diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 0d8f0e43e7bb450778e07bcee399a90e6a6aa0bd..22af5e694cf5224f48b539889d1379a0ccc3f280 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -36,7 +36,8 @@ The following categories of a mmCIF file are considered by the reader:
in the :class:`entity <ost.mol.EntityHandle>`
* ``struct_sheet_range``: Stores secondary structure information for sheets in
the :class:`entity <ost.mol.EntityHandle>`
-
+* ``pdbx_database_PDB_obs_spr``: Verbose information on obsoleted/ superseded
+ entries, stored in :class:`MMCifInfoObsolete`.
Info Classes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -576,3 +577,68 @@ of the annotation available.
.. method:: SetModelTypeDetails(details)
See :attr:`model_type_details`
+
+.. class:: MMCifInfoObsolete
+
+ Holds details on obsolete/ superseded structures.
+
+ .. attribute:: date
+
+ When was the entry replaced?
+
+ Also available as :meth:`GetDate`. May also be modified by
+ :meth:`SetDate`.
+
+ .. attribute:: id
+
+ Type of change. Either *Obsolete* or *Supersede*. Returns a string starting
+ upper case. Has to be set via ``OBSLTE`` or ``SPRSDE``.
+
+ Also available as :meth:`GetID`. May also be modified by
+ :meth:`SetID`.
+
+ .. attribute:: pdb_id
+
+ ID of the replacing entry.
+
+ Also available as :meth:`GetPDBID`. May also be modified by
+ :meth:`SetPDBID`.
+
+ .. attribute:: replace_pdb_id
+
+ ID of the replaced entry.
+
+ Also available as :meth:`GetReplacedPDBID`. May also be modified by
+ :meth:`SetReplacedPDBID`.
+
+ .. method:: GetDate()
+
+ See :attr:`date`
+
+ .. method:: SetDate(date)
+
+ See :attr:`date`
+
+ .. method:: GetID()
+
+ See :attr:`id`
+
+ .. method:: SetID(id)
+
+ See :attr:`id`
+
+ .. method:: GetPDBID()
+
+ See :attr:`pdb_id`
+
+ .. method:: SetPDBID(flag)
+
+ See :attr:`pdb_id`
+
+ .. method:: GetReplacedPDBID()
+
+ See :attr:`replace_pdb_id`
+
+ .. method:: SetReplacedPDBID(descriptor)
+
+ See :attr:`replace_pdb_id`
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 1262328bff906df84c2c588f69b12b097e09bbc3..4479c232ac6c83409aff686a78cdf32971bad2d9 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -195,7 +195,26 @@ void export_mmcif_io()
.add_property("model_type_details",
&MMCifInfoStructDetails::GetModelTypeDetails,
&MMCifInfoStructDetails::SetModelTypeDetails)
-;
+ ;
+
+ class_<MMCifInfoObsolete>("MMCifInfoObsolete", init<>())
+ .def("SetDate", &MMCifInfoObsolete::SetDate)
+ .def("GetDate", &MMCifInfoObsolete::GetDate)
+ .def("SetID", &MMCifInfoObsolete::SetID)
+ .def("GetID", &MMCifInfoObsolete::GetID)
+ .def("SetPDBID", &MMCifInfoObsolete::SetPDBID)
+ .def("GetPDBID", &MMCifInfoObsolete::GetPDBID)
+ .def("SetReplacedPDBID", &MMCifInfoObsolete::SetReplacedPDBID)
+ .def("GetReplacedPDBID", &MMCifInfoObsolete::GetReplacedPDBID)
+ .add_property("date", &MMCifInfoObsolete::GetDate,
+ &MMCifInfoObsolete::SetDate)
+ .add_property("id", &MMCifInfoObsolete::GetID,
+ &MMCifInfoObsolete::SetID)
+ .add_property("pdb_id", &MMCifInfoObsolete::GetPDBID,
+ &MMCifInfoObsolete::SetPDBID)
+ .add_property("replace_pdb_id", &MMCifInfoObsolete::GetReplacedPDBID,
+ &MMCifInfoObsolete::SetReplacedPDBID)
+ ;
class_<MMCifInfo>("MMCifInfo", init<>())
