diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 240c7a6ab52714c8f3f2b5beb1210a88c648e498..78e126def7cf2b67171435e5c2f9efe49ee43de2 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -40,7 +40,10 @@ The following categories of a mmCIF file are considered by the reader:
* ``struct_ref`` stored in :class:`MMCifInfoStructRef`
* ``struct_ref_seq`` stored in :class:`MMCifInfoStructRefSeq`
* ``struct_ref_seq_dif`` stored in :class:`MMCifInfoStructRefDif`
-* ``database_pdb_rev`` stored in :class:`MMCifInfoRevisions`
+* ``database_pdb_rev`` (mmCIF dictionary version < 5) stored in
+ :class:`MMCifInfoRevisions`
+* ``pdbx_audit_revision_history`` and ``pdbx_audit_revision_details``
+ (mmCIF dictionary version >= 5) used to fill :class:`MMCifInfoRevisions`
Notes:
@@ -257,8 +260,8 @@ of the annotation available.
.. method:: SetRevisionsDateOriginal(date)
- Set the date, when this entry first entered the PDB.
- See :meth:`MMCifInfoRevisions.SetDateOriginal`.
+ Set the date, when this entry first entered the PDB. Ignored if it was set
+ in the past. See :meth:`MMCifInfoRevisions.SetDateOriginal`.
.. class:: MMCifInfoCitation
@@ -965,7 +968,8 @@ of the annotation available.
.. attribute:: first_release
Index + 1 of the revision releasing this entry. If the value is 0, was not
- set yet.
+ set yet. Set first time we encounter a :meth:`GetStatus` value of
+ "full release" (mmCIF versions < 5) or "Initial release" (current mmCIF).
:type: :class:`int`
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 5fc9d576bb27ab05c8a59b8ec72cc3e1043fdc3f..49cd8e16c9901a6d2132ca91c2b7d66f7e11f19d 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -675,7 +675,7 @@ private:
String replaced_pdb_id_; ///< replaced entry
};
-/// \brief container class for information on file revisions (database_pdb_rev)
+/// \brief Container class for information on file revisions
///
class DLLEXPORT_OST_IO MMCifInfoRevisions {
public:
@@ -701,19 +701,16 @@ public:
{
if (num_.size() && (num_.back() >= num)) {
std::stringstream ss;
- ss << "'num' component of 'database_pdb_rev' category has to increase ";
- ss << "with every revision, last was ";
- ss << num_.back();
- ss << ", trying to add ";
- ss << num;
+ ss << "Unique ID of revision has to increase with every revision, "
+ << "last was " << num_.back() << ", trying to add " << num;
throw IOException(ss.str());
- }
+ }
num_.push_back(num);
date_.push_back(date);
status_.push_back(status);
- // set first release date if not already occuoied
+ // set first release date if not already occupied
if (first_release_ == 0) {
- if (status == "full release") {
+ if (status == "full release" || status == "Initial release") {
first_release_ = status_.size();
}
}
@@ -1023,7 +1020,10 @@ public:
/// \param date
void SetRevisionsDateOriginal(String date)
{
- revisions_.SetDateOriginal(date);
+ // only set once
+ if (revisions_.GetDateOriginal() == "?") {
+ revisions_.SetDateOriginal(date);
+ }
}
/// \brief Add a revision to history
@@ -1051,7 +1051,7 @@ private:
Real resolution_;
MMCifInfoStructDetails struct_details_; ///< mmCIF struct category
MMCifInfoObsolete obsolete_; ///< obsolete/ superseded entry
- MMCifInfoRevisions revisions_; ///< database_pdb_rev category
+ MMCifInfoRevisions revisions_; ///< list of revisions
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 bbee2014c766b2c8b6589be70a035855c959e7ae..abd02fe6e153746cc2df08c56cfdb60c698e8880 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -87,6 +87,11 @@ void MMCifReader::ClearState()
bu_assemblies_.clear();
helix_list_.clear();
strand_list_.clear();
+ his_revision_ordinal_avail_ = false;
+ det_revision_ordinal_avail_ = false;
+ revision_dates_.clear();
+ revision_types_.clear();
+ database_PDB_rev_added_ = false;
}
void MMCifReader::SetRestrictChains(const String& restrict_chains)
@@ -331,6 +336,7 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[SRSD_DETAILS]=header.GetIndex("details");
cat_available = true;
} else if (header.GetCategory()=="database_PDB_rev") {
+ // THIS IS FOR mmCIF versions < 5
category_ = DATABASE_PDB_REV;
// mandatory items
this->TryStoreIdx(DPI_NUM, "num", header);
@@ -339,6 +345,33 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[DPI_DATE_ORIGINAL] = header.GetIndex("date_original");
indices_[DPI_STATUS] = header.GetIndex("status");
cat_available = true;
+ } else if (header.GetCategory()=="pdbx_audit_revision_history") {
+ // THIS IS FOR mmCIF versions >= 5
+ category_ = PDBX_AUDIT_REVISION_HISTORY;
+ // mandatory items
+ this->TryStoreIdx(PARH_REVISION_DATE, "revision_date", header);
+ // optional items
+ indices_[PARH_ORDINAL] = header.GetIndex("ordinal");
+ // TOCHECK: shouldn't ordinal be mandatory??
