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libcifpp
Commit ab2dd4b7 by Maarten L. Hekkelman
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Merge branch 'trunk' into develop

parents 8bbcba76 be773165
Showing with 307 additions and 57 deletions
.gitignore
...@@ -6,8 +6,8 @@ tools/symop-map-generator ...@@ -6,8 +6,8 @@ tools/symop-map-generator
test/unit-test test/unit-test
test/pdb2cif-test test/pdb2cif-test
test/rename-compound-test test/rename-compound-test
tools/update-dictionary-script tools/update-libcifpp-data
data/ data/components.cif*
CMakeSettings.json CMakeSettings.json
msvc/ msvc/
Testing/ Testing/
......
CMakeLists.txt
...@@ -87,14 +87,14 @@ endif() ...@@ -87,14 +87,14 @@ endif()
# When CCP4 is sourced in the environment, we can recreate the symmetry operations table # When CCP4 is sourced in the environment, we can recreate the symmetry operations table
if(EXISTS "${CCP4}") if(EXISTS "${CCP4}")
if(RECREATE_SYMOP_DATA AND NOT EXISTS "${CLIBD}/syminfo.lib") if(CIFPP_RECREATE_SYMOP_DATA AND NOT EXISTS "${CLIBD}/syminfo.lib")
message(WARNING "Symop data table recreation requested, but file syminfo.lib was not found in ${CLIBD}") message(WARNING "Symop data table recreation requested, but file syminfo.lib was not found in ${CLIBD}")
set(RECREATE_SYMOP_DATA OFF) set(CIFPP_RECREATE_SYMOP_DATA OFF)
else() else()
option(RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON) option(CIFPP_RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
endif() endif()
else() else()
set(RECREATE_SYMOP_DATA OFF) set(CIFPP_RECREATE_SYMOP_DATA OFF)
message("Not trying to recreate SymOpTable_data.hpp since CCP4 is not defined") message("Not trying to recreate SymOpTable_data.hpp since CCP4 is not defined")
endif() endif()
...@@ -154,16 +154,16 @@ else() ...@@ -154,16 +154,16 @@ else()
find_program(MRC mrc) find_program(MRC mrc)
if(MRC) if(MRC)
option(USE_RSRC "Use mrc to create resources" ON) option(CIFPP_USE_RSRC "Use mrc to create resources" ON)
else() else()
message("Using resources not possible since mrc was not found") message("Using resources not possible since mrc was not found")
endif() endif()
if(USE_RSRC STREQUAL "ON") if(CIFPP_USE_RSRC STREQUAL "ON")
set(USE_RSRC 1) set(CIFPP_USE_RSRC 1)
message("Using resources compiled with ${MRC}") message("Using resources compiled with ${MRC}")
add_compile_definitions(USE_RSRC) add_compile_definitions(CIFPP_USE_RSRC)
endif() endif()
endif() endif()
...@@ -204,7 +204,7 @@ string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC) ...@@ -204,7 +204,7 @@ string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY) configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
# SymOp data table # SymOp data table
if(RECREATE_SYMOP_DATA) if(CIFPP_RECREATE_SYMOP_DATA)
# The tool to create the table # The tool to create the table
add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp") add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp")
...@@ -287,16 +287,17 @@ if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") ...@@ -287,16 +287,17 @@ if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
target_link_options(cifpp PRIVATE -undefined dynamic_lookup) target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
endif (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") endif (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
# download the components.cif file from CCD option(CIFPP_DOWNLOAD_CCD "Download the CCD file components.cif during installation" OFF)
set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/data/components.cif) if(CIFPP_DOWNLOAD_CCD)
# download the components.cif file from CCD
set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/data/components.cif)
if (NOT EXISTS ${COMPONENTS_CIF}) if (NOT EXISTS ${COMPONENTS_CIF})
if (NOT EXISTS ${PROJECT_SOURCE_DIR}/data) if (NOT EXISTS ${PROJECT_SOURCE_DIR}/data)
