tortoize-2.0.15/0000755000175000017500000000000014773215600013323 5ustar maartenmaartentortoize-2.0.15/.github/0000755000175000017500000000000014773215600014663 5ustar maartenmaartentortoize-2.0.15/.github/workflows/0000755000175000017500000000000014773215600016720 5ustar maartenmaartentortoize-2.0.15/.github/workflows/cmake-multi-platform.yml0000644000175000017500000000222714773215600023500 0ustar maartenmaartenname: multi platform test on: push: branches: [ "trunk", "develop" ] pull_request: branches: [ "trunk" ] jobs: build: runs-on: ubuntu-latest strategy: fail-fast: false steps: - uses: actions/checkout@v3 with: submodules: true - name: Set reusable strings id: strings shell: bash run: echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT" - name: Install dependencies Ubuntu run: > sudo apt-get update && sudo apt-get install catch2 nlohmann-json3-dev libeigen3-dev - name: Configure CMake run: > cmake -B ${{ steps.strings.outputs.build-output-dir }} -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=ON -S ${{ github.workspace }} - name: Build run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config Release - name: Test working-directory: ${{ steps.strings.outputs.build-output-dir }} run: ctest --build-config Release --output-on-failure -R tortoize-unit-test env: LIBCIFPP_DATA_DIR: ${{ steps.strings.outputs.build-output-dir }}/_deps/cifpp-src/rsrc tortoize-2.0.15/.gitignore0000644000175000017500000000014314773215600015311 0ustar maartenmaarten.vscode tortoize .vs/ build node_modules .gdb_history docroot/css docroot/scripts src/revision.hpp tortoize-2.0.15/.gitmodules0000644000175000017500000000036414773215600015503 0ustar maartenmaarten[submodule "libconfig"] path = libconfig url = https://github.com/mhekkel/libconfig.git [submodule "gxrio"] path = gxrio url = https://github.com/mhekkel/gxrio.git [submodule "dssp"] path = dssp url = https://github.com/PDB-REDO/dssp.git tortoize-2.0.15/CMakeLists.txt0000644000175000017500000001321514773215600016065 0ustar maartenmaarten# SPDX-License-Identifier: BSD-2-Clause # Copyright (c) 2021 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. cmake_minimum_required(VERSION 3.25) # set the project name project(tortoize VERSION 2.0.15 LANGUAGES CXX) list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") include(FindOrFetch) include(GNUInstallDirs) include(CheckFunctionExists) include(CheckIncludeFiles) include(CheckLibraryExists) include(CMakePackageConfigHelpers) include(GenerateExportHeader) include(CTest) set(CXX_EXTENSIONS OFF) set(CMAKE_CXX_STANDARD 20) set(CMAKE_CXX_STANDARD_REQUIRED ON) if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers") elseif(MSVC) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4") endif() # Optionally build a version to be installed inside CCP4 option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4" OFF) if(BUILD_FOR_CCP4) if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4}) message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced") else() list(APPEND CMAKE_MODULE_PATH "$ENV{CCP4}") list(APPEND CMAKE_PREFIX_PATH "$ENV{CCP4}") set(CMAKE_INSTALL_PREFIX "$ENV{CCP4}") if(WIN32) set(BUILD_SHARED_LIBS ON) endif() endif() endif() if(MSVC) # make msvc standards compliant... add_compile_options(/permissive-) add_link_options(/NODEFAULTLIB:library) 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}) endif() # Create a revision file, containing the current git version info, if any include(VersionString) write_version_header(${PROJECT_SOURCE_DIR}/src) # Optionally use mrc to create resources find_package(Mrc QUIET) if(MRC_FOUND) option(USE_RSRC "Use mrc to create resources" ON) else() message(STATUS "Not using resources since mrc was not found") set(USE_RSRC OFF) endif() if(USE_RSRC) set(USE_RSRC 1) add_compile_definitions(USE_RSRC) endif() # Optionally build a webservice option(BUILD_WEBSERVICE "Build a version with a webservice daemon" OFF) # libraries set(CMAKE_THREAD_PREFER_PTHREAD) set(THREADS_PREFER_PTHREAD_FLAG) find_package(Threads) find_package(nlohmann_json REQUIRED) find_or_fetch_package(mcfp VERSION 1.3.5 GIT_REPOSITORY https://github.com/mhekkel/libmcfp GIT_TAG b6c62a3) find_or_fetch_package(cifpp VERSION 7 GIT_REPOSITORY https://github.com/PDB-REDO/libcifpp.git GIT_TAG v7.0.9 VARIABLES "CIFPP_SHARE_DIR") if (NOT TARGET dssp) add_subdirectory(dssp EXCLUDE_FROM_ALL) endif() add_executable(tortoize ${PROJECT_SOURCE_DIR}/src/tortoize.cpp ${PROJECT_SOURCE_DIR}/src/tortoize-main.cpp) if(USE_RSRC) list(APPEND RESOURCES ${PROJECT_SOURCE_DIR}/rsrc/rama-data.bin ${PROJECT_SOURCE_DIR}/rsrc/torsion-data.bin ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic ${CIFPP_SHARE_DIR}/mmcif_ma.dic) mrc_target_resources(tortoize ${RESOURCES}) endif() target_include_directories(tortoize PRIVATE ${PROJECT_BINARY_DIR}) target_link_libraries(tortoize dssp::dssp cifpp::cifpp mcfp::mcfp) target_compile_definitions(tortoize PUBLIC NOMINMAX=1) install(TARGETS tortoize RUNTIME DESTINATION ${BIN_INSTALL_DIR} ) if(NOT USE_RSRC) install(FILES ${PROJECT_SOURCE_DIR}/rsrc/rama-data.bin ${PROJECT_SOURCE_DIR}/rsrc/torsion-data.bin DESTINATION ${CIFPP_SHARE_DIR}) endif() if(BUILD_WEBSERVICE) find_package(zeep 6 REQUIRED) if(NOT USE_RSRC) message(FATAL_ERROR "Web service needs mrc/resources") endif() add_executable(tortoized ${PROJECT_SOURCE_DIR}/src/tortoize.cpp ${PROJECT_SOURCE_DIR}/src/tortoize-server-main.cpp ) target_link_libraries(tortoized dssp::dssp cifpp::cifpp mcfp::mcfp zeep::zeep) mrc_target_resources(tortoized ${RESOURCES} ${CMAKE_CURRENT_SOURCE_DIR}/docroot/) install(TARGETS tortoized RUNTIME DESTINATION ${SBIN_INSTALL_DIR} ) set(TORTOIZED_EXE "${CMAKE_INSTALL_FULL_SBINDIR}/tortoized") set(TORTOIZED_PID "/var/run/tortoized") configure_file(tortoized.service.in ${CMAKE_CURRENT_BINARY_DIR}/tortoized.service @ONLY) install(FILES "${CMAKE_CURRENT_BINARY_DIR}/tortoized.service" DESTINATION "/etc/systemd/system") endif() # manual install(FILES doc/tortoize.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) # Test code if(BUILD_TESTING) add_subdirectory(test) endif() tortoize-2.0.15/LICENSE0000644000175000017500000000247714773215600014342 0ustar maartenmaartenBSD-2-Clause License Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute All rights reserved. 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. tortoize-2.0.15/README.md0000644000175000017500000000176614773215600014614 0ustar maartenmaartenTortoize ======== [![github CI](https://github.com/PDB-REDO/tortoize/actions/workflows/cmake-multi-platform.yml/badge.svg)](https://github.com/PDB-REDO/tortoize/actions) Application to calculate ramachandran z-scores. Building -------- The easiest way to install tortoize is by installing [CCP4](https://www.ccp4.ac.uk/download/index.php) It is possible to install tortoize on Linux without having CCP4. In that case you will have install some dependencies first. On Debian this boils down to: ```console sudo apt-get update && sudo apt-get install libcatch2-dev nlohmann-json3-dev libeigen3-dev ``` And on Ubuntu, slightly different: ```console sudo apt-get update && sudo apt-get install catch2 nlohmann-json3-dev libeigen3-dev ``` After that, building and installing should be as simple as: ```console git clone https://github.com/PDB-REDO/tortoize.git cd tortoize cmake -S . -B build cmake --build build sudo cmake --install build ``` Usage ----- See [manual page](doc/tortoize.pdf) for more info. tortoize-2.0.15/babel.config.js0000644000175000017500000000031414773215600016170 0ustar maartenmaarten{ presets: [ [ "@babel/env", { "targets": { "edge": "17", "firefox": "60", "chrome": "67", "safari": "11.1", }, "useBuiltIns": "usage", "corejs": "3.8.2", } ] ] }tortoize-2.0.15/changelog0000644000175000017500000000144414773215600015200 0ustar maartenmaartenVersion 2.0.15 - Fix loading data tables on big-endian machines Version 2.0.14 - Remove dependency on libzeep, unless building a web service of course Version 2.0.13 - Changes required to build on Windows Version 2.0.12 - new version string module Version 2.0.11 - Don't stop when a residue is not complete according to DSSP - Building for CCP4 Version 2.0.10 - Fix in logic, do not crash on modfied residues Version 2.0.9 - Using libdssp from now on Version 2.0.8 - Based on new libcifpp Version 2.0.7 - Added simple unit-test Version 2.0.6 - Update for new libcifpp Version 2.0.5 - Fixed a crashing bug when fed with unknown amino acids - Replacing ASX and GLX with ASP and GLU Version 2.0.4 - Should be easier to make Version 2.0.2 - Added cmake build files Version 2.0.0 - Total rewrite tortoize-2.0.15/cmake/0000755000175000017500000000000014773215600014403 5ustar maartenmaartentortoize-2.0.15/cmake/FindOrFetch.cmake0000644000175000017500000000232414773215600017541 0ustar maartenmaarten# CMake module to find a package, or fetch it in case it is not found locally cmake_minimum_required(VERSION 3.25) function(find_or_fetch_package _package) set(flags VERBOSE) set(options VERSION GIT_REPOSITORY GIT_TAG) set(variables VARIABLES) cmake_parse_arguments(FOF_OPTIONS "${flags}" "${options}" "${variables}" ${ARGN}) if(NOT _package) message(FATAL_ERROR "TARGET option is missing") endif() if(TARGET "${_package}" OR ${_package}_FOUND) return(PROPAGATE ${FOF_OPTIONS_VARIABLES}) endif() find_package("${_package}" ${FOF_OPTIONS_VERSION} QUIET) if(${FOF_OPTIONS_VARIABLES}) message(NOTICE "fof cifpp data dir: ${CIFPP_SHARE_DIR}") endif() if(${_package}_FOUND) return(PROPAGATE ${FOF_OPTIONS_VARIABLES}) endif() include(FetchContent) if(NOT FOF_OPTIONS_GIT_REPOSITORY) message("Package ${_package} not found and GIT_REPOSITORY option is missing") endif() if(NOT FOF_OPTIONS_GIT_TAG) message("Package ${_package} not found and GIT_TAG option is missing") endif() FetchContent_Declare( "${_package}" GIT_REPOSITORY ${FOF_OPTIONS_GIT_REPOSITORY} GIT_TAG ${FOF_OPTIONS_GIT_TAG}) FetchContent_MakeAvailable("${_package}") return(PROPAGATE ${FOF_OPTIONS_VARIABLES}) endfunction()tortoize-2.0.15/cmake/VersionString.cmake0000644000175000017500000002314514773215600020226 0ustar maartenmaarten# SPDX-License-Identifier: BSD-2-Clause # Copyright (c) 2021-2023 Maarten L. Hekkelman # 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. # This cmake extension writes out a revision.hpp file in a specified directory. # The file will contain a C++ inline function that can be used to write out # version information. cmake_minimum_required(VERSION 3.15) # We want the revision.hpp file to be updated whenever the status of the # git repository changes. Use the same technique as in GetGitRevisionDescription.cmake # from https://github.com/rpavlik/cmake-modules #[=======================================================================[.rst: .. command:: write_version_header Write a file named revision.hpp containing version info:: write_version_header( [FILE_NAME ] [LIB_NAME ] ) This command will generate the code to write a file name revision.hpp in the directory ````. ``FILE_NAME`` Specify the name of the file to create, default is ``revision.hpp``. ``LIB_NAME`` Specify the library name which will be used as a prefix part for the variables contained in the revision file. #]=======================================================================] # Record the location of this module now, not at the time the CMakeLists.txt # is being processed get_filename_component(_current_cmake_module_dir ${CMAKE_CURRENT_LIST_FILE} PATH) # First locate a .git file or directory. function(_get_git_dir _start_dir _variable) set(cur_dir "${_start_dir}") set(git_dir "${_start_dir}/.git") while(NOT EXISTS "${git_dir}") # .git dir not found, search parent directories set(prev_dir "${cur_dir}") get_filename_component(cur_dir "${cur_dir}" DIRECTORY) if(cur_dir STREQUAL prev_dir OR cur_dir STREQUAL ${_start_dir}) # we are not in git since we either hit root or # the ${_start_dir} which should be the top set(${_variable} "" PARENT_SCOPE) return() endif() set(git_dir "${cur_dir}/.git") endwhile() set(${_variable} "${git_dir}" PARENT_SCOPE) endfunction() # Locate the git refspec hash and load the hash # This code locates the file containing the git refspec/hash # and loads it. Doing it this way assures that each time the git # repository changes the revision.hpp file gets out of date. function(_get_git_hash _data_dir _variable) # Be pessimistic set(_variable "" PARENT_SCOPE) # Load git package if needed if(NOT GIT_FOUND) find_package(Git QUIET) endif() # And fail if not found if(NOT GIT_FOUND) return() endif() # Locate the nearest .git file or directory _get_git_dir(${CMAKE_CURRENT_SOURCE_DIR} GIT_DIR) # And fail if not found if("${GIT_DIR}" STREQUAL "") 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(IS_DIRECTORY ${GIT_DIR}) set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD") else() # 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 not 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 ${git_worktree_dir} git_worktree_dir) _get_git_dir("${git_worktree_dir}" GIT_DIR) set(HEAD_SOURCE_FILE "${git_worktree_dir}/HEAD") endif() endif() # Fail if the 'head' file was not found if(NOT EXISTS "${HEAD_SOURCE_FILE}") return() endif() # Make a copy of the head file set(HEAD_FILE "${_data_dir}/HEAD") configure_file("${HEAD_SOURCE_FILE}" "${HEAD_FILE}" COPYONLY) # Now we create a cmake file that will read the contents of this # head file in the appropriate way file(WRITE "${_data_dir}/grab-ref.cmake.in" [[ 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}" "@VERSION_STRING_DATA@/head-ref" COPYONLY) else() configure_file("@GIT_DIR@/packed-refs" "@VERSION_STRING_DATA@/packed-refs" COPYONLY) file(READ "@VERSION_STRING_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" "@VERSION_STRING_DATA@/head-ref" COPYONLY) endif() if(NOT HEAD_HASH) file(READ "@VERSION_STRING_DATA@/head-ref" HEAD_HASH LIMIT 1024) string(STRIP "${HEAD_HASH}" HEAD_HASH) endif() ]]) configure_file("${VERSION_STRING_DATA}/grab-ref.cmake.in" "${VERSION_STRING_DATA}/grab-ref.cmake" @ONLY) # Include the aforementioned file, this will define # the HEAD_HASH variable we're looking for include("${VERSION_STRING_DATA}/grab-ref.cmake") set(${_variable} "${HEAD_HASH}" PARENT_SCOPE) endfunction() # Create a revision file, containing the current git version info, if any function(write_version_header dir) set(flags ) set(options LIB_NAME FILE_NAME) set(sources ) cmake_parse_arguments(VERSION_STRING_OPTION "${flags}" "${options}" "${sources}" ${ARGN}) # parameter check if(NOT IS_DIRECTORY ${dir}) message(FATAL_ERROR "First parameter to write_version_header should be a directory where the final revision.hpp file will be placed") endif() if(VERSION_STRING_OPTION_FILE_NAME) set(file_name "${VERSION_STRING_OPTION_FILE_NAME}") else() set(file_name "revision.hpp") endif() # Where to store intermediate files set(VERSION_STRING_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/VersionString") if(NOT EXISTS "${VERSION_STRING_DATA}") file(MAKE_DIRECTORY "${VERSION_STRING_DATA}") endif() # Load the git hash using the wizzard-like code above. _get_git_hash("${VERSION_STRING_DATA}" GIT_HASH) # If git was found, fetch the git description string if(GIT_HASH) execute_process( COMMAND "${GIT_EXECUTABLE}" describe --dirty --match=build WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" RESULT_VARIABLE res OUTPUT_VARIABLE out ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) if(res EQUAL 0) set(REVISION_STRING "${out}") else() message(STATUS "Git hash not found, does this project has a 'build' tag?") endif() else() message(STATUS "Git hash not found") endif() # Check the revision string, if it matches we fill in the required info if(REVISION_STRING MATCHES "build-([0-9]+)-g([0-9a-f]+)(-dirty)?") set(BUILD_NUMBER ${CMAKE_MATCH_1}) if(CMAKE_MATCH_3) set(REVISION_GIT_TAGREF "${CMAKE_MATCH_2}*") else() set(REVISION_GIT_TAGREF "${CMAKE_MATCH_2}") endif() string(TIMESTAMP REVISION_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC) else() set(REVISION_GIT_TAGREF "") set(BUILD_NUMBER 0) set(REVISION_DATE_TIME "") endif() if(VERSION_STRING_OPTION_LIB_NAME) set(VAR_PREFIX "${VERSION_STRING_OPTION_LIB_NAME}") set(IDENT_PREFIX "${VERSION_STRING_OPTION_LIB_NAME}_") set(BOOL_IS_MAIN "false") else() set(VAR_PREFIX "") set(IDENT_PREFIX "") set(BOOL_IS_MAIN "true") endif() configure_file("${_current_cmake_module_dir}/revision.hpp.in" "${dir}/${file_name}" @ONLY) endfunction() tortoize-2.0.15/cmake/revision.hpp.in0000644000175000017500000000563314773215600017366 0ustar maartenmaarten// This file was generated by VersionString.cmake #pragma once #include constexpr const char k@VAR_PREFIX@ProjectName[] = "@PROJECT_NAME@"; constexpr const char k@VAR_PREFIX@VersionNumber[] = "@PROJECT_VERSION@"; constexpr int k@VAR_PREFIX@BuildNumber = @BUILD_NUMBER@; constexpr const char k@VAR_PREFIX@RevisionGitTag[] = "@REVISION_GIT_TAGREF@"; constexpr const char k@VAR_PREFIX@RevisionDate[] = "@REVISION_DATE_TIME@"; #ifndef VERSION_INFO_DEFINED #define VERSION_INFO_DEFINED 1 namespace version_info_v1_1 { class version_info_base { public: static void write_version_string(std::ostream &os, bool verbose) { auto s_main = registered_main(); if (s_main != nullptr) s_main->write(os, verbose); if (verbose) { for (auto lib = registered_libraries(); lib != nullptr; lib = lib->m_next) { os << "-\n"; lib->write(os, verbose); } } } protected: version_info_base(const char *name, const char *version, int build_number, const char *git_tag, const char *revision_date, bool is_main) : m_name(name) , m_version(version) , m_build_number(build_number) , m_git_tag(git_tag) , m_revision_date(revision_date) { if (is_main) registered_main() = this; else { auto &s_head = registered_libraries(); m_next = s_head; s_head = this; } } void write(std::ostream &os, bool verbose) { os << m_name << " version " << m_version << '\n'; if (verbose) { if (m_build_number != 0) { os << "build: " << m_build_number << ' ' << m_revision_date << '\n'; if (m_git_tag[0] != 0) os << "git tag: " << m_git_tag << '\n'; } } } using version_info_ptr = version_info_base *; static version_info_ptr ®istered_main() { static version_info_ptr s_main = nullptr; return s_main; } static version_info_ptr ®istered_libraries() { static version_info_ptr s_head = nullptr; return s_head; } const char *m_name; const char *m_version; int m_build_number; const char *m_git_tag; const char *m_revision_date; version_info_base *m_next = nullptr; }; template class version_info : public version_info_base { public: using implementation_type = T; version_info(const char *name, const char *version, int build_number, const char *git_tag, const char *revision_date, bool is_main) : version_info_base(name, version, build_number, git_tag, revision_date, is_main) { } }; } // namespace version_info_v1_1 inline void write_version_string(std::ostream &os, bool verbose) { version_info_v1_1::version_info_base::write_version_string(os, verbose); } #endif const class version_info_@IDENT_PREFIX@impl : public version_info_v1_1::version_info { public: version_info_@IDENT_PREFIX@impl() : version_info(k@VAR_PREFIX@ProjectName, k@VAR_PREFIX@VersionNumber, k@VAR_PREFIX@BuildNumber, k@VAR_PREFIX@RevisionGitTag, k@VAR_PREFIX@RevisionDate, @BOOL_IS_MAIN@) { } } s_version_info_@IDENT_PREFIX@instance; tortoize-2.0.15/doc/0000755000175000017500000000000014773215600014070 5ustar maartenmaartentortoize-2.0.15/doc/tortoize.10000644000175000017500000000330214773215600016027 0ustar maartenmaarten.TH tortoize 1 "2021-08-31" "version 2.0.2" "User Commands" .if n .ad l .nh .SH NAME tortoize \- Calculate ramachandran z-scores .SH SYNOPSIS tortoize [OPTION] input [output] .SH DESCRIPTION Tortoize validates protein structure models by checking the Ramachandran plot and side-chain rotamer distributions. Quality Z-scores are given at the residue level and at the model level (ramachandran-z and torsions-z). Higher scores are better. To compare models or to describe the reliability of the model Z-scores jackknife- based standard deviations are also reported (ramachandran-jackknife-sd and torsion-jackknife-sd). .SH OPTIONS The input file can be either mmCIF or PDB format and the file may be gzip or bzip2 compressed. .sp The output is a json file, if no file name is specified the output is written to \fIstdout\fR. .TP \fB--dict\fR= Specify a dictionary file containing restraints for residues specific to this file. .TP \fB--log\fR= Write a log with diagnostic information to this file. .SH REFERENCES References: .TP \fBSobolev et al.\fR A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure (2020), DOI: \fIhttps://doi.org/10.1016/j.str.2020.08.005\fR .TP \fBVan Beusekom et al.\fR Homology-based loop modeling yields more complete crystallographic protein structures, IUCrJ (2018), DOI: \fIhttps://doi.org/10.1107/S2052252518010552\fR .TP \fBHooft et al.\fR Objectively judging the quality of a protein structure from a Ramachandran plot, CABIOS (1993), DOI: \fIhttps://doi.org/10.1093/bioinformatics/13.4.425 \fR .SH AUTHOR Written by Maarten L. Hekkelman .SH "REPORTING BUGS" Report bugs at https://github.com/PDB-REDO/tortoize/issues tortoize-2.0.15/doc/tortoize.html0000644000175000017500000000575414773215600016650 0ustar maartenmaartenContent-type: text/html; charset=UTF-8 Man page of tortoize

