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https://github.com/PDB-REDO/libcifpp.git
synced 2026-06-04 22:14:24 +08:00
Compare commits
12 Commits
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cdfb0d9497 | ||
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cff099596e | ||
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8d96e513bd | ||
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cdefd063e2 |
4
.gitignore
vendored
4
.gitignore
vendored
@@ -6,8 +6,8 @@ tools/symop-map-generator
|
||||
test/unit-test
|
||||
test/pdb2cif-test
|
||||
test/rename-compound-test
|
||||
tools/update-dictionary-script
|
||||
data/
|
||||
tools/update-libcifpp-data
|
||||
data/components.cif*
|
||||
CMakeSettings.json
|
||||
msvc/
|
||||
Testing/
|
||||
|
||||
@@ -25,7 +25,7 @@
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
# set the project name
|
||||
project(cifpp VERSION 2.0.1 LANGUAGES CXX)
|
||||
project(cifpp VERSION 2.0.3 LANGUAGES CXX)
|
||||
|
||||
list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
|
||||
|
||||
@@ -87,14 +87,14 @@ endif()
|
||||
|
||||
# When CCP4 is sourced in the environment, we can recreate the symmetry operations table
|
||||
if(EXISTS "${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}")
|
||||
set(RECREATE_SYMOP_DATA OFF)
|
||||
set(CIFPP_RECREATE_SYMOP_DATA OFF)
|
||||
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option(RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)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option(CIFPP_RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)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()
|
||||
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")
|
||||
endif()
|
||||
|
||||
@@ -154,16 +154,16 @@ else()
|
||||
find_program(MRC mrc)
|
||||
|
||||
if(MRC)
|
||||
option(USE_RSRC "Use mrc to create resources" ON)
|
||||
option(CIFPP_USE_RSRC "Use mrc to create resources" ON)
|
||||
else()
|
||||
message("Using resources not possible since mrc was not found")
|
||||
endif()
|
||||
|
||||
if(USE_RSRC STREQUAL "ON")
|
||||
set(USE_RSRC 1)
|
||||
if(CIFPP_USE_RSRC STREQUAL "ON")
|
||||
set(CIFPP_USE_RSRC 1)
|
||||
|
||||
message("Using resources compiled with ${MRC}")
|
||||
add_compile_definitions(USE_RSRC)
|
||||
add_compile_definitions(CIFPP_USE_RSRC)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
@@ -204,7 +204,7 @@ string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
|
||||
configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
|
||||
|
||||
# SymOp data table
|
||||
if(RECREATE_SYMOP_DATA)
|
||||
if(CIFPP_RECREATE_SYMOP_DATA)
|
||||
# The tool to create the table
|
||||
|
||||
add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp")
|
||||
@@ -287,16 +287,17 @@ if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
|
||||
target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
|
||||
endif (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
|
||||
|
||||
# download the components.cif file from CCD
|
||||
set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/data/components.cif)
|
||||
option(CIFPP_DOWNLOAD_CCD "Download the CCD file components.cif during installation" OFF)
|
||||
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)
|
||||
file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
|
||||
endif()
|
||||
if (NOT EXISTS ${PROJECT_SOURCE_DIR}/data)
|
||||
file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
|
||||
endif()
|
||||
|
||||
# if(${CMAKE_VERSION} VERSION_LESS "3.19.0")
|
||||
find_program(GUNZIP gunzip)
|
||||
|
||||
if(GUNZIP)
|
||||
@@ -309,25 +310,15 @@ if (NOT EXISTS ${COMPONENTS_CIF})
|
||||
file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF}
|
||||
SHOW_PROGRESS)
|
||||
endif()
|
||||
# else()
|
||||
# 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})
|
||||
endif()
|
||||
|
||||
add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
|
||||
|
||||
if(UNIX)
|
||||
option(INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" OFF)
|
||||
