tortoize-2.0.5/0000775000175000017500000000000014177415663013255 5ustar maartenmaartentortoize-2.0.5/.gitignore0000664000175000017500000000006614177415663015247 0ustar maartenmaarten.vscode tortoize .vs/ build node_modules .gdb_history tortoize-2.0.5/CMakeLists.txt0000664000175000017500000001152614177415663016022 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 3.15) # set the project name project(tortoize VERSION 2.0.5 LANGUAGES CXX) list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") include(GNUInstallDirs) include(CheckFunctionExists) include(CheckIncludeFiles) include(CheckLibraryExists) include(CMakePackageConfigHelpers) include(Dart) include(FindFilesystem) include(GenerateExportHeader) set(CXX_EXTENSIONS OFF) set(CMAKE_CXX_STANDARD 17) set(CMAKE_CXX_STANDARD_REQUIRED ON) find_package(Filesystem REQUIRED) if("${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() if(NOT "$ENV{CCP4}" STREQUAL "") set(BUILD_SHARED_LIBS ON) set(CCP4 $ENV{CCP4}) list(PREPEND CMAKE_MODULE_PATH "${CCP4}/Lib") list(APPEND CMAKE_PREFIX_PATH ${CCP4}) if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) set(CMAKE_PREFIX_PATH ${CCP4}) endif() endif() if(MSVC) # make msvc standards compliant... add_compile_options(/permissive-) macro(get_WIN32_WINNT version) if (WIN32 AND CMAKE_SYSTEM_VERSION) set(ver ${CMAKE_SYSTEM_VERSION}) string(REPLACE "." "" ver ${ver}) string(REGEX REPLACE "([0-9])" "0\\1" ver ${ver}) set(${version} "0x${ver}") endif() endmacro() get_WIN32_WINNT(ver) add_definitions(-D_WIN32_WINNT=${ver}) # On Windows, do not install in the system location if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND NOT BUILD_FOR_CCP4) message(STATUS "The library and auxiliary files will be installed in $ENV{LOCALAPPDATA}/${PROJECT_NAME}") set(CMAKE_INSTALL_PREFIX "$ENV{LOCALAPPDATA}/${PROJECT_NAME}" CACHE PATH "..." FORCE) endif() endif() if(UNIX AND NOT APPLE) # On Linux, install in the $HOME/.local folder by default if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) message(WARNING "The library and auxiliary files will be installed in $ENV{HOME}/.local") set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "..." FORCE) endif() endif() # Create a revision file, containing the current git version info, if any include(VersionString) write_version_header() # Optionally use mrc to create resources find_package(Mrc) if(MRC_FOUND) option(USE_RSRC "Use mrc to create resources" ON) else() message(WARNING "Not using resources since mrc was not found") endif() if(USE_RSRC STREQUAL "ON") set(USE_RSRC 1) add_compile_definitions(USE_RSRC) endif() # libraries set(CMAKE_THREAD_PREFER_PTHREAD) set(THREADS_PREFER_PTHREAD_FLAG) find_package(Threads) find_package(cifpp 2.0.0 REQUIRED) find_package(zeep 5.1.4 REQUIRED) find_package(Boost COMPONENTS program_options REQUIRED) add_executable(tortoize ${PROJECT_SOURCE_DIR}/src/tortoize.cpp ${TORTOIZE_RESOURCE}) if(USE_RSRC) mrc_target_resources(tortoize ${CMAKE_SOURCE_DIR}/rsrc/rama-data.bin ${CMAKE_SOURCE_DIR}/rsrc/torsion-data.bin ${CIFPP_SHARE_DIR}/mmcif_pdbx_v50.dic) endif() target_include_directories(tortoize PRIVATE cifpp::cifpp ${CMAKE_SOURCE_DIR}/include ${CMAKE_BINARY_DIR}) target_link_libraries(tortoize cifpp::cifpp zeep::zeep std::filesystem Boost::program_options) install(TARGETS ${PROJECT_NAME} RUNTIME DESTINATION ${BIN_INSTALL_DIR} ) if(NOT USE_RSRC) install(FILES ${CMAKE_SOURCE_DIR}/rsrc/rama-data.bin ${CMAKE_SOURCE_DIR}/rsrc/torsion-data.bin DESTINATION ${CIFPP_SHARE_DIR}) endif() # # manual # install(FILES doc/tortoize.1 DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1) # manual install(FILES doc/tortoize.