file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/data/) file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
endif() endif()
# if(${CMAKE_VERSION} VERSION_LESS "3.19.0")
find_program(GUNZIP gunzip) find_program(GUNZIP gunzip)
if(GUNZIP) if(GUNZIP)
...@@ -309,25 +310,15 @@ if (NOT EXISTS ${COMPONENTS_CIF}) ...@@ -309,25 +310,15 @@ if (NOT EXISTS ${COMPONENTS_CIF})
file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF} file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF}
SHOW_PROGRESS) SHOW_PROGRESS)
endif() endif()
# else() endif()
# file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz ${COMPONENTS_CIF}.gz
# SHOW_PROGRESS)
# file(ARCHIVE_EXTRACT INPUT ${COMPONENTS_CIF}.gz
# DESTINATION ${CMAKE_SOURCE_DIR}/data/
# VERBOSE)
# endif()
endif()
add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF}) add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
endif()
if(UNIX) if(UNIX)
option(INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" OFF) option(CIFPP_INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" OFF)
if(INSTALL_UPDATE_SCRIPT) set(CIFPP_CACHE_DIR "/var/cache/libcifpp" CACHE STRING "The cache directory to use")
set(CIFPP_CACHE_DIR "/var/cache/libcifpp")
if(NOT "${CIFPP_CACHE_DIR}" STREQUAL "OFF")
target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}") target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
endif()
endif()
endif() endif()
generate_export_header(cifpp generate_export_header(cifpp
...@@ -337,7 +328,9 @@ set(INCLUDE_INSTALL_DIR ${CMAKE_INSTALL_INCLUDEDIR} ) ...@@ -337,7 +328,9 @@ set(INCLUDE_INSTALL_DIR ${CMAKE_INSTALL_INCLUDEDIR} )
set(LIBRARY_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} ) set(LIBRARY_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} )
set(SHARE_INSTALL_DIR ${CMAKE_INSTALL_DATADIR}/libcifpp) set(SHARE_INSTALL_DIR ${CMAKE_INSTALL_DATADIR}/libcifpp)
target_compile_definitions(cifpp PUBLIC DATA_DIR="${CMAKE_INSTALL_PREFIX}/${SHARE_INSTALL_DIR}") set(CIFPP_DATA_DIR "${CMAKE_INSTALL_PREFIX}/${SHARE_INSTALL_DIR}" CACHE STRING "The directory containing the provided data files")
target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
# Install rules # Install rules
...@@ -369,7 +362,7 @@ install( ...@@ -369,7 +362,7 @@ install(
install(FILES install(FILES
${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic ${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic ${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic
${PROJECT_SOURCE_DIR}/data/components.cif ${COMPONENTS_CIF}
DESTINATION ${SHARE_INSTALL_DIR} DESTINATION ${SHARE_INSTALL_DIR}
) )
...@@ -421,7 +414,7 @@ option(CIFPP_BUILD_TESTS "Build test exectuables" OFF) ...@@ -421,7 +414,7 @@ option(CIFPP_BUILD_TESTS "Build test exectuables" OFF)
if(CIFPP_BUILD_TESTS) if(CIFPP_BUILD_TESTS)
if(USE_RSRC) if(CIFPP_USE_RSRC)
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj
COMMAND ${MRC} -o ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic ${COFF_SPEC} COMMAND ${MRC} -o ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic ${COFF_SPEC}
) )
...@@ -468,12 +461,12 @@ message("Will install in ${CMAKE_INSTALL_PREFIX}") ...@@ -468,12 +461,12 @@ message("Will install in ${CMAKE_INSTALL_PREFIX}")
# Optionally install the update scripts for CCD and dictionary files # Optionally install the update scripts for CCD and dictionary files
if(INSTALL_UPDATE_SCRIPT) if(CIFPP_INSTALL_UPDATE_SCRIPT)
set(CIFPP_CRON_DIR "$ENV{DESTDIR}/etc/cron.weekly") set(CIFPP_CRON_DIR "$ENV{DESTDIR}/etc/cron.weekly")
configure_file(${CMAKE_SOURCE_DIR}/tools/update-dictionary-script.in update-dictionary-script @ONLY) configure_file(${CMAKE_SOURCE_DIR}/tools/update-libcifpp-data.in update-libcifpp-data @ONLY)
install( install(
FILES ${CMAKE_CURRENT_BINARY_DIR}/update-dictionary-script FILES ${CMAKE_CURRENT_BINARY_DIR}/update-libcifpp-data
DESTINATION ${CIFPP_CRON_DIR} DESTINATION ${CIFPP_CRON_DIR}
PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE WORLD_READ PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE WORLD_READ
) )
...@@ -482,13 +475,14 @@ if(INSTALL_UPDATE_SCRIPT) ...@@ -482,13 +475,14 @@ if(INSTALL_UPDATE_SCRIPT)
install(DIRECTORY DESTINATION "$ENV{DESTDIR}/etc/libcifpp/cache-update.d") install(DIRECTORY DESTINATION "$ENV{DESTDIR}/etc/libcifpp/cache-update.d")
# a config to, to make it complete # a config to, to make it complete
if(NOT EXISTS "$ENV{DESTDIR}/etc/libcifpp.conf")
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf [[# Uncomment the next line to enable automatic updates file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf [[# Uncomment the next line to enable automatic updates
# update=true # update=true
]]) ]])
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf DESTINATION "$ENV{DESTDIR}/etc") install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf DESTINATION "$ENV{DESTDIR}/etc")
install(CODE "message(\"A configuration file has been written to $ENV{DESTDIR}/etc/libcifpp.conf, please edit this file to enable automatic updates\")")
endif()
target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}") target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
install(CODE "message(\"A configuration file has been written to $ENV{DESTDIR}/etc/libcifpp.conf, please edit this file to enable automatic updates\")")
endif() endif()
changelog
...@@ -3,6 +3,13 @@ Version 3.0.0 ...@@ -3,6 +3,13 @@ Version 3.0.0
performance reasons. performance reasons.
- Upgraded mmcif::Structure - Upgraded mmcif::Structure
Version 2.0.2
- Added configuration flag to disable downloading CCD data during build
Note that there are now two flags for CCD data:
DOWNLOAD_CCD to enable downloading during build
INSTALL_UPDATE_SCRIPT to install an update mechanism for this file
- Updated unit tests to work even if no CCD data is available
Version 2.0.1 Version 2.0.1
- Fixed the generator for the symmetry operator table - Fixed the generator for the symmetry operator table
......
data/ccd-subset.cif 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
examples/pdb1cbs.ent deleted 100644 → 0
This source diff could not be displayed because it is too large. You can view the blob instead.
src/CifUtils.cpp
...@@ -1270,6 +1270,9 @@ void addDataDirectory(std::filesystem::path dataDir) ...@@ -1270,6 +1270,9 @@ void addDataDirectory(std::filesystem::path dataDir)
void addFileResource(const std::string &name, std::filesystem::path dataFile) void addFileResource(const std::string &name, std::filesystem::path dataFile)
{ {
if (not fs::exists(dataFile))
throw std::runtime_error("Attempt to add a file resource for " + name + " that does not exist: " + dataFile.string());
gLocalResources[name] = dataFile; gLocalResources[name] = dataFile;
} }
......
src/Compound.cpp
...@@ -457,7 +457,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id) ...@@ -457,7 +457,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
{ {
ccd = cif::loadResource("components.cif"); ccd = cif::loadResource("components.cif");
if (not ccd) if (not ccd)
throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-dictionary-script to fetch the data."); throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-libcifpp-data to fetch the data.");
} }
else else
ccd.reset(new std::ifstream(mCompoundsFile)); ccd.reset(new std::ifstream(mCompoundsFile));
...@@ -484,7 +484,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id) ...@@ -484,7 +484,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
{ {
ccd = cif::loadResource("components.cif"); ccd = cif::loadResource("components.cif");
if (not ccd) if (not ccd)
throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-dictionary-script to fetch the data."); throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-libcifpp-data to fetch the data.");
} }
else else
ccd.reset(new std::ifstream(mCompoundsFile)); ccd.reset(new std::ifstream(mCompoundsFile));
......
