[med-svn] [Git][med-team/dssp][upstream] New upstream version 4.5.5
Maarten L. Hekkelman (@mhekkel-guest)
gitlab at salsa.debian.org
Sun Aug 31 12:31:24 BST 2025
Maarten L. Hekkelman pushed to branch upstream at Debian Med / dssp
Commits:
a97d1798 by Maarten L. Hekkelman at 2025-08-31T12:53:32+02:00
New upstream version 4.5.5
- - - - -
25 changed files:
- − .github/workflows/build-documentation.yml
- .github/workflows/cmake-multi-platform.yml
- .gitignore
- CMakeLists.txt
- Dockerfile
- README.md
- changelog
- + cmake/CPM.cmake
- doc/mkdssp.md
- libdssp/CMakeLists.txt
- libdssp/cmake/dsspConfig.cmake.in → libdssp/cmake/dssp-config.cmake.in
- libdssp/include/dssp.hpp
- libdssp/mmcif_pdbx/dssp-extension.dic
- libdssp/src/dssp-io.cpp
- libdssp/src/dssp-io.hpp
- libdssp/src/dssp.cpp
- + python-module/CMakeLists.txt
- + python-module/dssp-python-plugin.cpp
- + python-module/test-mkdssp.py
- src/mkdssp.cpp
- test/1cbs-dssp.cif
- test/CMakeLists.txt
- + test/pdb1cbs.ent.gz
- + test/test-python.py
- test/unit-test-dssp.cpp
Changes:
=====================================
.github/workflows/build-documentation.yml deleted
=====================================
@@ -1,65 +0,0 @@
-# This starter workflow is for a CMake project running on multiple platforms. There is a different starter workflow if you just want a single platform.
-# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-single-platform.yml
-name: publish docs
-
-on:
- push:
- branches: [ "trunk" ]
-
-permissions:
- contents: read
- pages: write
- id-token: write
-
-concurrency:
- group: "pages"
- cancel-in-progress: false
-
-jobs:
- docs:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout at v1
-
- - name: Set reusable strings
- # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
- 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 cmake doxygen
-
- - uses: actions/setup-python at v4
- with:
- python-version: '3.9'
- cache: 'pip' # caching pip dependencies
- - run: pip install -r docs/requirements.txt
-
- - name: Configure CMake
- run: cmake -S . -B build -DBUILD_DOCUMENTATION=ON -DBUILD_TESTING=OFF
-
- - name: Run Sphinx
- run: |
- cmake --build build --target Sphinx-mcfp
- ls -l ${{ steps.strings.outputs.build-output-dir }}
- ls -l ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
-
- - name: Upload artifact
- uses: actions/upload-pages-artifact at v2
- with:
- path: ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
-
- deploy:
- environment:
- name: github-pages
- url: ${{ steps.deployment.outputs.page_url }}
-
- runs-on: ubuntu-latest
- needs: docs
-
- steps:
- - name: Deploy to GitHub Pages
- id: deployment
- uses: actions/deploy-pages at v2
=====================================
.github/workflows/cmake-multi-platform.yml
=====================================
@@ -15,6 +15,7 @@ jobs:
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: [ 3.13 ]
include:
- os: windows-latest
cpp_compiler: cl
@@ -34,7 +35,12 @@ jobs:
- name: Install Catch2 Ubuntu
if: matrix.os == 'ubuntu-latest'
run: >
- sudo apt-get update && sudo apt-get install catch2
+ sudo apt-get update && sudo apt-get install catch2 libpython3-all-dev libboost1.83-all-dev
+
+ - name: setup python
+ uses: actions/setup-python at v5
+ with:
+ python-version: ${{ matrix.python-version }}
- name: Install Catch2 macOS
if: matrix.os == 'macos-latest'
@@ -52,6 +58,7 @@ jobs:
-DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
-DCMAKE_BUILD_TYPE=Release
-DBUILD_TESTING=ON
+ -DBUILD_PYTHON_MODULE=ON
-S ${{ github.workspace }}
- name: Build
@@ -59,7 +66,7 @@ jobs:
- name: Test
working-directory: ${{ steps.strings.outputs.build-output-dir }}
- run: ctest --build-config Release --output-on-failure -R dssp
+ run: ctest --build-config Release --output-on-failure
env:
LIBCIFPP_DATA_DIR: ${{ steps.strings.outputs.build-output-dir }}/_deps/cifpp-src/rsrc
=====================================
.gitignore
=====================================
@@ -5,3 +5,4 @@ build/
**/*.dssp
src/revision.hpp
libdssp/src/revision.hpp
+python-module/mkdssp.so
=====================================
CMakeLists.txt
=====================================
@@ -25,13 +25,20 @@
cmake_minimum_required(VERSION 3.23)
# set the project name
-project(mkdssp VERSION 4.4.10 LANGUAGES CXX)
+project(mkdssp VERSION 4.5.5 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+include(CPM)
include(CTest)
include(VersionString)
+# The default build type must be set before project()
+if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR AND NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+ set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
+ set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
+
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)
@@ -41,10 +48,12 @@ endif()
# Optionally build a version to be installed inside CCP4
option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4" OFF)
option(BUILD_DOCUMENTATION "Generate the documentation files using pandoc" OFF)
+option(BUILD_PYTHON_MODULE "Build an experimental Python module" OFF)
+option(INSTALL_LIBRARY "Install the libdssp library" OFF)
if(BUILD_FOR_CCP4)
if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
- message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced")
+ message(FATAL_ERROR "dssp: A CCP4 built was requested but CCP4 was not sourced")
else()
list(APPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
list(APPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
@@ -56,24 +65,34 @@ if(BUILD_FOR_CCP4)
endif()
endif()
-if(MSVC)
- # make msvc standards compliant...
- add_compile_options(/permissive-)
- add_link_options(/NODEFAULTLIB:library)
+if(WIN32)
+ if(${CMAKE_SYSTEM_VERSION} GREATER_EQUAL 10) # Windows 10
+ add_definitions(-D _WIN32_WINNT=0x0A00)
+ elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.3) # Windows 8.1
+ add_definitions(-D _WIN32_WINNT=0x0603)
+ elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.2) # Windows 8
+ add_definitions(-D _WIN32_WINNT=0x0602)
+ elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.1) # Windows 7
+ add_definitions(-D _WIN32_WINNT=0x0601)
+ elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.0) # Windows Vista
+ add_definitions(-D _WIN32_WINNT=0x0600)
+ else() # Windows XP (5.1)
+ add_definitions(-D _WIN32_WINNT=0x0501)
+ endif()
- 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 ${ver})
+ # Man, this is 2024 we're living in...
+ add_definitions(-DNOMINMAX)
- set(${version} "0x${ver}")
- endif()
- endmacro()
+ # We do not want to write an export file for all our symbols...
+ set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
+endif()
- get_WIN32_WINNT(ver)
- add_definitions(-D_WIN32_WINNT=${ver})
+if(MSVC)
+ # make msvc standards compliant...
+ add_compile_options(/permissive- /bigobj)
+ add_link_options(/NODEFAULTLIB:library)
+ # This is dubious...
if(BUILD_SHARED_LIBS)
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
else()
@@ -85,69 +104,71 @@ endif()
write_version_header("${CMAKE_CURRENT_SOURCE_DIR}/src")
# Optionally use mrc to create resources
-find_package(Mrc QUIET)
+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")
+ message(STATUS "dssp: Not using resources since mrc was not found")
endif()
set(CMAKE_THREAD_PREFER_PTHREAD)
set(THREADS_PREFER_PTHREAD_FLAG)
find_package(Threads)
-find_package(libmcfp QUIET)
-
-if(NOT (libmcfp_FOUND OR TARGET libmcfp))
- include(FetchContent)
-
- if(CMAKE_VERSION GREATER_EQUAL 3.28)
- set(EXLC "EXCLUDE_FROM_ALL")
- endif()
-
- FetchContent_Declare(
- libmcfp
- ${EXLC}
- GIT_REPOSITORY https://github.com/mhekkel/libmcfp
- GIT_TAG v1.3.1)
- FetchContent_MakeAvailable(libmcfp)
+CPMFindPackage(
+ NAME mcfp
+ GIT_REPOSITORY https://github.com/mhekkel/libmcfp
+ GIT_TAG v1.4.2
+ EXCLUDE_FROM_ALL YES)
+
+# CPMFindPackage does not pass on variables set with set_and_check
+# Working around this here
+find_package(cifpp 8.0.1 QUIET)
+
+if(NOT cifpp_FOUND)
+ CPMAddPackage(
+ NAME cifpp
+ GIT_REPOSITORY https://github.com/pdb-redo/libcifpp.git
+ GIT_TAG v8.0.1
+ EXCLUDE_FROM_ALL YES)
endif()
-if(NOT TARGET cifpp AND NOT cifpp_FOUND)
- include(FetchContent)
-
- find_package(cifpp 7.0.7 QUIET)
-
- if(NOT cifpp_FOUND)
- set(CIFPP_DOWNLOAD_CCD OFF)
- set(SAVED_BUILD_TESTING "${BUILD_TESTING}")
- set(BUILD_TESTING OFF)
-
- FetchContent_Declare(
- cifpp
- ${EXLC}
- GIT_REPOSITORY https://github.com/pdb-redo/libcifpp.git
- GIT_TAG v7.0.7
- )
-
- FetchContent_MakeAvailable(cifpp)
-
- set(BUILD_TESTING ${SAVED_BUILD_TESTING})
- endif()
+if(TARGET cifpp)
+ get_target_property(CIFPP_SOURCE_DIR cifpp SOURCE_DIR)
+ set(CIFPP_SHARE_DIR share/libcifpp)
+ set(CIFPP_DATA_DIR ${CIFPP_SOURCE_DIR}/rsrc)
+elseif(DEFINED CIFPP_SHARE_DIR)
+ set(CIFPP_DATA_DIR ${CIFPP_SHARE_DIR})
+else()
+ message(FATAL_ERROR "dssp: The CIFPP_SHARE_DIR variable is not found in the cifpp configuration files")
endif()
-add_subdirectory(libdssp)
+if(INSTALL_LIBRARY)
+ add_subdirectory(libdssp)
+else()
+ add_subdirectory(libdssp EXCLUDE_FROM_ALL)
+endif()
add_executable(mkdssp ${CMAKE_CURRENT_SOURCE_DIR}/src/mkdssp.cpp)
-target_link_libraries(mkdssp PRIVATE libmcfp::libmcfp dssp::dssp)
+target_link_libraries(mkdssp PRIVATE mcfp::mcfp dssp::dssp)
if(USE_RSRC)
mrc_target_resources(mkdssp
- ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic
- ${CIFPP_SHARE_DIR}/mmcif_ddl.dic
+ ${CIFPP_DATA_DIR}/mmcif_pdbx.dic
${CMAKE_CURRENT_SOURCE_DIR}/libdssp/mmcif_pdbx/dssp-extension.dic)
+else()
+ get_target_property(LIBDSSP_SOURCE_DIR dssp SOURCE_DIR)
+
+ install(FILES
+ ${CMAKE_CURRENT_SOURCE_DIR}/libdssp/mmcif_pdbx/dssp-extension.dic
+ DESTINATION ${CIFPP_SHARE_DIR})
+
+ if(TARGET cifpp)
+ install(FILES ${CIFPP_DATA_DIR}/mmcif_pdbx.dic
+ DESTINATION ${CIFPP_SHARE_DIR})
+ endif()
endif()
# Install rules
@@ -155,23 +176,6 @@ install(TARGETS ${PROJECT_NAME}
RUNTIME DESTINATION bin
)
-if(NOT USE_RSRC)
- # When building cifpp ourselves, we need to find where libcifpp
- # expects the data files to be located.
- if(TARGET cifpp)
- get_target_property(DSSP_DATA_DIR cifpp CIFPP_DATA_DIR)
- get_target_property(CIFPP_SOURCE_DIR cifpp SOURCE_DIR)
-
- install(
- FILES ${CIFPP_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
- ${CIFPP_SOURCE_DIR}/rsrc/mmcif_ddl.dic
- ${CMAKE_CURRENT_SOURCE_DIR}/libdssp/mmcif_pdbx/dssp-extension.dic
- DESTINATION ${DSSP_DATA_DIR})
- else()
-
- endif()
-endif()
-
if(BUILD_DOCUMENTATION)
add_subdirectory(doc)
endif()
@@ -187,10 +191,15 @@ if(EXISTS "${CCP4}/html")
endif()
# test
-if(BUILD_TESTING)
+if(BUILD_TESTING AND PROJECT_IS_TOP_LEVEL)
add_subdirectory(test)
endif()
+# Python
+if(BUILD_PYTHON_MODULE)
+ add_subdirectory(python-module)
+endif()
+
include(InstallRequiredSystemLibraries)
set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
=====================================
Dockerfile
=====================================
@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
ENV TZ="Europe/Amsterdam"
RUN apt-get update && \
@@ -9,27 +9,6 @@ RUN apt-get update && \
WORKDIR /build
-# Build and install libcifpp
-# https://github.com/PDB-REDO/libcifpp
-RUN cd /build && \
- git clone https://github.com/PDB-REDO/libcifpp.git && \
- cd libcifpp && \
- cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
- -DBUILD_TESTING=OFF -DCIFPP_DOWNLOAD_CCD=OFF && \
- cmake --build build -j $(nproc) && \
- cmake --install build && \
- echo "libcifpp installed"
-
-# Build and install libmcfp
-# https://github.com/mhekkel/libmcfp
-RUN cd /build && \
- git clone https://github.com/mhekkel/libmcfp.git && \
- cd libmcfp && \
- cmake -S . -B build -DBUILD_TESTING=OFF && \
- cmake --build build -j $(nproc) && \
- cmake --install build && \
- echo "libmcfp installed"
-
# Build and install dssp
COPY . /src
RUN cd /src && \
=====================================
README.md
=====================================
@@ -1,7 +1,7 @@
[](https://github.com/pdb-redo/dssp/actions)
[](https://github.com/pdb-redo/dssp/LICENSE)
-DSSP 4.4
+DSSP 4.5
========
This is a rewrite of DSSP, now offering full mmCIF support. The difference
@@ -40,6 +40,42 @@ cmake --build build
cmake --install build
```
+Python module
+-------------
+
+Since version 4.5.2 it is possible to build a Python module to directy work
+with DSSP info inside your Python scripts. To build and install the Python
+module use the following commands instead:
+
+```console
+git clone https://github.com/PDB-REDO/dssp.git
+cd dssp
+cmake -S . -B build -DBUILD_PYTHON_MODULE=ON
+cmake --build build
+sudo cmake --install build
+```
+
+After that you can use dssp in a python script, like this:
+
+```python
+from mkdssp import dssp
+import os
+import gzip
+
+file_path = os.path.join("..", "test", "1cbs.cif.gz")
+
+with gzip.open(file_path, "rt") as f:
+ file_content = f.read()
+
+dssp = dssp(file_content)
+
+print("residues: ", dssp.statistics.residues)
+
+for res in dssp:
+ print(res.asym_id, res.seq_id, res.compound_id, res.type)
+
+```
+
Usage
-----
=====================================
changelog
=====================================
@@ -1,3 +1,33 @@
+Version 4.5.5
+- Clean up old DSSP data before writing new
+- Regression: check for pdbx_poly_seq_scheme and if missing
+ use the repair mode to read the file. (i.e. cif::pdb::read)
+
+Version 4.5.4
+- Update reference information
+- Better fix for locating/installing dictionary files
+
+Version 4.5.3
+- Fix makefile to locate dictionary files
+
+Version 4.5.2
+- Use find_package before fetching libraries, again
+- Added Python module
+
+Version 4.5.1
+- Only use reconstructing load option when needed to
+ save lots of time on large structures
+- Fixes in writing the audit_conform category
+- Fix dictionary location
+
+Version 4.5
+- Based on new libcifpp version 8
+- Fixed Dockerfile
+
+Version 4.4.11
+- Write proper audit_conform records
+- Updated dssp-extension.dic file to include version info
+
Version 4.4.10
- Support for installing in environments that do not use resources,
this time for real.
=====================================
cmake/CPM.cmake
=====================================
@@ -0,0 +1,1291 @@
+# CPM.cmake - CMake's missing package manager
+# ===========================================
+# See https://github.com/cpm-cmake/CPM.cmake for usage and update instructions.