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) tortoize-2.0.5/LICENSE0000664000175000017500000000247214177415663014267 0ustar maartenmaartenSPDX-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.tortoize-2.0.5/README.md0000664000175000017500000000135414177415663014537 0ustar maartenmaartenTortoize ======== Application to calculate ramachandran z-scores. Building -------- Make sure you install [libcif++](https://github.com/PDB-REDO/libcifpp) and [libzeep](https://github.com/mhekkel/libzeep) first before building. After that, building should be as easy as typing: ``` git clone https://github.com/PBD-REDO/tortoize.git cd tortoize mkdir build cd build cmake .. cmake --build . --config Release ctest -C Release cmake --install . ``` This will install the `tortoize` program in `$HOME/.local/bin`. If you want to install elsewhere, specify the prefix with the [CMAKE_INSTALL_PREFIX](https://cmake.org/cmake/help/v3.21/variable/CMAKE_INSTALL_PREFIX.html) variable. Usage ----- See [manual page](doc/tortoize.pdf) for more info. tortoize-2.0.5/babel.config.js0000664000175000017500000000031414177415663016122 0ustar maartenmaarten{ presets: [ [ "@babel/env", { "targets": { "edge": "17", "firefox": "60", "chrome": "67", "safari": "11.1", }, "useBuiltIns": "usage", "corejs": "3.8.2", } ] ] }tortoize-2.0.5/changelog0000664000175000017500000000034114177415663015125 0ustar maartenmaartenVersion 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 rewritetortoize-2.0.5/cmake/0000775000175000017500000000000014177415663014335 5ustar maartenmaartentortoize-2.0.5/cmake/FindFilesystem.cmake0000664000175000017500000000432714177415663020272 0ustar maartenmaarten# Simplistic reimplementation of https://github.com/vector-of-bool/CMakeCM/blob/master/modules/FindFilesystem.cmake if(TARGET std::filesystem) return() endif() cmake_minimum_required(VERSION 3.10) include(CMakePushCheckState) include(CheckIncludeFileCXX) include(CheckCXXSourceCompiles) cmake_push_check_state() set(CMAKE_CXX_STANDARD 17) check_include_file_cxx("filesystem" _CXX_FILESYSTEM_HAVE_HEADER) mark_as_advanced(_CXX_FILESYSTEM_HAVE_HEADER) set(code [[ #include #include int main() { auto cwd = std::filesystem::current_path(); return EXIT_SUCCESS; } ]]) if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS_EQUAL 8.4.0) # >> https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed set(CXX_FILESYSTEM_NO_LINK_NEEDED 0) else() # Check a simple filesystem program without any linker flags check_cxx_source_compiles("${code}" CXX_FILESYSTEM_NO_LINK_NEEDED) endif() if(CXX_FILESYSTEM_NO_LINK_NEEDED) set(_found 1) else() set(prev_libraries ${CMAKE_REQUIRED_LIBRARIES}) # Add the libstdc++ flag set(CMAKE_REQUIRED_LIBRARIES ${prev_libraries} -lstdc++fs) check_cxx_source_compiles("${code}" CXX_FILESYSTEM_STDCPPFS_NEEDED) set(_found ${CXX_FILESYSTEM_STDCPPFS_NEEDED}) if(NOT CXX_FILESYSTEM_STDCPPFS_NEEDED) # Try the libc++ flag set(CMAKE_REQUIRED_LIBRARIES ${prev_libraries} -lc++fs) check_cxx_source_compiles("${code}" CXX_FILESYSTEM_CPPFS_NEEDED) set(_found ${CXX_FILESYSTEM_CPPFS_NEEDED}) endif() endif() if(_found) add_library(std::filesystem INTERFACE IMPORTED) set_property(TARGET std::filesystem APPEND PROPERTY INTERFACE_COMPILE_FEATURES cxx_std_17) if(CXX_FILESYSTEM_NO_LINK_NEEDED) # Nothing to add... elseif(CXX_FILESYSTEM_STDCPPFS_NEEDED) set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME stdc++fs) elseif(CXX_FILESYSTEM_CPPFS_NEEDED) set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME c++fs) endif() endif() cmake_pop_check_state() set(Filesystem_FOUND ${_found} CACHE BOOL "TRUE if we can run a program using std::filesystem" FORCE) if(Filesystem_FIND_REQUIRED AND NOT Filesystem_FOUND) message(FATAL_ERROR "Cannot run simple program using std::filesystem") endif() tortoize-2.0.5/cmake/GetGitRevisionDescription.cmake0000664000175000017500000002245714177415663022457 0ustar maartenmaarten# - Returns a version string from Git # # These functions force a re-configure on each git commit so that you can # trust the values of the variables in your build system. # # get_git_head_revision( [ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR]) # # Returns the refspec and sha hash of the current head revision # # git_describe( [ ...]) # # Returns the results of git describe on the source tree, and adjusting # the output so that it tests false if an error occurs. # # git_describe_working_tree( [ ...]) # # Returns the results of git describe on the working tree (--dirty option), # and adjusting the output so that it tests false if an error occurs. # # git_get_exact_tag( [ ...]) # # Returns the results of git describe --exact-match on the source tree, # and