test/HEM.cif 0 → 100644
This diff is collapsed. Click to expand it.
test/REA.cif 0 → 100644
data_REA
#
_chem_comp.id REA
_chem_comp.name "RETINOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H28 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2016-10-18
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces 3KV
_chem_comp.formula_weight 300.435
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code REA
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1CBS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
REA C1 C1 C 0 1 N N N 21.972 29.831 16.739 -4.684 0.932 -0.497 C1 REA 1
REA C2 C2 C 0 1 N N N 20.921 30.524 15.841 -5.837 0.190 -1.176 C2 REA 2
REA C3 C3 C 0 1 N N N 20.245 29.635 14.848 -6.441 -0.798 -0.171 C3 REA 3
REA C4 C4 C 0 1 N N N 19.555 28.479 15.488 -5.418 -1.903 0.100 C4 REA 4
REA C5 C5 C 0 1 N N N 20.389 27.812 16.587 -4.082 -1.301 0.429 C5 REA 5
REA C6 C6 C 0 1 N N N 21.425 28.446 17.218 -3.756 -0.048 0.161 C6 REA 6
REA C7 C7 C 0 1 N N N 22.242 27.851 18.297 -2.457 0.396 0.516 C7 REA 7
REA C8 C8 C 0 1 N N N 21.868 26.977 19.240 -1.363 -0.229 0.007 C8 REA 8
REA C9 C9 C 0 1 N N N 22.705 26.434 20.286 -0.076 0.257 0.298 C9 REA 9
REA C10 C10 C 0 1 N N N 22.159 25.536 21.131 1.022 -0.370 -0.213 C10 REA 10
REA C11 C11 C 0 1 N N N 22.875 24.924 22.234 2.306 0.115 0.077 C11 REA 11
REA C12 C12 C 0 1 N N N 22.237 24.026 22.990 3.405 -0.513 -0.435 C12 REA 12
REA C13 C13 C 0 1 N N N 22.856 23.377 24.125 4.689 -0.028 -0.144 C13 REA 13
REA C14 C14 C 0 1 N N N 22.135 22.473 24.834 5.787 -0.655 -0.656 C14 REA 14
REA C15 C15 C 0 1 N N N 22.563 21.710 26.016 7.077 -0.265 -0.244 C15 REA 15
REA C16 C16 C 0 1 N N N 22.238 30.737 17.948 -5.246 1.886 0.559 C16 REA 16
REA C17 C17 C 0 1 N N N 23.292 29.620 15.948 -3.911 1.737 -1.544 C17 REA 17
REA C18 C18 C 0 1 N N N 19.791 26.449 16.947 -3.056 -2.175 1.103 C18 REA 18
REA C19 C19 C 0 1 N N N 24.181 26.841 20.385 0.090 1.471 1.175 C19 REA 19
REA C20 C20 C 0 1 N N N 24.303 23.747 24.489 4.855 1.186 0.733 C20 REA 20
REA O1 O1 O 0 1 N N N 23.640 21.075 25.978 7.210 0.553 0.648 O1 REA 21
REA O2 O2 O 0 1 N N N 21.840 21.712 27.037 8.166 -0.798 -0.840 O2 REA 22
REA H21 H21 H 0 1 N N N 20.147 30.955 16.494 -6.598 0.905 -1.490 H21 REA 23
REA H22 H22 H 0 1 N N N 21.425 31.330 15.288 -5.462 -0.353 -2.044 H22 REA 24
REA H31 H31 H 0 1 N N N 19.501 30.227 14.295 -6.673 -0.278 0.759 H31 REA 25