tortoize

Section: User Commands (1)
Updated: 2021-08-31
Index Return to Main Contents
 

NAME

tortoize - Calculate ramachandran z-scores  

SYNOPSIS

tortoize [OPTION] input [output]  

DESCRIPTION

Tortoize validates protein structure models by checking the Ramachandran plot and side-chain rotamer distributions. Quality Z-scores are given at the residue level and at the model level (ramachandran-z and torsions-z). Higher scores are better. To compare models or to describe the reliability of the model Z-scores jackknife- based standard deviations are also reported (ramachandran-jackknife-sd and torsion-jackknife-sd).  

OPTIONS

The input file can be either mmCIF or PDB format and the file may be gzip or bzip2 compressed.

The output is a json file, if no file name is specified the output is written to stdout.

--dict=<file>
Specify a dictionary file containing restraints for residues specific to this file.
--log=<file>
Write a log with diagnostic information to this file.
 

REFERENCES

References:
Sobolev et al.
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure (2020), DOI: https://doi.org/10.1016/j.str.2020.08.005
Van Beusekom et al.
Homology-based loop modeling yields more complete crystallographic protein structures, IUCrJ (2018), DOI: https://doi.org/10.1107/S2052252518010552
Hooft et al.
Objectively judging the quality of a protein structure from a Ramachandran plot, CABIOS (1993), DOI: https://doi.org/10.1093/bioinformatics/13.4.425
 

AUTHOR

Written by Maarten L. Hekkelman <maarten@hekkelman.com>  

REPORTING BUGS

Report bugs at https://github.com/PDB-REDO/tortoize/issues

 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
REFERENCES
AUTHOR
REPORTING BUGS
This document was created by man2html, using the manual pages.
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[:μN٢rblQ7 B|/w;,YȝRgT$Zd^}rrEhɥF9s;O8n]1~ק>q8B_ffLQgW{ˆ7;Цá{J+gwGCun.~DjVqN k鶃 {a]0լuY#`s?|cp}fNؤC q@sp׫] ixm:V.wZ?6ТU%B?M p*X=?pg1W}pC}" 7{C%Sƞۨ0$(N)v!щ֋*ηu[ۍ&3l&XQ)^ }KɮY/̞>stream 2021-08-31T16:02:09+02:00 2021-08-31T16:02:09+02:00 groff version 1.22.4 Untitled endstream endobj 2 0 obj <>endobj xref 0 21 0000000000 65535 f 0000002159 00000 n 0000020744 00000 n 0000002100 00000 n 0000001940 00000 n 0000000182 00000 n 0000001920 00000 n 0000002224 00000 n 0000003119 00000 n 0000012188 00000 n 0000002711 00000 n 0000007930 00000 n 0000002347 00000 n 0000003782 00000 n 0000002265 00000 n 0000002295 00000 n 0000004122 00000 n 0000008250 00000 n 0000012643 00000 n 0000003687 00000 n 0000019321 00000 n trailer << /Size 21 /Root 1 0 R /Info 2 0 R /ID [<148FDE25E23D3F0D44524B5B279AEBD4><148FDE25E23D3F0D44524B5B279AEBD4>] >> startxref 20898 %%EOF tortoize-2.0.15/docroot/0000755000175000017500000000000014773215600014774 5ustar maartenmaartentortoize-2.0.15/docroot/images/0000755000175000017500000000000014773215600016241 5ustar maartenmaartentortoize-2.0.15/docroot/images/PDB_logo_rect_medium.svg0000644000175000017500000001112614773215600022765 0ustar maartenmaarten tortoize-2.0.15/docroot/index.html0000644000175000017500000000646414773215600017003 0ustar maartenmaarten ]> Tortoize web service
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Tortoize, calculate Ramachandran Z-scores

Sobolev et al. A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure (2020), DOI: 10.1016/j.str.2020.08.005