adjusting the output so that it tests false if there was no exact # matching tag. # # git_local_changes() # # Returns either "CLEAN" or "DIRTY" with respect to uncommitted changes. # Uses the return code of "git diff-index --quiet HEAD --". # Does not regard untracked files. # # Requires CMake 2.6 or newer (uses the 'function' command) # # Original Author: # 2009-2020 Ryan Pavlik # http://academic.cleardefinition.com # # Copyright 2009-2013, Iowa State University. # Copyright 2013-2020, Ryan Pavlik # Copyright 2013-2020, Contributors # SPDX-License-Identifier: BSL-1.0 # Distributed under the Boost Software License, Version 1.0. # (See accompanying file LICENSE_1_0.txt or copy at # http://www.boost.org/LICENSE_1_0.txt) if(__get_git_revision_description) return() endif() set(__get_git_revision_description YES) # We must run the following at "include" time, not at function call time, # to find the path to this module rather than the path to a calling list file get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH) # Function _git_find_closest_git_dir finds the next closest .git directory # that is part of any directory in the path defined by _start_dir. # The result is returned in the parent scope variable whose name is passed # as variable _git_dir_var. If no .git directory can be found, the # function returns an empty string via _git_dir_var. # # Example: Given a path C:/bla/foo/bar and assuming C:/bla/.git exists and # neither foo nor bar contain a file/directory .git. This wil return # C:/bla/.git # function(_git_find_closest_git_dir _start_dir _git_dir_var) set(cur_dir "${_start_dir}") set(git_dir "${_start_dir}/.git") while(NOT EXISTS "${git_dir}") # .git dir not found, search parent directories set(git_previous_parent "${cur_dir}") get_filename_component(cur_dir "${cur_dir}" DIRECTORY) if(cur_dir STREQUAL git_previous_parent) # We have reached the root directory, we are not in git set(${_git_dir_var} "" PARENT_SCOPE) return() endif() set(git_dir "${cur_dir}/.git") endwhile() set(${_git_dir_var} "${git_dir}" PARENT_SCOPE) endfunction() function(get_git_head_revision _refspecvar _hashvar) _git_find_closest_git_dir("${CMAKE_CURRENT_SOURCE_DIR}" GIT_DIR) if("${ARGN}" STREQUAL "ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR") set(ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR TRUE) else() set(ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR FALSE) endif() if(NOT "${GIT_DIR}" STREQUAL "") file(RELATIVE_PATH _relative_to_source_dir "${CMAKE_SOURCE_DIR}" "${GIT_DIR}") if("${_relative_to_source_dir}" MATCHES "[.][.]" AND NOT ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR) # We've gone above the CMake root dir. set(GIT_DIR "") endif() endif() if("${GIT_DIR}" STREQUAL "") set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE) set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE) return() endif() # Check if the current source dir is a git submodule or a worktree. # In both cases .git is a file instead of a directory. # if(NOT IS_DIRECTORY ${GIT_DIR}) # The following git command will return a non empty string that # points to the super project working tree if the current # source dir is inside a git submodule. # Otherwise the command will return an empty string. # execute_process( COMMAND "${GIT_EXECUTABLE}" rev-parse --show-superproject-working-tree WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" OUTPUT_VARIABLE out ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) if(NOT "${out}" STREQUAL "") # If out is empty, GIT_DIR/CMAKE_CURRENT_SOURCE_DIR is in a submodule file(READ ${GIT_DIR} submodule) string(REGEX REPLACE "gitdir: (.*)$" "\\1" GIT_DIR_RELATIVE ${submodule}) string(STRIP ${GIT_DIR_RELATIVE} GIT_DIR_RELATIVE) get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH) get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE) set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD") else() # GIT_DIR/CMAKE_CURRENT_SOURCE_DIR is in a worktree file(READ ${GIT_DIR} worktree_ref) # The .git directory contains a path to the worktree information directory # inside the parent git repo of the worktree. # string(REGEX REPLACE "gitdir: (.