|
||||
{"end_auth_asym_id", re.auth_asym_id()},
|
||||
{"end_auth_seq_id", re.auth_seq_id()}
|
||||
{ "beg_auth_comp_id", rb.compound_id() },
|
||||
{ "beg_auth_asym_id", rb.auth_asym_id() },
|
||||
{ "beg_auth_seq_id", rb.auth_seq_id() },
|
||||
{ "end_auth_comp_id", re.compound_id() },
|
||||
{ "end_auth_asym_id", re.auth_asym_id() },
|
||||
{ "end_auth_seq_id", re.auth_seq_id() }
|
||||
|
||||
// { "pdbx_PDB_helix_class", vS(39, 40) },
|
||||
// { "details", vS(41, 70) },
|
||||
|
||||
146
src/mkdssp.cpp
146
src/mkdssp.cpp
@@ -1,17 +1,17 @@
|
||||
/*-
|
||||
* 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
|
||||
@@ -29,37 +29,32 @@
|
||||
#endif
|
||||
|
||||
#include <exception>
|
||||
#include <iostream>
|
||||
#include <filesystem>
|
||||
#include <fstream>
|
||||
#include <iostream>
|
||||
|
||||
#include <cfg.hpp>
|
||||
#include <gxrio.hpp>
|
||||
#include <pdbx++.hpp>
|
||||
|
||||
#include <boost/format.hpp>
|
||||
#include <boost/date_time/gregorian/formatters.hpp>
|
||||
|
||||
#include "DSSP.hpp"
|
||||
|
||||
#include <boost/program_options.hpp>
|
||||
|
||||
#include "dssp_wrapper.hpp"
|
||||
#include "revision.hpp"
|
||||
|
||||
namespace fs = std::filesystem;
|
||||
namespace po = boost::program_options;
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// recursively print exception whats:
|
||||
void print_what (const std::exception& e)
|
||||
void print_what(const std::exception &e)
|
||||
{
|
||||
std::cerr << e.what() << std::endl;
|
||||
try
|
||||
{
|
||||
std::rethrow_if_nested(e);
|
||||
}
|
||||
catch (const std::exception& nested)
|
||||
catch (const std::exception &nested)
|
||||
{
|
||||
std::cerr << " >> ";
|
||||
print_what(nested);
|
||||
@@ -68,102 +63,78 @@ void print_what (const std::exception& e)
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
int d_main(int argc, const char* argv[])
|
||||
int d_main(int argc, const char *argv[])
|
||||
{
|
||||
using namespace std::literals;
|
||||
|
||||
po::options_description visible_options(argv[0] + " [options] input-file [output-file]"s);
|
||||
visible_options.add_options()
|
||||
("dict", po::value<std::vector<std::string>>(),
|
||||
"Dictionary file containing restraints for residues in this specific target, can be specified multiple times.")
|
||||
("output-format", po::value<std::string>(), "Output format, can be either 'dssp' for classic DSSP or 'mmcif' for annotated mmCIF. The default is chosen based on the extension of the output file, if any.")