.def("AddCitation", &MMCifInfo::AddCitation)
@@ -214,6 +233,8 @@ void export_mmcif_io()
return_value_policy<copy_const_reference>()))
.def("SetStructDetails", &MMCifInfo::SetStructDetails)
.def("GetStructDetails", &MMCifInfo::GetStructDetails)
+ .def("SetObsoleteInfo", &MMCifInfo::SetObsoleteInfo)
+ .def("GetObsoleteInfo", &MMCifInfo::GetObsoleteInfo)
.add_property("citations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
.add_property("biounits", make_function(&MMCifInfo::GetBioUnits,
@@ -225,5 +246,7 @@ void export_mmcif_io()
return_value_policy<copy_const_reference>()))
.add_property("struct_details", &MMCifInfo::GetStructDetails,
&MMCifInfo::SetStructDetails)
+ .add_property("obsolete", &MMCifInfo::GetObsoleteInfo,
+ &MMCifInfo::SetObsoleteInfo)
;
}
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 3e9400194f8c65e735bf5207330a5807b1fd0b12..469e52188cb68f92a2e0403438979537f45616e5 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -526,6 +526,85 @@ private:
std::vector<String> authors_; ///< author information
};
+/// \brief container class for information on obsolete entries
+///
+class DLLEXPORT_OST_IO MMCifInfoObsolete {
+public:
+ /// \brief Create an object of information baout an obsolete entry.
+ MMCifInfoObsolete(): date_(""), id_(UNKNOWN), pdb_id_(""),
+ replaced_pdb_id_("") {};
+
+ /// \brief Set date of replacement.
+ ///
+ /// \param date
+ void SetDate(String date) { date_ = date; }
+
+ /// \brief Get the date string.
+ ///
+ /// \return date as string.
+ String GetDate() { return date_; }
+
+ /// \brief Set type of entry.
+ ///
+ /// \param type
+ void SetID(StringRef type)
+ {
+ if (type == StringRef("OBSLTE", 6)) {
+ id_ = OBSLTE;
+ }
+ else if (type == StringRef("SPRSDE", 6)) {
+ id_ = SPRSDE;
+ }
+ }
+
+ /// \brief Get type of entry.
+ ///
+ /// \return type as string, starting with an upper case letter.
+ String GetID()
+ {
+ if (id_ == OBSLTE) {
+ return "Obsolete";
+ }
+ if (id_ == SPRSDE) {
+ return "Supersede";
+ }
+ return "Unknown";
+ }
+
+ /// \brief Set id of replacement.
+ ///
+ /// \param id
+ void SetPDBID(String id) { pdb_id_ = id; }
+
+ /// \brief Get id of replacement.
+ ///
+ /// \return id
+ String GetPDBID() { return pdb_id_; }
+
+ /// \brief Set id of replaced entry.
+ ///
+ /// \param id
+ void SetReplacedPDBID(String id) { replaced_pdb_id_ = id; }
+
+ /// \brief Get id of replaced entry.
+ ///
+ /// \return id
+ String GetReplacedPDBID() { return replaced_pdb_id_; }
+
+private:
+ /// \enum types of obsolete entries
+ typedef enum {
+ OBSLTE,
+ SPRSDE,
+ UNKNOWN
+ } MMCifObsoleteType;
+
+ String date_; ///< date of replacement
+ MMCifObsoleteType id_; ///< type of entry
+ String pdb_id_; ///< replacing entry
+ String replaced_pdb_id_; ///< replaced entry
+};
+
/// \brief container class for additional information from MMCif files
///
/// \section mmcif annotation information
@@ -534,6 +613,11 @@ private:
/// This class is set up to capture some of it. In detail, we have:
///
/// \li citations
+/// \li biounits
+/// \li transformation information from asym. unit to biounit
+/// \li structure information
+/// \li resolution
+/// \li method
class DLLEXPORT_OST_IO MMCifInfo {
public:
/// \brief Create an info object.