+ his_revision_ordinal_avail_ = (indices_[PARH_ORDINAL] != -1);
+ cat_available = true;
+ } else if (header.GetCategory()=="pdbx_audit_revision_details") {
+ // THIS IS FOR mmCIF versions >= 5
+ category_ = PDBX_AUDIT_REVISION_DETAILS;
+ // mandatory items
+ this->TryStoreIdx(PARD_TYPE, "type", header);
+ // optional items
+ indices_[PARD_REVISION_ORDINAL] = header.GetIndex("revision_ordinal");
+ // TOCHECK: shouldn't ordinal be mandatory??
+ det_revision_ordinal_avail_ = (indices_[PARD_REVISION_ORDINAL] != -1);
+ cat_available = true;
+ } else if (header.GetCategory()=="pdbx_database_status") {
+ // THIS IS FOR mmCIF versions >= 5
+ category_ = PDBX_DATABASE_STATUS;
+ // optional items
+ indices_[PDS_RECVD_INITIAL_DEPOSITION_DATE]
+ = header.GetIndex("recvd_initial_deposition_date");
+ cat_available = true;
}
category_counts_[category_]++;
return cat_available;
@@ -1352,6 +1385,53 @@ void MMCifReader::ParseDatabasePDBRev(const std::vector<StringRef>& columns)
status = StringRef("", 0);
}
info_.AddRevision(num, date.str(), status.str());
+ database_PDB_rev_added_ = true;
+}
+
+void MMCifReader::ParsePdbxAuditRevisionHistory(
+ const std::vector<StringRef>& columns) {
+ int num;
+ StringRef date;
+ // get ordinal (or count)
+ if (his_revision_ordinal_avail_) {
+ num = this->TryGetInt(columns[indices_[PARH_ORDINAL]],
+ "pdbx_audit_revision_history.ordinal");
+ } else if (revision_dates_.empty()) {
+ num = 0;
+ } else {
+ num = revision_dates_.begin()->first + 1;
+ }
+ // get date
+ date = columns[indices_[PARH_REVISION_DATE]];
+ // add to map
+ revision_dates_[num] = date.str();
+}
+
+void MMCifReader::ParsePdbxAuditRevisionDetails(
+ const std::vector<StringRef>& columns) {
+ int num;
+ StringRef type;
+ // get ordinal (or count)
+ if (det_revision_ordinal_avail_) {
+ num = this->TryGetInt(columns[indices_[PARD_REVISION_ORDINAL]],
+ "pdbx_audit_revision_details.revision_ordinal");
+ } else if (revision_types_.empty()) {
+ num = 0;
+ } else {
+ num = revision_types_.begin()->first + 1;
+ }
+ // get type
+ type = columns[indices_[PARD_TYPE]];
+ // add to map
+ revision_types_[num] = type.str();
+}
+
+void MMCifReader::ParsePdbxDatabaseStatus(
+ const std::vector<StringRef>& columns) {
+ const int idx = indices_[PDS_RECVD_INITIAL_DEPOSITION_DATE];
+ if (idx != -1) {
+ info_.SetRevisionsDateOriginal(columns[idx].str());
+ }
}
void MMCifReader::OnDataRow(const StarLoopDesc& header,
@@ -1430,6 +1510,18 @@ void MMCifReader::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing database_PDB_rev entry");
this->ParseDatabasePDBRev(columns);
break;
+ case PDBX_AUDIT_REVISION_HISTORY:
+ LOG_TRACE("processing pdbx_audit_revision_history entry");
+ this->ParsePdbxAuditRevisionHistory(columns);
+ break;
+ case PDBX_AUDIT_REVISION_DETAILS:
+ LOG_TRACE("processing pdbx_audit_revision_details entry");
+ this->ParsePdbxAuditRevisionDetails(columns);
+ break;
+ case PDBX_DATABASE_STATUS:
+ LOG_TRACE("processing pdbx_database_status entry");