*)$" "\\1" git_worktree_dir ${worktree_ref}) string(STRIP ${git_worktree_dir} git_worktree_dir) _git_find_closest_git_dir("${git_worktree_dir}" GIT_DIR) set(HEAD_SOURCE_FILE "${git_worktree_dir}/HEAD") endif() else() set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD") endif() set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data") if(NOT EXISTS "${GIT_DATA}") file(MAKE_DIRECTORY "${GIT_DATA}") endif() if(NOT EXISTS "${HEAD_SOURCE_FILE}") return() endif() set(HEAD_FILE "${GIT_DATA}/HEAD") configure_file("${HEAD_SOURCE_FILE}" "${HEAD_FILE}" COPYONLY) configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in" "${GIT_DATA}/grabRef.cmake" @ONLY) include("${GIT_DATA}/grabRef.cmake") set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE) set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE) endfunction() function(git_describe _var) if(NOT GIT_FOUND) find_package(Git QUIET) endif() get_git_head_revision(refspec hash) if(NOT GIT_FOUND) set(${_var} "GIT-NOTFOUND" PARENT_SCOPE) return() endif() if(NOT hash) set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE) return() endif() # TODO sanitize #if((${ARGN}" MATCHES "&&") OR # (ARGN MATCHES "||") OR # (ARGN MATCHES "\\;")) # message("Please report the following error to the project!") # message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}") #endif() #message(STATUS "Arguments to execute_process: ${ARGN}") execute_process( COMMAND "${GIT_EXECUTABLE}" describe --tags --always ${hash} ${ARGN} WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" RESULT_VARIABLE res OUTPUT_VARIABLE out ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) if(NOT res EQUAL 0) set(out "${out}-${res}-NOTFOUND") endif() set(${_var} "${out}" PARENT_SCOPE) endfunction() function(git_describe_working_tree _var) if(NOT GIT_FOUND) find_package(Git QUIET) endif() if(NOT GIT_FOUND) set(${_var} "GIT-NOTFOUND" PARENT_SCOPE) return() endif() execute_process( COMMAND "${GIT_EXECUTABLE}" describe --dirty ${ARGN} WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" RESULT_VARIABLE res OUTPUT_VARIABLE out ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) if(NOT res EQUAL 0) set(out "${out}-${res}-NOTFOUND") endif() set(${_var} "${out}" PARENT_SCOPE) endfunction() function(git_get_exact_tag _var) git_describe(out --exact-match ${ARGN}) set(${_var} "${out}" PARENT_SCOPE) endfunction() function(git_local_changes _var) if(NOT GIT_FOUND) find_package(Git QUIET) endif() get_git_head_revision(refspec hash) if(NOT GIT_FOUND) set(${_var} "GIT-NOTFOUND" PARENT_SCOPE) return() endif() if(NOT hash) set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE) return() endif() execute_process( COMMAND "${GIT_EXECUTABLE}" diff-index --quiet HEAD -- WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" RESULT_VARIABLE res OUTPUT_VARIABLE out ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) if(res EQUAL 0) set(${_var} "CLEAN" PARENT_SCOPE) else() set(${_var} "DIRTY" PARENT_SCOPE) endif() endfunction() tortoize-2.0.5/cmake/GetGitRevisionDescription.cmake.in0000664000175000017500000000251214177415663023052 0ustar maartenmaarten# # Internal file for GetGitRevisionDescription.cmake # # Requires CMake 2.6 or newer (uses the 'function' command) # # Original Author: # 2009-2010 Ryan Pavlik # http://academic.cleardefinition.com # Iowa State University HCI Graduate Program/VRAC # # Copyright 2009-2012, Iowa State University # Copyright 2011-2015, Contributors # Distributed under the Boost Software License, Version 1.0. # (See accompanying file LICENSE_1_0.txt or copy at # http://www.boost.org/LICENSE_1_0.txt) # SPDX-License-Identifier: BSL-1.0 set(HEAD_HASH) file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024) string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS) if(HEAD_CONTENTS MATCHES "ref") # named branch string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}") if(EXISTS "@GIT_DIR@/${HEAD_REF}") configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY) else() configure_file("@GIT_DIR@/packed-refs" "@GIT_DATA@/packed-refs" COPYONLY) file(READ "@GIT_DATA@/packed-refs" PACKED_REFS) if(${PACKED_REFS} MATCHES "([0-9a-z]*) ${HEAD_REF}") set(HEAD_HASH "${CMAKE_MATCH_1}") endif() endif() else() # detached HEAD configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY) endif() if(NOT HEAD_HASH) file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024) string(STRIP "${HEAD_HASH}" HEAD_HASH) endif() tortoize-2.0.5/cmake/VersionString.cmake0000664000175000017500000000603414177415663020156 0ustar maartenmaarten# SPDX-License-Identifier: BSD-2-Clause # Copyright (c) 2021 NKI/AVL, Netherlands Cancer Institute # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # 1. Redistributions of source code must retain the above copyright notice, this # list of conditions and the following disclaimer # 2. Redistributions in binary form must reproduce the above copyright notice, # this list of conditions and the following disclaimer in the documentation # and/or other materials provided with the distribution. # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND # ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED # WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR # ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES # (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; # LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND # ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. cmake_minimum_required(VERSION 3.15) # Create a revision file, containing the current git version info, if any function(write_version_header) include(GetGitRevisionDescription) if(NOT(GIT-NOTFOUND OR HEAD-HASH-NOTFOUND)) git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty) if(BUILD_VERSION_STRING MATCHES "build-([0-9]+)-g([0-9a-f]+)(-dirty)?") set(BUILD_GIT_TAGREF "${CMAKE_MATCH_2}") if(CMAKE_MATCH_3) set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}*") else() set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}") endif() endif() else() set(BUILD_VERSION_STRING "no git info available") endif() include_directories(${CMAKE_BINARY_DIR} PRIVATE) string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC) if(ARGC GREATER 0) set(VAR_PREFIX "${ARGV0}") endif() file(WRITE "${CMAKE_BINARY_DIR}/revision.hpp.in" [[// Generated revision file #pragma once #include const char k@VAR_PREFIX@ProjectName[] = "@PROJECT_NAME@"; const char k@VAR_PREFIX@VersionNumber[] = "@PROJECT_VERSION@"; const char k@VAR_PREFIX@VersionGitTag[] = "@BUILD_GIT_TAGREF@"; const char k@VAR_PREFIX@BuildInfo[] = "@BUILD_VERSION_STRING@"; const char k@VAR_PREFIX@BuildDate[] = "@BUILD_DATE_TIME@"; inline void write_version_string(std::ostream &os, bool verbose) { os << k@VAR_PREFIX@ProjectName << " version " << k@VAR_PREFIX@VersionNumber << std::endl; if (verbose) { os << "build: " << k@VAR_PREFIX@BuildInfo << ' ' << k@VAR_PREFIX@BuildDate << std::endl; if (k@VAR_PREFIX@VersionGitTag[0] != 0) os << "git tag: " << k@VAR_PREFIX@VersionGitTag << std::endl; } } ]]) configure_file("${CMAKE_BINARY_DIR}/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY) endfunction() tortoize-2.0.5/doc/0000775000175000017500000000000014177415663014022 5ustar maartenmaartentortoize-2.0.5/doc/tortoize.10000664000175000017500000000330214177415663015761 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-2.0.5/doc/tortoize.html0000664000175000017500000000575414177415663016602 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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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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3383C!h3333338L""ӈ)3{&333331$GB -#L,5\Ĭ04{-=Lm,Y2B3Mɋ04W4/#Y4JJCLmMcԻMC\C04̿F4\ɫ#CE6N&4 5M +D6-ɞmjkVFieE9#hsr,z{fffffxl%溙A61fcä9e:hg>\^uq3RatͨqY*^]f"X&]yfr̶~9 rь33333]& qi6e`eZ&%CBTbY~sgG0L@@@00k$ H9`eFXAܚT0`i̞;ۊɒ{^KgfI&^tCdI`I0LR[]%3nNL ) ͰѮ3` 337r4~q Vc^tY&Ѳ$ Aqӳ{3WrfQPt`A`+{333333LL)6Y8rEM7mL_6Ĉs5CZFI Ѐ 33Lͻr.+}Bif5DAfg8ffffffkc=n3E$2Lz)/\geZhcaF)ai™iiF&&F)نF&,`irfffpdya`i̎6`iYfffpxI욅jigqALBn!{MffffffmHM`i’[ۗ\eYM333333\H6).]L͏H 338 Kw]FPfffffLDH5#F?F"~\RL04qH7BsQcLvlrWPՙ%gpe1/b~ufffff8bYGF &ƞ& ^333333gE80L4MN4W761 ffffff䃲ģL%\Xh0L熴4 @6Lͼ.4j047SF\K04ۖ3333333ƢYȵ(fhJ8v)7NY]blYrYeLڶbKojV9< )hi$1O-Z0ed2e _WmTqZp>[8 _"H[ "4ot9/[sI.