REA H32 H32 H 0 1 N N N 21.001 29.250 14.148 -7.349 -1.234 -0.586 H32 REA 26
REA H41 H41 H 0 1 N N N 18.613 28.835 15.931 -5.756 -2.511 0.938 H41 REA 27
REA H42 H42 H 0 1 N N N 19.335 27.730 14.713 -5.322 -2.531 -0.786 H42 REA 28
REA H7 H7 H 0 1 N N N 23.276 28.162 18.329 -2.337 1.230 1.191 H7 REA 29
REA H8 H8 H 0 1 N N N 20.840 26.645 19.217 -1.482 -1.100 -0.622 H8 REA 30
REA H10 H10 H 0 1 N N N 21.127 25.256 20.977 0.903 -1.241 -0.842 H10 REA 31
REA H11 H11 H 0 1 N N N 23.902 25.189 22.440 2.425 0.985 0.706 H11 REA 32
REA H12 H12 H 0 1 N N N 21.216 23.774 22.743 3.286 -1.383 -1.063 H12 REA 33
REA H14 H14 H 0 1 N N N 21.127 22.292 24.490 5.667 -1.451 -1.376 H14 REA 34
REA H161 H161 H 0 0 N N N 22.984 30.265 18.604 -5.802 1.316 1.303 H161 REA 35
REA H162 H162 H 0 0 N N N 22.618 31.709 17.601 -4.426 2.415 1.044 H162 REA 36
REA H163 H163 H 0 0 N N N 21.302 30.887 18.506 -5.911 2.605 0.081 H163 REA 37
REA H171 H171 H 0 0 N N N 24.033 29.127 16.595 -4.598 2.394 -2.077 H171 REA 38
REA H172 H172 H 0 0 N N N 23.095 28.989 15.069 -3.146 2.335 -1.050 H172 REA 39
REA H173 H173 H 0 0 N N N 23.683 30.595 15.620 -3.439 1.054 -2.251 H173 REA 40
REA H181 H181 H 0 0 N N N 20.397 25.979 17.736 -3.448 -3.187 1.201 H181 REA 41
REA H182 H182 H 0 0 N N N 18.761 26.584 17.308 -2.145 -2.194 0.503 H182 REA 42
REA H183 H183 H 0 0 N N N 19.786 25.804 16.056 -2.831 -1.775 2.092 H183 REA 43
REA H191 H191 H 0 0 N N N 24.647 26.327 21.238 0.171 1.159 2.216 H191 REA 44
REA H192 H192 H 0 0 N N N 24.702 26.559 19.458 0.993 2.008 0.885 H192 REA 45
REA H193 H193 H 0 0 N N N 24.252 27.929 20.529 -0.774 2.125 1.058 H193 REA 46
REA H201 H201 H 0 0 N N N 24.620 23.168 25.369 5.026 0.871 1.762 H201 REA 47
REA H202 H202 H 0 0 N N N 24.965 23.516 23.641 5.707 1.771 0.386 H202 REA 48
REA H203 H203 H 0 0 N N N 24.360 24.822 24.717 3.952 1.795 0.685 H203 REA 49
REA HO2 HO2 H 0 1 N N N 22.244 21.180 27.713 9.006 -0.469 -0.490 HO2 REA 50
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
REA C1 C2 SING N N 1
REA C1 C6 SING N N 2
REA C1 C16 SING N N 3
REA C1 C17 SING N N 4
REA C2 C3 SING N N 5
REA C2 H21 SING N N 6
REA C2 H22 SING N N 7
REA C3 C4 SING N N 8
REA C3 H31 SING N N 9
REA C3 H32 SING N N 10
REA C4 C5 SING N N 11
REA C4 H41 SING N N 12
REA C4 H42 SING N N 13
REA C5 C6 DOUB N N 14
REA C5 C18 SING N N 15
REA C6 C7 SING N N 16
REA C7 C8 DOUB N E 17
REA C7 H7 SING N N 18
REA C8 C9 SING N N 19
REA C8 H8 SING N N 20
REA C9 C10 DOUB N E 21