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#endif // -------------------------------------------------------------------- int pr_main(int argc, char *argv[]) { using namespace std::literals; auto &config = mcfp::config::instance(); config.init("tortoize [options] input [output]", mcfp::make_option("help,h", "Display help message"), mcfp::make_option("version", "Print version"), mcfp::make_option("verbose,v", "verbose output"), mcfp::make_option("log", "Write log to this file"), mcfp::make_option>("dict", "Dictionary file containing restraints for residues in this specific target, can be specified multiple times."), mcfp::make_hidden_option("build", "Build a binary data table") ); config.parse(argc, argv); // -------------------------------------------------------------------- if (config.has("version")) { write_version_string(std::cout, config.has("verbose")); exit(0); } if (config.has("help")) { std::cout << config << std::endl << std::endl << R"(Tortoize validates protein structure models by checking the Ramachandran plot and side-chain rotamer distributions. Quality Z-scores are given at the residue level and at the model level (ramachandran-z and torsions-z). Higher scores are better. To compare models or to describe the reliability of the model Z-scores jackknife- based standard deviations are also reported (ramachandran-jackknife-sd and torsion-jackknife-sd). References: - Sobolev et al. A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure (2020), DOI: https://doi.org/10.1016/j.str.2020.08.005 - Van Beusekom et al. Homology-based loop modeling yields more complete crystallographic protein structures, IUCrJ (2018), DOI: https://doi.org/10.1107/S2052252518010552 - Hooft et al. Objectively judging the quality of a protein structure from a Ramachandran plot, CABIOS (1993), DOI: https://doi.org/10.1093/bioinformatics/13.4.425 )" << std::endl << std::endl; exit(0); } if (config.has("build")) { buildDataFile(config.get("build")); exit(0); } if (config.operands().empty()) { std::cerr << "Input file not specified" << std::endl; exit(1); } cif::VERBOSE = config.count("verbose"); if (config.has("log")) { if (config.operands().size() != 2) { std::cerr << "If you specify a log file, you should also specify an output file" << std::endl; exit(1); } std::string logFile = config.get("log"); // open the log file int fd = open(logFile.c_str(), O_CREAT | O_RDWR, 0644); if (fd < 0) throw std::runtime_error("Opening log file " + logFile + " failed: " + strerror(errno)); // redirect stdout and stderr to the log file dup2(fd, STDOUT_FILENO); dup2(fd, STDERR_FILENO); close(fd); } if (config.has("dict")) { for (auto dict : config.get>("dict")) cif::compound_factory::instance().push_dictionary(dict); } // -------------------------------------------------------------------- json data = tortoize_calculate(config.operands().front()); if (config.operands().size() == 2) { std::ofstream of(config.operands().back()); if (not of.is_open()) { std::cerr << "Could not open output file" << std::endl; exit(1); } of << data; } else std::cout << data << std::endl; return 0; } // -------------------------------------------------------------------- // 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; try { result = pr_main(argc, argv); } catch (std::exception &ex) { print_what(ex); exit(1); } return result; } tortoize-2.0.15/src/tortoize-server-main.cpp0000644000175000017500000001737014773215600020733 0ustar maartenmaarten/*- * SPDX-License-Identifier: BSD-2-Clause * * Copyright (c) 2025 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. */ #include "revision.hpp" #include "tortoize.hpp" #include #include #include #include #include #include #include #include namespace fs = std::filesystem; using json = nlohmann::json; #ifdef _MSC_VER # include // MSVC stdlib.h definitions # define STDIN_FILENO 0 # define STDOUT_FILENO 1 # define STDERR_FILENO 2 #endif // -------------------------------------------------------------------- class tortoize_html_controller : public zeep::http::html_controller { public: tortoize_html_controller() : zeep::http::html_controller("tortoize") { mount("{css,scripts,fonts,images,favicon}/", &tortoize_html_controller::handle_file); mount("{favicon.ico,browserconfig.xml,manifest.json}", &tortoize_html_controller::handle_file); mount("", &tortoize_html_controller::index); } void index(const zeep::http::request &request, const zeep::http::scope &scope, zeep::http::reply &reply) { get_template_processor().create_reply_from_template("index", scope, reply); } }; // -------------------------------------------------------------------- class tortoize_rest_controller : public zeep::http::rest_controller { public: tortoize_rest_controller() : zeep::http::rest_controller("") , m_tempdir(fs::temp_directory_path() / "tortoize-ws") { fs::create_directories(m_tempdir); map_post_request("tortoize", &tortoize_rest_controller::calculate, "data", "dict"); } json calculate(const std::string &file, const std::string &dict) { // First store dictionary, just in case fs::path dictFile; if (not dict.empty()) { dictFile = m_tempdir / ("dict-" + std::to_string(m_next_dict_nr++)); std::ofstream tmpFile(dictFile); tmpFile << dict; cif::compound_factory::instance().push_dictionary(dictFile); } try { // -------------------------------------------------------------------- json data{ { "software", { { "name", "tortoize" }, { "version", kVersionNumber }, { "reference", "Sobolev et al. A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure (2020)" }, { "reference-doi", "https://doi.org/10.1016/j.str.2020.08.005" } } } }; // -------------------------------------------------------------------- struct membuf : public std::streambuf { membuf(char *text, size_t length) { this->setg(text, text, text + length); } } buffer(const_cast(file.data()), file.length()); cif::gzio::istream in(&buffer); cif::file f = cif::pdb::read(in); if (f.empty()) throw std::runtime_error("Invalid mmCIF or PDB file"); std::set models; for (auto r : f.front()["atom_site"]) { if (not r["pdbx_PDB_model_num"].empty()) models.insert(r["pdbx_PDB_model_num"].as()); } if (models.empty()) models.insert(0); for (auto model : models) { cif::mm::structure structure(f, model); data["model"][std::to_string(model)] = calculateZScores(structure); } if (not dictFile.empty()) { cif::compound_factory::instance().pop_dictionary(); fs::remove(dictFile); } return data; } catch (...) { std::error_code ec; if (not dictFile.empty()) { cif::compound_factory::instance().pop_dictionary(); fs::remove(dictFile); } throw; } } fs::path m_tempdir; size_t m_next_dict_nr = 1; }; int start_server(int argc, char *argv[]) { using namespace std::literals; namespace zh = zeep::http; cif::compound_factory::init(true); int result = 0; auto &config = mcfp::config::instance(); config.init("tortoize server [options] start|stop|status|reload", mcfp::make_option("help,h", "Display help message"), mcfp::make_option("version", "Print version"), mcfp::make_option("verbose,v", "verbose output"), mcfp::make_option("address", "0.0.0.0", "External address"), mcfp::make_option("port", 10350, "Port to listen to"), mcfp::make_option("user,u", "www-data", "User to run the daemon"), mcfp::make_option("no-daemon,F", "Do not fork into background")); config.parse(argc, argv); // -------------------------------------------------------------------- if (config.has("version")) { write_version_string(std::cout, config.has("verbose")); exit(0); } if (config.has("help")) { std::cout << config << std::endl; exit(0); } if (config.operands().empty()) { std::cerr << "Missing command, should be one of start, stop, status or reload" << std::endl; exit(1); } cif::VERBOSE = config.count("verbose"); std::string user = config.get("user"); std::string address = config.get("address"); uint16_t port = config.get("port"); zh::daemon server([&]() { auto s = new zeep::http::server(); #if DEBUG s->set_template_processor(new zeep::http::file_based_html_template_processor("docroot")); #else s->set_template_processor(new zeep::http::rsrc_based_html_template_processor()); #endif s->add_controller(new tortoize_rest_controller()); s->add_controller(new