for write_data_files=off

.github/workflows/build-documentation.yml

@@ -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@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@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 ${{ steps.strings.outputs.build-output-dir }} -DBUILD_DOCUMENTATION=ON -DBUILD_TESTING=OFF
-
-    - name: Run Sphinx
-      run: |
-        cmake --build ${{ steps.strings.outputs.build-output-dir }} --target Sphinx-libcifpp
-        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@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@v2

.github/workflows/cmake-multi-platform.yml

@@ -45,15 +45,13 @@ jobs:
         cmake -B ${{ steps.strings.outputs.build-output-dir }}
         -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
         -DCMAKE_BUILD_TYPE=Release
+        -DCIFPP_DOWNLOAD_CCD=OFF
         -S ${{ github.workspace }}
         
     - name: Build
       run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config Release
-      
+
     - name: Test
       working-directory: ${{ steps.strings.outputs.build-output-dir }}
       run: ctest --build-config Release --output-on-failure
 
-    - name: Install
-      if: matrix.os != 'windows-latest'
-      run: sudo cmake --install ${{ steps.strings.outputs.build-output-dir }} --config Release

.gitignore

@@ -2,7 +2,7 @@ build/
 .vscode/
 .vs/
 tools/update-libcifpp-data
-rsrc/components.cif*
+data/components.cif*
 CMakeSettings.json
 msvc/
 src/revision.hpp

CMakeLists.txt

@@ -66,22 +66,28 @@ if(NOT(BUILD_FOR_CCP4 AND WIN32))
 	option(BUILD_SHARED_LIBS "Build a shared library instead of a static one" OFF)
 endif()
 
-if(BUILD_FOR_CCP4)
-	unset(CIFPP_DOWNLOAD_CCD)
-	unset(CIFPP_INSTALL_UPDATE_SCRIPT)
-else()
-	# Lots of code depend on the availability of the components.cif file
-	option(CIFPP_DOWNLOAD_CCD "Download the CCD file components.cif during installation" ON)
+# Lots of code depend on the availability of the components.cif file
+option(CIFPP_DOWNLOAD_CCD "Download the CCD file components.cif during installation" ON)
 
-	# An optional cron script can be installed to keep the data files up-to-date
-	if(UNIX AND NOT APPLE)
-		option(CIFPP_INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" ON)
-	endif()
+# An optional cron script can be installed to keep the data files up-to-date
+if("${CMAKE_SYSTEM_NAME}" STREQUAL "Linux" AND NOT BUILD_FOR_CCP4)
+	option(CIFPP_INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" ON)
 endif()
 
+# Optionally avoid installing data files (requires privileges at inconvenient moments)
+option(WRITE_DATA_FILES "Write data files during installation" ON)
+
 # When CCP4 is sourced in the environment, we can recreate the symmetry operations table
-if(EXISTS "$ENV{CCP4}/lib/data/syminfo.lib")
-	option(CIFPP_RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
+if(EXISTS "$ENV{CCP4}")
+	if(EXISTS "$ENV{CCP4}/lib/data/syminfo.lib")
+		option(CIFPP_RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
+	else()
+		set(CIFPP_RECREATE_SYMOP_DATA OFF)
+		message(WARNING "Symop data table recreation requested, but file syminfo.lib was not found in $ENV{CLIBD}")
+	endif()
+else()
+	set(CIFPP_RECREATE_SYMOP_DATA OFF)
+	message("Not trying to recreate symop_table_data.hpp since CCP4 is not defined")
 endif()
 
 # CCP4 build
@@ -206,28 +212,20 @@ endif()
 
 find_package(ZLIB REQUIRED)
 
-# Using Eigen3 is a bit of a thing. We don't want to build it completely since we
-# only need a couple of header files. Nothing special. But often, eigen3 is already
-# installed and then we prefer that.
-find_package(Eigen3 3.4 QUIET)
+find_package(Eigen3 QUIET)
 
-if(Eigen3_FOUND AND TARGET Eigen3::Eigen)
+if(Eigen3_FOUND)
 	get_target_property(EIGEN_INCLUDE_DIR Eigen3::Eigen INTERFACE_INCLUDE_DIRECTORIES)
 else()
-	# Create a private copy of eigen3 and populate it only, no need to build
-	FetchContent_Declare(
-		my-eigen3
+	ExternalProject_Add(
+		local_Eigen3
 		GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
 		GIT_TAG 3.4.0
+		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/external
 	)
 