REA C9 C19 SING N N 22
REA C10 C11 SING N N 23
REA C10 H10 SING N N 24
REA C11 C12 DOUB N E 25
REA C11 H11 SING N N 26
REA C12 C13 SING N N 27
REA C12 H12 SING N N 28
REA C13 C14 DOUB N E 29
REA C13 C20 SING N N 30
REA C14 C15 SING N N 31
REA C14 H14 SING N N 32
REA C15 O1 DOUB N N 33
REA C15 O2 SING N N 34
REA C16 H161 SING N N 35
REA C16 H162 SING N N 36
REA C16 H163 SING N N 37
REA C17 H171 SING N N 38
REA C17 H172 SING N N 39
REA C17 H173 SING N N 40
REA C18 H181 SING N N 41
REA C18 H182 SING N N 42
REA C18 H183 SING N N 43
REA C19 H191 SING N N 44
REA C19 H192 SING N N 45
REA C19 H193 SING N N 46
REA C20 H201 SING N N 47
REA C20 H202 SING N N 48
REA C20 H203 SING N N 49
REA O2 HO2 SING N N 50
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
REA SMILES ACDLabs 12.01 "C1(CCCC(=C1\C=C\C(=C\C=C\C(=C\C(=O)O)C)C)C)(C)C"
REA InChI InChI 1.03 "InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+"
REA InChIKey InChI 1.03 SHGAZHPCJJPHSC-YCNIQYBTSA-N
REA SMILES_CANONICAL CACTVS 3.385 "CC1=C(\C=C\C(C)=C\C=C\C(C)=C\C(O)=O)C(C)(C)CCC1"
REA SMILES CACTVS 3.385 "CC1=C(C=CC(C)=CC=CC(C)=CC(O)=O)C(C)(C)CCC1"
REA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C(=O)O)/C)/C"
REA SMILES "OpenEye OEToolkits" 1.7.6 "CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC(=O)O)C)C"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
REA "SYSTEMATIC NAME" ACDLabs 12.01 "retinoic acid"
REA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
REA "Create component" 1999-07-08 RCSB
REA "Modify descriptor" 2011-06-04 RCSB
REA "Other modification" 2016-10-18 RCSB
#
test/rename-compound-test.cpp
...@@ -20,9 +20,10 @@ int main(int argc, char* argv[]) ...@@ -20,9 +20,10 @@ int main(int argc, char* argv[])
if (argc == 3) if (argc == 3)
testdir = argv[2]; testdir = argv[2];
if (std::filesystem::exists(testdir / ".."/"data"/"components.cif")) if (std::filesystem::exists(testdir / ".."/"data"/"ccd-subset.cif"))
cif::addFileResource("components.cif", testdir / ".."/"data"/"components.cif"); cif::addFileResource("components.cif", testdir / ".."/"data"/"ccd-subset.cif");
mmcif::CompoundFactory::instance().pushDictionary(testdir / "REA.cif");
mmcif::CompoundFactory::instance().pushDictionary(testdir / "RXA.cif"); mmcif::CompoundFactory::instance().pushDictionary(testdir / "RXA.cif");
mmcif::File f(testdir / ".."/"examples"/"1cbs.cif.gz"); mmcif::File f(testdir / ".."/"examples"/"1cbs.cif.gz");
......