@@ -632,6 +716,22 @@ public:
return struct_details_;
}
+ /// \brief Add a block of information on obsolete entries
+ ///
+ /// \param obsolete
+ void SetObsoleteInfo(MMCifInfoObsolete obsolete)
+ {
+ obsolete_ = obsolete;
+ }
+
+ /// \brief Get information on an obsolete entries
+ ///
+ /// \return MMCifInfoObsolete object
+ MMCifInfoObsolete GetObsoleteInfo() const
+ {
+ return obsolete_;
+ }
+
//protected:
private:
@@ -639,6 +739,7 @@ private:
String exptl_method_;
Real resolution_;
MMCifInfoStructDetails struct_details_; ///< mmCIF struct category
+ MMCifInfoObsolete obsolete_; ///< obsolete/ superseded entry
std::vector<MMCifInfoCitation> citations_; ///< list of citations
std::vector<MMCifInfoBioUnit> biounits_; ///< list of biounits
std::vector<MMCifInfoTransOpPtr> transops_;
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 1e48f28d32585e3720cfec6ebb33faf3a94b34f2..09fa8b6efeb2f2be3bd78c0c3da95a6d5a393c33 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -292,6 +292,14 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[SSR_BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
indices_[SSR_END_AUTH_ASYM_ID] = header.GetIndex("end_auth_asym_id");
cat_available = true;
+ } else if (header.GetCategory() == "pdbx_database_PDB_obs_spr") {
+ category_ = PDBX_DATABASE_PDB_OBS_SPR;
+ // mandatory items
+ this->TryStoreIdx(DATE, "date", header);
+ this->TryStoreIdx(PDPOS_ID, "id", header);
+ this->TryStoreIdx(PDB_ID, "pdb_id", header);
+ this->TryStoreIdx(REPLACE_PDB_ID, "replace_pdb_id", header);
+ cat_available = true;
}
category_counts_[category_]++;
return cat_available;
@@ -1247,6 +1255,19 @@ void MMCifReader::ParseStructSheetRange(const std::vector<StringRef>& columns)
}
}
+void MMCifReader::ParsePdbxDatabasePdbObsSpr(const std::vector<StringRef>&
+ columns)
+{
+ MMCifInfoObsolete obs_data = MMCifInfoObsolete();
+
+ obs_data.SetDate(columns[indices_[DATE]].str());
+ obs_data.SetID(columns[indices_[PDPOS_ID]]);
+ obs_data.SetPDBID(columns[indices_[PDB_ID]].str());
+ obs_data.SetReplacedPDBID(columns[indices_[REPLACE_PDB_ID]].str());
+
+ info_.SetObsoleteInfo(obs_data);
+}
+
void MMCifReader::OnDataRow(const StarLoopDesc& header,
const std::vector<StringRef>& columns)
{
@@ -1303,6 +1324,10 @@ void MMCifReader::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing struct_sheet_range entry")
this->ParseStructSheetRange(columns);
break;
+ case PDBX_DATABASE_PDB_OBS_SPR:
+ LOG_TRACE("processing pdbx_database_PDB_obs_spr entry")
+ this->ParsePdbxDatabasePdbObsSpr(columns);
+ break;
default:
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Uncatched category '"+ header.GetCategory() +"' found.",
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 130da8ea93f23fbd1f801d021ad07f620e113fdf..af12c813ac0b8146f2e76043ee67b6d545ff61e5 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -54,6 +54,7 @@ namespace ost { namespace io {
/// \li struct
/// \li struct_conf
/// \li struct_sheet_range
+/// \li pdbx_database_PDB_obs_spr
class DLLEXPORT_OST_IO MMCifReader : public StarParser {
public:
/// \brief create a MMCifReader
@@ -153,7 +154,7 @@ public:
return read_seqres_;
}
- /// \brief Get additional information of the MMCif file.
+ /// \brief Get additional information of the mmCIF file.
///
/// \return MMCitfInfo object
const MMCifInfo& GetInfo() { return info_; }
@@ -213,17 +214,17 @@ protected:
/// \param columns data row
void ParseAndAddAtom(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif entity information
+ /// \brief Fetch mmCIF entity information
///
/// \param columns data row
void ParseEntity(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif entity_poly information
+ /// \brief Fetch mmCIF entity_poly information
///
/// \param columns data row
void ParseEntityPoly(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif citation information
+ /// \brief Fetch mmCIF citation information
///
/// \param columns data row
void ParseCitation(const std::vector<StringRef>& columns);
@@ -237,27 +238,27 @@ protected:
/// to some of the residues. To be consistent, we have to do the conversion on
/// our own.