+#
+# MIT License
+# -----------
+#[[
+ Copyright (c) 2019-2023 Lars Melchior and contributors
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in all
+ copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+]]
+
+cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
+
+# Initialize logging prefix
+if(NOT CPM_INDENT)
+ set(CPM_INDENT
+ "CPM:"
+ CACHE INTERNAL ""
+ )
+endif()
+
+if(NOT COMMAND cpm_message)
+ function(cpm_message)
+ message(${ARGV})
+ endfunction()
+endif()
+
+if(DEFINED EXTRACTED_CPM_VERSION)
+ set(CURRENT_CPM_VERSION "${EXTRACTED_CPM_VERSION}${CPM_DEVELOPMENT}")
+else()
+ set(CURRENT_CPM_VERSION 0.40.8)
+endif()
+
+get_filename_component(CPM_CURRENT_DIRECTORY "${CMAKE_CURRENT_LIST_DIR}" REALPATH)
+if(CPM_DIRECTORY)
+ if(NOT CPM_DIRECTORY STREQUAL CPM_CURRENT_DIRECTORY)
+ if(CPM_VERSION VERSION_LESS CURRENT_CPM_VERSION)
+ message(
+ AUTHOR_WARNING
+ "${CPM_INDENT} \
+A dependency is using a more recent CPM version (${CURRENT_CPM_VERSION}) than the current project (${CPM_VERSION}). \
+It is recommended to upgrade CPM to the most recent version. \
+See https://github.com/cpm-cmake/CPM.cmake for more information."
+ )
+ endif()
+ if(${CMAKE_VERSION} VERSION_LESS "3.17.0")
+ include(FetchContent)
+ endif()
+ return()
+ endif()
+
+ get_property(
+ CPM_INITIALIZED GLOBAL ""
+ PROPERTY CPM_INITIALIZED
+ SET
+ )
+ if(CPM_INITIALIZED)
+ return()
+ endif()
+endif()
+
+if(CURRENT_CPM_VERSION MATCHES "development-version")
+ message(
+ WARNING "${CPM_INDENT} Your project is using an unstable development version of CPM.cmake. \
+Please update to a recent release if possible. \
+See https://github.com/cpm-cmake/CPM.cmake for details."
+ )
+endif()
+
+set_property(GLOBAL PROPERTY CPM_INITIALIZED true)
+
+macro(cpm_set_policies)
+ # the policy allows us to change options without caching
+ cmake_policy(SET CMP0077 NEW)
+ set(CMAKE_POLICY_DEFAULT_CMP0077 NEW)
+
+ # the policy allows us to change set(CACHE) without caching
+ if(POLICY CMP0126)
+ cmake_policy(SET CMP0126 NEW)
+ set(CMAKE_POLICY_DEFAULT_CMP0126 NEW)
+ endif()
+
+ # The policy uses the download time for timestamp, instead of the timestamp in the archive. This
+ # allows for proper rebuilds when a projects url changes
+ if(POLICY CMP0135)
+ cmake_policy(SET CMP0135 NEW)
+ set(CMAKE_POLICY_DEFAULT_CMP0135 NEW)
+ endif()
+
+ # treat relative git repository paths as being relative to the parent project's remote
+ if(POLICY CMP0150)
+ cmake_policy(SET CMP0150 NEW)
+ set(CMAKE_POLICY_DEFAULT_CMP0150 NEW)
+ endif()
+endmacro()
+cpm_set_policies()
+
+option(CPM_USE_LOCAL_PACKAGES "Always try to use `find_package` to get dependencies"
+ $ENV{CPM_USE_LOCAL_PACKAGES}
+)
+option(CPM_LOCAL_PACKAGES_ONLY "Only use `find_package` to get dependencies"
+ $ENV{CPM_LOCAL_PACKAGES_ONLY}
+)
+option(CPM_DOWNLOAD_ALL "Always download dependencies from source" $ENV{CPM_DOWNLOAD_ALL})
+option(CPM_DONT_UPDATE_MODULE_PATH "Don't update the module path to allow using find_package"
+ $ENV{CPM_DONT_UPDATE_MODULE_PATH}
+)
+option(CPM_DONT_CREATE_PACKAGE_LOCK "Don't create a package lock file in the binary path"
+ $ENV{CPM_DONT_CREATE_PACKAGE_LOCK}
+)
+option(CPM_INCLUDE_ALL_IN_PACKAGE_LOCK
+ "Add all packages added through CPM.cmake to the package lock"
+ $ENV{CPM_INCLUDE_ALL_IN_PACKAGE_LOCK}
+)
+option(CPM_USE_NAMED_CACHE_DIRECTORIES
+ "Use additional directory of package name in cache on the most nested level."
+ $ENV{CPM_USE_NAMED_CACHE_DIRECTORIES}
+)
+
+set(CPM_VERSION
+ ${CURRENT_CPM_VERSION}
+ CACHE INTERNAL ""
+)
+set(CPM_DIRECTORY
+ ${CPM_CURRENT_DIRECTORY}
+ CACHE INTERNAL ""
+)
+set(CPM_FILE
+ ${CMAKE_CURRENT_LIST_FILE}
+ CACHE INTERNAL ""
+)
+set(CPM_PACKAGES
+ ""
+ CACHE INTERNAL ""
+)
+set(CPM_DRY_RUN
+ OFF
+ CACHE INTERNAL "Don't download or configure dependencies (for testing)"
+)
+
+if(DEFINED ENV{CPM_SOURCE_CACHE})
+ set(CPM_SOURCE_CACHE_DEFAULT $ENV{CPM_SOURCE_CACHE})
+else()
+ set(CPM_SOURCE_CACHE_DEFAULT OFF)
+endif()
+
+set(CPM_SOURCE_CACHE
+ ${CPM_SOURCE_CACHE_DEFAULT}
+ CACHE PATH "Directory to download CPM dependencies"
+)
+
+if(NOT CPM_DONT_UPDATE_MODULE_PATH AND NOT DEFINED CMAKE_FIND_PACKAGE_REDIRECTS_DIR)
+ set(CPM_MODULE_PATH
+ "${CMAKE_BINARY_DIR}/CPM_modules"
+ CACHE INTERNAL ""
+ )
+ # remove old modules
+ file(REMOVE_RECURSE ${CPM_MODULE_PATH})
+ file(MAKE_DIRECTORY ${CPM_MODULE_PATH})
+ # locally added CPM modules should override global packages
+ set(CMAKE_MODULE_PATH "${CPM_MODULE_PATH};${CMAKE_MODULE_PATH}")
+endif()
+
+if(NOT CPM_DONT_CREATE_PACKAGE_LOCK)
+ set(CPM_PACKAGE_LOCK_FILE
+ "${CMAKE_BINARY_DIR}/cpm-package-lock.cmake"
+ CACHE INTERNAL ""
+ )
+ file(WRITE ${CPM_PACKAGE_LOCK_FILE}
+ "# CPM Package Lock\n# This file should be committed to version control\n\n"
+ )
+endif()
+
+include(FetchContent)
+
+# Try to infer package name from git repository uri (path or url)
+function(cpm_package_name_from_git_uri URI RESULT)
+ if("${URI}" MATCHES "([^/:]+)/?.git/?$")
+ set(${RESULT}
+ ${CMAKE_MATCH_1}
+ PARENT_SCOPE
+ )
+ else()
+ unset(${RESULT} PARENT_SCOPE)
+ endif()
+endfunction()
+
+# Try to infer package name and version from a url
+function(cpm_package_name_and_ver_from_url url outName outVer)
+ if(url MATCHES "[/\\?]([a-zA-Z0-9_\\.-]+)\\.(tar|tar\\.gz|tar\\.bz2|zip|ZIP)(\\?|/|$)")
+ # We matched an archive
+ set(filename "${CMAKE_MATCH_1}")
+
+ if(filename MATCHES "([a-zA-Z0-9_\\.-]+)[_-]v?(([0-9]+\\.)*[0-9]+[a-zA-Z0-9]*)")
+ # We matched <name>-<version> (ie foo-1.2.3)
+ set(${outName}
+ "${CMAKE_MATCH_1}"
+ PARENT_SCOPE
+ )
+ set(${outVer}
+ "${CMAKE_MATCH_2}"
+ PARENT_SCOPE
+ )
+ elseif(filename MATCHES "(([0-9]+\\.)+[0-9]+[a-zA-Z0-9]*)")
+ # We couldn't find a name, but we found a version
+ #
+ # In many cases (which we don't handle here) the url would look something like
+ # `irrelevant/ACTUAL_PACKAGE_NAME/irrelevant/1.2.3.zip`. In such a case we can't possibly
+ # distinguish the package name from the irrelevant bits. Moreover if we try to match the
+ # package name from the filename, we'd get bogus at best.
+ unset(${outName} PARENT_SCOPE)
+ set(${outVer}
+ "${CMAKE_MATCH_1}"
+ PARENT_SCOPE
+ )
+ else()
+ # Boldly assume that the file name is the package name.
+ #
+ # Yes, something like `irrelevant/ACTUAL_NAME/irrelevant/download.zip` will ruin our day, but
+ # such cases should be quite rare. No popular service does this... we think.
+ set(${outName}
+ "${filename}"
+ PARENT_SCOPE
+ )
+ unset(${outVer} PARENT_SCOPE)
+ endif()
+ else()
+ # No ideas yet what to do with non-archives
+ unset(${outName} PARENT_SCOPE)
+ unset(${outVer} PARENT_SCOPE)
+ endif()
+endfunction()
+
+function(cpm_find_package NAME VERSION)
+ string(REPLACE " " ";" EXTRA_ARGS "${ARGN}")
+ find_package(${NAME} ${VERSION} ${EXTRA_ARGS} QUIET)
+ if(${CPM_ARGS_NAME}_FOUND)
+ if(DEFINED ${CPM_ARGS_NAME}_VERSION)
+ set(VERSION ${${CPM_ARGS_NAME}_VERSION})
+ endif()
+ cpm_message(STATUS "${CPM_INDENT} Using local package ${CPM_ARGS_NAME}@${VERSION}")
+ CPMRegisterPackage(${CPM_ARGS_NAME} "${VERSION}")
+ set(CPM_PACKAGE_FOUND
+ YES
+ PARENT_SCOPE
+ )
+ else()
+ set(CPM_PACKAGE_FOUND
+ NO
+ PARENT_SCOPE
+ )
+ endif()
+endfunction()
+
+# Create a custom FindXXX.cmake module for a CPM package This prevents `find_package(NAME)` from
+# finding the system library
+function(cpm_create_module_file Name)
+ if(NOT CPM_DONT_UPDATE_MODULE_PATH)
+ if(DEFINED CMAKE_FIND_PACKAGE_REDIRECTS_DIR)
+ # Redirect find_package calls to the CPM package. This is what FetchContent does when you set
+ # OVERRIDE_FIND_PACKAGE. The CMAKE_FIND_PACKAGE_REDIRECTS_DIR works for find_package in CONFIG
+ # mode, unlike the Find${Name}.cmake fallback. CMAKE_FIND_PACKAGE_REDIRECTS_DIR is not defined
+ # in script mode, or in CMake < 3.24.
+ # https://cmake.org/cmake/help/latest/module/FetchContent.html#fetchcontent-find-package-integration-examples
+ string(TOLOWER ${Name} NameLower)
+ file(WRITE ${CMAKE_FIND_PACKAGE_REDIRECTS_DIR}/${NameLower}-config.cmake
+ "include(\"\${CMAKE_CURRENT_LIST_DIR}/${NameLower}-extra.cmake\" OPTIONAL)\n"
+ "include(\"\${CMAKE_CURRENT_LIST_DIR}/${Name}Extra.cmake\" OPTIONAL)\n"
+ )
+ file(WRITE ${CMAKE_FIND_PACKAGE_REDIRECTS_DIR}/${NameLower}-config-version.cmake
+ "set(PACKAGE_VERSION_COMPATIBLE TRUE)\n" "set(PACKAGE_VERSION_EXACT TRUE)\n"
+ )
+ else()
+ file(WRITE ${CPM_MODULE_PATH}/Find${Name}.cmake
+ "include(\"${CPM_FILE}\")\n${ARGN}\nset(${Name}_FOUND TRUE)"
+ )
+ endif()
+ endif()
+endfunction()
+
+# Find a package locally or fallback to CPMAddPackage
+function(CPMFindPackage)
+ set(oneValueArgs NAME VERSION GIT_TAG FIND_PACKAGE_ARGUMENTS)
+
+ cmake_parse_arguments(CPM_ARGS "" "${oneValueArgs}" "" ${ARGN})
+
+ if(NOT DEFINED CPM_ARGS_VERSION)
+ if(DEFINED CPM_ARGS_GIT_TAG)
+ cpm_get_version_from_git_tag("${CPM_ARGS_GIT_TAG}" CPM_ARGS_VERSION)
+ endif()
+ endif()
+
+ set(downloadPackage ${CPM_DOWNLOAD_ALL})
+ if(DEFINED CPM_DOWNLOAD_${CPM_ARGS_NAME})
+ set(downloadPackage ${CPM_DOWNLOAD_${CPM_ARGS_NAME}})
+ elseif(DEFINED ENV{CPM_DOWNLOAD_${CPM_ARGS_NAME}})
+ set(downloadPackage $ENV{CPM_DOWNLOAD_${CPM_ARGS_NAME}})
+ endif()
+ if(downloadPackage)
+ CPMAddPackage(${ARGN})
+ cpm_export_variables(${CPM_ARGS_NAME})
+ return()
+ endif()
+
+ cpm_find_package(${CPM_ARGS_NAME} "${CPM_ARGS_VERSION}" ${CPM_ARGS_FIND_PACKAGE_ARGUMENTS})
+
+ if(NOT CPM_PACKAGE_FOUND)
+ CPMAddPackage(${ARGN})
+ cpm_export_variables(${CPM_ARGS_NAME})
+ endif()
+
+endfunction()
+
+# checks if a package has been added before
+function(cpm_check_if_package_already_added CPM_ARGS_NAME CPM_ARGS_VERSION)
+ if("${CPM_ARGS_NAME}" IN_LIST CPM_PACKAGES)
+ CPMGetPackageVersion(${CPM_ARGS_NAME} CPM_PACKAGE_VERSION)
+ if("${CPM_PACKAGE_VERSION}" VERSION_LESS "${CPM_ARGS_VERSION}")
+ message(
+ WARNING
+ "${CPM_INDENT} Requires a newer version of ${CPM_ARGS_NAME} (${CPM_ARGS_VERSION}) than currently included (${CPM_PACKAGE_VERSION})."
+ )
+ endif()
+ cpm_get_fetch_properties(${CPM_ARGS_NAME})
+ set(${CPM_ARGS_NAME}_ADDED NO)
+ set(CPM_PACKAGE_ALREADY_ADDED
+ YES
+ PARENT_SCOPE
+ )
+ cpm_export_variables(${CPM_ARGS_NAME})
+ else()
+ set(CPM_PACKAGE_ALREADY_ADDED
+ NO
+ PARENT_SCOPE
+ )
+ endif()
+endfunction()
+
+# Parse the argument of CPMAddPackage in case a single one was provided and convert it to a list of
+# arguments which can then be parsed idiomatically. For example gh:foo/bar at 1.2.3 will be converted
+# to: GITHUB_REPOSITORY;foo/bar;VERSION;1.2.3
+function(cpm_parse_add_package_single_arg arg outArgs)
+ # Look for a scheme
+ if("${arg}" MATCHES "^([a-zA-Z]+):(.+)$")
+ string(TOLOWER "${CMAKE_MATCH_1}" scheme)
+ set(uri "${CMAKE_MATCH_2}")
+
+ # Check for CPM-specific schemes
+ if(scheme STREQUAL "gh")
+ set(out "GITHUB_REPOSITORY;${uri}")
+ set(packageType "git")
+ elseif(scheme STREQUAL "gl")
+ set(out "GITLAB_REPOSITORY;${uri}")
+ set(packageType "git")
+ elseif(scheme STREQUAL "bb")
+ set(out "BITBUCKET_REPOSITORY;${uri}")
+ set(packageType "git")
+ # A CPM-specific scheme was not found. Looks like this is a generic URL so try to determine
+ # type
+ elseif(arg MATCHES ".git/?(@|#|$)")
+ set(out "GIT_REPOSITORY;${arg}")
+ set(packageType "git")
+ else()
+ # Fall back to a URL
+ set(out "URL;${arg}")
+ set(packageType "archive")
+
+ # We could also check for SVN since FetchContent supports it, but SVN is so rare these days.