tortoize_html_controller()); return s; }, "tortoized"); std::string command = config.operands().front(); if (command == "start") { std::cout << "starting server at http://" << address << ':' << port << '/' << std::endl; if (config.has("no-daemon")) result = server.run_foreground(address, port); else result = server.start(address, port, 2, 2, user); // server.start(vm.count("no-daemon"), address, port, 2, user); // // result = daemon::start(vm.count("no-daemon"), port, user); } else if (command == "stop") result = server.stop(); else if (command == "status") result = server.status(); else if (command == "reload") result = server.reload(); else { std::cerr << "Invalid command" << std::endl; result = 1; } return result; } // -------------------------------------------------------------------- // 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; try { result = start_server(argc, argv); } catch (std::exception &ex) { print_what(ex); exit(1); } return result; } tortoize-2.0.15/src/tortoize.cpp0000644000175000017500000006372114773215600016506 0ustar maartenmaarten/*- * 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. */ #include "tortoize.hpp" #include "revision.hpp" #include #include #include namespace fs = std::filesystem; using json = nlohmann::json; // -------------------------------------------------------------------- // simple integer compression, based somewhat on MRS code class OBitStream { public: OBitStream(std::vector &buffer) : m_buffer(buffer) { m_buffer.push_back(0); } OBitStream(const OBitStream &) = delete; OBitStream &operator=(const OBitStream &) = delete; void writebit(bool bit) { if (bit) m_buffer.back() |= 1 << m_bitOffset; if (--m_bitOffset < 0) { m_buffer.push_back(0); m_bitOffset = 7; } } // write fixed size void write(uint32_t value, int bits) { while (bits-- > 0) { if (value & (1UL << bits)) m_buffer.back() |= 1 << m_bitOffset; if (--m_bitOffset < 0) { m_buffer.push_back(0); m_bitOffset = 7; } } } void sync() { writebit(0); while (m_bitOffset != 7) writebit(1); } const uint8_t *data() const { return m_buffer.data(); } size_t size() const { return m_buffer.size(); } friend void WriteArray(OBitStream &bs, const std::vector &data); private: std::vector &m_buffer; int m_bitOffset = 7; }; class IBitStream { public: IBitStream(const uint8_t *data) : m_data(data) , m_byte(*m_data++) , m_bitOffset(7) { } IBitStream(const OBitStream &bits) : IBitStream(bits.data()) { } IBitStream(const IBitStream &) = delete; IBitStream &operator=(const IBitStream &) = delete; uint32_t read(int bc) { uint32_t result = 0; while (bc > 0) { static const uint8_t kM[] = { 0x00, 0x01, 0x03, 0x07, 0x0F, 0x1F, 0x3F, 0x7F, 0xFF }; int bw = m_bitOffset + 1; if (bw > bc) bw = bc; m_bitOffset -= bw; result = result << bw | (kM[bw] & (m_byte >> (m_bitOffset + 1))); if (m_bitOffset < 0) { m_byte = *m_data++; m_bitOffset = 7; } bc -= bw; } return result; } friend std::vector ReadArray(IBitStream &bs); private: const uint8_t *m_data; uint8_t m_byte; int m_bitOffset; }; // -------------------------------------------------------------------- // Arrays // This is a simplified version of the array compression routines in MRS // Only supported datatype is uint32_t and only supported width it 24 bit. struct Selector { int32_t databits; uint32_t span; } const kSelectors[16] = { { 0, 1 }, { -4, 1 }, { -2, 1 }, { -2, 2 }, { -1, 1 }, { -1, 2 }, { -1, 4 }, { 0, 1 }, { 0, 2 }, { 0, 4 }, { 1, 1 }, { 1, 2 }, { 1, 4 }, { 2, 1 }, { 2, 2 }, { 4, 1 } }; // store ints of at most 24 bits, should be enough. const uint32_t kStartWidth = 8, kMaxWidth = 24; inline uint32_t bitWidth(uint32_t v) { uint32_t result = 0; while (v > 0) { v >>= 1; ++result; } return result; } void CompressSimpleArraySelector(OBitStream &inBits, const std::vector &inArray) { int32_t width = kStartWidth; int32_t bn[4]; uint32_t dv[4]; uint32_t bc = 0; auto a = inArray.begin(), e = inArray.end(); while (a != e or bc > 0) { while (bc < 4 and a != e) { dv[bc] = *a++; bn[bc] = bitWidth(dv[bc]); ++bc; } uint32_t s = 0; int32_t c = bn[0] - kMaxWidth; for (uint32_t i = 1; i < 16; ++i) { if (kSelectors[i].span > bc) continue; int32_t w = width + kSelectors[i].databits; if (static_cast(w) > kMaxWidth) continue; bool fits = true; int32_t waste = 0; switch (kSelectors[i].span) { case 4: fits = fits and bn[3] <= w; waste += w - bn[3]; [[fallthrough]]; case 3: fits = fits and bn[2] <= w; waste += w - bn[2]; [[fallthrough]]; case 2: fits = fits and bn[1] <= w; waste += w - bn[1]; [[fallthrough]]; case 1: fits = fits and bn[0] <= w; waste += w - bn[0]; } if (fits == false) continue; int32_t n = (kSelectors[i].span - 1) * 4 - waste; if (n > c) { s = i; c = n; } } if (s == 0) width = kMaxWidth; else width += kSelectors[s].databits; uint32_t n = kSelectors[s].span; inBits.write(s, 4); if (width > 0) { for (uint32_t i = 0; i < n; ++i) inBits.write(dv[i], width); } bc -= n; if (bc > 0) { for (uint32_t i = 0; i < (4 - n); ++i) { bn[i] = bn[i + n]; dv[i] = dv[i + n]; } } } } void DecompressSimpleArraySelector(IBitStream &inBits, std::vector &outArray) { uint32_t width = kStartWidth; uint32_t span = 0; // The array should be initialized to the expected size! auto size = outArray.size(); auto a = outArray.begin(); while (size-- > 0) { if (span == 0) { uint32_t selector = inBits.read(4); span = kSelectors[selector].span; if (selector == 0) width = kMaxWidth; else width += kSelectors[selector].databits; } if (width > 0) *a++ = inBits.read(width); else *a++ = 0; --span; } } // -------------------------------------------------------------------- enum class SecStrType : char { helix = 'H', strand = 'E', other = '.', cis = 'c', prepro = 'p' }; std::ostream &operator<<(std::ostream &os, SecStrType ss) { switch (ss) { case SecStrType::helix: os << "helix"; break; case SecStrType::strand: os << "strand"; break; case SecStrType::other: os << "other"; break; case SecStrType::cis: os << "cis"; break; case SecStrType::prepro: os << "prepro"; break; } return os; } std::string to_string(SecStrType ss) { switch (ss) { case SecStrType::helix: return "helix"; break; case SecStrType::strand: return "strand"; break; case SecStrType::other: return "other"; break; case SecStrType::cis: return "cis"; break; case SecStrType::prepro: return "prepro"; break; } throw std::runtime_error("Invalid sec structure"); } // -------------------------------------------------------------------- // The header for the data blocks as written in de resource struct StoredData { char aa[3]; SecStrType ss; float mean, mean_vs_random, sd, sd_vs_random, binSpacing; uint32_t offset; // offset into compressed data area }; class Data { friend class DataTable; public: Data(Data &&d) : aa(d.aa) , ss(d.ss) , mean(d.mean) , sd(d.sd) , mean_vs_random(d.mean_vs_random) , sd_vs_random(d.sd_vs_random) , binSpacing(d.binSpacing) , counts(move(d.counts)) , dim(d.dim) , d2(d.d2) { } Data(const Data &) = delete; Data &operator=(const Data &) = delete; Data(const char *type, const std::string &aa, SecStrType ss, std::istream &is); Data(bool torsion, const StoredData &data, const uint8_t *bits); void store(StoredData &data, std::vector &databits); float interpolatedCount(float phi, float a2) const; float zscore(float a1, float a2) const { return (interpolatedCount(a1, a2) - mean) / sd; } void dump() const { for (size_t i = 0; i < counts.size(); ++i) { float a1, a2; std::tie(a1, a2) = angles(i); std::cout << a1 << ' ' << a2 << ' ' << counts[i] << std::endl; } } private: std::string aa; SecStrType ss; float mean, sd, mean_vs_random, sd_vs_random; float binSpacing; std::vector counts; // calculated size_t dim; bool d2; float count(size_t a1Ix, size_t a2Ix) const { a1Ix %= dim; a2Ix %= dim; return static_cast(d2 ? counts.at(a1Ix * dim + a2Ix) : counts.at(a1Ix)); } size_t index(float a1, float a2 = 0) const { size_t x = 0, y = 0; if (d2) { x = static_cast((a1 + 180) / binSpacing); y = static_cast((a2 + 180) / binSpacing); } else y = static_cast((a1 + 180) / binSpacing); return x * static_cast(std::rint(360 / binSpacing)) + y; } std::tuple angles(size_t index) const { size_t x = index / dim; size_t y = index % dim; return std::make_tuple(x * binSpacing - 180, y * binSpacing - 180); } }; Data::Data(const char *type, const std::string &aa, SecStrType ss, std::istream &is) : aa(aa) , ss(ss) { // example: // 14400 bins, aver 19.2878, sd 15.4453, binspacing 3 // torsion vs random: 2.0553 2.8287 static const std::regex kRX1(R"((\d+) bins, aver ([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?), sd ([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?), binspacing ([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?))"), kRX2(R"((torsion|rama) vs random: ([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?) ([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?))"); std::string line; getline(is, line); d2 = strcmp(type, "torsion") != 0 or std::set{ "CYS", "SER", "THR", "VAL" }.count(aa) == 0; std::smatch m; if (not std::regex_match(line, m, kRX1)) throw std::runtime_error("Invalid file"); size_t nBins = stoi(m[1]); mean = stof(m[2]); sd = stof(m[3]); binSpacing = stof(m[4]); dim = static_cast(360 / binSpacing); if ((d2 and nBins != dim * dim) or (not d2 and nBins != dim)) throw std::runtime_error("Unexpected number of bins"); counts.resize(nBins); getline(is, line); if (not std::regex_match(line, m, kRX2) or m[1] != type) throw std::runtime_error("Invalid file"); mean_vs_random = stof(m[2]); sd_vs_random = stof(m[3]); for (size_t i = 0; i < nBins; ++i) { float a1 = 0, a2 = 0; uint32_t count; if (d2) is >> a1 >> a2 >> count; else is >> a1 >> count; if (is.eof()) throw std::runtime_error("truncated file?"); counts.at(index(a1, a2)) = count; } } Data::Data(bool torsion, const StoredData &data, const uint8_t *databits) { aa.assign(data.aa, data.aa + 3); ss = data.ss; mean = data.mean; mean_vs_random = data.mean_vs_random; sd = data.sd; sd_vs_random = data.sd_vs_random; binSpacing = data.binSpacing; d2 = not torsion or std::set{ "CYS", "SER", "THR", "VAL" }.count(aa) == 0; size_t nBins = static_cast(360 / binSpacing); dim = nBins; if (d2) nBins *= nBins; counts.insert(counts.begin(), nBins, 0); IBitStream bits(databits + data.offset); DecompressSimpleArraySelector(bits, counts); } void Data::store(StoredData &data, std::vector &databits) { assert(aa.length() == 3); copy(aa.begin(), aa.end(), data.aa); data.ss = ss; data.mean = mean; data.sd = sd; data.mean_vs_random = mean_vs_random; data.sd_vs_random = sd_vs_random; data.offset = static_cast(databits.size()); data.binSpacing = binSpacing; OBitStream bits(databits); CompressSimpleArraySelector(bits, counts); bits.sync(); } float Data::interpolatedCount(float a1, float a2) const { const size_t N = dim; float result; if (d2) { size_t a1FloorIx = static_cast(N * (a1 + 180) / 360); size_t a2FloorIx = static_cast(N * (a2 + 180) / 360); size_t a1CeilIx = (a1FloorIx + 1); size_t a2CeilIx = (a2FloorIx + 1); float a1FloorAngle = (a1FloorIx * 360.0f) / N - 180; float a2FloorAngle = (a2FloorIx * 360.0f) / N - 180; float a1CeilAngle = (a1CeilIx * 360.0f) / N - 180; float a2CeilAngle = (a2CeilIx * 360.0f) / N - 180; float a1Factor = a1CeilIx > a1FloorIx ? (a1 - a1FloorAngle) / (a1CeilAngle - a1FloorAngle) : 1; float a2Factor = a2CeilIx > a2FloorIx ? (a2 - a2FloorAngle) / (a2CeilAngle - a2FloorAngle) : 1; float c1 = count(a1FloorIx, a2FloorIx) + (count(a1CeilIx, a2FloorIx) - count(a1FloorIx, a2FloorIx)) * a1Factor; float c2 = count(a1FloorIx, a2CeilIx) + (count(a1CeilIx, a2CeilIx) - count(a1FloorIx, a2CeilIx)) * a1Factor; result = c1 + (c2 - c1) * a2Factor; } else { size_t a1FloorIx = static_cast(N * (a1 + 180) / 360); size_t a1CeilIx = (a1FloorIx + 1); float a1FloorAngle = (a1FloorIx * 360.0f) / N - 180; float a1CeilAngle = (a1CeilIx * 360.0f) / N - 180; float a1Factor = a1CeilIx > a1FloorIx ? (a1 - a1FloorAngle) / (a1CeilAngle - a1FloorAngle) : 1; result = count(a1FloorIx, 0) + (count(a1CeilIx, 0) - count(a1FloorIx, 0)) * a1Factor; } return result; } void buildDataFile(const fs::path &dir) { using namespace std::literals; if constexpr (std::endian::native == std::endian::big) throw std::logic_error("Sorry, this code works on little endian machines only"); // first read the global mean and sd float mean_torsion, sd_torsion, mean_ramachandran, sd_ramachandran; std::ifstream in(dir / "zscores_proteins.txt"); std::string line; const std::regex krx(R"((Rama|Rota): average ([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?), sd ([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?))"); while (getline(in, line)) { std::smatch m; if (not std::regex_match(line, m, krx)) continue; if (m[1] == "Rama") { mean_ramachandran = stof(m[2]); sd_ramachandran = stof(m[3]); } else { mean_torsion = stof(m[2]); sd_torsion = stof(m[3]); } } std::vector data; std::vector bits; // first ramachandran counts for (auto aa : cif::compound_factory::kAAMap) { for (std::pair ss : { std::make_pair(SecStrType::helix, "helix"), std::make_pair(SecStrType::strand, "strand"), std::make_pair(SecStrType::other, "other") }) { auto p = dir / ("rama_count_"s + ss.second + '_' + aa.first + ".txt"); if (not fs::exists(p)) continue; std::ifstream f(p); Data d("rama", aa.first, ss.first, f); StoredData sd = {}; d.store(sd, bits); data.push_back(sd); } } for (std::tuple ss : { std::make_tuple(SecStrType::cis, "PRO", "cis_PRO"), std::make_tuple(SecStrType::prepro, "***", "prepro_all_noGIV"), std::make_tuple(SecStrType::prepro, "GLY", "prepro_GLY"), std::make_tuple(SecStrType::prepro, "IV_", "prepro_ILEVAL") }) { auto p = dir / ("rama_count_"s + std::get<2>(ss) + ".txt"); if (not fs::exists(p)) continue; std::ifstream f(p); Data d("rama", std::get<1>(ss), std::get<0>(ss), f); StoredData sd = {}; d.store(sd, bits); data.push_back(sd); } data.push_back({}); if (fs::exists("rama-data.bin")) fs::remove("rama-data.bin"); std::ofstream out("rama-data.bin", std::ios::binary); if (not out.is_open()) throw std::runtime_error("Could not create rama-data.bin file"); out.write(reinterpret_cast(&mean_ramachandran), sizeof(mean_ramachandran)); out.write(reinterpret_cast(&sd_ramachandran), sizeof(sd_ramachandran)); out.write(reinterpret_cast(data.data()), data.size() * sizeof(StoredData)); out.write(reinterpret_cast(bits.data()), bits.size()); out.close(); data.clear(); bits.clear(); // next torsion counts for (auto aa : cif::compound_factory::kAAMap) { for (std::pair ss : { std::make_pair(SecStrType::helix, "helix"), std::make_pair(SecStrType::strand, "strand"), std::make_pair(SecStrType::other, "other") }) { auto p = dir / ("torsion_count_"s + ss.second + '_' + aa.first + ".txt"); if (not fs::exists(p)) continue; std::ifstream f(p); Data d("torsion", aa.first, ss.first, f); StoredData sd = {}; d.store(sd, bits); data.push_back(sd); } } data.push_back({}); if (fs::exists("torsion-data.bin")) fs::remove("torsion-data.bin"); out.open("torsion-data.bin", std::ios::binary); if (not out.is_open()) throw std::runtime_error("Could not create torsion-data.bin file"); out.write(reinterpret_cast(&mean_torsion), sizeof(mean_torsion)); out.write(reinterpret_cast(&sd_torsion), sizeof(sd_torsion)); out.write(reinterpret_cast(data.data()), data.size() * sizeof(StoredData)); out.write(reinterpret_cast(bits.data()), bits.size()); out.close(); } // -------------------------------------------------------------------- class DataTable { public: static DataTable &instance() { static DataTable sInstance; return sInstance; } const Data &loadTorsionData(const std::string &aa, SecStrType ss) const; const Data &loadRamachandranData(const std::string &aa, SecStrType ss) const; float mean_torsion() const { return m_mean_torsion; } float sd_torsion() const { return m_sd_torsion; } float mean_ramachandran() const { return m_mean_ramachandran; } float sd_ramachandran() const { return m_sd_ramachandran; } private: DataTable(const DataTable &) = delete; DataTable &operator=(const DataTable &) = delete; DataTable(); void load(const char *name, std::vector &table, float &mean, float &sd); std::vector m_torsion, m_ramachandran; float m_mean_torsion, m_sd_torsion, m_mean_ramachandran, m_sd_ramachandran; }; DataTable::DataTable() { load("torsion-data.bin", m_torsion, m_mean_torsion, m_sd_torsion); load("rama-data.bin", m_ramachandran, m_mean_ramachandran, m_sd_ramachandran); } const Data &DataTable::loadTorsionData(const