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libcifpp
Commit a9e9f86c by Maarten L. Hekkelman
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Renaming internal use of mmcif_pdbx dictionary. It was wrong to use the name mmcif_pdbx_v50

parent a2c52713
Showing with 30 additions and 32 deletions
CMakeLists.txt
...@@ -362,7 +362,7 @@ install( ...@@ -362,7 +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.dic
${COMPONENTS_CIF} ${COMPONENTS_CIF}
DESTINATION ${SHARE_INSTALL_DIR} DESTINATION ${SHARE_INSTALL_DIR}
) )
...@@ -435,7 +435,7 @@ if(CIFPP_BUILD_TESTS) ...@@ -435,7 +435,7 @@ if(CIFPP_BUILD_TESTS)
target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp Boost::boost) target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp Boost::boost)
if(CIFPP_USE_RSRC) if(CIFPP_USE_RSRC)
mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic) mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx.dic)
endif() endif()
if(MSVC) if(MSVC)
......
examples/example.cpp
...@@ -8,7 +8,6 @@ namespace fs = std::filesystem; ...@@ -8,7 +8,6 @@ namespace fs = std::filesystem;
int main() int main()
{ {
cif::file file; cif::file file;
file.load_dictionary("mmcif_pdbx_v50");
file.load("1cbs.cif.gz"); file.load("1cbs.cif.gz");
auto& db = file.front(); auto& db = file.front();
......
include/cif++/structure/Compound.hpp
...@@ -46,7 +46,7 @@ class Compound; ...@@ -46,7 +46,7 @@ class Compound;
struct CompoundAtom; struct CompoundAtom;
class CompoundFactoryImpl; class CompoundFactoryImpl;
/// \brief The bond type as defined in the CCD, possible values taken from the mmcif_pdbx_v50 file /// \brief The bond type as defined in the CCD, possible values taken from the mmcif_pdbx file
enum class BondType enum class BondType
{ {
sing, // 'single bond' sing, // 'single bond'
......
src/Cif++.cpp
...@@ -1798,7 +1798,7 @@ auto Category::erase(iterator pos) -> iterator ...@@ -1798,7 +1798,7 @@ auto Category::erase(iterator pos) -> iterator
} }
// links are created based on the _pdbx_item_linked_group_list entries // links are created based on the _pdbx_item_linked_group_list entries
// in mmcif_pdbx_v50.dic dictionary. // in mmcif_pdbx.dic dictionary.
// //
// For each link group in _pdbx_item_linked_group_list // For each link group in _pdbx_item_linked_group_list
// a std::set of keys from one category is mapped to another. // a std::set of keys from one category is mapped to another.
......
src/cif/file.cpp
...@@ -61,7 +61,8 @@ bool file::is_valid() ...@@ -61,7 +61,8 @@ bool file::is_valid()
load_dictionary(); load_dictionary();
} }
bool result = true; bool result = not empty();
for (auto &d : *this) for (auto &d : *this)
result = d.is_valid() and result; result = d.is_valid() and result;
...@@ -76,9 +77,10 @@ void file::load_dictionary() ...@@ -76,9 +77,10 @@ void file::load_dictionary()
if (audit_conform and not audit_conform->empty()) if (audit_conform and not audit_conform->empty())
{ {
std::string name; std::string name;
cif::tie(name) = audit_conform->front().get("name"); cif::tie(name) = audit_conform->front().get("dict_name");
load_dictionary(name); if (not name.empty())
load_dictionary(name);
} }
} }
...@@ -158,10 +160,9 @@ void file::load(std::istream &is) ...@@ -158,10 +160,9 @@ void file::load(std::istream &is)
p.parse_file(); p.parse_file();
if (saved != nullptr) if (saved != nullptr)
{
set_validator(saved); set_validator(saved);
(void)is_valid(); else
} load_dictionary();
} }
void file::save(const std::filesystem::path &p) const void file::save(const std::filesystem::path &p) const
......