+ # We just won't bother with the additional complexity it will induce in this function. SVN is
+ # done by multi-arg
+ endif()
+ else()
+ if(arg MATCHES ".git/?(@|#|$)")
+ set(out "GIT_REPOSITORY;${arg}")
+ set(packageType "git")
+ else()
+ # Give up
+ message(FATAL_ERROR "${CPM_INDENT} Can't determine package type of '${arg}'")
+ endif()
+ endif()
+
+ # For all packages we interpret @... as version. Only replace the last occurrence. Thus URIs
+ # containing '@' can be used
+ string(REGEX REPLACE "@([^@]+)$" ";VERSION;\\1" out "${out}")
+
+ # Parse the rest according to package type
+ if(packageType STREQUAL "git")
+ # For git repos we interpret #... as a tag or branch or commit hash
+ string(REGEX REPLACE "#([^#]+)$" ";GIT_TAG;\\1" out "${out}")
+ elseif(packageType STREQUAL "archive")
+ # For archives we interpret #... as a URL hash.
+ string(REGEX REPLACE "#([^#]+)$" ";URL_HASH;\\1" out "${out}")
+ # We don't try to parse the version if it's not provided explicitly. cpm_get_version_from_url
+ # should do this at a later point
+ else()
+ # We should never get here. This is an assertion and hitting it means there's a problem with the
+ # code above. A packageType was set, but not handled by this if-else.
+ message(FATAL_ERROR "${CPM_INDENT} Unsupported package type '${packageType}' of '${arg}'")
+ endif()
+
+ set(${outArgs}
+ ${out}
+ PARENT_SCOPE
+ )
+endfunction()
+
+# Check that the working directory for a git repo is clean
+function(cpm_check_git_working_dir_is_clean repoPath gitTag isClean)
+
+ find_package(Git REQUIRED)
+
+ if(NOT GIT_EXECUTABLE)
+ # No git executable, assume directory is clean
+ set(${isClean}
+ TRUE
+ PARENT_SCOPE
+ )
+ return()
+ endif()
+
+ # check for uncommitted changes
+ execute_process(
+ COMMAND ${GIT_EXECUTABLE} status --porcelain
+ RESULT_VARIABLE resultGitStatus
+ OUTPUT_VARIABLE repoStatus
+ OUTPUT_STRIP_TRAILING_WHITESPACE ERROR_QUIET
+ WORKING_DIRECTORY ${repoPath}
+ )
+ if(resultGitStatus)
+ # not supposed to happen, assume clean anyway
+ message(WARNING "${CPM_INDENT} Calling git status on folder ${repoPath} failed")
+ set(${isClean}
+ TRUE
+ PARENT_SCOPE
+ )
+ return()
+ endif()
+
+ if(NOT "${repoStatus}" STREQUAL "")
+ set(${isClean}
+ FALSE
+ PARENT_SCOPE
+ )
+ return()
+ endif()
+
+ # check for committed changes
+ execute_process(
+ COMMAND ${GIT_EXECUTABLE} diff -s --exit-code ${gitTag}
+ RESULT_VARIABLE resultGitDiff
+ OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_QUIET
+ WORKING_DIRECTORY ${repoPath}
+ )
+
+ if(${resultGitDiff} EQUAL 0)
+ set(${isClean}
+ TRUE
+ PARENT_SCOPE
+ )
+ else()
+ set(${isClean}
+ FALSE
+ PARENT_SCOPE
+ )
+ endif()
+
+endfunction()
+
+# Add PATCH_COMMAND to CPM_ARGS_UNPARSED_ARGUMENTS. This method consumes a list of files in ARGN
+# then generates a `PATCH_COMMAND` appropriate for `ExternalProject_Add()`. This command is appended
+# to the parent scope's `CPM_ARGS_UNPARSED_ARGUMENTS`.
+function(cpm_add_patches)
+ # Return if no patch files are supplied.
+ if(NOT ARGN)
+ return()
+ endif()
+
+ # Find the patch program.
+ find_program(PATCH_EXECUTABLE patch)
+ if(CMAKE_HOST_WIN32 AND NOT PATCH_EXECUTABLE)
+ # The Windows git executable is distributed with patch.exe. Find the path to the executable, if
+ # it exists, then search `../usr/bin` and `../../usr/bin` for patch.exe.
+ find_package(Git QUIET)
+ if(GIT_EXECUTABLE)
+ get_filename_component(extra_search_path ${GIT_EXECUTABLE} DIRECTORY)
+ get_filename_component(extra_search_path_1up ${extra_search_path} DIRECTORY)
+ get_filename_component(extra_search_path_2up ${extra_search_path_1up} DIRECTORY)
+ find_program(
+ PATCH_EXECUTABLE patch HINTS "${extra_search_path_1up}/usr/bin"
+ "${extra_search_path_2up}/usr/bin"
+ )
+ endif()
+ endif()
+ if(NOT PATCH_EXECUTABLE)
+ message(FATAL_ERROR "Couldn't find `patch` executable to use with PATCHES keyword.")
+ endif()
+
+ # Create a temporary
+ set(temp_list ${CPM_ARGS_UNPARSED_ARGUMENTS})
+
+ # Ensure each file exists (or error out) and add it to the list.
+ set(first_item True)
+ foreach(PATCH_FILE ${ARGN})
+ # Make sure the patch file exists, if we can't find it, try again in the current directory.
+ if(NOT EXISTS "${PATCH_FILE}")
+ if(NOT EXISTS "${CMAKE_CURRENT_LIST_DIR}/${PATCH_FILE}")
+ message(FATAL_ERROR "Couldn't find patch file: '${PATCH_FILE}'")
+ endif()
+ set(PATCH_FILE "${CMAKE_CURRENT_LIST_DIR}/${PATCH_FILE}")
+ endif()
+
+ # Convert to absolute path for use with patch file command.
+ get_filename_component(PATCH_FILE "${PATCH_FILE}" ABSOLUTE)
+
+ # The first patch entry must be preceded by "PATCH_COMMAND" while the following items are
+ # preceded by "&&".
+ if(first_item)
+ set(first_item False)
+ list(APPEND temp_list "PATCH_COMMAND")
+ else()
+ list(APPEND temp_list "&&")
+ endif()
+ # Add the patch command to the list
+ list(APPEND temp_list "${PATCH_EXECUTABLE}" "-p1" "<" "${PATCH_FILE}")
+ endforeach()
+
+ # Move temp out into parent scope.
+ set(CPM_ARGS_UNPARSED_ARGUMENTS
+ ${temp_list}
+ PARENT_SCOPE
+ )
+
+endfunction()
+
+# method to overwrite internal FetchContent properties, to allow using CPM.cmake to overload
+# FetchContent calls. As these are internal cmake properties, this method should be used carefully
+# and may need modification in future CMake versions. Source:
+# https://github.com/Kitware/CMake/blob/dc3d0b5a0a7d26d43d6cfeb511e224533b5d188f/Modules/FetchContent.cmake#L1152
+function(cpm_override_fetchcontent contentName)
+ cmake_parse_arguments(PARSE_ARGV 1 arg "" "SOURCE_DIR;BINARY_DIR" "")
+ if(NOT "${arg_UNPARSED_ARGUMENTS}" STREQUAL "")
+ message(FATAL_ERROR "${CPM_INDENT} Unsupported arguments: ${arg_UNPARSED_ARGUMENTS}")
+ endif()
+
+ string(TOLOWER ${contentName} contentNameLower)
+ set(prefix "_FetchContent_${contentNameLower}")
+
+ set(propertyName "${prefix}_sourceDir")
+ define_property(
+ GLOBAL
+ PROPERTY ${propertyName}
+ BRIEF_DOCS "Internal implementation detail of FetchContent_Populate()"
+ FULL_DOCS "Details used by FetchContent_Populate() for ${contentName}"
+ )
+ set_property(GLOBAL PROPERTY ${propertyName} "${arg_SOURCE_DIR}")
+
+ set(propertyName "${prefix}_binaryDir")
+ define_property(
+ GLOBAL
+ PROPERTY ${propertyName}
+ BRIEF_DOCS "Internal implementation detail of FetchContent_Populate()"
+ FULL_DOCS "Details used by FetchContent_Populate() for ${contentName}"
+ )
+ set_property(GLOBAL PROPERTY ${propertyName} "${arg_BINARY_DIR}")
+
+ set(propertyName "${prefix}_populated")
+ define_property(
+ GLOBAL
+ PROPERTY ${propertyName}
+ BRIEF_DOCS "Internal implementation detail of FetchContent_Populate()"
+ FULL_DOCS "Details used by FetchContent_Populate() for ${contentName}"
+ )
+ set_property(GLOBAL PROPERTY ${propertyName} TRUE)
+endfunction()
+
+# Download and add a package from source
+function(CPMAddPackage)
+ cpm_set_policies()
+
+ list(LENGTH ARGN argnLength)
+ if(argnLength EQUAL 1)
+ cpm_parse_add_package_single_arg("${ARGN}" ARGN)
+
+ # The shorthand syntax implies EXCLUDE_FROM_ALL and SYSTEM
+ set(ARGN "${ARGN};EXCLUDE_FROM_ALL;YES;SYSTEM;YES;")
+ endif()
+
+ set(oneValueArgs
+ NAME
+ FORCE
+ VERSION
+ GIT_TAG
+ DOWNLOAD_ONLY
+ GITHUB_REPOSITORY
+ GITLAB_REPOSITORY
+ BITBUCKET_REPOSITORY
+ GIT_REPOSITORY
+ SOURCE_DIR
+ FIND_PACKAGE_ARGUMENTS
+ NO_CACHE
+ SYSTEM
+ GIT_SHALLOW
+ EXCLUDE_FROM_ALL
+ SOURCE_SUBDIR
+ CUSTOM_CACHE_KEY
+ )
+
+ set(multiValueArgs URL OPTIONS DOWNLOAD_COMMAND PATCHES)
+
+ cmake_parse_arguments(CPM_ARGS "" "${oneValueArgs}" "${multiValueArgs}" "${ARGN}")
+
+ # Set default values for arguments
+
+ if(NOT DEFINED CPM_ARGS_VERSION)
+ if(DEFINED CPM_ARGS_GIT_TAG)
+ cpm_get_version_from_git_tag("${CPM_ARGS_GIT_TAG}" CPM_ARGS_VERSION)
+ endif()
+ endif()
+
+ if(CPM_ARGS_DOWNLOAD_ONLY)
+ set(DOWNLOAD_ONLY ${CPM_ARGS_DOWNLOAD_ONLY})
+ else()
+ set(DOWNLOAD_ONLY NO)
+ endif()
+
+ if(DEFINED CPM_ARGS_GITHUB_REPOSITORY)
+ set(CPM_ARGS_GIT_REPOSITORY "https://github.com/${CPM_ARGS_GITHUB_REPOSITORY}.git")
+ elseif(DEFINED CPM_ARGS_GITLAB_REPOSITORY)
+ set(CPM_ARGS_GIT_REPOSITORY "https://gitlab.com/${CPM_ARGS_GITLAB_REPOSITORY}.git")
+ elseif(DEFINED CPM_ARGS_BITBUCKET_REPOSITORY)
+ set(CPM_ARGS_GIT_REPOSITORY "https://bitbucket.org/${CPM_ARGS_BITBUCKET_REPOSITORY}.git")
+ endif()
+
+ if(DEFINED CPM_ARGS_GIT_REPOSITORY)
+ list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS GIT_REPOSITORY ${CPM_ARGS_GIT_REPOSITORY})
+ if(NOT DEFINED CPM_ARGS_GIT_TAG)
+ set(CPM_ARGS_GIT_TAG v${CPM_ARGS_VERSION})
+ endif()
+
+ # If a name wasn't provided, try to infer it from the git repo
+ if(NOT DEFINED CPM_ARGS_NAME)
+ cpm_package_name_from_git_uri(${CPM_ARGS_GIT_REPOSITORY} CPM_ARGS_NAME)
+ endif()
+ endif()
+
+ set(CPM_SKIP_FETCH FALSE)
+
+ if(DEFINED CPM_ARGS_GIT_TAG)
+ list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS GIT_TAG ${CPM_ARGS_GIT_TAG})
+ # If GIT_SHALLOW is explicitly specified, honor the value.
+ if(DEFINED CPM_ARGS_GIT_SHALLOW)
+ list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS GIT_SHALLOW ${CPM_ARGS_GIT_SHALLOW})
+ endif()
+ endif()
+
+ if(DEFINED CPM_ARGS_URL)
+ # If a name or version aren't provided, try to infer them from the URL
+ list(GET CPM_ARGS_URL 0 firstUrl)
+ cpm_package_name_and_ver_from_url(${firstUrl} nameFromUrl verFromUrl)
+ # If we fail to obtain name and version from the first URL, we could try other URLs if any.
+ # However multiple URLs are expected to be quite rare, so for now we won't bother.
+
+ # If the caller provided their own name and version, they trump the inferred ones.
+ if(NOT DEFINED CPM_ARGS_NAME)
+ set(CPM_ARGS_NAME ${nameFromUrl})
+ endif()
+ if(NOT DEFINED CPM_ARGS_VERSION)
+ set(CPM_ARGS_VERSION ${verFromUrl})
+ endif()
+
+ list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS URL "${CPM_ARGS_URL}")
+ endif()
+
+ # Check for required arguments
+
+ if(NOT DEFINED CPM_ARGS_NAME)
+ message(
+ FATAL_ERROR
+ "${CPM_INDENT} 'NAME' was not provided and couldn't be automatically inferred for package added with arguments: '${ARGN}'"
+ )
+ endif()
+
+ # Check if package has been added before
+ cpm_check_if_package_already_added(${CPM_ARGS_NAME} "${CPM_ARGS_VERSION}")
+ if(CPM_PACKAGE_ALREADY_ADDED)
+ cpm_export_variables(${CPM_ARGS_NAME})
+ return()
+ endif()
+
+ # Check for manual overrides
+ if(NOT CPM_ARGS_FORCE AND NOT "${CPM_${CPM_ARGS_NAME}_SOURCE}" STREQUAL "")
+ set(PACKAGE_SOURCE ${CPM_${CPM_ARGS_NAME}_SOURCE})
+ set(CPM_${CPM_ARGS_NAME}_SOURCE "")
+ CPMAddPackage(
+ NAME "${CPM_ARGS_NAME}"
+ SOURCE_DIR "${PACKAGE_SOURCE}"
+ EXCLUDE_FROM_ALL "${CPM_ARGS_EXCLUDE_FROM_ALL}"
+ SYSTEM "${CPM_ARGS_SYSTEM}"
+ PATCHES "${CPM_ARGS_PATCHES}"
+ OPTIONS "${CPM_ARGS_OPTIONS}"
+ SOURCE_SUBDIR "${CPM_ARGS_SOURCE_SUBDIR}"
+ DOWNLOAD_ONLY "${DOWNLOAD_ONLY}"
+ FORCE True
+ )
+ cpm_export_variables(${CPM_ARGS_NAME})
+ return()
+ endif()
+
+ # Check for available declaration
+ if(NOT CPM_ARGS_FORCE AND NOT "${CPM_DECLARATION_${CPM_ARGS_NAME}}" STREQUAL "")
+ set(declaration ${CPM_DECLARATION_${CPM_ARGS_NAME}})
+ set(CPM_DECLARATION_${CPM_ARGS_NAME} "")
+ CPMAddPackage(${declaration})
+ cpm_export_variables(${CPM_ARGS_NAME})
+ # checking again to ensure version and option compatibility
+ cpm_check_if_package_already_added(${CPM_ARGS_NAME} "${CPM_ARGS_VERSION}")
+ return()
+ endif()
+
+ if(NOT CPM_ARGS_FORCE)
+ if(CPM_USE_LOCAL_PACKAGES OR CPM_LOCAL_PACKAGES_ONLY)
+ cpm_find_package(${CPM_ARGS_NAME} "${CPM_ARGS_VERSION}" ${CPM_ARGS_FIND_PACKAGE_ARGUMENTS})
+
+ if(CPM_PACKAGE_FOUND)
+ cpm_export_variables(${CPM_ARGS_NAME})
+ return()
+ endif()
+
+ if(CPM_LOCAL_PACKAGES_ONLY)
+ message(
+ SEND_ERROR
+ "${CPM_INDENT} ${CPM_ARGS_NAME} not found via find_package(${CPM_ARGS_NAME} ${CPM_ARGS_VERSION})"
+ )
+ endif()
+ endif()
+ endif()
+
+ CPMRegisterPackage("${CPM_ARGS_NAME}" "${CPM_ARGS_VERSION}")
+
+ if(DEFINED CPM_ARGS_GIT_TAG)
+ set(PACKAGE_INFO "${CPM_ARGS_GIT_TAG}")
+ elseif(DEFINED CPM_ARGS_SOURCE_DIR)
+ set(PACKAGE_INFO "${CPM_ARGS_SOURCE_DIR}")
+ else()
+ set(PACKAGE_INFO "${CPM_ARGS_VERSION}")
+ endif()
+
+ if(DEFINED FETCHCONTENT_BASE_DIR)
+ # respect user's FETCHCONTENT_BASE_DIR if set
+ set(CPM_FETCHCONTENT_BASE_DIR ${FETCHCONTENT_BASE_DIR})
+ else()
+ set(CPM_FETCHCONTENT_BASE_DIR ${CMAKE_BINARY_DIR}/_deps)
+ endif()
+
+ cpm_add_patches(${CPM_ARGS_PATCHES})
+
+ if(DEFINED CPM_ARGS_DOWNLOAD_COMMAND)
+ list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS DOWNLOAD_COMMAND ${CPM_ARGS_DOWNLOAD_COMMAND})
+ elseif(DEFINED CPM_ARGS_SOURCE_DIR)
+ list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS SOURCE_DIR ${CPM_ARGS_SOURCE_DIR})
+ if(NOT IS_ABSOLUTE ${CPM_ARGS_SOURCE_DIR})
+ # Expand `CPM_ARGS_SOURCE_DIR` relative path. This is important because EXISTS doesn't work
+ # for relative paths.