-	FetchContent_GetProperties(my-eigen3)
-
-	if(NOT my-eigen3_POPULATED)
-		FetchContent_Populate(my-eigen3)
-	endif()
-
-	set(EIGEN_INCLUDE_DIR ${my-eigen3_SOURCE_DIR})
+	set(EIGEN3_D local_Eigen3)
+	set(EIGEN_INCLUDE_DIR ${CMAKE_CURRENT_BINARY_DIR}/external/include/eigen3)
 endif()
 
 include(FindFilesystem)
@@ -338,12 +336,15 @@ target_include_directories(cifpp
 	"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
 	PRIVATE
-	"${BOOST_REGEX_INCLUDE_DIR}"
 	"${EIGEN_INCLUDE_DIR}"
+	"${BOOST_REGEX_INCLUDE_DIR}"
 )
 
-target_link_libraries(cifpp
-	PUBLIC Threads::Threads ZLIB::ZLIB ${CIFPP_REQUIRED_LIBRARIES})
+target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB ${CIFPP_REQUIRED_LIBRARIES})
+
+if(${EIGEN3_D})
+	add_dependencies(cifpp ${EIGEN3_D})
+endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 	target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -351,7 +352,7 @@ endif(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 
 if(CIFPP_DOWNLOAD_CCD)
 	# download the components.cif file from CCD
-	set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/rsrc/components.cif)
+	set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/data/components.cif)
 
 	if(EXISTS ${COMPONENTS_CIF})
 		file(SIZE ${COMPONENTS_CIF} CCD_FILE_SIZE)
@@ -363,25 +364,27 @@ if(CIFPP_DOWNLOAD_CCD)
 	endif()
 
 	if(NOT EXISTS ${COMPONENTS_CIF})
+		if(NOT EXISTS ${PROJECT_SOURCE_DIR}/data)
+			file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
+		endif()
+
 		# Since the file(DOWNLOAD) command in cmake does not use
 		# compression, we try to download the gzipped version and
 		# decompress it ourselves.
 		find_program(GUNZIP gunzip)
 
-		if(WIN32 OR GUNZIP STREQUAL "GUNZIP-NOTFOUND")
-			file(DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF}
-				SHOW_PROGRESS STATUS CCD_FETCH_STATUS)
-		else()
+		if(GUNZIP)
 			if(NOT EXISTS "${COMPONENTS_CIF}.gz")
 				file(DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz ${COMPONENTS_CIF}.gz
 					SHOW_PROGRESS STATUS CCD_FETCH_STATUS)
 			endif()
 
 			add_custom_command(OUTPUT ${COMPONENTS_CIF}
-				COMMAND "${GUNZIP}" ${COMPONENTS_CIF}.gz
-				WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/rsrc/)
-
-			add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
+				COMMAND ${GUNZIP} ${COMPONENTS_CIF}.gz
+				WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
+		else()
+			file(DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF}
+				SHOW_PROGRESS STATUS CCD_FETCH_STATUS)
 		endif()
 
 		# Do not continue if downloading went wrong
@@ -391,6 +394,8 @@ if(CIFPP_DOWNLOAD_CCD)
 			message(FATAL_ERROR "Error trying to download CCD file: ${CCD_FETCH_STATUS}")
 		endif()
 	endif()
+
+	add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
 endif()
 
 # Installation directories
@@ -459,22 +464,24 @@ install(
 	COMPONENT Devel
 )
 
-install(FILES
-	${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
-	${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
-	${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic
-	${COMPONENTS_CIF}
-	DESTINATION ${CIFPP_DATA_DIR}
-)
-
-if(CIFPP_CACHE_DIR)
+if(WRITE_DATA_FILES)
 	install(FILES
 		${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
 		${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
 		${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic
 		${COMPONENTS_CIF}
-		DESTINATION ${CIFPP_CACHE_DIR}
+		DESTINATION ${CIFPP_DATA_DIR}
 	)
+
+	if(CIFPP_CACHE_DIR)
+		install(FILES
+			${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
+			${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
+			${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic
+			${COMPONENTS_CIF}
+			DESTINATION ${CIFPP_CACHE_DIR}
+		)
+	endif()
 endif()
 
 set(CONFIG_TEMPLATE_FILE ${PROJECT_SOURCE_DIR}/cmake/cifpp-config.cmake.in)
@@ -509,6 +516,7 @@ write_basic_package_version_file(
 )
 
 if(BUILD_TESTING)
+
 	# We're using the older version 2 of Catch2
 	FetchContent_Declare(
 		Catch2
@@ -535,7 +543,7 @@ if(BUILD_TESTING)
 		add_executable(${CIFPP_TEST} ${CIFPP_TEST_SOURCE} "${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp")
 