std::string &aa, SecStrType ss) const { auto i = find_if(m_torsion.begin(), m_torsion.end(), [aa, ss](auto &d) { return d.aa == aa and d.ss == ss; }); if (i == m_torsion.end()) throw std::runtime_error("Data missing for aa = " + aa + " and ss = '" + static_cast(ss) + '\''); return *i; } const Data &DataTable::loadRamachandranData(const std::string &aa, SecStrType ss) const { std::vector::const_iterator i; switch (ss) { case SecStrType::cis: i = find_if(m_ramachandran.begin(), m_ramachandran.end(), [](auto &d) { return d.ss == SecStrType::cis and d.aa == "PRO"; }); break; case SecStrType::prepro: i = find_if(m_ramachandran.begin(), m_ramachandran.end(), [aa](auto &d) { bool result = false; if (d.ss == SecStrType::prepro) { if (aa == "GLY") result = d.aa == "GLY"; else if (aa == "ILE" or aa == "VAL") result = d.aa == "IV_"; else result = d.aa == "***"; } return result; }); break; default: i = find_if(m_ramachandran.begin(), m_ramachandran.end(), [aa, ss](auto &d) { return d.aa == aa and d.ss == ss; }); break; } if (i == m_ramachandran.end()) throw std::runtime_error("Data missing for aa = " + aa + " and ss = '" + static_cast(ss) + '\''); return *i; } template void byteswap(T &v) { T result; char *pv = (char *)&v; char *presult = (char *)&result; int size = sizeof(T); for (int i = 0; i < size; i++) presult[size - 1 - i] = pv[i]; v = result; } void DataTable::load(const char *name, std::vector &table, float &mean, float &sd) { using namespace std::literals; auto rfd = cif::load_resource(name); if (not rfd) throw std::runtime_error("Missing resource "s + name); rfd->seekg(0, rfd->end); auto size = rfd->tellg(); rfd->seekg(0, rfd->beg); float *fv = new float[size / sizeof(float) + 1]; rfd->read(reinterpret_cast(fv), size); mean = fv[0]; sd = fv[1]; StoredData *data = reinterpret_cast(fv + 2); if constexpr (std::endian::native == std::endian::big) { byteswap(mean); byteswap(sd); } size_t ix = 0; while (data[ix].aa[0] != 0) ++ix; size_t n = ix; const uint8_t *bits = reinterpret_cast(fv + 2) + (n + 1) * sizeof(StoredData); for (ix = 0; ix < n; ++ix) { if constexpr (std::endian::native == std::endian::big) { byteswap(data[ix].mean); byteswap(data[ix].mean_vs_random); byteswap(data[ix].sd); byteswap(data[ix].sd_vs_random); byteswap(data[ix].binSpacing); byteswap(data[ix].offset); } table.emplace_back(strcmp(name, "torsion-data.bin") == 0, data[ix], bits); } } // -------------------------------------------------------------------- float jackknife(const std::vector &zScorePerResidue) { // jackknife variance estimate, see: https://en.wikipedia.org/wiki/Jackknife_resampling const size_t N = zScorePerResidue.size(); double zScoreSum = accumulate(zScorePerResidue.begin(), zScorePerResidue.end(), 0.0); std::vector scores(N); DataTable &tbl = DataTable::instance(); double scoreSum = 0; for (size_t i = 0; i < zScorePerResidue.size(); ++i) { double score = (zScoreSum - zScorePerResidue[i]) / (N - 1); score = (score - tbl.mean_ramachandran()) / tbl.sd_ramachandran(); scores[i] = score; scoreSum += score; } double avg = scoreSum / N; double sumD = accumulate(scores.begin(), scores.end(), 0.0, [avg](double a, double z) { return a + (z - avg) * (z - avg); }); return static_cast(std::sqrt((N - 1) * sumD / N)); } // -------------------------------------------------------------------- json calculateZScores(const cif::mm::structure &structure) { dssp dssp(structure, 3, false); auto &tbl = DataTable::instance(); double ramaZScoreSum = 0; size_t ramaZScoreCount = 0; double torsZScoreSum = 0; size_t torsZScoreCount = 0; json residues; std::vector ramaZScorePerResidue, torsZScorePerResidue; for (auto &poly : structure.polymers()) { for (size_t i = 1; i + 1 < poly.size(); ++i) { auto &res = poly[i]; auto phi = res.phi(); auto psi = res.psi(); if (phi == 360 or psi == 360) continue; std::string aa = res.get_compound_id(); json residue = { { "asymID", res.get_asym_id() }, { "seqID", res.get_seq_id() }, { "compID", aa }, { "pdb", { { "strandID", res.get_auth_asym_id() }, { "seqNum", std::stoi(res.get_auth_seq_id()) }, { "compID", aa }, { "insCode", res.get_pdb_ins_code() } } } }; // remap some common modified amino acids if (aa == "MSE") { if (cif::VERBOSE > 1) std::cerr << "Replacing MSE with MET" << std::endl; aa = "MET"; } else if (aa == "HYP") { if (cif::VERBOSE > 1) std::cerr << "Replacing HYP with PRO" << std::endl; aa = "PRO"; } else if (aa == "ASX") { if (cif::VERBOSE > 1) std::cerr << "Replacing ASX with ASP" << std::endl; aa = "ASP"; } else if (aa == "GLX") { if (cif::VERBOSE > 1) std::cerr << "Replacing GLX with GLU" << std::endl; aa = "GLU"; } else if (not cif::compound_factory::instance().kAAMap.count(aa)) { if (cif::VERBOSE > 0) std::cerr << "Replacing " << aa << " with ALA" << std::endl; aa = "ALA"; } SecStrType tors_ss, rama_ss; try { switch (dssp[{ res.get_asym_id(), res.get_seq_id() }].type()) { case dssp::structure_type::Alphahelix: tors_ss = SecStrType::helix; break; case dssp::structure_type::Strand: tors_ss = SecStrType::strand; break; default: tors_ss = SecStrType::other; break; } } catch (const std::out_of_range &e) { if (cif::VERBOSE > 0) std::cerr << "Residue " << res << " is missing in DSSP" << std::endl; continue; } if (aa != "PRO" and poly[i + 1].get_compound_id() == "PRO") rama_ss = SecStrType::prepro; else if (aa == "PRO" && res.is_cis()) rama_ss = SecStrType::cis; else rama_ss = tors_ss; // TODO: #pragma warning "todo" (but the question now is, what is here to do???) auto &rd = tbl.loadRamachandranData(aa, rama_ss); auto zr = rd.zscore(phi, psi); residue["ramachandran"] = { { "ss-type", to_string(rama_ss) }, { "z-score", zr } }; ramaZScorePerResidue.push_back(zr); ramaZScoreSum += zr; ++ramaZScoreCount; try { float zt = nanf("1"); auto chiCount = res.nr_of_chis(); if (chiCount) { float chi1 = res.chi(0); float chi2 = chiCount > 1 ? res.chi(1) : 0; auto &td = tbl.loadTorsionData(aa, tors_ss); zt = td.zscore(chi1, chi2); torsZScoreSum += zt; ++torsZScoreCount; torsZScorePerResidue.push_back(zt); residue["torsion"] = { { "ss-type", to_string(tors_ss) }, { "z-score", zt } }; } } catch (const std::exception &e) { if (cif::VERBOSE > 0) std::cerr << e.what() << '\n'; } residues.push_back(residue); } } float ramaVsRand = static_cast(ramaZScoreSum / ramaZScoreCount); float torsVsRand = static_cast(torsZScoreSum / torsZScoreCount); float jackknifeRama = jackknife(ramaZScorePerResidue); float jackknifeTors = jackknife(torsZScorePerResidue); return { { "ramachandran-z", ((ramaVsRand - tbl.mean_ramachandran()) / tbl.sd_ramachandran()) }, { "ramachandran-jackknife-sd", jackknifeRama }, { "torsion-z", ((torsVsRand - tbl.mean_torsion()) / tbl.sd_torsion()) }, { "torsion-jackknife-sd", jackknifeTors }, { "residues", residues }, }; } // -------------------------------------------------------------------- json tortoize_calculate(const fs::path &xyzin) { json data{ { "software", { { "name", "tortoize" }, { "version", kVersionNumber }, { "reference", "Sobolev et al. A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure (2020)" }, { "reference-doi", "https://doi.org/10.1016/j.str.2020.08.005" } } } }; // -------------------------------------------------------------------- cif::file f = cif::pdb::read(xyzin); if (f.empty()) throw std::runtime_error("Invalid or empty mmCIF/PDB file"); std::set models; for (auto r : f.front()["atom_site"]) { if (not r["pdbx_PDB_model_num"].empty()) models.insert(r["pdbx_PDB_model_num"].as()); } if (models.empty()) models.insert(0); for (auto model : models) { cif::mm::structure structure(f, model); data["model"][std::to_string(model)] = calculateZScores(structure); } return data; }tortoize-2.0.15/src/tortoize.hpp0000644000175000017500000000320214773215600016477 0ustar maartenmaarten/*- * 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. */ #include #include void buildDataFile(const std::filesystem::path &dir); nlohmann::json calculateZScores(const cif::mm::structure& structure); nlohmann::json tortoize_calculate(const std::filesystem::path &xyzin); tortoize-2.0.15/test/0000755000175000017500000000000014773215600014302 5ustar maartenmaartentortoize-2.0.15/test/1cbs.cif.gz0000644000175000017500000011047314773215600016242 0ustar maartenmaartenʳ_1cbs.cif\s⸲Py`O్:@9@&@2ske|$[m<띙RZV-ޚi(UaP7O%`aqko${~3OP?