+ this->ParsePdbxDatabaseStatus(columns);
+ break;
default:
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Uncatched category '"+ header.GetCategory() +"' found.",
@@ -1689,6 +1781,23 @@ void MMCifReader::OnEndData()
// create secondary structure from struct_conf info
this->AssignSecStructure(ent_handle_);
+ // add revision history for new style mmCIFs (only if no old data there)
+ if (!database_PDB_rev_added_) {
+ std::map<int, String>::const_iterator rd_it, rt_it;
+ for (rd_it = revision_dates_.begin(); rd_it != revision_dates_.end();
+ ++rd_it) {
+ // look for status
+ const int num = rd_it->first;
+ const String& date = rd_it->second;
+ if ( his_revision_ordinal_avail_ && det_revision_ordinal_avail_
+ && revision_types_.find(num) != revision_types_.end()) {
+ info_.AddRevision(num, date, revision_types_[num]);
+ } else {
+ info_.AddRevision(num, date, "?");
+ }
+ }
+ }
+
LOG_INFO("imported "
<< chain_count_ << " chains, "
<< residue_count_ << " residues, "
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index a8e35f52cf543ca6f744224d88723caef4d16b42..55a195652092481182c644dd3f936e7b3593b2bc 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -298,6 +298,21 @@ protected:
/// \param columns data row
void ParseDatabasePDBRev(const std::vector<StringRef>& columns);
+ /// \brief Fetch mmCIF pdbx_audit_revision_history information
+ ///
+ /// \param columns data row
+ void ParsePdbxAuditRevisionHistory(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF pdbx_audit_revision_details information
+ ///
+ /// \param columns data row
+ void ParsePdbxAuditRevisionDetails(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF pdbx_database_status information
+ ///
+ /// \param columns data row
+ void ParsePdbxDatabaseStatus(const std::vector<StringRef>& columns);
+
/// \brief Fetch mmCIF struct information
///
/// \param columns data row
@@ -531,6 +546,23 @@ private:
DPI_STATUS, ///< status of a revision
} DatabasePDBRevItems;
+ /// \enum categories of the pdbx_audit_revision_history category
+ typedef enum {
+ PARH_ORDINAL, ///< unique identifier
+ PARH_REVISION_DATE, ///< revision date
+ } PdbxAuditRevisionHistoryItems;
+
+ /// \enum categories of the pdbx_audit_revision_details category
+ typedef enum {
+ PARD_REVISION_ORDINAL, ///< link to pdbx_audit_revision_history.ordinal
+ PARD_TYPE, ///< type classification of the revision
+ } PdbxAuditRevisionDetailsItems;
+
+ /// \enum categories of the pdbx_database_status category
+ typedef enum {
+ PDS_RECVD_INITIAL_DEPOSITION_DATE, ///< date of initial deposition
+ } PdbxDatabaseStatusItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
@@ -551,6 +583,9 @@ private:
STRUCT_REF_SEQ,
STRUCT_REF_SEQ_DIF,
DATABASE_PDB_REV,
+ PDBX_AUDIT_REVISION_HISTORY,
+ PDBX_AUDIT_REVISION_DETAILS,
+ PDBX_DATABASE_STATUS,
DONT_KNOW
} MMCifCategory;
@@ -621,6 +656,12 @@ private:
MMCifHSVector helix_list_; ///< for storing struct_conf sec.struct. data