 		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp Catch2::Catch2)
-		target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")
+		target_include_directories(${CIFPP_TEST} PRIVATE ${EIGEN_INCLUDE_DIR})
 
 		if(MSVC)
 			# Specify unwind semantics so that MSVC knowns how to handle exceptions
@@ -561,7 +569,7 @@ if(CIFPP_INSTALL_UPDATE_SCRIPT)
 		else()
 			set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/cron.weekly" CACHE PATH "The cron directory, for the update script")
 		endif()
-	elseif(${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD")
+	elseif(UNIX) # assume all others are like FreeBSD...
 		set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/periodic/weekly" CACHE PATH "The cron directory, for the update script")
 	else()
 		message(FATAL_ERROR "Don't know where to install the update script")
@@ -599,7 +607,7 @@ set(CPACK_SOURCE_TGZ ON)
 set(CPACK_SOURCE_TBZ2 OFF)
 set(CPACK_SOURCE_TXZ OFF)
 set(CPACK_SOURCE_TZ OFF)
-set(CPACK_SOURCE_IGNORE_FILES "/rsrc/components.cif;/build;/.vscode;/.git")
+set(CPACK_SOURCE_IGNORE_FILES "/data/components.cif;/build;/.vscode;/.git")
 set(CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}")
 set(CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME})
 include(CPack)

README.md

@@ -1,34 +1,10 @@
-[![github CI](https://github.com/pdb-redo/libcifpp/actions/workflows/cmake-multi-platform.yml/badge.svg)](https://github.com/pdb-redo/libcifpp/actions)
-[![GitHub License](https://img.shields.io/github/license/pdb-redo/libcifpp)](https://github.com/pdb-redo/libcifpp/LICENSE)
-
 # libcifpp
 
-As the name implies, this library was originally written to work with mmCIF files
-using C++ as programming language. The design of this library leanes heavily on
-the structure of CIF files. These files can be thought of as a text dump of a
-relational databank with, often but not always, a very strict schema describing
-the data. These schema's are called dictionaries.
-
-Using information from the content of a mmCIF file and an optional schema,
-libcifpp allows you to access the data in the file as a collection of datablock
-each containing a collection of categories with rows of data. The categories can
-be searched for data using queries written in regular C++ syntax. When a dictionary
-was specified, inserted data is checked for validity. Likewise removal of data
-may result in cascaded removal of linked data in other categories using
-parent/child relationship information.
-
-Since there were still many programs using the legacy PDB format at the time
-development started, a layer was added that converts data to and from PDB format
-into mmCIF format. This means you can manipulate PDB files as if they were
-normal mmCIF files.
-
-Apart from this basic functionality, libcifpp also offers code to help with
-symmetry calculations, 3d manipulations and obtaining information from the CCD
-[Chemical Component Dictionary](https://www.wwpdb.org/data/ccd).
+This library contains code to work with mmCIF and legacy PDB files.
 
 ## Documentation
 
-The documentation can be found at [github.io](https://pdb-redo.github.io/libcifpp/)
+The documentation can be found at https://www.hekkelman.com/libcifpp-doc/
 
 ## Synopsis
 
@@ -88,138 +64,54 @@ int main(int argc, char *argv[])
 You might be able to use libcifpp from a package manager used by your
 OS distribution. But most likely this package will be out-of-date.
 Therefore it is recommended to build *libcifpp* from code. It is not
-hard to do. But it is recommended to read the following instructions
-carefully.
+hard to do.
 
 ### Requirements
 
 The code for this library was written in C++17. You therefore need a
-recent compiler to build it. For the development gcc >= 9.4 and clang >= 9.0
+recent compiler to build it. For the development gcc 9.4 and clang 9.0
 have been used as well as MSVC version 2019.
 