src/pdb/PDB2Cif.cpp
...@@ -6055,10 +6055,11 @@ void ReadPDBFile(std::istream &pdbFile, cif::File &cifFile) ...@@ -6055,10 +6055,11 @@ void ReadPDBFile(std::istream &pdbFile, cif::File &cifFile)
{ {
PDBFileParser p; PDBFileParser p;
cifFile.loadDictionary("mmcif_pdbx_v50");
p.Parse(pdbFile, cifFile); p.Parse(pdbFile, cifFile);
cifFile.loadDictionary("mmcif_pdbx");
if (not cifFile.isValid() and cif::VERBOSE >= 0) if (not cifFile.isValid() and cif::VERBOSE >= 0)
std::cerr << "Resulting mmCIF file is not valid!" << std::endl; std::cerr << "Resulting mmCIF file is not valid!" << std::endl;
} }
src/structure/Compound.cpp
...@@ -416,7 +416,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const fs::path &file, std::shared_ptr<C ...@@ -416,7 +416,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const fs::path &file, std::shared_ptr<C
else else
{ {
// A CCD components file, validate it first // A CCD components file, validate it first
cifFile.load_dictionary("mmcif_pdbx_v50"); cifFile.load_dictionary("mmcif_pdbx");
if (not cifFile.is_valid()) if (not cifFile.is_valid())
throw std::runtime_error("Invalid compound file"); throw std::runtime_error("Invalid compound file");
......
src/structure/Structure.cpp
...@@ -1297,7 +1297,7 @@ void File::load(const std::filesystem::path &path) ...@@ -1297,7 +1297,7 @@ void File::load(const std::filesystem::path &path)
cif::File::load(in); cif::File::load(in);
// validate, otherwise lots of functionality won't work // validate, otherwise lots of functionality won't work
loadDictionary("mmcif_pdbx_v50"); loadDictionary("mmcif_pdbx");
if (not isValid() and cif::VERBOSE >= 0) if (not isValid() and cif::VERBOSE >= 0)
std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl; std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl;
} }
......
test/dssp-test.cpp
...@@ -64,7 +64,7 @@ bool init_unit_test() ...@@ -64,7 +64,7 @@ bool init_unit_test()
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 // do this now, avoids the need for installing
cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic"); cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// initialize CCD location // initialize CCD location
cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif"); cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
...@@ -76,12 +76,9 @@ bool init_unit_test() ...@@ -76,12 +76,9 @@ bool init_unit_test()
BOOST_AUTO_TEST_CASE(dssp_1) BOOST_AUTO_TEST_CASE(dssp_1)
{ {
// using namespace mmcif;
cif::file f(gTestDir / "1cbs.cif"); cif::file f(gTestDir / "1cbs.cif");
f.load_dictionary("mmcif_pdbx_v50");
BOOST_CHECK(f.is_valid()); BOOST_ASSERT(f.is_valid());
std::ifstream t(gTestDir / "1cbs-dssp-test.tsv"); std::ifstream t(gTestDir / "1cbs-dssp-test.tsv");
......
test/rename-compound-test.cpp
...@@ -19,8 +19,8 @@ int main(int argc, char* argv[]) ...@@ -19,8 +19,8 @@ int main(int argc, char* argv[])
if (std::filesystem::exists(testdir / ".." / "data" / "ccd-subset.cif")) if (std::filesystem::exists(testdir / ".." / "data" / "ccd-subset.cif"))
cif::add_file_resource("components.cif", testdir / ".." / "data" / "ccd-subset.cif"); cif::add_file_resource("components.cif", testdir / ".." / "data" / "ccd-subset.cif");
if (std::filesystem::exists(testdir / ".." / "rsrc" / "mmcif_pdbx_v50.dic")) if (std::filesystem::exists(testdir / ".." / "rsrc" / "mmcif_pdbx.dic"))
cif::add_file_resource("mmcif_pdbx_v50.dic", testdir / ".." / "rsrc" / "mmcif_pdbx_v50.dic"); cif::add_file_resource("mmcif_pdbx.dic", testdir / ".." / "rsrc" / "mmcif_pdbx.dic");
mmcif::CompoundFactory::instance().pushDictionary(testdir / "REA.cif"); mmcif::CompoundFactory::instance().pushDictionary(testdir / "REA.cif");
mmcif::CompoundFactory::instance().pushDictionary(testdir / "RXA.cif"); mmcif::CompoundFactory::instance().pushDictionary(testdir / "RXA.cif");
......