if(INSTALL_UPDATE_SCRIPT)
|
||||
set(CIFPP_CACHE_DIR "/var/cache/libcifpp")
|
||||
if(NOT "${CIFPP_CACHE_DIR}" STREQUAL "OFF")
|
||||
target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
|
||||
endif()
|
||||
endif()
|
||||
option(CIFPP_INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" OFF)
|
||||
set(CIFPP_CACHE_DIR "/var/cache/libcifpp" CACHE STRING "The cache directory to use")
|
||||
target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
|
||||
endif()
|
||||
|
||||
generate_export_header(cifpp
|
||||
@@ -337,7 +328,9 @@ set(INCLUDE_INSTALL_DIR ${CMAKE_INSTALL_INCLUDEDIR} )
|
||||
set(LIBRARY_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} )
|
||||
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
|
||||
|
||||
@@ -369,7 +362,7 @@ install(
|
||||
install(FILES
|
||||
${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
|
||||
${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic
|
||||
${PROJECT_SOURCE_DIR}/data/components.cif
|
||||
${COMPONENTS_CIF}
|
||||
DESTINATION ${SHARE_INSTALL_DIR}
|
||||
)
|
||||
|
||||
@@ -421,7 +414,7 @@ option(CIFPP_BUILD_TESTS "Build test exectuables" OFF)
|
||||
|
||||
if(CIFPP_BUILD_TESTS)
|
||||
|
||||
if(USE_RSRC)
|
||||
if(CIFPP_USE_RSRC)
|
||||
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}
|
||||
)
|
||||
@@ -468,12 +461,12 @@ message("Will install in ${CMAKE_INSTALL_PREFIX}")
|
||||
|
||||
# Optionally install the update scripts for CCD and dictionary files
|
||||
|
||||
if(INSTALL_UPDATE_SCRIPT)
|
||||
if(CIFPP_INSTALL_UPDATE_SCRIPT)
|
||||
set(CIFPP_CRON_DIR "$ENV{DESTDIR}/etc/cron.weekly")
|
||||
|
||||
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(
|
||||
FILES ${CMAKE_CURRENT_BINARY_DIR}/update-dictionary-script
|
||||
FILES ${CMAKE_CURRENT_BINARY_DIR}/update-libcifpp-data
|
||||
DESTINATION ${CIFPP_CRON_DIR}
|
||||
PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE WORLD_READ
|
||||
)
|
||||
@@ -482,13 +475,14 @@ if(INSTALL_UPDATE_SCRIPT)
|
||||
install(DIRECTORY DESTINATION "$ENV{DESTDIR}/etc/libcifpp/cache-update.d")
|
||||
|
||||
# a config to, to make it complete
|
||||
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf [[# Uncomment the next line to enable automatic updates
|
||||
if(NOT EXISTS "$ENV{DESTDIR}/etc/libcifpp.conf")
|
||||
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf [[# Uncomment the next line to enable automatic updates
|
||||
# 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}")
|
||||
|
||||
install(CODE "message(\"A configuration file has been written to $ENV{DESTDIR}/etc/libcifpp.conf, please edit this file to enable automatic updates\")")
|
||||
endif()
|
||||
|
||||
|
||||
11
changelog
11
changelog
@@ -1,3 +1,14 @@
|
||||
Version 2.0.3
|
||||
- Fixed reading mmCIF files where model numbers are used and
|
||||
model number 1 is missing.
|
||||
|
||||
Version 2.0.2
|
||||
- Added configuration flag to disable downloading CCD data during build
|
||||
Note that there are now two flags for CCD data:
|
||||
DOWNLOAD_CCD to enable downloading during build
|
||||
INSTALL_UPDATE_SCRIPT to install an update mechanism for this file
|
||||
- Updated unit tests to work even if no CCD data is available
|
||||
|
||||
Version 2.0.1
|
||||
- Fixed the generator for the symmetry operator table
|
||||
|
||||
|
||||
2396
data/ccd-subset.cif
Normal file
2396
data/ccd-subset.cif
Normal file
File diff suppressed because it is too large
Load Diff
@@ -22,9 +22,7 @@ int main()
|
||||
<< "residues with an OXT are:" << std::endl;
|
||||
|
||||
for (const auto& [asym, comp, seqnr]: db.find<std::string,std::string,int>(
|
||||
cif::Key("label_atom_id") == "OXT",
|
||||
{ "label_asym_id", "label_comp_id", "label_seq_id" }
|
||||
))
|
||||
cif::Key("label_atom_id") == "OXT", "label_asym_id", "label_comp_id", "label_seq_id"))
|
||||
{
|
||||
std::cout << asym << ' ' << comp << ' ' << seqnr << std::endl;
|
||||
}
|
||||
|
||||
1573
examples/pdb1cbs.ent
1573
examples/pdb1cbs.ent
File diff suppressed because it is too large
Load Diff
Binary file not shown.