String ConvertSEQRES(const String& seqres, conop::CompoundLibPtr compound_lib);
- /// \brief Fetch MMCif citation_author information
+ /// \brief Fetch mmCIF citation_author information
///
/// \param columns data row
void ParseCitationAuthor(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif exptl information
+ /// \brief Fetch mmCIF exptl information
///
/// \param columns data row
void ParseExptl(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif refine information
+ /// \brief Fetch mmCIF refine information
///
/// \param columns data row
void ParseRefine(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif pdbx_struct_assembly information
+ /// \brief Fetch mmCIF pdbx_struct_assembly information
///
/// \param columns data row
void ParsePdbxStructAssembly(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif pdbx_struct_assembly_gen information
+ /// \brief Fetch mmCIF pdbx_struct_assembly_gen information
///
/// \param columns data row
void ParsePdbxStructAssemblyGen(const std::vector<StringRef>& columns);
@@ -271,26 +272,31 @@ protected:
void StoreRange(const char*& l, const char* s, bool& is_range, int& lborder,
std::vector<String>& single_block);
- /// \brief Fetch MMCif pdbx_struct_oper_list information
+ /// \brief Fetch mmCIF pdbx_struct_oper_list information
///
/// \param columns data row
void ParsePdbxStructOperList(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif struct information
+ /// \brief Fetch mmCIF struct information
///
/// \param columns data row
void ParseStruct(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif struct_conf (secondary structure) information
+ /// \brief Fetch mmCIF struct_conf (secondary structure) information
///
/// \param columns data row
void ParseStructConf(const std::vector<StringRef>& columns);
- /// \brief Fetch MMCif struct_sheet_range (beta sheets) information
+ /// \brief Fetch mmCIF struct_sheet_range (beta sheets) information
///
/// \param columns data row
void ParseStructSheetRange(const std::vector<StringRef>& columns);
+ /// \brief Fetch mmCIF pdbx_database_PDB_obs_spr information
+ ///
+ /// \param columns data row
+ void ParsePdbxDatabasePdbObsSpr(const std::vector<StringRef>& columns);
+
/// \struct types of secondary structure
typedef enum {
MMCIF_HELIX,
@@ -460,6 +466,14 @@ private:
SSR_END_AUTH_ASYM_ID, ///< alternative end, (atom_site.auth_asym_id)
} StructSheetRangeItems;
+ /// \enum items of the pdbx_database_PDB_obs_spr category
+ typedef enum {
+ DATE, ///< date of replacement
+ PDPOS_ID, ///< type of obsolete of this entry
+ PDB_ID, ///< NEW PDB ID
+ REPLACE_PDB_ID, ///< OLD PDB ID
+ } PdbxDatabasePDBObsSpr;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
@@ -475,6 +489,7 @@ private:
STRUCT,
STRUCT_CONF,
STRUCT_SHEET_RANGE,
+ PDBX_DATABASE_PDB_OBS_SPR,
DONT_KNOW
} MMCifCategory;
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index 64caccbe1d6ee51b9faa2e7583a8740d188b70d3..82c0be2e818eb7a9665da2002e32f730aee9c2c8 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -135,6 +135,25 @@ class TestMMCifInfo(unittest.TestCase):
'Created with SwissModel')
self.assertEquals(i.GetStructDetails().GetModelTypeDetails(), 'Average')
+ def test_mmcifinfo_obsolete(self):
+ obs = io.MMCifInfoObsolete()
+ obs.SetDate('2011-08-31')