|
||||
("min-pp-stretch", po::value<short>(), "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3")
|
||||
("write-other", "If set, write the type OTHER for loops, default is to leave this out")
|
||||
auto &config = cfg::config::instance();
|
||||
|
||||
// ("components", po::value<std::string>(), "Location of the components.cif file from CCD")
|
||||
// ("extra-compounds", po::value<std::string>(), "File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
|
||||
("mmcif-dictionary", po::value<std::string>(), "Path to the mmcif_pdbx.dic file to use instead of default")
|
||||
config.init(
|
||||
cfg::make_option<std::string>("output-format", "Output format, can be either 'dssp' for classic DSSP or 'mmcif' for annotated mmCIF. The default is chosen based on the extension of the output file, if any."),
|
||||
cfg::make_option<short>("min-pp-stretch", 3, "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3"),
|
||||
cfg::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
|
||||
|
||||
("help,h", "Display help message")
|
||||
("version", "Print version")
|
||||
("verbose,v", "verbose output")
|
||||
;
|
||||
|
||||
po::options_description hidden_options("hidden options");
|
||||
hidden_options.add_options()
|
||||
("xyzin,i", po::value<std::string>(), "coordinates file")
|
||||
("output,o", po::value<std::string>(), "Output to this file")
|
||||
("debug,d", po::value<int>(), "Debug level (for even more verbose output)")
|
||||
// cfg::make_option("components", po::value<std::string, "Location of the components.cif file from CCD")
|
||||
// cfg::make_option("extra-compounds", po::value<std::string, "File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
|
||||
cfg::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"),
|
||||
|
||||
// ("compounds", po::value<std::string>(), "Location of the components.cif file from CCD, alias")
|
||||
;
|
||||
cfg::make_option("help,h", "Display help message"),
|
||||
cfg::make_option("version", "Print version"),
|
||||
cfg::make_option("verbose,v", "verbose output"),
|
||||
|
||||
po::options_description cmdline_options;
|
||||
cmdline_options.add(visible_options).add(hidden_options);
|
||||
cfg::make_hidden_option<int>("debug,d", "Debug level (for even more verbose output)"));
|
||||
|
||||
po::positional_options_description p;
|
||||
p.add("xyzin", 1);
|
||||
p.add("output", 1);
|
||||
|
||||
po::variables_map vm;
|
||||
po::store(po::command_line_parser(argc, argv).options(cmdline_options).positional(p).run(), vm);
|
||||
|
||||
po::notify(vm);
|
||||
config.parse(argc, argv);
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
if (vm.count("version"))
|
||||
if (config.has("version"))
|
||||
{
|
||||
write_version_string(std::cout, vm.count("verbose"));
|
||||
write_version_string(std::cout, config.has("verbose"));
|
||||
exit(0);
|
||||
}
|
||||
|
||||
if (vm.count("help"))
|
||||
if (config.has("help"))
|
||||
{
|
||||
std::cerr << visible_options << std::endl;
|
||||
std::cerr << "Usage: mkdssp [options] input-file [output-file]" << std::endl
|
||||
<< std::endl
|
||||
<< config << std::endl;
|
||||
exit(0);
|
||||
}
|
||||
|
||||
if (vm.count("xyzin") == 0)
|
||||
|
||||
if (config.operands().empty())
|
||||
{
|
||||
std::cerr << "Input file not specified" << std::endl;
|
||||
exit(1);
|
||||
}
|
||||
|
||||
if (vm.count("output-format") and vm["output-format"].as<std::string>() != "dssp" and vm["output-format"].as<std::string>() != "mmcif")
|
||||
if (config.has("output-format") and config.get<std::string>("output-format") != "dssp" and config.get<std::string>("output-format") != "mmcif")
|
||||
{
|
||||
std::cerr << "Output format should be one of 'dssp' or 'mmcif'" << std::endl;
|
||||
exit(1);
|
||||
}
|
||||
|
||||
cif::VERBOSE = vm.count("verbose") != 0;
|
||||
if (vm.count("debug"))
|
||||
cif::VERBOSE = vm["debug"].as<int>();