=;2Èl}xK[HզoX8xh[ JO藸4㛤Kdž"˲SUX)_Mt-'*(S/c}j}l ۵Ct-=xBBD {Iߤ&Q iʾy.e:+"mQٜHB;t(_чf s釨s`ST5}S{k#_eyG6bj5|~Ʊ5J@.G%?MI{E}` > F,8Gzv=pXz.;R ȔLv CO;qZoA+MpV+5~o_EgnIxQC¦n&I}ˊZ4n S'DzG-a8hriڀȽnsȸ C`I7<./Txm S +sLC:SyeO #`:|=Gth0N6t? *FQ!B@+0/&vrlwǭ<$]ݘmBfW~]0/dsê<[껎5(\4A +{WT(XQUFUv3QU'8BTã4A}vMb*s%3QmØ$FUg&(VED>Ex{j0j#u) 6L]W e2}cr7^߾N֫eF}xLe|\4F p{x|Mxw!_wt~\h|y}YN >Ht2cّ.iXfs;,;#CpZg"('\b!gLy F:$݋ItdĺF7]zn D"Ut9ts w"˻Fځyo4۩lpd=DMw!F&<ȋ>oTTx'$\ H8Y7ip iLot. d:TNZM8nbh(h=NoZUd} c$X&5*h5x,|MsZFU^]^]%B* qvp1n[υ)qxe( (B_osk];\}^\p'6u0P8x Qfր'ASՀ `(O7EnsENDE z(ro ӎN1#DE Nt8 N1zb&(8EۀN1kb: KN1u(INg#Sn)èSXSNhP)r5]KEοS\ XT쇛 F}Hw&nU5qRu$:@m;Cbp9BTs Rvcy{> 1 F`{oUʣ˚i??s2Z74խj"uv/ApOGagŻ*M˫PgM6y@0 y!X9P:9]pgoKV;o?73j@3,R6fd.C*vz },~^yALR\&mlXcmZ6Sj+:&ɝrmquEx =5aXIh~ƴԓ+IԷFa$m % qۛV%JFa7Zc@uȳQpGKT &^7vt;.sKOxg|oef8{uCqR[PO{\ qJy?g7ObURC-O$3$G@gނjLmPHT|;Y7) oc%t[3vϒEt;+c\B8^Dk yr<| 84} Km-a ϤwjLR tio|NqHx}LS &w֠^ *nM:շ[5ɕ]rҸl?RCX&+'r+qaN{'LVcTY zoo̢ sņx A8)Ml,^}t#%Tqn/EPlŰf*s` *$,OkVo;5 gfn*$̯ 17xMӵ, b8rjXf@q-ճ$ڬ$@8pL9M$[>'ӹ\.GҐ/Ŭg+cSԉˣzh܋0MɚnCYJdj2`cbFp&`>0,cimv/À,(k17][2pȧ}>e)jvo0 0(&!E!Y Ր4.j %bk$ )$-8mF/Cˡ%ZW$|RhNZ͉|tkOV{v54ZjX5+W\^.b.5^ ~W[N/DWDDWug4rBnIun +Ȕ1~Lg:'l'>]}6k|ʿ:Y<׎[3{Q~Z(Wu"d\/o `!{j4{@-̎ '*LE>[v! 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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. */ #include #include "tortoize.hpp" #include #include namespace fs = std::filesystem; using json = nlohmann::json; // -------------------------------------------------------------------- // -------------------------------------------------------------------- fs::path gTestDir = fs::current_path(); int main(int argc, char *argv[]) { Catch::Session session; // There must be exactly one instance // Build a new parser on top of Catch2's #if CATCH22 using namespace Catch::clara; #else // Build a new parser on top of Catch2's using namespace Catch::Clara; #endif auto cli = session.cli() // Get Catch2's command line parser | Opt(gTestDir, "data-dir") // bind variable to a new option, with a hint string ["-D"]["--data-dir"] // the option names it will respond to ("The directory containing the data files") // description string for the help output | Opt(cif::VERBOSE, "verbose")["-v"]["--cif-verbose"]("Flag for cif::VERBOSE"); // Now pass the new composite back to Catch2 so it uses that session.cli(cli); // Let Catch2 (using Clara) parse the command line int returnCode = session.applyCommandLine(argc, argv); if (returnCode != 0) // Indicates a command line error return returnCode; cif::add_data_directory(gTestDir / ".." / "rsrc"); return session.run(); } // -------------------------------------------------------------------- TEST_CASE("first_test") { auto a = tortoize_calculate(gTestDir / "1cbs.cif.gz"); std::ifstream bf(gTestDir / "1cbs.json"); json b = nlohmann::json::parse(bf); auto ma = a["model"]["1"]; auto mb = b["model"]["1"]; CHECK_THAT(ma["ramachandran-jackknife-sd"].template get(), Catch::Matchers::WithinRel(mb["ramachandran-jackknife-sd"].template get(), 0.1)); CHECK_THAT(ma["ramachandran-z"].template get(), Catch::Matchers::WithinRel(mb["ramachandran-z"].template get(), 0.1)); CHECK_THAT(ma["torsion-jackknife-sd"].template get(), Catch::Matchers::WithinRel(mb["torsion-jackknife-sd"].template get(), 0.1)); CHECK_THAT(ma["torsion-z"].template get(), Catch::Matchers::WithinRel(mb["torsion-z"].template get(), 0.1)); }tortoize-2.0.15/tortoized.service.in0000644000175000017500000000044614773215600017341 0ustar maartenmaarten[Unit] Description=The diricore web service After=network.target Wants=network-online.target [Service] Restart=on-failure Type=forking PIDFile=@TORTOIZED_PID@ ExecStart=@TORTOIZED_EXE@ start ExecReload=@TORTOIZED_EXE@ reload ExecStop=@TORTOIZED_EXE@ stop [Install] WantedBy=multi-user.target tortoize-2.0.15/webapp/0000755000175000017500000000000014773215600014601 5ustar maartenmaartentortoize-2.0.15/webapp/index.js0000644000175000017500000000347514773215600016257 0ustar maartenmaartenimport "core-js/stable"; import "regenerator-runtime/runtime"; import bsCustomFileInput from 'bs-custom-file-input'; class Tortoize { constructor(form) { this.form = document.forms['tortoize-form']; this.table = document.getElementById('tortoize-table'); this.alert = document.getElementById('tortoize-alert'); this.form.addEventListener('submit', (evt) => this.handleSubmit(evt)); this.alert.classList.add('invisible'); } handleSubmit(event) { if (event) event.preventDefault(); const data = new FormData(this.form); this.table.style.display = 'none'; this.alert.classList.add('invisible'); let wasOK; fetch('tortoize', { credentials: 'include', method: 'post', body: data }).then(r => { wasOK = r.ok; return r.json(); }).then(r => { // console.log(r); if (r.model) this.process(r.model); else if (r.error) throw r.error; else throw 'Reply does not contain data'; }).catch(err => { console.log(err); this.alert.textContent = `Could not calculate rama z-score: ${err}`; this.alert.classList.remove('invisible'); }); } process(model) { const tbody = this.table.querySelector('tbody'); [...tbody.querySelectorAll('tr')].forEach(row => tbody.removeChild(row)); for (const [id, data] of Object.entries(model)) { const row = document.createElement("tr"); const tdid = document.createElement("td"); tdid.textContent = id; row.appendChild(tdid); for (const f of ['ramachandran', 'torsion']) { const td = document.createElement('td'); td.textContent = (+data[`${f}-z`]).toFixed(2) + " ± " + (+data[`${f}-jackknife-sd`]).toFixed(2); row.appendChild(td); } tbody.appendChild(row); } this.table.style.display = 'unset'; } } window.addEventListener('load', () => { bsCustomFileInput.init(); new Tortoize(); });tortoize-2.0.15/webpack.config.js0000644000175000017500000000460314773215600016544 0ustar maartenmaartenconst MiniCssExtractPlugin = require('mini-css-extract-plugin'); const { CleanWebpackPlugin } = require('clean-webpack-plugin'); const webpack = require('webpack'); const TerserPlugin = require('terser-webpack-plugin'); const UglifyJsPlugin = require('uglifyjs-webpack-plugin'); const path = require('path'); const SCRIPTS = path.resolve(__dirname, "webapp"); const SCSS = path.resolve(__dirname, "scss"); const DEST = path.resolve(__dirname, "docroot/scripts"); module.exports = (env) => { const PRODUCTION = env != null && env.PRODUCTION; const webpackConf = { entry: { 'pdb-redo-style': path.resolve(SCSS, "pdb-redo-bootstrap.scss"), 'index': path.resolve(SCRIPTS, 'index.js') }, output: { path: DEST, clean: true }, module: { rules: [ { test: /\.js/, exclude: /node_modules/, use: { loader: "babel-loader", options: { presets: ['@babel/preset-env'] } } }, { test: /\.(eot|svg|ttf|woff(2)?)(\?v=\d+\.\d+\.\d+)?/, loader: 'file-loader', options: { name: '[name].[ext]', outputPath: 'fonts/', publicPath: '../fonts/' } }, { test: /\.(sa|sc|c)ss$/i, use: [ MiniCssExtractPlugin.loader, "css-loader", "postcss-loader", "sass-loader" ] }, { test: /\.woff(2)?(\?v=[0-9]\.[0-9]\.[0-9])?$/, include: path.resolve(__dirname, './node_modules/bootstrap-icons/font/fonts'), type: 'asset/resource', generator: { filename: '../fonts/[name][ext]' } }, { test: /\.png$/, type: 'asset/resource', generator: { filename: '../images/[name][ext]' } } ] }, resolve: { extensions: ['.js', '.scss'], }, plugins: [ new MiniCssExtractPlugin({ filename: "../css/[name].css" }), new CleanWebpackPlugin({ verbose: true, cleanOnceBeforeBuildPatterns: [ path.resolve(__dirname, 'scripts'), path.resolve(__dirname, 'fonts') ] })], optimization: { minimizer: [] } }; if (PRODUCTION) { webpackConf.mode = "production"; webpackConf.optimization.minimizer.push( new TerserPlugin({ /* additional options here */ }), new UglifyJsPlugin({ parallel: 4 }) ); } else { webpackConf.mode = "development"; webpackConf.devtool = 'source-map'; webpackConf.plugins.push(new webpack.optimize.AggressiveMergingPlugin()) } return webpackConf; }; tortoize-2.0.15/yarn.lock0000644000175000017500000046153214773215600015161 0ustar maartenmaarten# THIS IS AN AUTOGENERATED FILE. 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