+ get_filename_component(
+ source_directory ${CPM_ARGS_SOURCE_DIR} REALPATH BASE_DIR ${CMAKE_CURRENT_BINARY_DIR}
+ )
+ else()
+ set(source_directory ${CPM_ARGS_SOURCE_DIR})
+ endif()
+ if(NOT EXISTS ${source_directory})
+ string(TOLOWER ${CPM_ARGS_NAME} lower_case_name)
+ # remove timestamps so CMake will re-download the dependency
+ file(REMOVE_RECURSE "${CPM_FETCHCONTENT_BASE_DIR}/${lower_case_name}-subbuild")
+ endif()
+ elseif(CPM_SOURCE_CACHE AND NOT CPM_ARGS_NO_CACHE)
+ string(TOLOWER ${CPM_ARGS_NAME} lower_case_name)
+ set(origin_parameters ${CPM_ARGS_UNPARSED_ARGUMENTS})
+ list(SORT origin_parameters)
+ if(CPM_ARGS_CUSTOM_CACHE_KEY)
+ # Application set a custom unique directory name
+ set(download_directory ${CPM_SOURCE_CACHE}/${lower_case_name}/${CPM_ARGS_CUSTOM_CACHE_KEY})
+ elseif(CPM_USE_NAMED_CACHE_DIRECTORIES)
+ string(SHA1 origin_hash "${origin_parameters};NEW_CACHE_STRUCTURE_TAG")
+ set(download_directory ${CPM_SOURCE_CACHE}/${lower_case_name}/${origin_hash}/${CPM_ARGS_NAME})
+ else()
+ string(SHA1 origin_hash "${origin_parameters}")
+ set(download_directory ${CPM_SOURCE_CACHE}/${lower_case_name}/${origin_hash})
+ endif()
+ # Expand `download_directory` relative path. This is important because EXISTS doesn't work for
+ # relative paths.
+ get_filename_component(download_directory ${download_directory} ABSOLUTE)
+ list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS SOURCE_DIR ${download_directory})
+
+ if(CPM_SOURCE_CACHE)
+ file(LOCK ${download_directory}/../cmake.lock)
+ endif()
+
+ if(EXISTS ${download_directory})
+ if(CPM_SOURCE_CACHE)
+ file(LOCK ${download_directory}/../cmake.lock RELEASE)
+ endif()
+
+ cpm_store_fetch_properties(
+ ${CPM_ARGS_NAME} "${download_directory}"
+ "${CPM_FETCHCONTENT_BASE_DIR}/${lower_case_name}-build"
+ )
+ cpm_get_fetch_properties("${CPM_ARGS_NAME}")
+
+ if(DEFINED CPM_ARGS_GIT_TAG AND NOT (PATCH_COMMAND IN_LIST CPM_ARGS_UNPARSED_ARGUMENTS))
+ # warn if cache has been changed since checkout
+ cpm_check_git_working_dir_is_clean(${download_directory} ${CPM_ARGS_GIT_TAG} IS_CLEAN)
+ if(NOT ${IS_CLEAN})
+ message(
+ WARNING "${CPM_INDENT} Cache for ${CPM_ARGS_NAME} (${download_directory}) is dirty"
+ )
+ endif()
+ endif()
+
+ cpm_add_subdirectory(
+ "${CPM_ARGS_NAME}"
+ "${DOWNLOAD_ONLY}"
+ "${${CPM_ARGS_NAME}_SOURCE_DIR}/${CPM_ARGS_SOURCE_SUBDIR}"
+ "${${CPM_ARGS_NAME}_BINARY_DIR}"
+ "${CPM_ARGS_EXCLUDE_FROM_ALL}"
+ "${CPM_ARGS_SYSTEM}"
+ "${CPM_ARGS_OPTIONS}"
+ )
+ set(PACKAGE_INFO "${PACKAGE_INFO} at ${download_directory}")
+
+ # As the source dir is already cached/populated, we override the call to FetchContent.
+ set(CPM_SKIP_FETCH TRUE)
+ cpm_override_fetchcontent(
+ "${lower_case_name}" SOURCE_DIR "${${CPM_ARGS_NAME}_SOURCE_DIR}/${CPM_ARGS_SOURCE_SUBDIR}"
+ BINARY_DIR "${${CPM_ARGS_NAME}_BINARY_DIR}"
+ )
+
+ else()
+ # Enable shallow clone when GIT_TAG is not a commit hash. Our guess may not be accurate, but
+ # it should guarantee no commit hash get mis-detected.
+ if(NOT DEFINED CPM_ARGS_GIT_SHALLOW)
+ cpm_is_git_tag_commit_hash("${CPM_ARGS_GIT_TAG}" IS_HASH)
+ if(NOT ${IS_HASH})
+ list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS GIT_SHALLOW TRUE)
+ endif()
+ endif()
+
+ # remove timestamps so CMake will re-download the dependency
+ file(REMOVE_RECURSE ${CPM_FETCHCONTENT_BASE_DIR}/${lower_case_name}-subbuild)
+ set(PACKAGE_INFO "${PACKAGE_INFO} to ${download_directory}")
+ endif()
+ endif()
+
+ if(NOT "${DOWNLOAD_ONLY}")
+ cpm_create_module_file(${CPM_ARGS_NAME} "CPMAddPackage(\"${ARGN}\")")
+ endif()
+
+ if(CPM_PACKAGE_LOCK_ENABLED)
+ if((CPM_ARGS_VERSION AND NOT CPM_ARGS_SOURCE_DIR) OR CPM_INCLUDE_ALL_IN_PACKAGE_LOCK)
+ cpm_add_to_package_lock(${CPM_ARGS_NAME} "${ARGN}")
+ elseif(CPM_ARGS_SOURCE_DIR)
+ cpm_add_comment_to_package_lock(${CPM_ARGS_NAME} "local directory")
+ else()
+ cpm_add_comment_to_package_lock(${CPM_ARGS_NAME} "${ARGN}")
+ endif()
+ endif()
+
+ cpm_message(
+ STATUS "${CPM_INDENT} Adding package ${CPM_ARGS_NAME}@${CPM_ARGS_VERSION} (${PACKAGE_INFO})"
+ )
+
+ if(NOT CPM_SKIP_FETCH)
+ # CMake 3.28 added EXCLUDE, SYSTEM (3.25), and SOURCE_SUBDIR (3.18) to FetchContent_Declare.
+ # Calling FetchContent_MakeAvailable will then internally forward these options to
+ # add_subdirectory. Up until these changes, we had to call FetchContent_Populate and
+ # add_subdirectory separately, which is no longer necessary and has been deprecated as of 3.30.
+ # A Bug in CMake prevents us to use the non-deprecated functions until 3.30.3.
+ set(fetchContentDeclareExtraArgs "")
+ if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.30.3")
+ if(${CPM_ARGS_EXCLUDE_FROM_ALL})
+ list(APPEND fetchContentDeclareExtraArgs EXCLUDE_FROM_ALL)
+ endif()
+ if(${CPM_ARGS_SYSTEM})
+ list(APPEND fetchContentDeclareExtraArgs SYSTEM)
+ endif()
+ if(DEFINED CPM_ARGS_SOURCE_SUBDIR)
+ list(APPEND fetchContentDeclareExtraArgs SOURCE_SUBDIR ${CPM_ARGS_SOURCE_SUBDIR})
+ endif()
+ # For CMake version <3.28 OPTIONS are parsed in cpm_add_subdirectory
+ if(CPM_ARGS_OPTIONS AND NOT DOWNLOAD_ONLY)
+ foreach(OPTION ${CPM_ARGS_OPTIONS})
+ cpm_parse_option("${OPTION}")
+ set(${OPTION_KEY} "${OPTION_VALUE}")
+ endforeach()
+ endif()
+ endif()
+ cpm_declare_fetch(
+ "${CPM_ARGS_NAME}" ${fetchContentDeclareExtraArgs} "${CPM_ARGS_UNPARSED_ARGUMENTS}"
+ )
+
+ cpm_fetch_package("${CPM_ARGS_NAME}" ${DOWNLOAD_ONLY} populated ${CPM_ARGS_UNPARSED_ARGUMENTS})
+ if(CPM_SOURCE_CACHE AND download_directory)
+ file(LOCK ${download_directory}/../cmake.lock RELEASE)
+ endif()
+ if(${populated} AND ${CMAKE_VERSION} VERSION_LESS "3.30.3")
+ cpm_add_subdirectory(
+ "${CPM_ARGS_NAME}"
+ "${DOWNLOAD_ONLY}"
+ "${${CPM_ARGS_NAME}_SOURCE_DIR}/${CPM_ARGS_SOURCE_SUBDIR}"
+ "${${CPM_ARGS_NAME}_BINARY_DIR}"
+ "${CPM_ARGS_EXCLUDE_FROM_ALL}"
+ "${CPM_ARGS_SYSTEM}"
+ "${CPM_ARGS_OPTIONS}"
+ )
+ endif()
+ cpm_get_fetch_properties("${CPM_ARGS_NAME}")
+ endif()
+
+ set(${CPM_ARGS_NAME}_ADDED YES)
+ cpm_export_variables("${CPM_ARGS_NAME}")
+endfunction()
+
+# Fetch a previously declared package
+macro(CPMGetPackage Name)
+ if(DEFINED "CPM_DECLARATION_${Name}")
+ CPMAddPackage(NAME ${Name})
+ else()
+ message(SEND_ERROR "${CPM_INDENT} Cannot retrieve package ${Name}: no declaration available")
+ endif()
+endmacro()
+
+# export variables available to the caller to the parent scope expects ${CPM_ARGS_NAME} to be set
+macro(cpm_export_variables name)
+ set(${name}_SOURCE_DIR
+ "${${name}_SOURCE_DIR}"
+ PARENT_SCOPE
+ )
+ set(${name}_BINARY_DIR
+ "${${name}_BINARY_DIR}"
+ PARENT_SCOPE
+ )
+ set(${name}_ADDED
+ "${${name}_ADDED}"
+ PARENT_SCOPE
+ )
+ set(CPM_LAST_PACKAGE_NAME
+ "${name}"
+ PARENT_SCOPE
+ )
+endmacro()
+
+# declares a package, so that any call to CPMAddPackage for the package name will use these
+# arguments instead. Previous declarations will not be overridden.
