From a1d54b48b9702276115237f4f535243184acaafe Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 14 Oct 2019 16:34:35 +0200
Subject: [PATCH] SCHWED-4368: Read revision version numbers from mmCIF files.
---
modules/io/src/mol/mmcif_reader.cc | 23 +++++++++++--------
modules/io/src/mol/mmcif_reader.hh | 19 ++++++++++++++-
modules/io/tests/test_mmcif_reader.cc | 18 ++++++++++++++-
.../io/tests/testfiles/mmcif/3IMJ_rev_new.cif | 2 +-
4 files changed, 50 insertions(+), 12 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 3641b2e0d..9e8413853 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -87,7 +87,7 @@ void MMCifReader::ClearState()
bu_assemblies_.clear();
helix_list_.clear();
strand_list_.clear();
- revision_dates_.clear();
+ revisions_.clear();
revision_types_.clear();
database_PDB_rev_added_ = false;
}
@@ -339,6 +339,8 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
category_ = PDBX_AUDIT_REVISION_HISTORY;
// mandatory items
this->TryStoreIdx(PARH_ORDINAL, "ordinal", header);
+ this->TryStoreIdx(PARH_MAJOR, "major_revision", header);
+ this->TryStoreIdx(PARH_MINOR, "minor_revision", header);
this->TryStoreIdx(PARH_REVISION_DATE, "revision_date", header);
cat_available = true;
} else if (header.GetCategory()=="pdbx_audit_revision_details") {
@@ -1423,8 +1425,12 @@ void MMCifReader::ParsePdbxAuditRevisionHistory(
int num = this->TryGetInt(columns[indices_[PARH_ORDINAL]],
"pdbx_audit_revision_history.ordinal");
StringRef date = columns[indices_[PARH_REVISION_DATE]];
+ int major = this->TryGetInt(columns[indices_[PARH_MAJOR]],
+ "pdbx_audit_revision_history.major_revision");
+ int minor = this->TryGetInt(columns[indices_[PARH_MINOR]],
+ "pdbx_audit_revision_history.minor_revision");
// add to map
- revision_dates_[num] = date.str();
+ revisions_.push_back(MMCifRevisionDesc(num, date.str(), major, minor));
}
void MMCifReader::ParsePdbxAuditRevisionDetails(
@@ -1779,17 +1785,16 @@ void MMCifReader::OnEndData()
// 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;
- for (rd_it = revision_dates_.begin(); rd_it != revision_dates_.end();
- ++rd_it) {
+ std::vector<MMCifRevisionDesc>::const_iterator r_it;
+ for (r_it = revisions_.begin(); r_it != revisions_.end(); ++r_it) {
// look for status
- const int num = rd_it->first;
- const String& date = rd_it->second;
+ const int num = r_it->num;
std::map<int, String>::const_iterator rt_it = revision_types_.find(num);
if (rt_it != revision_types_.end()) {
- info_.AddRevision(num, date, rt_it->second);
+ info_.AddRevision(num, r_it->date, rt_it->second, r_it->major,
+ r_it->minor);
} else {
- info_.AddRevision(num, date, "?");
+ info_.AddRevision(num, r_it->date, "?", r_it->major, r_it->minor);
}
}
}
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 4a58d567b..e7d0e6bcb 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -546,6 +546,8 @@ private:
typedef enum {
PARH_ORDINAL, ///< unique identifier
PARH_REVISION_DATE, ///< revision date
+ PARH_MAJOR, ///< major version
+ PARH_MINOR, ///< minor version
} PdbxAuditRevisionHistoryItems;
/// \enum categories of the pdbx_audit_revision_details category
@@ -621,6 +623,21 @@ private:
} MMCifPSAEntry;
typedef std::map<String, MMCifPSAEntry> MMCifPSAMap;
+ /// \struct keeping track of revision information