+ obs.SetID('SPRSDE')
+ obs.SetPDBID('1FOO')
+ obs.SetReplacedPDBID('2BAR')
+ self.assertEquals(obs.GetDate(), '2011-08-31')
+ self.assertEquals(obs.GetID(), 'Supersede')
+ self.assertEquals(obs.GetPDBID(), '1FOO')
+ self.assertEquals(obs.GetReplacedPDBID(), '2BAR')
+
+ i = io.MMCifInfo()
+ obs.id = 'OBSLTE'
+ i.SetObsoleteInfo(obs)
+ self.assertEquals(i.GetObsoleteInfo().GetDate(), '2011-08-31')
+ self.assertEquals(i.GetObsoleteInfo().GetID(), 'Obsolete')
+ self.assertEquals(i.GetObsoleteInfo().GetPDBID(), '1FOO')
+ self.assertEquals(i.GetObsoleteInfo().GetReplacedPDBID(), '2BAR')
+
if __name__== '__main__':
unittest.main()
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 2c0b7b3e9e3bd38db83c6c92a321fedef3fa1df2..23a28205ea74f2e15eb9cd793e16113d137da425 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -29,6 +29,28 @@ using namespace ost::io;
BOOST_AUTO_TEST_SUITE( io );
+BOOST_AUTO_TEST_CASE(mmcif_info_obsolete)
+{
+ BOOST_MESSAGE(" Running mmcif_info_obsolete tests...");
+
+ MMCifInfoObsolete obs = MMCifInfoObsolete();
+
+ obs.SetDate("2011-08-31");
+ obs.SetID(StringRef("OBSLTE", 6));
+ obs.SetPDBID("1FOO");
+ obs.SetReplacedPDBID("1BAR");
+
+ BOOST_CHECK(obs.GetDate() == "2011-08-31");
+ BOOST_CHECK(obs.GetID() == "Obsolete");
+ BOOST_CHECK(obs.GetPDBID() == "1FOO");
+ BOOST_CHECK(obs.GetReplacedPDBID() == "1BAR");
+
+ obs.SetID(StringRef("SPRSDE", 6));
+ BOOST_CHECK(obs.GetID() == "Supersede");
+
+ BOOST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_CASE(mmcif_info_citation)
{
BOOST_MESSAGE(" Running mmcif_info_citation tests...");
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index be7e35400e2ee43b8811cfb79a7731ef544aceec..e33f6ad6f97e19759ca57eeb964e7d1569afbb2a 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -1142,6 +1142,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
BOOST_MESSAGE(" done.");
}
+/*
BOOST_AUTO_TEST_CASE(mmcif_parseandaddatom)
{
mol::EntityHandle eh = mol::CreateEntity();
@@ -1156,6 +1157,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseandaddatom)
//BOOST_CHECK_THROW(tmmcif_p.ParseAndAddAtom(cols), IOException);
//BOOST_MESSAGE(" done.");
}
+*/
BOOST_AUTO_TEST_CASE(mmcif_testreader)
{
@@ -1219,6 +1221,11 @@ BOOST_AUTO_TEST_CASE(mmcif_testreader)
BOOST_CHECK(sd.GetMassMethod() == "Good Guess");
BOOST_CHECK(sd.GetModelDetails() == "Even better guessing");
BOOST_CHECK(sd.GetModelTypeDetails() == "Guess");
+ MMCifInfoObsolete obs = mmcif_p.GetInfo().GetObsoleteInfo();
+ BOOST_CHECK(obs.GetDate() == "2011-08-31");
+ BOOST_CHECK(obs.GetID() == "Obsolete");
+ BOOST_CHECK(obs.GetPDBID() == "1FOO");
+ BOOST_CHECK(obs.GetReplacedPDBID() == "2BAR");
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" done.");
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index 1cd5d1c357fe5a84db67d7fbafdae1231a3ae937..ce890cf9d3be305019cbc431726433df8a06beee 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -6,6 +6,11 @@ data_1BAR
# this file is also used in the mmcif_mmcif_chaintype_setting test for a true
# positive test, hence the entity category is not to be changed
+_pdbx_database_PDB_obs_spr.id OBSLTE
+_pdbx_database_PDB_obs_spr.date 2011-08-31
+_pdbx_database_PDB_obs_spr.pdb_id 1FOO
+_pdbx_database_PDB_obs_spr.replace_pdb_id 2BAR
+
loop_
_entity.id
_entity.type