ɤlv)Ø.i[8LfmioImilk֙}Be lillǘٹ|CȒŅYދWY3ǑeWhȬK@f#EW[ў6cJ;onxpl3">oignhg9ol9ldciY`f™Jgʩ ģ%eߜ[|InNUŗh(Z\\[8MB],GZ'ߖT^LDOhy kXgor Wqkn*~3e^ʗhyhmR\nFÓi/|Rnƨ header file. */ #undef HAVE_INTTYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_MEMORY_H /* Define if you have POSIX threads libraries and header files. */ #undef HAVE_PTHREAD /* Have PTHREAD_PRIO_INHERIT. */ #undef HAVE_PTHREAD_PRIO_INHERIT /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Define to 1 if ZEEP is found */ #undef HAVE_ZEEP /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Define to necessary symbol if this constant uses a non-standard name on your system. */ #undef PTHREAD_CREATE_JOINABLE /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* Use mrc to store resources */ #undef USE_RSRC tortoize-2.0.5/src/tortoize.cpp0000664000175000017500000010633214177415663016434 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 #include #include #include #include #include #include #include #include #include #include #include #include "cif++/Secondary.hpp" // #include "cif++/Statistics.hpp" #include "cif++/CifUtils.hpp" #include "cif++/Cif++.hpp" #include "cif++/Structure.hpp" #include "cif++/Compound.hpp" #include #include "revision.hpp" #ifdef _MSC_VER //MSVC stdlib.h definitions #define STDIN_FILENO 0 #define STDOUT_FILENO 1 #define STDERR_FILENO 2 #endif namespace po = boost::program_options; namespace fs = std::filesystem; namespace ba = boost::algorithm; using mmcif::Atom; using mmcif::Point; using mmcif::Structure; using mmcif::Monomer; using mmcif::Polymer; using json = zeep::json::element; // -------------------------------------------------------------------- // 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 initilialized 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; } // -------------------------------------------------------------------- // 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 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 * (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, a2; 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 = 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(fs::path dir) { using namespace std::literals; // 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: mmcif::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: mmcif::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; } void DataTable::load(const char* name, std::vector& table, float& mean, float& sd) { using namespace std::literals; auto rfd = cif::loadResource(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); const float* fv = new float[size / sizeof(float) + 1]; rfd->read(reinterpret_cast(const_cast(fv)), size); mean = fv[0]; sd = fv[1]; const StoredData* data = reinterpret_cast(fv + 2); 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) 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 sqrt((N - 1) * sumD / N); } // -------------------------------------------------------------------- json calculateZScores(const Structure& structure) { mmcif::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::tuple pdbID = structure.MapLabelToPDB(res.asymID(), res.seqID(), res.compoundID(), res.authSeqID()); json residue = { { "asymID", res.asymID() }, { "seqID", res.seqID() }, { "compID", res.compoundID() }, { "pdb", { { "strandID", std::get<0>(pdbID) }, { "seqNum", std::get<1>(pdbID) }, { "compID", std::get<2>(pdbID) }, { "insCode", std::get<3>(pdbID) } }} }; std::string aa = res.compoundID(); // 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 (mmcif::kAAMap.find(aa) == mmcif::kAAMap.end()) { if (cif::VERBOSE) std::cerr << "Replacing " << aa << " with ALA" << std::endl; aa = "ALA"; } SecStrType tors_ss, rama_ss; switch (dssp(res)) { case mmcif::ssAlphahelix: tors_ss = SecStrType::helix; break; case mmcif::ssStrand: tors_ss = SecStrType::strand; break; default: tors_ss = SecStrType::other; break; } if (aa != "PRO" and poly[i + 1].compoundID() == "PRO") rama_ss = SecStrType::prepro; else if (aa == "PRO" && res.isCis()) rama_ss = SecStrType::cis; else rama_ss = tors_ss; #pragma warning "todo" auto& rd = tbl.loadRamachandranData(aa, rama_ss); auto zr = rd.zscore(phi, psi); residue["ramachandran"] = { { "ss-type", boost::lexical_cast(rama_ss) }, { "z-score", zr } }; ramaZScorePerResidue.push_back(zr); ramaZScoreSum += zr; ++ramaZScoreCount; try { float zt = nan("1"); auto chiCount = res.nrOfChis(); 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", boost::lexical_cast(tors_ss) }, { "z-score", zt } }; } } catch (const std::exception& e) { if (cif::VERBOSE) std::cerr << e.what() << '\n'; } residues.push_back(residue); } } float ramaVsRand = ramaZScoreSum / ramaZScoreCount; float torsVsRand = 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 }, }; } // -------------------------------------------------------------------- #if WEBSERVICE 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; mmcif::CompoundFactory::instance().pushDictionary(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" } } } }; // -------------------------------------------------------------------- mmcif::File f(file.data(), file.length()); std::set models; for (auto r: f.data()["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) { Structure structure(f, model); data["model"][std::to_string(model)] = calculateZScores(structure); } if (not dictFile.empty()) { mmcif::CompoundFactory::instance().popDictionary(); fs::remove(dictFile); } return data; } catch (...) { std::error_code ec; if (not dictFile.empty()) { mmcif::CompoundFactory::instance().popDictionary(); 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; mmcif::CompoundFactory::init(true); int result = 0; po::options_description visible_options(PACKAGE_NAME " [options] input [output]"); visible_options.add_options() ("log", po::value(), "Write log to this file") ("help,h", "Display help message") ("version", "Print version") ("address", po::value()->default_value("0.0.0.0"), "External address") ("port", po::value()->default_value(10350), "Port to listen to") ("user,u", po::value()->default_value("www-data"), "User to run the daemon") ("no-daemon,F", "Do not fork into background" ) ("verbose,v", "verbose output") ; po::options_description hidden_options("hidden options"); hidden_options.add_options() ("command", po::value(), "The command to execute") ("debug,d", po::value(), "Debug level (for even more verbose output)") ; po::options_description cmdline_options; cmdline_options.add(visible_options).add(hidden_options); po::positional_options_description p; p.add("command", 1); po::variables_map vm; po::store(po::command_line_parser(argc, argv).options(cmdline_options).positional(p).run(), vm); po::notify(vm); // -------------------------------------------------------------------- std::string secret; if (vm.count("secret")) secret = vm["secret"].as(); else { secret = zeep::encode_base64(zeep::random_hash()); std::cerr << "starting with created secret " << secret << std::endl; } std::string user = vm["user"].as(); std::string address = vm["address"].as(); uint16_t port = vm["port"].as(); 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; }, PACKAGE_NAME ); std::string command = vm["command"].as(); if (command == "start") { std::cout << "starting server at http://" << address << ':' << port << '/' << std::endl; if (vm.count("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; } #endif // -------------------------------------------------------------------- int pr_main(int argc, char* argv[]) { using namespace std::literals; #if WEBSERVICE if (argc > 2 and argv[1] == "server"s) return start_server(argc - 1, argv + 1); #endif po::options_description visible_options(fs::path(argv[0]).filename().string() + " [options] input [output]"); visible_options.add_options() ("log", po::value(), "Write log to this file") ("dict", po::value>(), "Dictionary file containing restraints for residues in this specific target, can be specified multiple times.") ("help,h", "Display help message") ("version", "Print version") ("verbose,v", "verbose output") ; po::options_description hidden_options("hidden options"); hidden_options.add_options() ("xyzin", po::value(), "coordinates file") ("output", po::value(), "Output to this file") ("debug,d", po::value(), "Debug level (for even more verbose output)") ("build", po::value(), "Build a binary data