@@ -533,6 +533,8 @@ class Structure
|
||||
void loadData();
|
||||
void updateAtomIndex();
|
||||
|
||||
void loadAtomsForModel(StructureOpenOptions options);
|
||||
|
||||
File &mFile;
|
||||
size_t mModelNr;
|
||||
AtomView mAtoms;
|
||||
|
||||
@@ -8,5 +8,5 @@ Name: libcifpp
|
||||
Description: C++ library for the manipulation of mmCIF files.
|
||||
Version: @PACKAGE_VERSION@
|
||||
|
||||
Libs: -L${libdir} -lcifpp @PRIVATE_LIBS@
|
||||
Cflags: -I${includedir} @PRIVATE_INC_DIRS@
|
||||
Libs: -L${libdir} -lcifpp -lboost_regex -lboost_iostreams
|
||||
Cflags: -I${includedir} -pthread
|
||||
|
||||
@@ -1243,6 +1243,9 @@ void addDataDirectory(std::filesystem::path dataDir)
|
||||
|
||||
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;
|
||||
}
|
||||
|
||||
|
||||
@@ -457,7 +457,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
|
||||
{
|
||||
ccd = cif::loadResource("components.cif");
|
||||
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
|
||||
ccd.reset(new std::ifstream(mCompoundsFile));
|
||||
@@ -484,7 +484,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
|
||||
{
|
||||
ccd = cif::loadResource("components.cif");
|
||||
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
|
||||
ccd.reset(new std::ifstream(mCompoundsFile));
|
||||
@@ -636,17 +636,18 @@ void CompoundFactory::init(bool useThreadLocalInstanceOnly)
|
||||
CompoundFactory::CompoundFactory()
|
||||
: mImpl(nullptr)
|
||||
{
|
||||
auto ccd = cif::loadResource("components.cif");
|
||||
if (ccd)
|
||||
mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
|
||||
else if (cif::VERBOSE)
|
||||
std::cerr << "CCD components.cif file was not found" << std::endl;
|
||||
|
||||
const char *clibd_mon = getenv("CLIBD_MON");
|
||||
if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
|
||||
mImpl.reset(new CCP4CompoundFactoryImpl(clibd_mon));
|
||||
else if (cif::VERBOSE)
|
||||
std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
|
||||
|
||||
auto ccd = cif::loadResource("components.cif");
|
||||
if (ccd)
|
||||
mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
|
||||
else if (cif::VERBOSE)
|
||||
std::cerr << "CCD components.cif file was not found" << std::endl;
|
||||
}
|
||||
|
||||
CompoundFactory::~CompoundFactory()
|
||||
|
||||
@@ -1790,6 +1790,33 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
|
||||
|
||||
auto &atomCat = (*db)["atom_site"];
|
||||
|
||||
loadAtomsForModel(options);
|
||||
|
||||
// Check to see if we should actually load another model?
|
||||
if (mAtoms.empty() and mModelNr == 1)
|
||||
{
|
||||
std::optional<size_t> model_nr;
|
||||
cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
|
||||
if (model_nr and *model_nr != mModelNr)
|
||||
{
|
||||
if (cif::VERBOSE)
|
||||
std::cerr << "No atoms loaded for model 1, trying model " << *model_nr << std::endl;
|
||||
mModelNr = *model_nr;
|
||||
loadAtomsForModel(options);
|
||||
}
|
||||
}
|
||||
|
||||
if (mAtoms.empty())
|
||||
throw std::runtime_error("No atoms loaded, refuse to continue");
|
||||
|
||||
loadData();
|
||||
}
|
||||
|
||||
void Structure::loadAtomsForModel(StructureOpenOptions options)
|
||||
{
|
||||
auto db = mFile.impl().mDb;
|
||||
auto &atomCat = (*db)["atom_site"];
|
||||
|
||||
for (auto &a : atomCat)
|
||||
{
|
||||
std::string id, type_symbol;
|
||||
@@ -1805,10 +1832,9 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
|
||||
|
||||
mAtoms.emplace_back(new AtomImpl(*db, id, a));
|
||||
}
|
||||
|
||||
loadData();
|
||||
}
|
||||
|
||||
|
||||
Structure::Structure(const Structure &s)
|
||||
: mFile(s.mFile)
|
||||
, mModelNr(s.mModelNr)
|
||||
|
||||
253
test/HEM.cif
Normal file
253
test/HEM.cif
Normal file
@@ -0,0 +1,253 @@
|
||||
data_HEM
|
||||
#
|
||||
|
||||
_chem_comp.id HEM
|
||||
_chem_comp.name "PROTOPORPHYRIN IX CONTAINING FE"
|
||||
_chem_comp.type NON-POLYMER
|
||||
_chem_comp.pdbx_type HETAIN
|
||||
_chem_comp.formula "C34 H32 Fe N4 O4"
|
||||
_chem_comp.mon_nstd_parent_comp_id ?