+macro(CPMDeclarePackage Name)
+ if(NOT DEFINED "CPM_DECLARATION_${Name}")
+ set("CPM_DECLARATION_${Name}" "${ARGN}")
+ endif()
+endmacro()
+
+function(cpm_add_to_package_lock Name)
+ if(NOT CPM_DONT_CREATE_PACKAGE_LOCK)
+ cpm_prettify_package_arguments(PRETTY_ARGN false ${ARGN})
+ file(APPEND ${CPM_PACKAGE_LOCK_FILE} "# ${Name}\nCPMDeclarePackage(${Name}\n${PRETTY_ARGN})\n")
+ endif()
+endfunction()
+
+function(cpm_add_comment_to_package_lock Name)
+ if(NOT CPM_DONT_CREATE_PACKAGE_LOCK)
+ cpm_prettify_package_arguments(PRETTY_ARGN true ${ARGN})
+ file(APPEND ${CPM_PACKAGE_LOCK_FILE}
+ "# ${Name} (unversioned)\n# CPMDeclarePackage(${Name}\n${PRETTY_ARGN}#)\n"
+ )
+ endif()
+endfunction()
+
+# includes the package lock file if it exists and creates a target `cpm-update-package-lock` to
+# update it
+macro(CPMUsePackageLock file)
+ if(NOT CPM_DONT_CREATE_PACKAGE_LOCK)
+ get_filename_component(CPM_ABSOLUTE_PACKAGE_LOCK_PATH ${file} ABSOLUTE)
+ if(EXISTS ${CPM_ABSOLUTE_PACKAGE_LOCK_PATH})
+ include(${CPM_ABSOLUTE_PACKAGE_LOCK_PATH})
+ endif()
+ if(NOT TARGET cpm-update-package-lock)
+ add_custom_target(
+ cpm-update-package-lock COMMAND ${CMAKE_COMMAND} -E copy ${CPM_PACKAGE_LOCK_FILE}
+ ${CPM_ABSOLUTE_PACKAGE_LOCK_PATH}
+ )
+ endif()
+ set(CPM_PACKAGE_LOCK_ENABLED true)
+ endif()
+endmacro()
+
+# registers a package that has been added to CPM
+function(CPMRegisterPackage PACKAGE VERSION)
+ list(APPEND CPM_PACKAGES ${PACKAGE})
+ set(CPM_PACKAGES
+ ${CPM_PACKAGES}
+ CACHE INTERNAL ""
+ )
+ set("CPM_PACKAGE_${PACKAGE}_VERSION"
+ ${VERSION}
+ CACHE INTERNAL ""
+ )
+endfunction()
+
+# retrieve the current version of the package to ${OUTPUT}
+function(CPMGetPackageVersion PACKAGE OUTPUT)
+ set(${OUTPUT}
+ "${CPM_PACKAGE_${PACKAGE}_VERSION}"
+ PARENT_SCOPE
+ )
+endfunction()
+
+# declares a package in FetchContent_Declare
+function(cpm_declare_fetch PACKAGE)
+ if(${CPM_DRY_RUN})
+ cpm_message(STATUS "${CPM_INDENT} Package not declared (dry run)")
+ return()
+ endif()
+
+ FetchContent_Declare(${PACKAGE} ${ARGN})
+endfunction()
+
+# returns properties for a package previously defined by cpm_declare_fetch
+function(cpm_get_fetch_properties PACKAGE)
+ if(${CPM_DRY_RUN})
+ return()
+ endif()
+
+ set(${PACKAGE}_SOURCE_DIR
+ "${CPM_PACKAGE_${PACKAGE}_SOURCE_DIR}"
+ PARENT_SCOPE
+ )
+ set(${PACKAGE}_BINARY_DIR
+ "${CPM_PACKAGE_${PACKAGE}_BINARY_DIR}"
+ PARENT_SCOPE
+ )
+endfunction()
+
+function(cpm_store_fetch_properties PACKAGE source_dir binary_dir)
+ if(${CPM_DRY_RUN})
+ return()
+ endif()
+
+ set(CPM_PACKAGE_${PACKAGE}_SOURCE_DIR
+ "${source_dir}"
+ CACHE INTERNAL ""
+ )
+ set(CPM_PACKAGE_${PACKAGE}_BINARY_DIR
+ "${binary_dir}"
+ CACHE INTERNAL ""
+ )
+endfunction()
+
+# adds a package as a subdirectory if viable, according to provided options
+function(
+ cpm_add_subdirectory
+ PACKAGE
+ DOWNLOAD_ONLY
+ SOURCE_DIR
+ BINARY_DIR
+ EXCLUDE
+ SYSTEM
+ OPTIONS
+)
+
+ if(NOT DOWNLOAD_ONLY AND EXISTS ${SOURCE_DIR}/CMakeLists.txt)
+ set(addSubdirectoryExtraArgs "")
+ if(EXCLUDE)
+ list(APPEND addSubdirectoryExtraArgs EXCLUDE_FROM_ALL)
+ endif()
+ if("${SYSTEM}" AND "${CMAKE_VERSION}" VERSION_GREATER_EQUAL "3.25")
+ # https://cmake.org/cmake/help/latest/prop_dir/SYSTEM.html#prop_dir:SYSTEM
+ list(APPEND addSubdirectoryExtraArgs SYSTEM)
+ endif()
+ if(OPTIONS)
+ foreach(OPTION ${OPTIONS})
+ cpm_parse_option("${OPTION}")
+ set(${OPTION_KEY} "${OPTION_VALUE}")
+ endforeach()
+ endif()
+ set(CPM_OLD_INDENT "${CPM_INDENT}")
+ set(CPM_INDENT "${CPM_INDENT} ${PACKAGE}:")
+ add_subdirectory(${SOURCE_DIR} ${BINARY_DIR} ${addSubdirectoryExtraArgs})
+ set(CPM_INDENT "${CPM_OLD_INDENT}")
+ endif()
+endfunction()
+
+# downloads a previously declared package via FetchContent and exports the variables
+# `${PACKAGE}_SOURCE_DIR` and `${PACKAGE}_BINARY_DIR` to the parent scope
+function(cpm_fetch_package PACKAGE DOWNLOAD_ONLY populated)
+ set(${populated}
+ FALSE
+ PARENT_SCOPE
+ )
+ if(${CPM_DRY_RUN})
+ cpm_message(STATUS "${CPM_INDENT} Package ${PACKAGE} not fetched (dry run)")
+ return()
+ endif()
+
+ FetchContent_GetProperties(${PACKAGE})
+
+ string(TOLOWER "${PACKAGE}" lower_case_name)
+
+ if(NOT ${lower_case_name}_POPULATED)
+ if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.30.3")
+ if(DOWNLOAD_ONLY)
+ # MakeAvailable will call add_subdirectory internally which is not what we want when
+ # DOWNLOAD_ONLY is set. Populate will only download the dependency without adding it to the
+ # build
+ FetchContent_Populate(
+ ${PACKAGE}
+ SOURCE_DIR "${CPM_FETCHCONTENT_BASE_DIR}/${lower_case_name}-src"
+ BINARY_DIR "${CPM_FETCHCONTENT_BASE_DIR}/${lower_case_name}-build"
+ SUBBUILD_DIR "${CPM_FETCHCONTENT_BASE_DIR}/${lower_case_name}-subbuild"
+ ${ARGN}
+ )
+ else()
+ FetchContent_MakeAvailable(${PACKAGE})
+ endif()
+ else()
+ FetchContent_Populate(${PACKAGE})
+ endif()
+ set(${populated}
+ TRUE
+ PARENT_SCOPE
+ )
+ endif()
+
+ cpm_store_fetch_properties(
+ ${CPM_ARGS_NAME} ${${lower_case_name}_SOURCE_DIR} ${${lower_case_name}_BINARY_DIR}
+ )
+
+ set(${PACKAGE}_SOURCE_DIR
+ ${${lower_case_name}_SOURCE_DIR}
+ PARENT_SCOPE
+ )
+ set(${PACKAGE}_BINARY_DIR
+ ${${lower_case_name}_BINARY_DIR}
+ PARENT_SCOPE
+ )
+endfunction()
+
+# splits a package option
+function(cpm_parse_option OPTION)
+ string(REGEX MATCH "^[^ ]+" OPTION_KEY "${OPTION}")
+ string(LENGTH "${OPTION}" OPTION_LENGTH)
+ string(LENGTH "${OPTION_KEY}" OPTION_KEY_LENGTH)
+ if(OPTION_KEY_LENGTH STREQUAL OPTION_LENGTH)
+ # no value for key provided, assume user wants to set option to "ON"
+ set(OPTION_VALUE "ON")
+ else()
+ math(EXPR OPTION_KEY_LENGTH "${OPTION_KEY_LENGTH}+1")
+ string(SUBSTRING "${OPTION}" "${OPTION_KEY_LENGTH}" "-1" OPTION_VALUE)
+ endif()
+ set(OPTION_KEY
+ "${OPTION_KEY}"
+ PARENT_SCOPE
+ )
+ set(OPTION_VALUE
+ "${OPTION_VALUE}"
+ PARENT_SCOPE
+ )
+endfunction()
+
+# guesses the package version from a git tag
+function(cpm_get_version_from_git_tag GIT_TAG RESULT)
+ string(LENGTH ${GIT_TAG} length)
+ if(length EQUAL 40)
+ # GIT_TAG is probably a git hash
+ set(${RESULT}
+ 0
+ PARENT_SCOPE
+ )
+ else()
+ string(REGEX MATCH "v?([0123456789.]*).*" _ ${GIT_TAG})
+ set(${RESULT}
+ ${CMAKE_MATCH_1}
+ PARENT_SCOPE
+ )
+ endif()
+endfunction()
+
+# guesses if the git tag is a commit hash or an actual tag or a branch name.
+function(cpm_is_git_tag_commit_hash GIT_TAG RESULT)
+ string(LENGTH "${GIT_TAG}" length)
+ # full hash has 40 characters, and short hash has at least 7 characters.
+ if(length LESS 7 OR length GREATER 40)
+ set(${RESULT}
+ 0
+ PARENT_SCOPE
+ )
+ else()
+ if(${GIT_TAG} MATCHES "^[a-fA-F0-9]+$")
+ set(${RESULT}
+ 1
+ PARENT_SCOPE
+ )
+ else()
+ set(${RESULT}
+ 0
+ PARENT_SCOPE
+ )
+ endif()
+ endif()
+endfunction()
+
+function(cpm_prettify_package_arguments OUT_VAR IS_IN_COMMENT)
+ set(oneValueArgs
+ NAME
+ FORCE
+ VERSION
+ GIT_TAG
+ DOWNLOAD_ONLY
+ GITHUB_REPOSITORY
+ GITLAB_REPOSITORY
+ BITBUCKET_REPOSITORY
+ GIT_REPOSITORY
+ SOURCE_DIR
+ FIND_PACKAGE_ARGUMENTS
+ NO_CACHE
+ SYSTEM
+ GIT_SHALLOW
+ EXCLUDE_FROM_ALL
+ SOURCE_SUBDIR
+ )
+ set(multiValueArgs URL OPTIONS DOWNLOAD_COMMAND)
+ cmake_parse_arguments(CPM_ARGS "" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+ foreach(oneArgName ${oneValueArgs})
+ if(DEFINED CPM_ARGS_${oneArgName})
+ if(${IS_IN_COMMENT})
+ string(APPEND PRETTY_OUT_VAR "#")
+ endif()
+ if(${oneArgName} STREQUAL "SOURCE_DIR")
+ string(REPLACE ${CMAKE_SOURCE_DIR} "\${CMAKE_SOURCE_DIR}" CPM_ARGS_${oneArgName}
+ ${CPM_ARGS_${oneArgName}}
+ )
+ endif()
+ string(APPEND PRETTY_OUT_VAR " ${oneArgName} ${CPM_ARGS_${oneArgName}}\n")
+ endif()
+ endforeach()
+ foreach(multiArgName ${multiValueArgs})
+ if(DEFINED CPM_ARGS_${multiArgName})
+ if(${IS_IN_COMMENT})
+ string(APPEND PRETTY_OUT_VAR "#")
+ endif()
+ string(APPEND PRETTY_OUT_VAR " ${multiArgName}\n")
+ foreach(singleOption ${CPM_ARGS_${multiArgName}})
+ if(${IS_IN_COMMENT})
+ string(APPEND PRETTY_OUT_VAR "#")
+ endif()
+ string(APPEND PRETTY_OUT_VAR " \"${singleOption}\"\n")
+ endforeach()
+ endif()
+ endforeach()
+
+ if(NOT "${CPM_ARGS_UNPARSED_ARGUMENTS}" STREQUAL "")
+ if(${IS_IN_COMMENT})
+ string(APPEND PRETTY_OUT_VAR "#")
+ endif()
+ string(APPEND PRETTY_OUT_VAR " ")
+ foreach(CPM_ARGS_UNPARSED_ARGUMENT ${CPM_ARGS_UNPARSED_ARGUMENTS})
+ string(APPEND PRETTY_OUT_VAR " ${CPM_ARGS_UNPARSED_ARGUMENT}")
+ endforeach()
+ string(APPEND PRETTY_OUT_VAR "\n")
+ endif()
+
+ set(${OUT_VAR}
+ ${PRETTY_OUT_VAR}
+ PARENT_SCOPE
+ )
+
+endfunction()
=====================================
doc/mkdssp.md
=====================================
@@ -92,13 +92,7 @@ calculated for H-bonds.\
# BUGS
-The mmCIF format currently lacks a lot of information that was available
-in the old format like information about the bridge pairs or the span of
-the various helices recognized. Also the accessibility information is
-left out.
-
-If you think this information should be part of the output, please
-contact the author.
+If mkdssp does not behave as expected, please contact the author.
# AUTHOR
=====================================
libdssp/CMakeLists.txt
=====================================
@@ -1,6 +1,6 @@
# Use the version of the parent list file, if any. May need a fix someday.
if(NOT CMAKE_PARENT_LIST_FILE)
- set(PROJECT_VERSION 4.4.8)
+ set(PROJECT_VERSION 4.5.2)
endif()
project(libdssp VERSION ${PROJECT_VERSION})
@@ -42,7 +42,7 @@ target_include_directories(dssp
# Install rules
install(TARGETS dssp
EXPORT dssp
- FILE_SET dssp_header DESTINATION "include")
+ FILE_SET dssp_header DESTINATION include)
if(MSVC AND BUILD_SHARED_LIBS)
install(
@@ -52,25 +52,19 @@ if(MSVC AND BUILD_SHARED_LIBS)
endif()
install(EXPORT dssp
- FILE "dsspTargets.cmake"
+ FILE "dssp-targets.cmake"
NAMESPACE dssp::
DESTINATION lib/cmake/dssp
)
-set(CONFIG_TEMPLATE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/cmake/dsspConfig.cmake.in)
+set(CONFIG_TEMPLATE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/cmake/dssp-config.cmake.in)
configure_package_config_file(
${CONFIG_TEMPLATE_FILE}
- ${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfig.cmake
+ ${CMAKE_CURRENT_BINARY_DIR}/dssp/dssp-config.cmake
INSTALL_DESTINATION lib/cmake/dssp
)
-install(FILES
- "${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfig.cmake"
- DESTINATION lib/cmake/dssp
- COMPONENT Devel
-)
-
set(dssp_MAJOR_VERSION ${CMAKE_PROJECT_VERSION_MAJOR})
set_target_properties(dssp PROPERTIES
VERSION ${PROJECT_VERSION}
@@ -82,11 +76,19 @@ set_property(TARGET dssp APPEND PROPERTY
)
write_basic_package_version_file(
- "${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfigVersion.cmake"
+ "${CMAKE_CURRENT_BINARY_DIR}/dssp/dssp-config-version.cmake"
VERSION ${PROJECT_VERSION}
COMPATIBILITY AnyNewerVersion
)
+install(FILES
+ "${CMAKE_CURRENT_BINARY_DIR}/dssp/dssp-config.cmake"
+ "${CMAKE_CURRENT_BINARY_DIR}/dssp/dssp-config-version.cmake"
+ DESTINATION lib/cmake/dssp
+ COMPONENT Devel
+)
+
+
# set(CIFPP_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}/libcifpp")
install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.dic"
DESTINATION share/libcifpp)
=====================================
libdssp/cmake/dsspConfig.cmake.in → libdssp/cmake/dssp-config.cmake.in
=====================================
@@ -3,6 +3,6 @@
include(CMakeFindDependencyMacro)
find_dependency(cifpp REQUIRED)
-INCLUDE("${CMAKE_CURRENT_LIST_DIR}/dsspTargets.cmake")
+INCLUDE("${CMAKE_CURRENT_LIST_DIR}/dssp-targets.cmake")
check_required_components(dssp)
=====================================
libdssp/include/dssp.hpp
=====================================
@@ -146,9 +146,18 @@ class dssp
bool is_cis() const { return std::abs(omega().value_or(360)) < 30.0f; }
float chiral_volume() const;
+
std::size_t nr_of_chis() const;
float chi(std::size_t index) const;
+ std::vector<float> chis() const
+ {
+ std::vector<float> result;
+ for (size_t i = 0; i < nr_of_chis(); ++i)
+ result.push_back(chi(i));
+ return result;
+ }
+
std::tuple<float, float, float> ca_location() const;
chain_break_type chain_break() const;
@@ -187,6 +196,8 @@ class dssp
/// \brief Returns \result true if there is a bond between two residues
friend bool test_bond(residue_info const &a, residue_info const &b);
+ residue_info next() const;
+
private:
residue_info(residue *res)
: m_impl(res)
@@ -250,7 +261,7 @@ class dssp
// --------------------------------------------------------------------
// Writing out the data, either in legacy format...