table") ; po::options_description cmdline_options; cmdline_options.add(visible_options).add(hidden_options); 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); // -------------------------------------------------------------------- if (vm.count("version")) { write_version_string(std::cout, vm.count("verbose")); exit(0); } if (vm.count("help")) { std::cout << visible_options << 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 (vm.count("build")) { buildDataFile(vm["build"].as()); exit(0); } if (vm.count("xyzin") == 0) { std::cerr << "Input file not specified" << std::endl; exit(1); } cif::VERBOSE = vm.count("verbose") != 0; if (vm.count("debug")) cif::VERBOSE = vm["debug"].as(); if (vm.count("log")) { if (not vm.count("output")) { std::cerr << "If you specify a log file, you should also specify an output file" << std::endl; exit(1); } std::string logFile = vm["log"].as(); // 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 (vm.count("dict")) { for (auto dict: vm["dict"].as>()) mmcif::CompoundFactory::instance().pushDictionary(dict); } // -------------------------------------------------------------------- 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" } } } }; // -------------------------------------------------------------------- mmcif::File f(vm["xyzin"].as()); std::set models; for (auto r: f.data()["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) { Structure structure(f, model); data["model"][std::to_string(model)] = calculateZScores(structure); } if (vm.count("output")) { std::ofstream of(vm["output"].as()); 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); } } #if not defined(TORTOIZE_TEST_NO_MAIN) 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; } #endiftortoize-2.0.5/test/0000775000175000017500000000000014177415663014234 5ustar maartenmaartentortoize-2.0.5/test/unit-test.cpp0000664000175000017500000000003114177415663016666 0ustar maartenmaartenint main() { return 0; }tortoize-2.0.5/webapp/0000775000175000017500000000000014177415663014533 5ustar maartenmaartentortoize-2.0.5/webapp/index.js0000664000175000017500000000347514177415663016211 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[`${f}-jackknife-sd`]).toFixed(2); row.appendChild(td); } tbody.appendChild(row); } this.table.style.display = 'unset'; } } window.addEventListener('load', () => { bsCustomFileInput.init(); new Tortoize(); });tortoize-2.0.5/webpack.config.js0000664000175000017500000000374714177415663016506 0ustar maartenmaartenconst MiniCssExtractPlugin = require('mini-css-extract-plugin'); const { CleanWebpackPlugin } = require('clean-webpack-plugin'); const UglifyJsPlugin = require('uglify-js-plugin'); const webpack = require("webpack"); const SCRIPTS = __dirname + "/webapp/"; const SCSS = __dirname + "/scss/"; const DEST = __dirname + "/docroot/scripts/"; module.exports = (env) => { const webpackConf = { entry: { 'pdb-redo-style': SCSS + "pdb-redo-bootstrap.scss", 'index': SCRIPTS + 'index.js' }, module: { rules: [ { test: /\.js$/, 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: /\.(png)/, loader: 'file-loader', options: { name: '[name].[ext]', outputPath: 'images/', publicPath: '../images/' } }, { test: /\.s[ac]ss$/i, use: [ MiniCssExtractPlugin.loader, 'css-loader', 'sass-loader' ] } ] }, output: { path: DEST, filename: "./[name].js" }, plugins: [ new CleanWebpackPlugin({ cleanOnceBeforeBuildPatterns: [ 'css/**/*', 'scripts/**/*', 'fonts/**/*', '!images*' ] }), new webpack.ProvidePlugin({ $: 'jquery', jQuery: 'jquery', CodeMirror: 'codemirror' }), new MiniCssExtractPlugin({ filename: '../css/[name].css', chunkFilename: '../css/[id].css' }) ] }; const PRODUCTIE = env != null && env.PRODUCTIE; if (PRODUCTIE) { webpackConf.mode = "production"; webpackConf.plugins.push(new UglifyJsPlugin({parallel: 4})) } else { webpackConf.mode = "development"; webpackConf.devtool = 'source-map'; webpackConf.plugins.push(new webpack.optimize.AggressiveMergingPlugin()) } return webpackConf; }; tortoize-2.0.5/yarn.lock0000664000175000017500000037021314177415663015106 0ustar maartenmaarten# THIS IS AN AUTOGENERATED FILE. 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