|
||||
_chem_comp.pdbx_synonyms HEME
|
||||
_chem_comp.pdbx_formal_charge 0
|
||||
_chem_comp.pdbx_initial_date 1999-07-08
|
||||
_chem_comp.pdbx_modified_date 2020-06-17
|
||||
_chem_comp.pdbx_ambiguous_flag Y
|
||||
_chem_comp.pdbx_release_status REL
|
||||
_chem_comp.pdbx_replaced_by ?
|
||||
_chem_comp.pdbx_replaces MHM
|
||||
_chem_comp.formula_weight 616.487
|
||||
_chem_comp.one_letter_code ?
|
||||
_chem_comp.three_letter_code HEM
|
||||
_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 3IA3
|
||||
_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
|
||||
HEM CHA CHA C 0 1 N N N 2.748 -19.531 39.896 -2.161 -0.125 0.490 CHA HEM 1
|
||||
HEM CHB CHB C 0 1 N N N 3.258 -17.744 35.477 1.458 -3.419 0.306 CHB HEM 2
|
||||
HEM CHC CHC C 0 1 N N N 1.703 -21.900 33.637 4.701 0.169 -0.069 CHC HEM 3
|
||||
HEM CHD CHD C 0 1 N N N 1.149 -23.677 38.059 1.075 3.460 0.018 CHD HEM 4
|
||||
HEM C1A C1A C 0 1 Y N N 3.031 -18.673 38.872 -1.436 -1.305 0.380 C1A HEM 5
|
||||
HEM C2A C2A C 0 1 Y N N 3.578 -17.325 39.013 -2.015 -2.587 0.320 C2A HEM 6
|
||||
HEM C3A C3A C 0 1 Y N N 3.705 -16.820 37.785 -1.009 -3.500 0.270 C3A HEM 7
|
||||
HEM C4A C4A C 0 1 Y N N 3.256 -17.863 36.862 0.216 -2.803 0.298 C4A HEM 8
|
||||
HEM CMA CMA C 0 1 N N N 4.227 -15.469 37.393 -1.175 -4.996 0.197 CMA HEM 9
|
||||
HEM CAA CAA C 0 1 N N N 3.945 -16.670 40.296 -3.490 -2.893 0.314 CAA HEM 10
|
||||
HEM CBA CBA C 0 1 N N N 5.391 -17.138 40.581 -3.998 -2.926 -1.129 CBA HEM 11
|
||||
HEM CGA CGA C 0 1 N N N 6.095 -16.663 41.825 -5.473 -3.232 -1.136 CGA HEM 12
|
||||
HEM O1A O1A O 0 1 N N N 7.098 -15.928 41.683 -6.059 -3.405 -0.094 O1A HEM 13
|
||||
HEM O2A O2A O 0 1 N N N 5.657 -17.040 42.940 -6.137 -3.311 -2.300 O2A HEM 14
|
||||
HEM C1B C1B C 0 1 N N N 2.888 -18.698 34.579 2.664 -2.707 0.308 C1B HEM 15
|
||||
HEM C2B C2B C 0 1 N N N 2.933 -18.535 33.146 3.937 -3.328 0.418 C2B HEM 16
|
||||
HEM C3B C3B C 0 1 N N N 2.499 -19.716 32.632 4.874 -2.341 0.314 C3B HEM 17
|
||||
HEM C4B C4B C 0 1 N N N 2.187 -20.580 33.743 4.117 -1.079 0.139 C4B HEM 18
|
||||
HEM CMB CMB C 0 1 N N N 3.391 -17.290 32.422 4.203 -4.798 0.613 CMB HEM 19
|
||||
HEM CAB CAB C 0 1 N N N 2.345 -20.140 31.217 6.339 -2.497 0.365 CAB HEM 20
|
||||
HEM CBB CBB C 0 1 N N N 1.755 -19.492 30.233 6.935 -3.419 -0.385 CBB HEM 21
|
||||
HEM C1C C1C C 0 1 Y N N 1.395 -22.786 34.659 3.964 1.345 -0.174 C1C HEM 22
|
||||
HEM C2C C2C C 0 1 Y N N 0.854 -24.130 34.500 4.531 2.601 -0.445 C2C HEM 23
|
||||
HEM C3C C3C C 0 1 Y N N 0.689 -24.626 35.757 3.510 3.536 -0.437 C3C HEM 24
|
||||
HEM C4C C4C C 0 1 Y N N 1.139 -23.583 36.674 2.304 2.846 -0.139 C4C HEM 25
|