-The other requirement you really need to have installed on your computer
-is a version of [CMake](https://cmake.org). For now the minimum version
-is 3.16 but that may soon change into a higher version. You should also
-install the gui version of CMake to set build options easily, on Debian
-I prefer to use the curses version installed with `cmake-curses-gui`.
-
-It is very useful to have [mrc](https://github.com/mhekkel/mrc) available.
-However, this is only an option if you use Windows or an operating system
-using the ELF executable format (i.e. Linux or FreeBSD). MRC is a resource
-compiler that allows including data files into the executable making them
-easier to install.
-
-Other libraries you might want to install beforehand are:
+Other requirements are:
 
+- [cmake](https://cmake.org) A build tool.
+- [mrc](https://github.com/mhekkel/mrc), a resource compiler that
+  allows including data files into the executable making them easier to
+  install. Strictly speaking this is optional, but at the expense of
+  functionality.
 - [libeigen](https://eigen.tuxfamily.org/index.php?title=Main_Page), a
   library to do amongst others matrix calculations. This usually can be
   installed using your package manager, in Debian/Ubuntu it is called
   `libeigen3-dev`
 - [zlib](https://github.com/madler/zlib), the development version of this
   library. On Debian/Ubuntu this is the package `zlib1g-dev`.
-- [boost](https://www.boost.org), in Debian/Ubuntu this is `libboost-dev`.
-  
-  The Boost libraries are only needed in case you are using GCC due to a long
-  standing bug in GNU's implementation of std::regex. It simply crashes
-  on the regular expressions used in the mmcif_pdbx dictionary and so
-  we use the boost regex implementation instead.
+- [boost](https://www.boost.org).
+
+The Boost libraries are only needed in case you want to build the test
+code or if you are using GCC. That last condition is due to a long
+standing bug in the implementation of std::regex. It simply crashes
+on the regular expressions used in the mmcif_pdbx dictionary and so
+we use the boost regex implementation instead.
 
 ### Building
 
-First you need to download the code:
+Building the code is as simple as typing:
 
 ```console
- git clone https://github.com/PDB-REDO/libcifpp.git
+ git clone https://github.com/PDB-REDO/libcifpp.git --recurse-submodules
  cd libcifpp
+ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local -DCMAKE_BUILD_TYPE=Release
+ cmake --build build
+ cmake --install build
 ```
 
-You should start by considering where to install libcifpp. If you have
-sufficient permissions on your computer you perhaps should use the
-default but libcifpp can be configured to be installed anywhere
-including e.g. *$HOME/.local*.
-
-Next step is to configure, for this use the CMake gui application. If you
-installed the curses version of cmake you can type `ccmake`. On Windows
-you can use `cmake-gui.exe`.
-
-To install in the default location:
-
-```console
-ccmake -S . -B build
-```
-
-To install elsewhere, e.g. *$HOME/.local*:
-
-```console
-ccmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local
-```
-
-In the cmake window, start the configure command (use button or press 'c').
-After the first configure step you will see a list of settable options.
-Alter these to match your preferences. Most options are self explaining
-and contain a description. Some may need a bit more explanation:
-
-- CIFPP_DATA_DIR, this directory will be used to store initial versions
-  of the mmcif_pdbx dictionary as well as the optional CCD file.
-
-- CIFPP_DOWNLOAD_CCD
-
-  The CCD file is huge and perhaps you think you don't
-  need it. In that case you can leave this OFF. But that will limit the
-  use cases.
-
-- CIFPP_INSTALL_UPDATE_SCRIPT
-  
-  The files in CIFPP_DATA_DIR are quickly becoming out of date. On
-  FreeBSD and Linux you can install a script that updates these files
-  on a weekly basis.
-
-- CIFPP_CRON_DIR
-  
-  The directory where the update script is to be installed.
-
-- CIFPP_ETC_DIR
-  
-  The update script will only work if the file called *libcifpp.conf*
-  in this *etc* directory will contain an uncommented line with
-
-```console
-update=true
-```
-
-- CIFPP_CACHE_DIR
-
-  When you installed and enabled the update script, new files are
-  written to this directory.
-
-- CIFPP_RECREATE_SYMOP_DATA
-  
-  If you had CCP4 sourced into your environment, this option allows
-  you to recreate the symop data file.
-
-- BUILD_FOR_CCP4
-  
-  Build a special version of libcifpp to be installed in the CCP4
-  environment.
-
-After setting these options you can run the configure step again and
-then use generate to create the makefiles.
-
-Building and installing is then as simple as:
-
-```console
-cmake --build build
-cmake --install build
-```
-
-If this fails due to lack of permissions, you can try:
-
-```console
-sudo cmake --install build
-```
+This checks out the source code from github, creates a new directory
+where cmake stores its files. Run a configure, build the code and then
+it installs the library and auxiliary files.
 