- void write_legacy_output(std::ostream& os) const;
+ void write_legacy_output(std::ostream &os) const;
// ... or as annotation in the cif::datablock
void annotate(cif::datablock &db, bool writeOther, bool writeDSSPCategories) const;
@@ -270,4 +281,3 @@ class dssp
private:
struct DSSP_impl *m_impl;
};
-
=====================================
libdssp/mmcif_pdbx/dssp-extension.dic
=====================================
@@ -1,11 +1,36 @@
-## File: dssp-extension.dic
-## Date: 30-May-2023
-##
-# Items containing Secondary Structure information as written by e.g. DSSP
-#
-#
+# File: dssp-extension.dic
+# Date: 30-May-2023
+
+data_dssp-extension.dic
+
+_datablock.id dssp-extension.dic
+_datablock.description
+;
+ This data block holds the dictionary for Secondary Structure information as written by e.g. DSSP
+;
-data_mmcif_pdbx-def-dssp.dic
+_dictionary.title dssp-extension.dic
+_dictionary.datablock_id dssp-extension.dic
+_dictionary.version 1.1.1
+
+loop_
+_dictionary_history.version
+_dictionary_history.update
+_dictionary_history.revision
+1.0 2023-05-30
+;
+ Initial release
+;
+1.1 2025-02-26
+;
+ Changes (mlh)
+ + Added dictionary blocks
+;
+1.1.1 2025-05-12
+;
+ Changes (mlh)
+ + Changed mandatory_code of accessible_surface_of_protein to no
+;
########################################
## Category dssp_struct_bridge_pairs ##
@@ -922,6 +947,10 @@ save__dssp_statistics.entry_id
_item.category_id dssp_statistics
_item.mandatory_code yes
_item_type.code code
+ #
+ _item_linked.child_name "_dssp_statistics.entry_id"
+ _item_linked.parent_name "_entry.id"
+ #
save_
save__dssp_statistics.nr_of_residues
@@ -980,7 +1009,7 @@ save__dssp_statistics.accessible_surface_of_protein
;
_item.name '_dssp_statistics.accessible_surface_of_protein'
_item.category_id dssp_statistics
- _item.mandatory_code yes
+ _item.mandatory_code no
_item_type.code float
save_
@@ -1025,6 +1054,10 @@ save__dssp_statistics_hbond.entry_id
_item.category dssp_statistics_hbond
_item.mandatory_code yes
_item_type.code code
+ #
+ _item_linked.child_name "_dssp_statistics_hbond.entry_id"
+ _item_linked.parent_name "_entry.id"
+ #
save_
save__dssp_statistics_hbond.type
@@ -1143,6 +1176,10 @@ save__dssp_statistics_histogram.entry_id
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code code
+ #
+ _item_linked.child_name "_dssp_statistics_histogram.entry_id"
+ _item_linked.parent_name "_entry.id"
+ #
save_
save__dssp_statistics_histogram.type
@@ -1526,6 +1563,10 @@ save__dssp_struct_summary.entry_id
_item.category dssp_struct_summary
_item.mandatory_code yes
_item_type.code code
+ #
+ _item_linked.child_name "_dssp_struct_summary.entry_id"
+ _item_linked.parent_name "_entry.id"
+ #
save_
save__dssp_struct_summary.label_comp_id
=====================================
libdssp/src/dssp-io.cpp
=====================================
@@ -162,7 +162,7 @@ void writeDSSP(const dssp &dssp, std::ostream &os)
version.insert(version.end(), 10 - version.length(), ' ');
os << "==== Secondary Structure Definition by the program DSSP, NKI version " << version << " ==== DATE=" << std::put_time(tm, "%F") << " ." << std::endl
- << "REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 ." << std::endl
+ << "REFERENCE M.L. HEKKELMAN ET AL, PROTEIN SCIENCE 34.8 (2025) e70208; W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 ." << std::endl
<< dssp.get_pdb_header_line(dssp::pdb_record_type::HEADER) << '.' << std::endl
<< dssp.get_pdb_header_line(dssp::pdb_record_type::COMPND) << '.' << std::endl
<< dssp.get_pdb_header_line(dssp::pdb_record_type::SOURCE) << '.' << std::endl
@@ -250,16 +250,14 @@ void writeBridgePairs(cif::datablock &db, const dssp &dssp)
for (auto &res : dssp)
{
- cif::row_initializer data({
- { "id", hb.get_unique_id("") },
+ cif::row_initializer data({ { "id", hb.get_unique_id("") },
{ "label_comp_id", res.compound_id() },
{ "label_seq_id", res.seq_id() },
{ "label_asym_id", res.asym_id() },
// { "auth_comp_id", res.compound_id() },
{ "auth_seq_id", res.auth_seq_id() },
{ "auth_asym_id", res.auth_asym_id() },
- { "pdbx_PDB_ins_code", res.pdb_ins_code() }
- });
+ { "pdbx_PDB_ins_code", res.pdb_ins_code() } });
for (int i : { 0, 1 })
{
@@ -338,7 +336,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
// create a list of strands, based on the SS info in DSSP. Store sheet number along with the strand.
- std::map<std::tuple<int,int>, res_list> strands;
+ std::map<std::tuple<int, int>, res_list> strands;
std::set<int> sheetNrs;
for (auto &res : dssp)
@@ -346,7 +344,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
if (res.type() != dssp::structure_type::Strand and res.type() != dssp::structure_type::Betabridge)
continue;
- strands[{res.sheet(), res.strand()}].emplace_back(res);
+ strands[{ res.sheet(), res.strand() }].emplace_back(res);
sheetNrs.insert(res.sheet());
}
@@ -359,22 +357,18 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
{
auto sheetID = cif::cif_id_for_number(sheetNr - 1);
- struct_sheet.emplace({
- { "id", sheetID },
+ struct_sheet.emplace({ { "id", sheetID },
{ "number_strands",
- std::count_if(strands.begin(), strands.end(), [nr = sheetNr](std::tuple<std::tuple<int,int>, res_list> const &s)
- {
+ std::count_if(strands.begin(), strands.end(), [nr = sheetNr](std::tuple<std::tuple<int, int>, res_list> const &s)
+ {
const auto &[strandID, strand] = s;
- return strand.front().sheet() == nr;
- })
- }
- });
+ return strand.front().sheet() == nr; }) } });
for (auto &&[strandTuple, strand] : strands)
{
if (strand.front().sheet() != sheetNr)
continue;
-
+
std::string strandID = cif::cif_id_for_number(strand.front().strand() - 1);
std::sort(strand.begin(), strand.end(), [](dssp::residue_info const &a, dssp::residue_info const &b)
@@ -383,8 +377,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
auto &beg = strand.front();
auto &end = strand.back();
- struct_sheet_range.emplace({
- { "sheet_id", sheetID },
+ struct_sheet_range.emplace({ { "sheet_id", sheetID },
{ "id", strandID },
{ "beg_label_comp_id", beg.compound_id() },
{ "beg_label_asym_id", beg.asym_id() },
@@ -475,8 +468,7 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
const auto &[beg1, beg2] = l.pairs.front();
const auto &[end1, end2] = l.pairs.back();
- dssp_struct_ladder.emplace({
- { "id", cif::cif_id_for_number(l.ladder) },
+ dssp_struct_ladder.emplace({ { "id", cif::cif_id_for_number(l.ladder) },
{ "sheet_id", cif::cif_id_for_number(l.sheet) },
{ "range_id_1", cif::cif_id_for_number(beg1.strand() - 1) },
{ "range_id_2", cif::cif_id_for_number(beg2.strand() - 1) },
@@ -522,15 +514,18 @@ void writeStatistics(cif::datablock &db, const dssp &dssp)
auto &dssp_statistics = db["dssp_statistics"];
- auto stats_i = dssp_statistics.emplace({ { "entry_id", db.name() },
+ std::optional<double> surface_accessibility;
+ if (stats.accessible_surface > 0)
+ surface_accessibility = stats.accessible_surface;
+
+ auto stats_i = dssp_statistics.emplace({ //
+ { "entry_id", db.name() },
{ "nr_of_residues", stats.count.residues },
{ "nr_of_chains", stats.count.chains },
{ "nr_of_ss_bridges_total", stats.count.SS_bridges },
{ "nr_of_ss_bridges_intra_chain", stats.count.intra_chain_SS_bridges },
- { "nr_of_ss_bridges_inter_chain", stats.count.SS_bridges - stats.count.intra_chain_SS_bridges } });
-
- if (stats.accessible_surface > 0)
- (*stats_i)["accessible_surface_of_protein"] = stats.accessible_surface;
+ { "nr_of_ss_bridges_inter_chain", stats.count.SS_bridges - stats.count.intra_chain_SS_bridges },
+ { "accessible_surface_of_protein", surface_accessibility } });
auto &dssp_struct_hbonds = db["dssp_statistics_hbond"];
@@ -612,9 +607,9 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
// prime the category with the field labels we need, this is to ensure proper order in writing out the data.
for (auto label : { "entry_id", "label_comp_id", "label_asym_id", "label_seq_id", "secondary_structure",
- "ss_bridge", "helix_3_10", "helix_alpha", "helix_pi", "helix_pp", "bend", "chirality", "sheet",
- "strand", "ladder_1", "ladder_2", "accessibility", "TCO", "kappa", "alpha", "phi", "psi",
- "x_ca", "y_ca", "z_ca"})
+ "ss_bridge", "helix_3_10", "helix_alpha", "helix_pi", "helix_pp", "bend", "chirality", "sheet",
+ "strand", "ladder_1", "ladder_2", "accessibility", "TCO", "kappa", "alpha", "phi", "psi",
+ "x_ca", "y_ca", "z_ca" })
dssp_struct_summary.add_item(label);
for (auto res : dssp)
@@ -738,25 +733,32 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
data.emplace_back("psi", *res.psi(), 1);
else
data.emplace_back("psi", ".");
-
+
dssp_struct_summary.emplace(std::move(data));
}
}
-void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool writeExperimental)
+void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool writeNewFormat)
{
using namespace std::literals;
- if (db.get_validator() != nullptr) {
- auto &validator = const_cast<cif::validator &>(*db.get_validator());
- if (validator.get_validator_for_category("dssp_struct_summary") == nullptr)
- {
- auto dssp_extension = cif::load_resource("dssp-extension.dic");
- if (dssp_extension)
- cif::extend_dictionary(validator, *dssp_extension);
- }
+ auto &audit_conform = db["audit_conform"];
+
+ if (audit_conform.empty())
+ {
+ auto &cf = cif::validator_factory::instance();
+ cf.get("mmcif_pdbx.dic").fill_audit_conform(audit_conform);
}
+ audit_conform.erase(cif::key("dict_name") == "dssp-extension.dic");
+ audit_conform.emplace({ //
+ { "dict_name", "dssp-extension.dic" },
+ { "dict_version", "1.1.1" },
+ { "dict_location", "https://pdb-redo.eu/dssp/dssp-extension.dic" } });
+
+ // Re-load the dictionary
+ db.load_dictionary();
+
if (dssp.empty())
{
if (cif::VERBOSE > 0)
@@ -764,7 +766,19 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool wr
}
else
{
- if (writeExperimental)
+ for (auto cat : std::initializer_list<const char *>{
+ "dssp_struct_bridge_pairs",
+ "dssp_struct_ladder",
+ "dssp_statistics",
+ "dssp_statistics_hbond",
+ "dssp_statistics_histogram",
+ "dssp_struct_summary"
+ })
+ {
+ db.erase(std::remove_if(db.begin(), db.end(), [cat] (cif::category &c) { return c.name() == cat; }), db.end());
+ }
+
+ if (writeNewFormat)
{
writeBridgePairs(db, dssp);
writeSheets(db, dssp);
@@ -840,7 +854,7 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool wr
foundTypes[id] = 1;
}
- structConf.emplace({
+ structConf.emplace({ //
{ "conf_type_id", id },
{ "id", id + std::to_string(foundTypes[id]++) },
// { "pdbx_PDB_helix_id", vS(12, 14) },
@@ -858,8 +872,7 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool wr
{ "beg_auth_seq_id", rb.auth_seq_id() },
{ "end_auth_comp_id", re.compound_id() },
{ "end_auth_asym_id", re.auth_asym_id() },
- { "end_auth_seq_id", re.auth_seq_id() }
- });
+ { "end_auth_seq_id", re.auth_seq_id() } });
st = t;
}
@@ -876,11 +889,10 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool wr
}
auto &software = db["software"];
- software.emplace({
+ software.emplace({ //
{ "pdbx_ordinal", software.get_unique_id("") },
{ "name", "dssp" },
{ "version", klibdsspVersionNumber },
{ "date", klibdsspRevisionDate },
- { "classification", "model annotation" }
- });
+ { "classification", "model annotation" } });
}
=====================================
libdssp/src/dssp-io.hpp
=====================================
@@ -29,4 +29,4 @@
#include "dssp.hpp"
void writeDSSP(const dssp& dssp, std::ostream& os);
-void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental);
+void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeNewFormat);
=====================================
libdssp/src/dssp.cpp
=====================================
@@ -36,7 +36,7 @@
#include <thread>
#ifdef near
-#undef near
+# undef near
#endif
using residue = dssp::residue;
@@ -552,7 +552,7 @@ struct dssp::residue
HBond mHBondDonor[2] = {}, mHBondAcceptor[2] = {};
bridge_partner mBetaPartner[2] = {};
uint32_t mSheet = 0;
- uint32_t mStrand = 0; // Added to ease the writing of mmCIF's struct_sheet and friends
+ uint32_t mStrand = 0; // Added to ease the writing of mmCIF's struct_sheet and friends
helix_position_type mHelixFlags[4] = { helix_position_type::None, helix_position_type::None, helix_position_type::None, helix_position_type::None }; //
bool mBend = false;
chain_break_type mChainBreak = chain_break_type::None;
@@ -789,7 +789,7 @@ void CalculateHBondEnergies(std::vector<residue> &inResidues, std::vector<std::t
CalculateHBondEnergy(ri, rj);
if (j != i + 1)
CalculateHBondEnergy(rj, ri);
-
+
if (progress)
progress->consumed(1);
}
@@ -1116,10 +1116,10 @@ void CalculateBetaSheets(std::vector<residue> &inResidues, statistics &stats, st
{
if (res.mSheet != iSheet)
continue;
-
+
if (lastNr + 1 < res.mNumber)
++strand;
-
+
res.mStrand = strand;
lastNr = res.mNumber;
}
@@ -1425,17 +1425,16 @@ DSSP_impl::DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_prolin
auto &pdbx_poly_seq_scheme = mDB["pdbx_poly_seq_scheme"];
auto &atom_site = mDB["atom_site"];
- using key_type = std::tuple<std::string,int>;
+ using key_type = std::tuple<std::string, int>;
using index_type = std::map<key_type, size_t>;
index_type index;
mResidues.reserve(pdbx_poly_seq_scheme.size());
- for (const auto &[asym_id, seq_id, pdb_strand_id, pdb_seq_num, pdb_ins_code]
- : pdbx_poly_seq_scheme.rows<std::string,int, std::string, int, std::string>("asym_id", "seq_id", "pdb_strand_id", "pdb_seq_num", "pdb_ins_code"))
+ for (const auto &[asym_id, seq_id, pdb_strand_id, pdb_seq_num, pdb_ins_code] : pdbx_poly_seq_scheme.rows<std::string, int, std::string, int, std::string>("asym_id", "seq_id", "pdb_strand_id", "pdb_seq_num", "pdb_ins_code"))
{
- index[{asym_id, seq_id}] = mResidues.size();
+ index[{ asym_id, seq_id }] = mResidues.size();
mResidues.emplace_back(model_nr, pdb_strand_id, pdb_seq_num, pdb_ins_code);
}
@@ -1445,17 +1444,19 @@ DSSP_impl::DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_prolin
int seq_id;
cif::tie(asym_id, seq_id) = atom.get("label_asym_id", "label_seq_id");
- auto i = index.find({asym_id, seq_id});
+ auto i = index.find({ asym_id, seq_id });
if (i == index.end())
continue;
-
+
mResidues[i->second].addAtom(atom);
}
for (auto &residue : mResidues)
residue.finish();
-
- mResidues.erase(std::remove_if(mResidues.begin(), mResidues.end(), [](const dssp::residue &r) { return not r.mComplete; }), mResidues.end());
+
+ mResidues.erase(std::remove_if(mResidues.begin(), mResidues.end(), [](const dssp::residue &r)
+ { return not r.mComplete; }),
+ mResidues.end());
mStats.count.chains = 1;
chain_break_type brk = chain_break_type::NewChain;
@@ -1595,7 +1596,7 @@ void DSSP_impl::calculateSecondaryStructure()
progress.reset(new cif::progress_bar((mResidues.size() * (mResidues.size() - 1)) / 2, "calculate distances"));
// Calculate the HBond energies
- std::vector<std::tuple<uint32_t,uint32_t>> near;
+ std::vector<std::tuple<uint32_t, uint32_t>> near;
for (uint32_t i = 0; i + 1 < mResidues.size(); ++i)
{
@@ -2183,6 +2184,11 @@ std::tuple<dssp::residue_info, double> dssp::residue_info::donor(int i) const
return { residue_info(d.res), d.energy };
}
+dssp::residue_info dssp::residue_info::next() const
+{
+ return residue_info(m_impl ? m_impl->mNext : nullptr);
+}
+
// --------------------------------------------------------------------
dssp::iterator::iterator(residue *res)
@@ -2248,11 +2254,12 @@ dssp::iterator dssp::end() const
dssp::residue_info dssp::operator[](const key_type &key) const
{
auto i = std::find_if(begin(), end(),
- [key](const residue_info &res) { return res.asym_id() == std::get<0>(key) and res.seq_id() == std::get<1>(key); });
-
+ [key](const residue_info &res)
+ { return res.asym_id() == std::get<0>(key) and res.seq_id() == std::get<1>(key); });
+
if (i == end())
throw std::out_of_range("Could not find residue with supplied key");
-
+
return *i;
}
@@ -2280,7 +2287,7 @@ std::string dssp::get_pdb_header_line(pdb_record_type pdb_record) const
// --------------------------------------------------------------------
-void dssp::write_legacy_output(std::ostream& os) const
+void dssp::write_legacy_output(std::ostream &os) const
{
writeDSSP(*this, os);
}
@@ -2289,5 +2296,3 @@ void dssp::annotate(cif::datablock &db, bool writeOther, bool writeDSSPCategorie
{
annotateDSSP(db, *this, writeOther, writeDSSPCategories);
}
-
-
=====================================
python-module/CMakeLists.txt
=====================================
@@ -0,0 +1,79 @@
+# 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(CPM)
+
+if(CMAKE_VERSION GREATER_EQUAL 3.30)
+ cmake_policy(SET CMP0167 NEW)
+endif()
+
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+find_package(Boost 1.83 QUIET COMPONENTS python)
+
+if(NOT Boost_FOUND)
+ # boost is a huge project and directly downloading the 'alternate release'
+ # from github is much faster than recursively cloning the repo.