||||
HEM CMC CMC C 0 1 N N N 0.550 -24.782 33.175 5.991 2.880 -0.697 CMC HEM 26
|
||||
HEM CAC CAC C 0 1 N N N 0.164 -25.943 36.196 3.649 4.981 -0.692 CAC HEM 27
|
||||
HEM CBC CBC C 0 1 N N N 0.498 -27.158 35.750 4.201 5.407 -1.823 CBC HEM 28
|
||||
HEM C1D C1D C 0 1 N N N 1.550 -22.718 38.980 -0.102 2.753 0.298 C1D HEM 29
|
||||
HEM C2D C2D C 0 1 N N N 1.513 -22.879 40.415 -1.382 3.388 0.641 C2D HEM 30
|
||||
HEM C3D C3D C 0 1 N N N 1.951 -21.691 40.929 -2.283 2.389 0.774 C3D HEM 31
|
||||
HEM C4D C4D C 0 1 N N N 2.277 -20.826 39.811 -1.561 1.137 0.511 C4D HEM 32
|
||||
HEM CMD CMD C 0 1 N N N 1.055 -24.094 41.156 -1.639 4.863 0.811 CMD HEM 33
|
||||
HEM CAD CAD C 0 1 N N N 2.048 -21.326 42.352 -3.741 2.532 1.123 CAD HEM 34
|
||||
HEM CBD CBD C 0 1 N N N 0.741 -20.498 42.530 -4.573 2.563 -0.160 CBD HEM 35
|
||||
HEM CGD CGD C 0 1 N N N 0.578 -19.987 43.892 -6.032 2.706 0.189 CGD HEM 36
|
||||
HEM O1D O1D O 0 1 N N N 1.387 -19.103 44.303 -6.372 2.776 1.347 O1D HEM 37
|
||||
HEM O2D O2D O 0 1 N N N -0.401 -20.468 44.537 -6.954 2.755 -0.785 O2D HEM 38
|
||||
HEM NA NA N 0 1 Y N N 2.863 -18.969 37.554 -0.068 -1.456 0.321 NA HEM 39
|
||||
HEM NB NB N 0 1 N N N 2.439 -19.944 34.911 2.820 -1.386 0.207 NB HEM 40
|
||||
HEM NC NC N 0 1 Y N N 1.537 -22.509 35.976 2.604 1.506 -0.033 NC HEM 41
|
||||
HEM ND ND N 0 1 N N N 2.008 -21.465 38.663 -0.276 1.431 0.298 ND HEM 42
|
||||
HEM FE FE FE 0 0 N N N 2.196 -20.749 36.814 1.010 0.157 -0.060 FE HEM 43
|
||||
HEM HHB HHB H 0 1 N N N 3.587 -16.798 35.072 1.498 -4.508 0.309 HHB HEM 44
|
||||
HEM HHC HHC H 0 1 N N N 1.553 -22.268 32.633 5.786 0.229 -0.153 HHC HEM 45
|
||||
HEM HHD HHD H 0 1 N N N 0.802 -24.613 38.472 1.018 4.543 -0.083 HHD HEM 46
|
||||
HEM HMA HMA H 0 1 N N N 5.316 -15.524 37.249 -1.220 -5.306 -0.847 HMA HEM 47
|
||||
HEM HMAA HMAA H 0 0 N N N 3.749 -15.149 36.455 -0.328 -5.480 0.683 HMAA HEM 48
|
||||
HEM HMAB HMAB H 0 0 N N N 3.998 -14.743 38.187 -2.097 -5.285 0.702 HMAB HEM 49
|
||||
HEM HAA HAA H 0 1 N N N 3.905 -15.575 40.197 -3.662 -3.862 0.782 HAA HEM 50
|
||||
HEM HAAA HAAA H 0 0 N N N 3.268 -16.991 41.102 -4.024 -2.121 0.869 HAAA HEM 51
|
||||
HEM HBA HBA H 0 1 N N N 5.368 -18.237 40.627 -3.825 -1.956 -1.597 HBA HEM 52
|
||||
HEM HBAA HBAA H 0 0 N N N 6.004 -16.819 39.725 -3.464 -3.697 -1.684 HBAA HEM 53
|
||||
HEM HMB HMB H 0 1 N N N 3.319 -17.449 31.336 3.256 -5.336 0.660 HMB HEM 54
|
||||
HEM HMBA HMBA H 0 0 N N N 2.753 -16.442 32.711 4.794 -5.175 -0.222 HMBA HEM 55
|
||||
HEM HMBB HMBB H 0 0 N N N 4.435 -17.072 32.692 4.752 -4.948 1.543 HMBB HEM 56
|
||||
HEM HAB HAB H 0 1 N N N 2.770 -21.100 30.963 6.927 -1.863 1.011 HAB HEM 57