test/structure-test.cpp
...@@ -61,7 +61,7 @@ bool init_unit_test() ...@@ -61,7 +61,7 @@ bool init_unit_test()
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 // do this now, avoids the need for installing
cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic"); cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// initialize CCD location // initialize CCD location
cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif"); cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
...@@ -78,7 +78,7 @@ BOOST_AUTO_TEST_CASE(create_nonpoly_1) ...@@ -78,7 +78,7 @@ BOOST_AUTO_TEST_CASE(create_nonpoly_1)
cif::VERBOSE = 1; cif::VERBOSE = 1;
mmcif::File file; mmcif::File file;
file.loadDictionary("mmcif_pdbx_v50.dic"); file.loadDictionary("mmcif_pdbx.dic");
file.emplace("TEST"); // create a datablock file.emplace("TEST"); // create a datablock
mmcif::Structure structure(file); mmcif::Structure structure(file);
...@@ -180,7 +180,7 @@ _struct_asym.details ? ...@@ -180,7 +180,7 @@ _struct_asym.details ?
# #
)"_cf; )"_cf;
expected.loadDictionary("mmcif_pdbx_v50.dic"); expected.loadDictionary("mmcif_pdbx.dic");
if (not (expected.firstDatablock() == structure.datablock())) if (not (expected.firstDatablock() == structure.datablock()))
{ {
...@@ -280,7 +280,7 @@ _struct_asym.details ? ...@@ -280,7 +280,7 @@ _struct_asym.details ?
# #
)"_cf; )"_cf;
data.loadDictionary("mmcif_pdbx_v50.dic"); data.loadDictionary("mmcif_pdbx.dic");
mmcif::Structure s(data); mmcif::Structure s(data);
......
test/sugar-test.cpp
...@@ -61,7 +61,7 @@ bool init_unit_test() ...@@ -61,7 +61,7 @@ bool init_unit_test()
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 // do this now, avoids the need for installing
cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic"); cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// initialize CCD location // initialize CCD location
cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif"); cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
......
test/unit-test.cpp
...@@ -67,7 +67,7 @@ bool init_unit_test() ...@@ -67,7 +67,7 @@ bool init_unit_test()
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 // do this now, avoids the need for installing
cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic"); cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// initialize CCD location // initialize CCD location
cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif"); cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
...@@ -295,7 +295,6 @@ save__cat_2.desc ...@@ -295,7 +295,6 @@ save__cat_2.desc
cif::Validator validator("test", is_dict); cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -327,6 +326,7 @@ _cat_2.desc ...@@ -327,6 +326,7 @@ _cat_2.desc
std::istream is_data(&data_buffer); std::istream is_data(&data_buffer);
f.load(is_data); f.load(is_data);
f.setValidator(&validator);
auto &cat1 = f.firstDatablock()["cat_1"]; auto &cat1 = f.firstDatablock()["cat_1"];
auto &cat2 = f.firstDatablock()["cat_2"]; auto &cat2 = f.firstDatablock()["cat_2"];
......
test/unit-v2-test.cpp
...@@ -69,7 +69,7 @@ bool init_unit_test() ...@@ -69,7 +69,7 @@ bool init_unit_test()
// 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 // // do this now, avoids the need for installing
// cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic"); // cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// // initialize CCD location // // initialize CCD location
// cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif"); // cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
......
tools/update-dictionary-script
...@@ -43,7 +43,7 @@ fetch_dictionary () { ...@@ -43,7 +43,7 @@ fetch_dictionary () {
# fetch the dictionaries # 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/mmcif_pdbx.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" fetch_dictionary "/var/cache/libcifpp/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
# this one is not compressed # this one is not compressed
......
tools/update-libcifpp-data.in
...@@ -43,7 +43,7 @@ fetch_dictionary () { ...@@ -43,7 +43,7 @@ fetch_dictionary () {
# fetch the dictionaries # fetch the dictionaries
fetch_dictionary "@CIFPP_CACHE_DIR@/mmcif_pdbx_v50.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz" fetch_dictionary "@CIFPP_CACHE_DIR@/mmcif_pdbx.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
fetch_dictionary "@CIFPP_CACHE_DIR@/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz" fetch_dictionary "@CIFPP_CACHE_DIR@/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
# notify subscribers # notify subscribers
......
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