MMCifHSVector strand_list_; ///< for storing struct_conf sec.struct. data
MMCifInfoStructRefs struct_refs_;
+ // for storing revisions
+ bool his_revision_ordinal_avail_;
+ bool det_revision_ordinal_avail_;
+ std::map<int, String> revision_dates_;
+ std::map<int, String> revision_types_;
+ bool database_PDB_rev_added_;
};
}}
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index c5788c9238b030aa538e2629ce10504da94bb06a..83cba518f76fd002405e1a0f789fb43afc4b5f22 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -1352,4 +1352,68 @@ BOOST_AUTO_TEST_CASE(mmcif_test_chain_mappings)
BOOST_TEST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_test_revisions_old)
+{
+ BOOST_TEST_MESSAGE(" Running mmcif_test_revisions_old tests...");
+
+ // load data
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/3IMJ_rev_old.cif");
+ IOProfile profile;
+ MMCifReader mmcif_p(s, eh, profile);
+ BOOST_REQUIRE_NO_THROW(mmcif_p.Parse());
+ const MMCifInfo& info = mmcif_p.GetInfo();
+ const MMCifInfoRevisions& revs = info.GetRevisions();
+
+ // check items
+ BOOST_CHECK_EQUAL(revs.GetSize(), size_t(3));
+ BOOST_CHECK_EQUAL(revs.GetNum(0), 1);
+ BOOST_CHECK_EQUAL(revs.GetDate(0), String("2009-11-17"));
+ BOOST_CHECK_EQUAL(revs.GetStatus(0), String("full release"));
+ BOOST_CHECK_EQUAL(revs.GetNum(1), 2);
+ BOOST_CHECK_EQUAL(revs.GetDate(1), String("2011-07-13"));
+ BOOST_CHECK_EQUAL(revs.GetStatus(1), String("?"));
+ BOOST_CHECK_EQUAL(revs.GetNum(2), 3);
+ BOOST_CHECK_EQUAL(revs.GetDate(2), String("2012-12-12"));
+ BOOST_CHECK_EQUAL(revs.GetStatus(2), String("?"));
+ // check rest
+ BOOST_CHECK_EQUAL(revs.GetDateOriginal(), String("2009-08-10"));
+ BOOST_CHECK_EQUAL(revs.GetLastDate(), String("2012-12-12"));
+ BOOST_CHECK_EQUAL(revs.GetFirstRelease(), size_t(1));
+
+ BOOST_TEST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_test_revisions_new)
+{
+ BOOST_TEST_MESSAGE(" Running mmcif_test_revisions_new tests...");
+
+ // load data
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/3IMJ_rev_new.cif");
+ IOProfile profile;
+ MMCifReader mmcif_p(s, eh, profile);
+ BOOST_REQUIRE_NO_THROW(mmcif_p.Parse());
+ const MMCifInfo& info = mmcif_p.GetInfo();
+ const MMCifInfoRevisions& revs = info.GetRevisions();
+
+ // check items
+ BOOST_CHECK_EQUAL(revs.GetSize(), size_t(3));
+ BOOST_CHECK_EQUAL(revs.GetNum(0), 1);
+ BOOST_CHECK_EQUAL(revs.GetDate(0), String("2009-11-17"));
+ BOOST_CHECK_EQUAL(revs.GetStatus(0), String("Initial release"));
+ BOOST_CHECK_EQUAL(revs.GetNum(1), 2);
+ BOOST_CHECK_EQUAL(revs.GetDate(1), String("2011-07-13"));
+ BOOST_CHECK_EQUAL(revs.GetStatus(1), String("?"));
+ BOOST_CHECK_EQUAL(revs.GetNum(2), 3);
+ BOOST_CHECK_EQUAL(revs.GetDate(2), String("2012-12-12"));
+ BOOST_CHECK_EQUAL(revs.GetStatus(2), String("?"));
+ // check rest
+ BOOST_CHECK_EQUAL(revs.GetDateOriginal(), String("2009-08-10"));
+ BOOST_CHECK_EQUAL(revs.GetLastDate(), String("2012-12-12"));
+ BOOST_CHECK_EQUAL(revs.GetFirstRelease(), size_t(1));
+