|
||||
HEM HBB HBB H 0 1 N N N 1.719 -19.927 29.245 7.994 -3.600 -0.277 HBB HEM 58
|
||||
HEM HBBA HBBA H 0 0 N N N 1.308 -18.526 30.414 6.360 -3.987 -1.102 HBBA HEM 59
|
||||
HEM HMC HMC H 0 1 N N N 0.153 -25.793 33.346 6.554 1.949 -0.639 HMC HEM 60
|
||||
HEM HMCA HMCA H 0 0 N N N -0.196 -24.182 32.634 6.110 3.316 -1.689 HMCA HEM 61
|
||||
HEM HMCB HMCB H 0 0 N N N 1.472 -24.846 32.578 6.362 3.578 0.053 HMCB HEM 62
|
||||
HEM HAC HAC H 0 1 N N N -0.583 -25.916 36.975 3.303 5.694 0.042 HAC HEM 63
|
||||
HEM HBC HBC H 0 1 N N N 0.027 -28.035 36.169 4.614 4.696 -2.523 HBC HEM 64
|
||||
HEM HBCA HBCA H 0 0 N N N 1.239 -27.263 34.971 4.235 6.464 -2.043 HBCA HEM 65
|
||||
HEM HMD HMD H 0 1 N N N 1.142 -23.919 42.238 -0.715 5.415 0.639 HMD HEM 66
|
||||
HEM HMDA HMDA H 0 0 N N N 0.006 -24.304 40.902 -2.394 5.185 0.094 HMDA HEM 67
|
||||
HEM HMDB HMDB H 0 0 N N N 1.680 -24.954 40.872 -1.994 5.055 1.824 HMDB HEM 68
|
||||
HEM HAD HAD H 0 1 N N N 2.055 -22.216 42.999 -4.052 1.687 1.738 HAD HEM 69
|
||||
HEM HADA HADA H 0 0 N N N 2.943 -20.719 42.554 -3.893 3.459 1.677 HADA HEM 70
|
||||
HEM HBD HBD H 0 1 N N N 0.767 -19.646 41.835 -4.262 3.408 -0.775 HBD HEM 71
|
||||
HEM HBDA HBDA H 0 0 N N N -0.119 -21.141 42.290 -4.421 1.636 -0.714 HBDA HEM 72
|
||||
HEM H2A H2A H 0 1 N N N 6.201 -16.682 43.632 -7.082 -3.510 -2.254 H2A HEM 73
|
||||
HEM H2D H2D H 0 1 N N N -0.445 -20.063 45.395 -7.877 2.847 -0.512 H2D HEM 74
|
||||
HEM HHA HHA H 0 1 N N N 2.913 -19.150 40.893 -3.246 -0.188 0.567 HHA HEM 75
|
||||
# #
|
||||
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
|
||||
HEM CHA C1A SING N N 1
|
||||
HEM CHA C4D DOUB N N 2
|
||||
HEM CHA HHA SING N N 3
|
||||
HEM CHB C4A SING N N 4
|
||||
HEM CHB C1B DOUB N N 5
|
||||
HEM CHB HHB SING N N 6
|
||||
HEM CHC C4B SING N N 7
|
||||
HEM CHC C1C DOUB N N 8
|
||||
HEM CHC HHC SING N N 9
|
||||
HEM CHD C4C DOUB N N 10
|
||||
HEM CHD C1D SING N N 11
|
||||
HEM CHD HHD SING N N 12
|
||||
HEM C1A C2A DOUB Y N 13
|
||||
HEM C1A NA SING Y N 14
|
||||
HEM C2A C3A SING Y N 15
|
||||
HEM C2A CAA SING N N 16
|
||||
HEM C3A C4A DOUB Y N 17
|
||||
HEM C3A CMA SING N N 18
|
||||
HEM C4A NA SING Y N 19
|
||||
HEM CMA HMA SING N N 20
|
||||
HEM CMA HMAA SING N N 21
|
||||
HEM CMA HMAB SING N N 22
|
||||
HEM CAA CBA SING N N 23
|
||||
HEM CAA HAA SING N N 24
|
||||
HEM CAA HAAA SING N N 25
|
||||
HEM CBA CGA SING N N 26
|
||||
HEM CBA HBA SING N N 27
|
||||
HEM CBA HBAA SING N N 28
|
||||
HEM CGA O1A DOUB N N 29
|
||||
HEM CGA O2A SING N N 30
|
||||
HEM C1B C2B SING N N 31
|
||||
HEM C1B NB SING N N 32
|
||||
HEM C2B C3B DOUB N N 33
|
||||
HEM C2B CMB SING N N 34