|
||||
cif::VERBOSE = config.count("verbose");
|
||||
if (config.has("debug"))
|
||||
cif::VERBOSE = config.get<int>("debug");
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// Load extra CCD definitions, if any
|
||||
|
||||
// if (vm.count("compounds"))
|
||||
// cif::add_file_resource("components.cif", vm["compounds"].as<std::string>());
|
||||
// else if (vm.count("components"))
|
||||
// cif::add_file_resource("components.cif", vm["components"].as<std::string>());
|
||||
|
||||
// if (vm.count("extra-compounds"))
|
||||
// mmcif::CompoundFactory::instance().pushDictionary(vm["extra-compounds"].as<std::string>());
|
||||
|
||||
// if (config.has("compounds"))
|
||||
// cif::add_file_resource("components.cif", config.get<std::string>("compounds"));
|
||||
// else if (config.has("components"))
|
||||
// cif::add_file_resource("components.cif", config.get<std::string>("components"));
|
||||
|
||||
// if (config.has("extra-compounds"))
|
||||
// mmcif::CompoundFactory::instance().pushDictionary(config.get<std::string>("extra-compounds"));
|
||||
|
||||
// And perhaps a private mmcif_pdbx dictionary
|
||||
if (config.has("mmcif-dictionary"))
|
||||
cif::add_file_resource("mmcif_pdbx.dic", config.get<std::string>("mmcif-dictionary"));
|
||||
|
||||
if (vm.count("mmcif-dictionary"))
|
||||
cif::add_file_resource("mmcif_pdbx.dic", vm["mmcif-dictionary"].as<std::string>());
|
||||
|
||||
// if (vm.count("dict"))
|
||||
// {
|
||||
// for (auto dict: vm["dict"].as<std::vector<std::string>>())
|
||||
// mmcif::CompoundFactory::instance().pushDictionary(dict);
|
||||
// }
|
||||
|
||||
gxrio::ifstream in(vm["xyzin"].as<std::string>());
|
||||
gxrio::ifstream in(config.operands().front());
|
||||
if (not in.is_open())
|
||||
{
|
||||
std::cerr << "Could not open file" << std::endl;
|
||||
@@ -180,19 +151,21 @@ int d_main(int argc, const char* argv[])
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
short pp_stretch = 3;
|
||||
if (vm.count("min-pp-stretch"))
|
||||
pp_stretch = vm["min-pp-stretch"].as<short>();
|
||||
if (config.has("min-pp-stretch"))
|
||||
pp_stretch = config.get<short>("min-pp-stretch");
|
||||
|
||||
bool writeOther = vm.count("write-other");
|
||||
bool writeOther = config.has("write-other");
|
||||
|
||||
std::string fmt;
|
||||
if (vm.count("output-format"))
|
||||
fmt = vm["output-format"].as<std::string>();
|
||||
if (config.has("output-format"))
|
||||
fmt = config.get<std::string>("output-format");
|
||||
|
||||
if (fmt.empty() and vm.count("output"))
|
||||
fs::path output;
|
||||
if (config.operands().size() > 1)
|
||||
output = config.operands()[1];
|
||||
|
||||
if (fmt.empty() and not output.empty())
|
||||
{
|
||||
fs::path output = vm["output"].as<std::string>();
|
||||
|
||||
if (output.extension() == ".gz" or output.extension() == ".xz")
|
||||
output = output.stem();
|
||||
|
||||
@@ -204,9 +177,8 @@ int d_main(int argc, const char* argv[])
|
||||
|
||||
dssp::DSSP dssp(f.front(), 1, pp_stretch, fmt == "dssp");
|
||||
|
||||
if (vm.count("output"))
|
||||
if (not output.empty())
|
||||
{
|
||||
fs::path output = vm["output"].as<std::string>();
|
||||
gxrio::ofstream out(output);
|
||||
|
||||
if (not out.is_open())
|
||||
@@ -227,13 +199,13 @@ int d_main(int argc, const char* argv[])
|
||||
else
|
||||
annotateDSSP(f.front(), dssp, writeOther, std::cout);
|
||||
}
|
||||
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
int main(int argc, const char* argv[])
|
||||
int main(int argc, const char *argv[])
|
||||
{
|
||||
int result = 0;
|
||||
|
||||
@@ -244,7 +216,7 @@ int main(int argc, const char* argv[])
|
||||
#endif
|
||||
result = d_main(argc, argv);
|
||||
}
|
||||
catch (const std::exception& ex)
|
||||
catch (const std::exception &ex)
|
||||
{
|
||||
print_what(ex);
|
||||
exit(1);
|
||||
|
||||
Reference in New Issue
Block a user