diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9d700a34a01a9c17d2128d8c8062c78c9cebf1e1..8141de3b24adbb7d9ab0c00cdb92c9cb30fd8b46 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,7 +6,7 @@ cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
project(OpenStructure CXX C)
set (OST_VERSION_MAJOR 1)
set (OST_VERSION_MINOR 4)
-set (OST_VERSION_PATCH 0)
+set (OST_VERSION_PATCH 1)
set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
include(OST)
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index d3213357183cf73841d9d1386e612b6e0828ca40..824d70340208f61ac9959cddcff4902833f1bed4 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -171,7 +171,8 @@ void export_mmcif_io()
.add_property("details", make_function(&MMCifInfoStructRefSeqDif::GetDetails,
return_value_policy<copy_const_reference>()))
.add_property("seq_rnum", &MMCifInfoStructRefSeqDif::GetSeqRNum)
- .add_property("db_rnum", &MMCifInfoStructRefSeqDif::GetDBRNum)
+ .add_property("db_rnum", make_function(&MMCifInfoStructRefSeqDif::GetDBRNum,
+ return_value_policy<copy_const_reference>()))
;
typedef std::pair<int, int> IntPair;
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index e7f391894cab4e8ace515de79fa14f6e047fd683..e7d47078cc5ae4c9f3c4dabee23dd55c72dd12e1 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -168,7 +168,7 @@ MMCifInfoStructRef::GetAlignedSeq(const String& aid) const
}
MMCifInfoStructRefSeqDifPtr
-MMCifInfoStructRefSeq::AddDif(int seq_rnum, int db_rnum, const String& details)
+MMCifInfoStructRefSeq::AddDif(int seq_rnum, const String& db_rnum, const String& details)
{
MMCifInfoStructRefSeqDifPtr d(new MMCifInfoStructRefSeqDif(seq_rnum, db_rnum,
details));
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 593fed6f2b70e25c777454bd3e8d95db8554ef56..ca8da62036b5151ff38cbefe65645515be2b0851 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -817,8 +817,8 @@ public:
int GetSeqEnd() const { return seq_end_; }
int GetDBBegin() const { return db_begin_; }
int GetDBEnd() const { return db_end_; }
- MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, int db_num,
- const String& details);
+ MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, const String& db_rnum,
+ const String& details);
const std::vector<MMCifInfoStructRefSeqDifPtr>& GetDifs() const { return difs_; }
private:
String id_;
@@ -832,14 +832,14 @@ private:
class DLLEXPORT_OST_IO MMCifInfoStructRefSeqDif {
public:
- MMCifInfoStructRefSeqDif(int seq_rnum, int db_rnum, const String& details):
+ MMCifInfoStructRefSeqDif(int seq_rnum, const String& db_rnum, const String& details):
seq_rnum_(seq_rnum), db_rnum_(db_rnum), details_(details) {}
int GetSeqRNum() const { return seq_rnum_;}
- int GetDBRNum() const { return db_rnum_; }
+ const String& GetDBRNum() const { return db_rnum_; }
const String& GetDetails() const { return details_; }
private:
int seq_rnum_;
- int db_rnum_;
+ String db_rnum_;
String details_;
};
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index a4c9ca313f3dcdeb5f1434884cb57c00d72ab9df..93807f921e50c1457dc3cf7d0cc890375900183f 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -805,7 +805,7 @@ void MMCifReader::ParseCitation(const std::vector<StringRef>& columns)
}
}
if (indices_[YEAR] != -1) {
- if (columns[indices_[YEAR]][0]!='?') {
+ if (!is_undef(columns[indices_[YEAR]])) {
cit.SetYear(this->TryGetInt(columns[indices_[YEAR]], "citation.year"));
}
}
@@ -1542,33 +1542,30 @@ void MMCifReader::ParseStructRefSeq(const std::vector<StringRef>& columns)