|
||||
HEM C3B C4B SING N N 35
|
||||
HEM C3B CAB SING N N 36
|
||||
HEM C4B NB DOUB N N 37
|
||||
HEM CMB HMB SING N N 38
|
||||
HEM CMB HMBA SING N N 39
|
||||
HEM CMB HMBB SING N N 40
|
||||
HEM CAB CBB DOUB N N 41
|
||||
HEM CAB HAB SING N N 42
|
||||
HEM CBB HBB SING N N 43
|
||||
HEM CBB HBBA SING N N 44
|
||||
HEM C1C C2C SING Y N 45
|
||||
HEM C1C NC SING Y N 46
|
||||
HEM C2C C3C DOUB Y N 47
|
||||
HEM C2C CMC SING N N 48
|
||||
HEM C3C C4C SING Y N 49
|
||||
HEM C3C CAC SING N N 50
|
||||
HEM C4C NC SING Y N 51
|
||||
HEM CMC HMC SING N N 52
|
||||
HEM CMC HMCA SING N N 53
|
||||
HEM CMC HMCB SING N N 54
|
||||
HEM CAC CBC DOUB N N 55
|
||||
HEM CAC HAC SING N N 56
|
||||
HEM CBC HBC SING N N 57
|
||||
HEM CBC HBCA SING N N 58
|
||||
HEM C1D C2D SING N N 59
|
||||
HEM C1D ND DOUB N N 60
|
||||
HEM C2D C3D DOUB N N 61
|
||||
HEM C2D CMD SING N N 62
|
||||
HEM C3D C4D SING N N 63
|
||||
HEM C3D CAD SING N N 64
|
||||
HEM C4D ND SING N N 65
|
||||
HEM CMD HMD SING N N 66
|
||||
HEM CMD HMDA SING N N 67
|
||||
HEM CMD HMDB SING N N 68
|
||||
HEM CAD CBD SING N N 69
|
||||
HEM CAD HAD SING N N 70
|
||||
HEM CAD HADA SING N N 71
|
||||
HEM CBD CGD SING N N 72
|
||||
HEM CBD HBD SING N N 73
|
||||
HEM CBD HBDA SING N N 74
|
||||
HEM CGD O1D DOUB N N 75
|
||||
HEM CGD O2D SING N N 76
|
||||
HEM O2A H2A SING N N 77
|
||||
HEM O2D H2D SING N N 78
|
||||
HEM FE NA SING N N 79
|
||||
HEM FE NB SING N N 80
|
||||
HEM FE NC SING N N 81
|
||||
HEM FE ND SING N N 82
|
||||
# #
|
||||
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
|
||||
HEM SMILES ACDLabs 12.01 "C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O"
|
||||
HEM InChI InChI 1.03 "InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;"
|
||||
HEM InChIKey InChI 1.03 KABFMIBPWCXCRK-RGGAHWMASA-L
|
||||
HEM SMILES_CANONICAL CACTVS 3.385 "CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C"
|
||||
HEM SMILES CACTVS 3.385 "CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C"
|
||||
HEM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O"
|
||||
HEM SMILES "OpenEye OEToolkits" 1.7.6 "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O"
|
||||
# #
|
||||
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
|
||||
HEM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "3-[(5Z,10Z,14Z,19Z)-18-(2-carboxyethyl)-8,13-bis(ethenyl)-3,7,12,17-tetramethyl-21,23-dihydroporphyrin-2-yl]propanoic acid"
|
||||
HEM "SYSTEMATIC NAME" ACDLabs 12.01 "[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)dipropanoato(2-)]iron"
|
||||
# #
|
||||
loop_
|
||||
_pdbx_chem_comp_audit.comp_id
|
||||
_pdbx_chem_comp_audit.action_type