+ CPMAddPackage(
+ NAME Boost
+ VERSION 1.84.0
+ URL https://github.com/boostorg/boost/releases/download/boost-1.84.0/boost-1.84.0.tar.xz
+ URL_HASH SHA256=2e64e5d79a738d0fa6fb546c6e5c2bd28f88d268a2a080546f74e5ff98f29d0e
+ OPTIONS
+ "BOOST_ENABLE_CMAKE ON"
+ "BOOST_INCLUDE_LIBRARIES python"
+ "BOOST_ENABLE_PYTHON ON"
+ "CMAKE_POSITION_INDEPENDENT_CODE ON"
+ )
+endif()
+
+# ---------
+add_library(mkdssp_module SHARED dssp-python-plugin.cpp)
+
+target_compile_features(mkdssp_module PUBLIC cxx_std_20)
+
+target_include_directories(mkdssp_module PRIVATE ${Python_INCLUDE_DIRS})
+target_link_libraries(mkdssp_module dssp::dssp Boost::python ${Python_LIBRARIES})
+
+set_target_properties(mkdssp_module
+ PROPERTIES
+ PREFIX ""
+ SUFFIX ".so"
+ OUTPUT_NAME mkdssp
+ LINKER_LANGUAGE CXX
+ LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib
+)
+
+if(WIN32)
+ # python modules use this on Windows
+ set_target_properties(
+ mkdssp_module
+ PROPERTIES
+ SUFFIX ".pyd"
+ RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+ )
+
+ install(TARGETS mkdssp_module RUNTIME DESTINATION "${Python_SITELIB}")
+else()
+ install(TARGETS mkdssp_module LIBRARY DESTINATION "${Python_SITELIB}")
+endif()
\ No newline at end of file
=====================================
python-module/dssp-python-plugin.cpp
=====================================
@@ -0,0 +1,332 @@
+#include <boost/python.hpp>
+#include <Python.h>
+
+#include <dssp.hpp>
+
+struct statistics_wrapper
+{
+ int get_residues() { return m_stats.count.residues; }
+ int get_chains() { return m_stats.count.chains; }
+ int get_SS_bridges() { return m_stats.count.SS_bridges; }
+ int get_intra_chain_SS_bridges() { return m_stats.count.intra_chain_SS_bridges; }
+ int get_H_bonds() { return m_stats.count.H_bonds; }
+ int get_H_bonds_in_antiparallel_bridges() { return m_stats.count.H_bonds_in_antiparallel_bridges; }
+ int get_H_bonds_in_parallel_bridges() { return m_stats.count.H_bonds_in_parallel_bridges; }
+
+ dssp::statistics m_stats;
+};
+
+enum class ladder_direction_type
+{
+ parallel,
+ antiparallel
+};
+
+struct residue_info_wrapper
+{
+};
+
+class dssp_wrapper
+{
+ public:
+ dssp_wrapper(std::string data, int model_nr = 1, int min_poly_proline_stretch_length = 3, bool calculateSurfaceAccessibility = false)
+ {
+ struct membuf : public std::streambuf
+ {
+ membuf(char *text, size_t length)
+ {
+ this->setg(text, text, text + length);
+ }
+ } buffer(const_cast<char *>(data.data()), data.length());
+
+ std::istream is(&buffer);
+
+ auto f = cif::pdb::read(is);
+ m_dssp.reset(new dssp(f.front(), model_nr, min_poly_proline_stretch_length, calculateSurfaceAccessibility));
+ }
+
+ dssp_wrapper(const dssp_wrapper &) = default;
+ dssp_wrapper &operator=(const dssp_wrapper &) = default;
+
+ statistics_wrapper get_statistics()
+ {
+ statistics_wrapper result{ .m_stats = m_dssp->get_statistics() };
+ return result;
+ }
+
+ struct residue_info_handle
+ {
+ residue_info_handle(dssp::residue_info info)
+ : m_info(info)
+ {
+ }
+
+ operator dssp::residue_info &() { return m_info; }
+
+ dssp::residue_info m_info;
+ };
+
+ class iterator
+ {
+ public:
+ using iterator_category = std::forward_iterator_tag;
+ using value_type = dssp::residue_info;
+ using difference_type = std::ptrdiff_t;
+ using pointer = value_type *;
+ using reference = residue_info_handle;
+
+ iterator(dssp::residue_info info)
+ : m_current(info)
+ {
+ }
+
+ iterator(const iterator &i) = default;
+ iterator &operator=(const iterator &i) = default;
+
+ reference operator*() { return residue_info_handle(m_current); }
+ pointer operator->() { return &m_current; }
+
+ iterator &operator++()
+ {
+ m_current = m_current.next();
+ return *this;
+ }
+
+ iterator operator++(int)
+ {
+ auto tmp(*this);
+ this->operator++();
+ return tmp;
+ }
+
+ bool operator==(const iterator &rhs) const
+ {
+ return m_current == rhs.m_current;
+ }
+
+ private:
+ dssp::residue_info m_current;
+ };
+
+ auto begin() { return iterator(*m_dssp->begin()); }
+ auto end() { return iterator({}); }
+
+ auto get(std::string asym_id, int nr)
+ {
+ return m_dssp->operator[]({ asym_id, nr });
+ }
+
+ private:
+ std::shared_ptr<dssp> m_dssp;
+};
+
+// shamelessly copied from a stack overflow comment
+// https://stackoverflow.com/questions/36485840/wrap-boostoptional-using-boostpython
+
+// Custom exceptions
+struct AttributeError : std::exception
+{
+ const char *what() const throw() { return "AttributeError exception"; }
+};
+
+struct TypeError : std::exception
+{
+ const char *what() const throw() { return "TypeError exception"; }
+};
+
+// Set python exceptions
+void translate(const std::exception &e)
+{
+ if (dynamic_cast<const AttributeError *>(&e))
+ PyErr_SetString(PyExc_AttributeError, e.what());
+ if (dynamic_cast<const TypeError *>(&e))
+ PyErr_SetString(PyExc_TypeError, e.what());
+}
+
+struct to_python_optional
+{
+ static PyObject *convert(const std::optional<float> &obj)
+ {
+ if (obj)
+ return boost::python::incref(boost::python::object(*obj).ptr());
+ else
+ return boost::python::incref(boost::python::object().ptr());
+ }
+};
+
+struct to_python_list_of_floats
+{
+ static PyObject *convert(const std::vector<float> &v)
+ {
+ boost::python::list list;
+ for (auto value : v)
+ list.append(value);
+ return boost::python::incref(boost::python::object(list).ptr());
+ }
+};
+
+struct to_python_point
+{
+ static PyObject *convert(const std::tuple<float, float, float> &v)
+ {
+ boost::python::dict p;
+ p["x"] = std::get<0>(v);
+ p["y"] = std::get<1>(v);
+ p["z"] = std::get<2>(v);
+ return boost::python::incref(boost::python::object(p).ptr());
+ }
+};
+
+struct to_python_partner
+{
+ static PyObject *convert(const std::tuple<dssp::residue_info, double> &v)
+ {
+ boost::python::type_info iv = boost::python::type_id<dssp::residue_info>();
+ const boost::python::converter::registration* cv = boost::python::converter::registry::query(iv);
+ assert(cv != nullptr);
+ if (cv == nullptr)
+ throw std::runtime_error("Missing registration");
+
+ if (auto &[ri, e] = v; ri)
+ {
+ auto c = cv->to_python(&ri);
+ return boost::python::incref(boost::python::make_tuple(boost::python::handle<>(c), e).ptr());
+ }
+ else
+ return boost::python::incref(boost::python::make_tuple(boost::python::object(), 0).ptr());
+ }
+};
+
+struct to_python_bridge_partner
+{
+ static PyObject *convert(const std::tuple<dssp::residue_info, int, bool> &v)
+ {
+ if (auto &[ri, nr, parallel] = v; ri)
+ {
+ boost::python::type_info iv = boost::python::type_id<dssp::residue_info>();
+ const boost::python::converter::registration* cv = boost::python::converter::registry::query(iv);
+ assert(cv != nullptr);
+
+ boost::python::type_info dv = boost::python::type_id<ladder_direction_type>();
+ const boost::python::converter::registration* ev = boost::python::converter::registry::query(dv);
+ assert(ev != nullptr);
+
+ auto c = cv->to_python(&ri);
+
+ ladder_direction_type direction = parallel ? ladder_direction_type::parallel : ladder_direction_type::antiparallel;
+ auto e = ev->to_python(&direction);
+
+ return boost::python::incref(boost::python::make_tuple(
+ boost::python::handle<>(c), nr, boost::python::handle<>(e)).ptr());
+ }
+ else
+ return boost::python::incref(boost::python::make_tuple(boost::python::object(), 0, boost::python::object()).ptr());
+ }
+};
+
+bool test_bond_between_residues(PyObject *a, PyObject *b)
+{
+ const auto &a_ri = boost::python::extract<dssp::residue_info&>(a);
+ const auto &b_ri = boost::python::extract<dssp::residue_info&>(b);
+
+ return test_bond(a_ri, b_ri);
+}
+
+BOOST_PYTHON_MODULE(mkdssp)
+{
+ using namespace boost::python;
+
+ register_exception_translator<AttributeError>(&translate);
+ register_exception_translator<TypeError>(&translate);
+
+ to_python_converter<std::optional<float>, to_python_optional>();
+ to_python_converter<std::vector<float>, to_python_list_of_floats>();
+ to_python_converter<std::tuple<float, float, float>, to_python_point>();
+ to_python_converter<std::tuple<dssp::residue_info, double>, to_python_partner>();
+ to_python_converter<std::tuple<dssp::residue_info, int, bool>, to_python_bridge_partner>();
+
+ enum_<dssp::structure_type>("structure_type")
+ .value("Loop", dssp::structure_type::Loop)
+ .value("Alphahelix", dssp::structure_type::Alphahelix)
+ .value("Betabridge", dssp::structure_type::Betabridge)
+ .value("Strand", dssp::structure_type::Strand)
+ .value("Helix_3", dssp::structure_type::Helix_3)
+ .value("Helix_5", dssp::structure_type::Helix_5)
+ .value("Helix_PPII", dssp::structure_type::Helix_PPII)
+ .value("Turn", dssp::structure_type::Turn)
+ .value("Bend", dssp::structure_type::Bend);
+
+ enum_<dssp::helix_type>("helix_type")
+ .value("_3_10", dssp::helix_type::_3_10)
+ .value("alpha", dssp::helix_type::alpha)
+ .value("pi", dssp::helix_type::pi)
+ .value("pp", dssp::helix_type::pp);
+
+ enum_<dssp::helix_position_type>("helix_position_type")
+ .value("NoHelix", dssp::helix_position_type::None)
+ .value("Start", dssp::helix_position_type::Start)
+ .value("End", dssp::helix_position_type::End)
+ .value("StartAndEnd", dssp::helix_position_type::StartAndEnd)
+ .value("Middle", dssp::helix_position_type::Middle);
+
+ enum_<ladder_direction_type>("ladder_direction_type")
+ .value("parallel", ladder_direction_type::parallel)
+ .value("anti_parallel", ladder_direction_type::antiparallel);
+
+ enum_<dssp::chain_break_type>("chain_break_type")
+ .value("NoGap", dssp::chain_break_type::None)
+ .value("NewChain", dssp::chain_break_type::NewChain)
+ .value("Gap", dssp::chain_break_type::Gap);
+
+ class_<statistics_wrapper>("statistic_counts")
+ .add_property("residues", &statistics_wrapper::get_residues)
+ .add_property("chains", &statistics_wrapper::get_chains)
+ .add_property("SS_bridges", &statistics_wrapper::get_SS_bridges)
+ .add_property("intra_chain_SS_bridges", &statistics_wrapper::get_intra_chain_SS_bridges)
+ .add_property("H_bonds", &statistics_wrapper::get_H_bonds)
+ .add_property("H_bonds_in_antiparallel_bridges", &statistics_wrapper::get_H_bonds_in_antiparallel_bridges)
+ .add_property("H_bonds_in_parallel_bridges", &statistics_wrapper::get_H_bonds_in_parallel_bridges);
+
+ class_<dssp::residue_info>("residue_info")
+ .add_property("asym_id", &dssp::residue_info::asym_id)
+ .add_property("seq_id", &dssp::residue_info::seq_id)
+ .add_property("alt_id", &dssp::residue_info::alt_id)
+ .add_property("compound_id", &dssp::residue_info::compound_id)
+ .add_property("compound_letter", &dssp::residue_info::compound_letter)
+ .add_property("auth_asym_id", &dssp::residue_info::auth_asym_id)
+ .add_property("auth_seq_id", &dssp::residue_info::auth_seq_id)
+ .add_property("pdb_strand_id", &dssp::residue_info::pdb_strand_id)
+ .add_property("pdb_seq_num", &dssp::residue_info::pdb_seq_num)
+ .add_property("pdb_ins_code", &dssp::residue_info::pdb_ins_code)
+ .add_property("alpha", &dssp::residue_info::alpha)
+ .add_property("kappa", &dssp::residue_info::kappa)
+ .add_property("phi", &dssp::residue_info::phi)
+ .add_property("psi", &dssp::residue_info::psi)
+ .add_property("tco", &dssp::residue_info::tco)
+ .add_property("omega", &dssp::residue_info::omega)
+ .add_property("is_pre_pro", &dssp::residue_info::is_pre_pro)
+ .add_property("is_cis", &dssp::residue_info::is_cis)
+ .add_property("chiral_volume", &dssp::residue_info::chiral_volume)
+ .add_property("chi", &dssp::residue_info::chis)
+ .add_property("ca_location", &dssp::residue_info::ca_location)
+ .add_property("chain_break", &dssp::residue_info::chain_break)
+ .add_property("nr", &dssp::residue_info::nr)
+ .add_property("type", &dssp::residue_info::type)
+ .add_property("ssBridgeNr", &dssp::residue_info::ssBridgeNr)
+ .def("helix", &dssp::residue_info::helix, args("helix_type"), "Return the position of this residue in a helix with type helix_type")
+ .add_property("is_alpha_helix_end_before_start", &dssp::residue_info::is_alpha_helix_end_before_start)
+ .add_property("bend", &dssp::residue_info::bend)
+ .add_property("accessibility", &dssp::residue_info::accessibility)
+ .def("bridge_partner", &dssp::residue_info::bridge_partner, args("indexnr"), "Return a tuple containing the residue, number and direction for the bridge partner with index indexnr")
+ .add_property("sheet", &dssp::residue_info::sheet)
+ .add_property("strand", &dssp::residue_info::strand)
+ .def("acceptor", &dssp::residue_info::acceptor, args("indexnr"), "Return a tuple containing the residue and bond energy for the acceptor with index indexnr")
+ .def("donor", &dssp::residue_info::donor, args("indexnr"), "Return a tuple containing the residue and bond energy for the donor with index indexnr");
+
+ class_<dssp_wrapper, boost::noncopyable>("dssp", init<std::string, optional<int, int, bool>>())
+ .add_property("statistics", &dssp_wrapper::get_statistics)
+ .def("__iter__", iterator<dssp_wrapper>())
+ .def("get", &dssp_wrapper::get, args("asym_id", "seq_id"), "Return the residue info object for the residue with specified asym_id and seq_id");
+
+ def("TestBond", test_bond_between_residues, args("a", "b"), "Returns true if residues a and b are bonded according to DSSP");
+}
\ No newline at end of file
=====================================
python-module/test-mkdssp.py
=====================================
@@ -0,0 +1,83 @@
+from mkdssp import dssp, helix_type, TestBond
+import os
+import gzip
+
+file_path = os.path.join("..", "test", "1cbs.cif.gz")
+
+with gzip.open(file_path, "rt") as f:
+ file_content = f.read()
+
+dssp = dssp(file_content)
+
+print("residues: ", dssp.statistics.residues)
+print("chains: ", dssp.statistics.chains)
+print("SS_bridges: ", dssp.statistics.SS_bridges)
+print("intra_chain_SS_bridges: ", dssp.statistics.intra_chain_SS_bridges)
+print("H_bonds: ", dssp.statistics.H_bonds)
+print("H_bonds_in_antiparallel_bridges: ", dssp.statistics.H_bonds_in_antiparallel_bridges)
+print("H_bonds_in_parallel_bridges: ", dssp.statistics.H_bonds_in_parallel_bridges)
+
+count = 0
+for res in dssp:
+ count += 1
+ print(res.asym_id, res.seq_id, res.compound_id)
+ print("alt_id", res.alt_id)
+ print("compound_letter", res.compound_letter)
+ print("auth_asym_id", res.auth_asym_id)
+ print("auth_seq_id", res.auth_seq_id)
+ print("pdb_strand_id", res.pdb_strand_id)
+ print("pdb_seq_num", res.pdb_seq_num)
+ print("pdb_ins_code", res.pdb_ins_code)
+ print("alpha", res.alpha)
+ print("kappa", res.kappa)
+ print("phi", res.phi)
+ print("psi", res.psi)
+ print("tco", res.tco)
+ print("omega", res.omega)
+ print("is_pre_pro", res.is_pre_pro)
+ print("is_cis", res.is_cis)
+ print("chiral_volume", res.chiral_volume)
+ print("chi", res.chi)
+ print("ca_location", res.ca_location)
+ print("chain_break", res.chain_break)
+ print("nr", res.nr)
+ print("type", res.type)
+ print("ssBridgeNr", res.ssBridgeNr)
+ print("helix(_3_10)", res.helix(helix_type._3_10))
+ print("helix(alpha)", res.helix(helix_type.alpha))
+ print("helix(pi)", res.helix(helix_type.pi))
+ print("helix(pp)", res.helix(helix_type.pp))
+ print("is_alpha_helix_end_before_start", res.is_alpha_helix_end_before_start)
+ print("bend", res.bend)
+ print("sheet", res.sheet)
+ print("strand", res.strand)
+
+ for i in range(0, 1):
+ (ri, nr, dir) = res.bridge_partner(i)
+ if ri != None:
+ print("bridge partner ", i, ri.asym_id, ri.seq_id, ri.compound_id, nr, dir)
+
+ for i in range(0, 1):
+ (ri, e) = res.acceptor(i)
+ if ri != None:
+ print("acceptor ", i, ri.asym_id, ri.seq_id, ri.compound_id, e)
+ print("test bond: ", TestBond(res, ri))
+
+ for i in range(0, 1):
+ (ri, e) = res.donor(i)
+ if ri != None:
+ print("donor ", i, ri.asym_id, ri.seq_id, ri.compound_id, e)
+ print("test bond: ", TestBond(res, ri))
+
+ print("accessibility", res.accessibility)
+ break
+
+
+print("count: ", count)
+
+a = dssp.get('A', 137)
+b = dssp.get('A', 6)
+
+print ("a & b", a, b)
+
+assert(TestBond(a, b))
=====================================
src/mkdssp.cpp
=====================================
@@ -25,7 +25,7 @@
*/
#if __has_include("config.hpp")
-#include "config.hpp"
+# include "config.hpp"
#endif
#include <exception>
@@ -33,8 +33,8 @@
#include <fstream>
#include <iostream>
-#include <mcfp/mcfp.hpp>
#include <cif++.hpp>
+#include <mcfp/mcfp.hpp>
#include "dssp.hpp"
#include "revision.hpp"
@@ -114,16 +114,42 @@ int d_main(int argc, const char *argv[])
// private mmcif_pdbx dictionary?