test/structure-test.cpp
...@@ -24,7 +24,7 @@ ...@@ -24,7 +24,7 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/ */
#define BOOST_TEST_MODULE Structure_Test #define BOOST_TEST_ALTERNATIVE_INIT_API
#include <boost/test/included/unit_test.hpp> #include <boost/test/included/unit_test.hpp>
#include <stdexcept> #include <stdexcept>
...@@ -52,16 +52,23 @@ cif::File operator""_cf(const char* text, size_t length) ...@@ -52,16 +52,23 @@ cif::File operator""_cf(const char* text, size_t length)
std::filesystem::path gTestDir = std::filesystem::current_path(); std::filesystem::path gTestDir = std::filesystem::current_path();
BOOST_AUTO_TEST_CASE(init) bool init_unit_test()
{ {
// not a test, just initialize test dir cif::VERBOSE = 1;
// not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2) if (boost::unit_test::framework::master_test_suite().argc == 2)
gTestDir = boost::unit_test::framework::master_test_suite().argv[1]; gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
// do this now, avoids the need for installing
cif::addFileResource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
// initialize CCD location // initialize CCD location
if (std::filesystem::exists(gTestDir / ".."/"data"/"components.cif")) cif::addFileResource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
cif::addFileResource("components.cif", gTestDir / ".."/"data"/"components.cif");
mmcif::CompoundFactory::instance().pushDictionary(gTestDir / "HEM.cif");
return true;
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
test/unit-test.cpp
...@@ -24,7 +24,8 @@ ...@@ -24,7 +24,8 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/ */
#define BOOST_TEST_MODULE LibCifPP_Test #define BOOST_TEST_ALTERNATIVE_INIT_API
// #define BOOST_TEST_MODULE LibCifPP_Test
#include <boost/test/included/unit_test.hpp> #include <boost/test/included/unit_test.hpp>
#include <stdexcept> #include <stdexcept>
...@@ -53,23 +54,27 @@ cif::File operator""_cf(const char* text, size_t length) ...@@ -53,23 +54,27 @@ cif::File operator""_cf(const char* text, size_t length)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(init) bool init_unit_test()
{ {
// not a test, just initialize test dir cif::VERBOSE = 1;
// not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2) if (boost::unit_test::framework::master_test_suite().argc == 2)
gTestDir = boost::unit_test::framework::master_test_suite().argv[1]; gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
// do this now, avoids the need for installing
cif::addFileResource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
// initialize CCD location
cif::addFileResource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
return true;
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(ut1) BOOST_AUTO_TEST_CASE(ut1)
{ {
cif::VERBOSE = 1;
// do this now, avoids the need for installing
cif::addFileResource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
// using namespace mmcif; // using namespace mmcif;
auto f = R"(data_TEST auto f = R"(data_TEST
...@@ -1527,8 +1532,6 @@ BOOST_AUTO_TEST_CASE(bondmap_1) ...@@ -1527,8 +1532,6 @@ BOOST_AUTO_TEST_CASE(bondmap_1)
{ {
cif::VERBOSE = 2; cif::VERBOSE = 2;
cif::addFileResource("components.cif", gTestDir / ".." / "data" / "components.cif");
// sections taken from CCD compounds.cif // sections taken from CCD compounds.cif
auto components = R"( auto components = R"(
data_ASN data_ASN
......
tools/update-dictionary-script 0 → 100644
#!/bin/bash
set -e
if [ "$EUID" -ne 0 ]
then echo "Please run as root"
exit
fi
if [ -f /etc/libcifpp.conf ] ; then
. /etc/libcifpp.conf
fi
# check to see if we're supposed to run at all
if [ "$update" != "true" ] ; then
exit
fi
# if cache directory doesn't exist, exit.
if ! [ -d /var/cache/libcifpp ]; then
exit
fi
fetch_dictionary () {
dict=$1
source=$2
wget -O${dict}.gz ${source}
# be careful not to nuke an existing dictionary file
# extract to a temporary file first
gunzip -c ${dict}.gz > ${dict}-tmp
# then move the extracted file to the final location
mv ${dict}-tmp ${dict}
# and clean up afterwards
rm ${dict}.gz
}
# fetch the dictionaries
fetch_dictionary "/var/cache/libcifpp/mmcif_pdbx_v50.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
fetch_dictionary "/var/cache/libcifpp/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
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