|
||||
_pdbx_chem_comp_audit.date
|
||||
_pdbx_chem_comp_audit.processing_site
|
||||
HEM "Create component" 1999-07-08 RCSB
|
||||
HEM "Other modification" 2016-01-20 RCSB
|
||||
HEM "Modify synonyms" 2020-06-05 PDBE
|
||||
#
|
||||
_pdbx_chem_comp_synonyms.ordinal 1
|
||||
_pdbx_chem_comp_synonyms.comp_id HEM
|
||||
_pdbx_chem_comp_synonyms.name HEME
|
||||
_pdbx_chem_comp_synonyms.provenance ?
|
||||
_pdbx_chem_comp_synonyms.type ?
|
||||
##
|
||||
|
||||
188
test/REA.cif
Normal file
188
test/REA.cif
Normal file
@@ -0,0 +1,188 @@
|
||||
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
|
||||
#
|
||||
@@ -20,9 +20,10 @@ int main(int argc, char* argv[])
|
||||
if (argc == 3)
|
||||
testdir = argv[2];
|
||||
|
||||
if (std::filesystem::exists(testdir / ".."/"data"/"components.cif"))
|
||||
cif::addFileResource("components.cif", testdir / ".."/"data"/"components.cif");
|
||||
if (std::filesystem::exists(testdir / ".."/"data"/"ccd-subset.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::File f(testdir / ".."/"examples"/"1cbs.cif.gz");
|
||||
|
||||
@@ -24,7 +24,7 @@
|
||||
* 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 <stdexcept>
|
||||
@@ -52,16 +52,23 @@ cif::File operator""_cf(const char* text, size_t length)
|
||||
|
||||
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)
|
||||
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
|
||||
if (std::filesystem::exists(gTestDir / ".."/"data"/"components.cif"))
|
||||
cif::addFileResource("components.cif", gTestDir / ".."/"data"/"components.cif");
|
||||
cif::addFileResource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
|
||||
|
||||
mmcif::CompoundFactory::instance().pushDictionary(gTestDir / "HEM.cif");
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
@@ -24,7 +24,8 @@
|
||||
* 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 <stdexcept>
|
||||
@@ -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)
|
||||
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)
|
||||
{
|
||||
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;
|
||||
|
||||
auto f = R"(data_TEST
|
||||
@@ -1527,8 +1532,6 @@ BOOST_AUTO_TEST_CASE(bondmap_1)
|
||||
{
|
||||
cif::VERBOSE = 2;
|
||||
|
||||
cif::addFileResource("components.cif", gTestDir / ".." / "data" / "components.cif");
|
||||
|
||||
// sections taken from CCD compounds.cif
|
||||
auto components = R"(
|
||||
data_ASN
|
||||
|
||||
47
tools/update-dictionary-script
Normal file
47
tools/update-dictionary-script
Normal file
@@ -0,0 +1,47 @@
|
||||
#!/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"
|
||||
Reference in New Issue
Block a user