 Tests are created by default, and to test the code you can run:
 
 ```console
-ctest --test-dir build
+ cmake --build build
+ ctest --test-dir build
 ```

cmake/cifpp-config.cmake.in

@@ -2,7 +2,7 @@
 
 include("${CMAKE_CURRENT_LIST_DIR}/cifpp-targets.cmake")
 
-set_and_check(CIFPP_SHARE_DIR "@PACKAGE_CIFPP_DATA_DIR@")
+# set_and_check(CIFPP_SHARE_DIR "@PACKAGE_CIFPP_DATA_DIR@")
 
 include(CMakeFindDependencyMacro)
 

src/model.cpp

@@ -2006,10 +2006,7 @@ void structure::change_residue(residue &res, const std::string &newCompound,
 			continue;
 
 		if (a2.empty() or a2 == ".")
-		{
-			i->set_property("label_comp_id", newCompound);
 			remove_atom(*i);
-		}
 		else if (a1 != a2)
 		{
 			auto ra = r.front();

test/rename-compound-test.cpp

@@ -37,8 +37,8 @@ TEST_CASE("rename")
 {
 	cif::VERBOSE = 3;
 
-	if (std::filesystem::exists(gTestDir / ".." / "rsrc" / "ccd-subset.cif"))
-		cif::add_file_resource("components.cif", gTestDir / ".." / "rsrc" / "ccd-subset.cif");
+	if (std::filesystem::exists(gTestDir / ".." / "data" / "ccd-subset.cif"))
+		cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
 
 	if (std::filesystem::exists(gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic"))
 		cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");

test/test-main.cpp

@@ -30,7 +30,7 @@ int main(int argc, char *argv[])
 	cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
 
 	// initialize CCD location
-	cif::add_file_resource("components.cif", gTestDir / ".." / "rsrc" / "ccd-subset.cif");
+	cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
 
 	cif::compound_factory::instance().push_dictionary(gTestDir / "HEM.cif");
 

tools/update-libcifpp-data.in

@@ -10,7 +10,7 @@ euid=${EUID:-$(id -u)}
 
 if [ "${euid}" -ne 0 ]; then
 	echo "Please run as root"
-	exit 1
+	exit
 fi
 
 if [ -f "@CIFPP_ETC_DIR@/libcifpp.conf" ]; then
@@ -19,13 +19,12 @@ fi
 
 # check to see if we're supposed to run at all
 if [ "$update" != "true" ]; then
-	exit 0
+	exit
 fi
 
 # if cache directory doesn't exist, exit.
 if ! [ -d "@CIFPP_CACHE_DIR@" ]; then
-	echo "Cache directory '@CIFPP_CACHE_DIR@' does not exist"
-	exit 1
+	exit
 fi
 
 # Create a temp file in the right directory and
@@ -61,16 +60,12 @@ update_dictionary() {
 
 # Update the dictionaries
 
-update_dictionary "@CIFPP_CACHE_DIR@/components.cif" "https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
+update_dictionary "@CIFPP_CACHE_DIR@/components.cif" "https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
 update_dictionary "@CIFPP_CACHE_DIR@/mmcif_pdbx.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
 update_dictionary "@CIFPP_CACHE_DIR@/mmcif_ma.dic" "https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic"
 
-# notify subscribers, using find instead of run-parts to make it work on FreeBSD as well
+# notify subscribers, will fail on FreeBSD
 
-if [ -d "@CIFPP_ETC_DIR@/libcifpp/cache-update.d" ]; then
-	find "@CIFPP_ETC_DIR@/libcifpp/cache-update.d" \
-		-exec test -x {} \; -and -not -exec test -d {} \; \
-		-exec {} "@CIFPP_CACHE_DIR@" \;
+if [ -d "@CIFPP_ETC_DIR@/libcifpp/cache-update.d" ] && [ -x /bin/run-parts ]; then
+	run-parts --arg "@CIFPP_CACHE_DIR@" -- "@CIFPP_ETC_DIR@/libcifpp/cache-update.d"
 fi
-
-exit 0