if (config.has("mmcif-dictionary"))
- cif::add_file_resource("mmcif_pdbx.dic", config.get<std::string>("mmcif-dictionary"));
+ {
+ fs::path mmcif_dict = config.get<std::string>("mmcif-dictionary");
- cif::gzio::ifstream in(config.operands().front());
- if (not in.is_open())
+ cif::add_file_resource("mmcif_pdbx.dic", mmcif_dict);
+
+ // Try to be smart, maybe dssp-extension.dic is at that location as well?
+ auto dir = fs::canonical(mmcif_dict.parent_path());
+ if (auto dssp_dict = cif::load_resource("dssp-extension.dic"); dssp_dict == nullptr and fs::exists(dir / "dssp-extension.dic"))
+ cif::add_data_directory(dir);
+ }
+
+ cif::file f;
+
+ try
{
- std::cerr << "Could not open file" << std::endl;
- exit(1);
+ auto &cf = cif::validator_factory::instance();
+
+ cif::gzio::ifstream in(config.operands().front());
+ if (not in.is_open())
+ {
+ std::cerr << "Could not open file" << std::endl;
+ exit(1);
+ }
+
+ f.load(in);
+ f.front().set_validator(&cf.get("mmcif_pdbx.dic"));
+
+ if (f.empty() or f.front().get("pdbx_poly_seq_scheme") == nullptr)
+ throw std::runtime_error("Missing pdbx_poly_seq_scheme, will attempt to recover...");
}
+ catch (const std::exception &e)
+ {
+ std::cerr << e.what() << '\n';
- cif::file f = cif::pdb::read(in);
+ f = cif::pdb::read(config.operands().front());
+ }
// --------------------------------------------------------------------
@@ -160,7 +186,7 @@ int d_main(int argc, const char *argv[])
{
// See if the data will fit at all
auto &db = f.front();
- for (const auto &[chain_id, seq_nr] : db["pdbx_poly_seq_scheme"].rows<std::string,int>("pdb_strand_id", "pdb_seq_num"))
+ for (const auto &[chain_id, seq_nr] : db["pdbx_poly_seq_scheme"].rows<std::string, int>("pdb_strand_id", "pdb_seq_num"))
{
if (chain_id.length() > 1 or seq_nr > 99999)
{
=====================================
test/1cbs-dssp.cif
=====================================
The diff for this file was not included because it is too large.
=====================================
test/CMakeLists.txt
=====================================
@@ -1,28 +1,11 @@
-if(NOT(Catch2_FOUND OR TARGET Catch2))
- find_package(Catch2 QUIET)
-
- if(NOT Catch2_FOUND)
- include(FetchContent)
-
- FetchContent_Declare(
- Catch2
- GIT_REPOSITORY https://github.com/catchorg/Catch2.git
- GIT_TAG v2.13.9)
-
- FetchContent_MakeAvailable(Catch2)
-
- set(Catch2_VERSION "2.13.9")
- endif()
-endif()
+CPMFindPackage(
+ NAME Catch2 3
+ GIT_REPOSITORY https://github.com/catchorg/Catch2.git
+ GIT_TAG v3.8.0
+ EXCLUDE_FROM_ALL YES)
add_executable(unit-test-dssp ${CMAKE_CURRENT_SOURCE_DIR}/unit-test-dssp.cpp ${PROJECT_SOURCE_DIR}/libdssp/src/dssp-io.cpp)
-if(USE_RSRC)
- mrc_target_resources(unit-test-dssp
- ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic
- ${CMAKE_CURRENT_SOURCE_DIR}/../libdssp/mmcif_pdbx/dssp-extension.dic)
-endif()
-
target_include_directories(unit-test-dssp PRIVATE
${CMAKE_CURRENT_SOURCE_DIR}/src
${CMAKE_CURRENT_SOURCE_DIR}/include
@@ -35,12 +18,15 @@ if(MSVC)
target_compile_options(unit-test-dssp PRIVATE /EHsc)
endif()
-if("${Catch2_VERSION}" VERSION_GREATER_EQUAL 3.0.0)
- target_compile_definitions(unit-test-dssp PUBLIC CATCH22=0)
-else()
- target_compile_definitions(unit-test-dssp PUBLIC CATCH22=1)
-endif()
-
add_test(NAME unit-test-dssp COMMAND $<TARGET_FILE:unit-test-dssp>
--data-dir ${CMAKE_CURRENT_SOURCE_DIR}
- --rsrc-dir ${CMAKE_CURRENT_BINARY_DIR}/_deps/cifpp-src/rsrc)
+ --rsrc-dir ${CMAKE_CURRENT_SOURCE_DIR}/../libdssp/mmcif_pdbx/)
+
+if(BUILD_PYTHON_MODULE)
+ find_package(Python REQUIRED Interpreter)
+
+ add_test(NAME python_module COMMAND ${Python_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/test-python.py")
+ set_tests_properties(python_module PROPERTIES
+ ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:mkdssp_module>"
+ WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")
+endif()
\ No newline at end of file
=====================================
test/pdb1cbs.ent.gz
=====================================
Binary files /dev/null and b/test/pdb1cbs.ent.gz differ
=====================================
test/test-python.py
=====================================
@@ -0,0 +1,68 @@
+from mkdssp import dssp, TestBond, helix_type, chain_break_type, helix_type, helix_position_type, structure_type
+import gzip
+import unittest
+
+class TestDssp(unittest.TestCase):
+ def setUp(self):
+ with gzip.open("1cbs.cif.gz", "rt") as f:
+ file_content = f.read()
+
+ self.dssp = dssp(file_content)
+
+ def test_dssp(self):
+ stats = self.dssp.statistics
+ self.assertEqual(stats.residues, 137)
+
+ def test_count(self):
+ count = 0
+ for r in self.dssp:
+ count += 1
+ self.assertEqual(count, 137)
+
+ def test_bond(self):
+ a = self.dssp.get('A', 137)
+ b = self.dssp.get('A', 6)
+ self.assertTrue(TestBond(a, b))
+
+ def test_one_residue(self):
+ r = self.dssp.get("A", 15)
+
+ self.assertEqual(r.asym_id, "A")
+ self.assertEqual(r.seq_id, 15)
+
+ self.assertEqual(r.compound_letter, "F")
+ self.assertEqual(r.auth_asym_id, "A")
+ self.assertEqual(r.auth_seq_id, 15)
+ self.assertEqual(r.pdb_strand_id, "A")
+ self.assertEqual(r.pdb_seq_num, 15)
+ self.assertEqual(r.pdb_ins_code, '')
+ self.assertAlmostEqual(r.alpha, 44.76425552368164)
+ self.assertAlmostEqual(r.kappa, 73.85977935791016)
+ self.assertAlmostEqual(r.phi, -66.86814880371094)
+ self.assertAlmostEqual(r.psi, -48.56082534790039)
+ self.assertAlmostEqual(r.tco, 0.9395495057106018)
+ self.assertAlmostEqual(r.omega, 179.16152954101562)
+ self.assertEqual(r.is_pre_pro, False)
+ self.assertEqual(r.is_cis, False)
+ self.assertEqual(r.chiral_volume, 0.0)
+ # self.assertAlmostEqual(r.chi, [-170.86489868164062, 59.921932220458984])
+ # self.assertAlmostEqual(r.ca_location, {'x': 22.385000228881836, 'y': 17.197999954223633, 'z': 17.680999755859375})
+ self.assertEqual(r.chain_break, chain_break_type.NoGap)
+ self.assertEqual(r.nr, 15)
+ self.assertEqual(r.type, structure_type.Alphahelix)
+ self.assertEqual(r.ssBridgeNr, 0)
+ self.assertEqual(r.helix(helix_type._3_10), helix_position_type.NoHelix)
+ self.assertEqual(r.helix(helix_type.alpha), helix_position_type.Start)
+ self.assertEqual(r.helix(helix_type.pi), helix_position_type.NoHelix)
+ self.assertEqual(r.helix(helix_type.pp), helix_position_type.NoHelix)
+ self.assertEqual(r.is_alpha_helix_end_before_start, False)
+ self.assertEqual(r.bend, True)
+ self.assertEqual(r.sheet, 0)
+ self.assertEqual(r.strand, 0)
+
+ (acceptor, energy) = r.acceptor(0)
+ self.assertEqual(acceptor.seq_id, 17)
+ self.assertAlmostEqual(energy, -0.2)
+
+if __name__ == "__main__":
+ unittest.main()
\ No newline at end of file
=====================================
test/unit-test-dssp.cpp
=====================================
@@ -28,11 +28,7 @@
#define CATCH_CONFIG_RUNNER
-#if CATCH22
-# include <catch2/catch.hpp>
-#else
-# include <catch2/catch_all.hpp>
-#endif
+#include <catch2/catch_all.hpp>
#include "../libdssp/src/dssp-io.hpp"
#include "../src/revision.hpp"
@@ -67,12 +63,7 @@ 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
std::filesystem::path rsrc_dir;
@@ -103,7 +94,7 @@ TEST_CASE("ut_dssp")
{
using namespace std::literals;
- cif::file f(gTestDir / "1cbs.cif.gz");
+ auto f = cif::pdb::read(gTestDir / "1cbs.cif.gz");
REQUIRE(f.is_valid());
dssp dssp(f.front(), 1, 3, true);
@@ -119,7 +110,7 @@ TEST_CASE("ut_dssp")
std::string line_t, line_r;
CHECK((std::getline(test, line_t) and std::getline(reference, line_r)));
- char kHeaderLineStart[] = "==== Secondary Structure Definition by the program DSSP, NKI version 4.4.5 ====";
+ char kHeaderLineStart[] = "==== Secondary Structure Definition by the program DSSP, NKI version 4.5.4 ====";
memcpy(kHeaderLineStart + 69, kVersionNumber, strlen(kVersionNumber));
CHECK(line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
@@ -135,9 +126,14 @@ TEST_CASE("ut_dssp")
break;
if (line_t != line_r)
+ {
+ if (cif::starts_with(line_t, "REFERENCE ") and cif::starts_with(line_r, "REFERENCE "))
+ continue;
+
std::cerr << line_nr << std::endl
<< line_t << std::endl
<< line_r << std::endl;
+ }
if (line_t != line_r)
{
@@ -155,14 +151,14 @@ TEST_CASE("ut_mmcif_2")
using namespace std::literals;
using namespace cif::literals;
- cif::file f(gTestDir / "1cbs.cif.gz");
+ auto f = cif::pdb::read(gTestDir / "1cbs.cif.gz");
REQUIRE(f.is_valid());
dssp dssp(f.front(), 1, 3, true);
std::stringstream test;
- dssp.annotate(f.front(), true, false);
+ dssp.annotate(f.front(), true, true);
cif::file rf(gTestDir / "1cbs-dssp.cif");
@@ -187,7 +183,7 @@ TEST_CASE("ut_mmcif_2")
TEST_CASE("dssp_1")
{
- cif::file f(gTestDir / "1cbs.cif.gz");
+ auto f = cif::pdb::read(gTestDir / "1cbs.cif.gz");
REQUIRE(f.is_valid());
@@ -225,7 +221,7 @@ TEST_CASE("dssp_1")
TEST_CASE("dssp_2")
{
- cif::file f(gTestDir / "1cbs.cif.gz");
+ auto f = cif::pdb::read(gTestDir / "1cbs.cif.gz");
REQUIRE(f.is_valid());
@@ -262,7 +258,7 @@ TEST_CASE("dssp_2")
TEST_CASE("dssp_3")
{
- cif::file f(gTestDir / "1cbs.cif.gz");
+ auto f = cif::pdb::read(gTestDir / "1cbs.cif.gz");
REQUIRE(f.is_valid());
@@ -271,4 +267,17 @@ TEST_CASE("dssp_3")
dssp.annotate(f.front(), true, true);
// CHECK(f.is_valid());
+}
+
+// --------------------------------------------------------------------
+
+TEST_CASE("dssp_pdb")
+{
+ auto f = cif::pdb::read(gTestDir / "pdb1cbs.ent.gz");
+
+ REQUIRE(f.is_valid());
+
+ dssp dssp(f.front(), 1, 3, true);
+
+ dssp.annotate(f.front(), true, true);
}
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/dssp/-/commit/a97d1798e6f21e9acce6b3619019c2321aab1ccf
--
View it on GitLab: https://salsa.debian.org/med-team/dssp/-/commit/a97d1798e6f21e9acce6b3619019c2321aab1ccf
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