+ BOOST_TEST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/testfiles/mmcif/3IMJ_rev_new.cif b/modules/io/tests/testfiles/mmcif/3IMJ_rev_new.cif
new file mode 100644
index 0000000000000000000000000000000000000000..bbc66a30194ce5ff62fd84dd7a758728bc35ff29
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/3IMJ_rev_new.cif
@@ -0,0 +1,35 @@
+data_3IMJ
+# taken from 3IMJ.cif (new style)
+_entry.id 3IMJ
+#
+_audit_conform.dict_name mmcif_pdbx.dic
+_audit_conform.dict_version 5.281
+_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
+#
+_pdbx_database_status.entry_id 3IMJ
+_pdbx_database_status.status_code REL
+_pdbx_database_status.deposit_site RCSB
+_pdbx_database_status.process_site RCSB
+_pdbx_database_status.recvd_initial_deposition_date 2009-08-10
+_pdbx_database_status.status_code_sf REL
+_pdbx_database_status.status_code_mr ?
+_pdbx_database_status.SG_entry ?
+_pdbx_database_status.status_code_cs ?
+_pdbx_database_status.pdb_format_compatible Y
+#
+loop_
+_pdbx_audit_revision_history.ordinal
+_pdbx_audit_revision_history.data_content_type
+_pdbx_audit_revision_history.major_revision
+_pdbx_audit_revision_history.minor_revision
+_pdbx_audit_revision_history.revision_date
+1 'Structure model' 1 0 2009-11-17
+2 'Structure model' 1 1 2011-07-13
+3 'Structure model' 1 2 2012-12-12
+#
+_pdbx_audit_revision_details.ordinal 1
+_pdbx_audit_revision_details.revision_ordinal 1
+_pdbx_audit_revision_details.data_content_type 'Structure model'
+_pdbx_audit_revision_details.provider repository
+_pdbx_audit_revision_details.type 'Initial release'
+_pdbx_audit_revision_details.description ?
diff --git a/modules/io/tests/testfiles/mmcif/3IMJ_rev_old.cif b/modules/io/tests/testfiles/mmcif/3IMJ_rev_old.cif
new file mode 100644
index 0000000000000000000000000000000000000000..a85aef8364f1d443c74acbc586f877b7abe56c4f
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/3IMJ_rev_old.cif
@@ -0,0 +1,32 @@
+data_3IMJ
+# taken from 3IMJ.cif (old style)
+_entry.id 3IMJ
+#
+_audit_conform.dict_name mmcif_pdbx.dic
+_audit_conform.dict_version 4.026
+_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
+#
+loop_
+_database_PDB_rev.num
+_database_PDB_rev.date
+_database_PDB_rev.date_original
+_database_PDB_rev.mod_type
+_database_PDB_rev.replaces
+_database_PDB_rev.status
+1 2009-11-17 2009-08-10 0 3IMJ 'full release'
+2 2011-07-13 ? 1 3IMJ ?
+3 2012-12-12 ? 1 3IMJ ?
+#
+_pdbx_database_status.entry_id 3IMJ
+_pdbx_database_status.status_code REL
+_pdbx_database_status.deposit_site RCSB
+_pdbx_database_status.process_site RCSB
+_pdbx_database_status.status_code_sf REL
+_pdbx_database_status.status_code_mr ?
+_pdbx_database_status.SG_entry ?
+_pdbx_database_status.status_code_cs ?
+_pdbx_database_status.dep_release_code_coordinates 'HOLD FOR PUBLICATION'
+_pdbx_database_status.dep_release_code_struct_fact 'HOLD FOR PUBLICATION'
+_pdbx_database_status.dep_release_code_sequence 'RELEASE NOW'
+
+# NOTE: values modified to match new style numbers