void MMCifReader::ParseStructRefSeqDif(const std::vector<StringRef>& columns)
{
- String aln_id=columns[indices_[SRSD_ALIGN_ID]].str();
- std::pair<bool,int> db_rnum(true, -1);
- if (!is_undef(columns[indices_[SRSD_DB_RNUM]])) {
- db_rnum=this->TryGetInt(columns[indices_[SRSD_DB_RNUM]],
- "_struct_ref_seq_dif.pdbx_seq_db_seq_num",
- profile_.fault_tolerant);
-
- }
- std::pair<bool,int> seq_rnum(true, -1);
- if (!is_undef(columns[indices_[SRSD_SEQ_RNUM]])) {
- seq_rnum=this->TryGetInt(columns[indices_[SRSD_SEQ_RNUM]],
- "_struct_ref_seq_dif.seq_num",
- profile_.fault_tolerant);
-
- }
- if (!seq_rnum.first || !db_rnum.first) {
- return;
- }
+ String aln_id=columns[indices_[SRSD_ALIGN_ID]].str();
+ String db_rnum;
+ if (!is_undef(columns[indices_[SRSD_DB_RNUM]])) {
+ db_rnum=columns[indices_[SRSD_DB_RNUM]].str();
+ }
+ std::pair<bool,int> seq_rnum(true, -1);
+ if (!is_undef(columns[indices_[SRSD_SEQ_RNUM]])) {
+ seq_rnum=this->TryGetInt(columns[indices_[SRSD_SEQ_RNUM]],
+ "_struct_ref_seq_dif.seq_num",
+ profile_.fault_tolerant);
+
+ }
+ if (!seq_rnum.first) {
+ return;
+ }
String details;
if (indices_[SRSD_DETAILS]!=-1) {
details=columns[indices_[SRSD_DETAILS]].str();
- }
- bool found=false;
+ }
+ bool found=false;
for (MMCifInfoStructRefs::iterator i=struct_refs_.begin(),
e=struct_refs_.end(); i!=e; ++i) {
if (MMCifInfoStructRefSeqPtr s=(*i)->GetAlignedSeq(aln_id)) {
- s->AddDif(seq_rnum.second, db_rnum.second, details);
+ s->AddDif(seq_rnum.second, db_rnum, details);
found=true;
break;
}
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 6f6866622c49c5a6e2f0259339e3c6b5508f4024..3a1906df9ea7c8f7ffc0dae6f79fcc9a54b7972e 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -584,16 +584,20 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
tmmcif_h.SetCategory(StringRef("citation", 8));
tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("year", 4));
tmmcif_h.Add(StringRef("book_title", 10));
tmmcif_h.Add(StringRef("journal_abbrev", 14));
tmmcif_p.OnBeginLoop(tmmcif_h);
columns.push_back(StringRef("Foo", 3));
+ columns.push_back(StringRef("1979", 4));
columns.push_back(StringRef("The Guide", 9));
columns.push_back(StringRef(".", 1));
BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
+ BOOST_CHECK(tmmcif_p.GetInfo().GetCitations().back().GetYear() == 1979);
+
columns.pop_back();
columns.pop_back();
columns.push_back(StringRef(".", 1));
diff --git a/scripts/ost_startup.py.in b/scripts/ost_startup.py.in
index 73cf24e88ac07829f9b93f09b433ba27c2c5bf57..612b6485cf2515deffe6023f80e3ea4ea14e8ce5 100644
--- a/scripts/ost_startup.py.in
+++ b/scripts/ost_startup.py.in
@@ -30,20 +30,21 @@ _site_packs='python%d.%d/site-packages' % sys.version_info[0:2]
_base_dir=os.getenv('DNG_ROOT')
sys.path.insert(0, os.path.join(_base_dir, '@LIBDIR@', _site_packs))
-from ost import *
-import ost
+from ost import SetPrefixPath, GetSharedDataPath, conop
-ost.SetPrefixPath(_base_dir)
+SetPrefixPath(_base_dir)
def _InitRuleBasedProcessor():
- compound_lib_path=os.path.join(ost.GetSharedDataPath(), 'compounds.chemlib')
+ compound_lib_path=os.path.join(GetSharedDataPath(), 'compounds.chemlib')
if os.path.exists(compound_lib_path):
compound_lib=conop.CompoundLib.Load(compound_lib_path)
conop.SetDefaultLib(compound_lib)
- io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(compound_lib)
# switch to rule-based processor, if compound library is available
_InitRuleBasedProcessor()
+from ost import *
+import ost
+
import os.path
HistoryFile=os.path.expanduser('~/.ost_history')