+ struct MMCifRevisionDesc {
+ // silly GCC note: major() & minor() exist as macros...facepalm
+ MMCifRevisionDesc(int _num, const String& _date, int _major, int _minor)
+ : date(_date) {
+ num = _num;
+ major = _major;
+ minor = _minor;
+ }
+ int num; ///< unique identifier
+ String date; ///< revision date
+ int major; ///< major version
+ int minor; ///< minor version
+ };
+
// members
MMCifCategory category_;
int category_counts_[DONT_KNOW+1]; ///< overall no. of atom_site loops
@@ -653,7 +670,7 @@ private:
MMCifHSVector strand_list_; ///< for storing struct_conf sec.struct. data
MMCifInfoStructRefs struct_refs_;
// for storing revisions
- std::map<int, String> revision_dates_;
+ std::vector<MMCifRevisionDesc> revisions_;
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 2711bddcf..b3c9d7c23 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -1357,20 +1357,28 @@ BOOST_AUTO_TEST_CASE(mmcif_test_revisions_old)
const MMCifInfo& info = mmcif_p.GetInfo();
const MMCifInfoRevisions& revs = info.GetRevisions();
- // check items
+ // check items (note: version numbers only for new mmCIF versions)
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.GetMajor(0), -1);
+ BOOST_CHECK_EQUAL(revs.GetMinor(0), -1);
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.GetMajor(1), -1);
+ BOOST_CHECK_EQUAL(revs.GetMinor(1), -1);
BOOST_CHECK_EQUAL(revs.GetNum(2), 3);
BOOST_CHECK_EQUAL(revs.GetDate(2), String("2012-12-12"));
BOOST_CHECK_EQUAL(revs.GetStatus(2), String("?"));
+ BOOST_CHECK_EQUAL(revs.GetMajor(2), -1);
+ BOOST_CHECK_EQUAL(revs.GetMinor(2), -1);
// check rest
BOOST_CHECK_EQUAL(revs.GetDateOriginal(), String("2009-08-10"));
BOOST_CHECK_EQUAL(revs.GetLastDate(), String("2012-12-12"));
+ BOOST_CHECK_EQUAL(revs.GetLastMajor(), -1);
+ BOOST_CHECK_EQUAL(revs.GetLastMinor(), -1);
BOOST_CHECK_EQUAL(revs.GetFirstRelease(), size_t(1));
BOOST_TEST_MESSAGE(" done.");
@@ -1394,15 +1402,23 @@ BOOST_AUTO_TEST_CASE(mmcif_test_revisions_new)
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.GetMajor(0), 1);
+ BOOST_CHECK_EQUAL(revs.GetMinor(0), 0);
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.GetMajor(1), 1);
+ BOOST_CHECK_EQUAL(revs.GetMinor(1), 1);
BOOST_CHECK_EQUAL(revs.GetNum(2), 3);
BOOST_CHECK_EQUAL(revs.GetDate(2), String("2012-12-12"));
BOOST_CHECK_EQUAL(revs.GetStatus(2), String("?"));
+ BOOST_CHECK_EQUAL(revs.GetMajor(2), 2);
+ BOOST_CHECK_EQUAL(revs.GetMinor(2), 0);
// check rest
BOOST_CHECK_EQUAL(revs.GetDateOriginal(), String("2009-08-10"));
BOOST_CHECK_EQUAL(revs.GetLastDate(), String("2012-12-12"));
+ BOOST_CHECK_EQUAL(revs.GetLastMajor(), 2);
+ BOOST_CHECK_EQUAL(revs.GetLastMinor(), 0);
BOOST_CHECK_EQUAL(revs.GetFirstRelease(), size_t(1));
BOOST_TEST_MESSAGE(" done.");
diff --git a/modules/io/tests/testfiles/mmcif/3IMJ_rev_new.cif b/modules/io/tests/testfiles/mmcif/3IMJ_rev_new.cif
index bbc66a301..47ca475fc 100644
--- a/modules/io/tests/testfiles/mmcif/3IMJ_rev_new.cif
+++ b/modules/io/tests/testfiles/mmcif/3IMJ_rev_new.cif
@@ -25,7 +25,7 @@ _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
+3 'Structure model' 2 0 2012-12-12
#
_pdbx_audit_revision_details.ordinal 1
_pdbx_audit_revision_details.revision_ordinal 1
--
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