diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 9189aecece5345a60ec850332af0fca826e14603..45ebdf60c4dcd6fdac658c24ad70a10190623430 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,13 @@
+Changes in Release 1.7.1
+--------------------------------------------------------------------------------
+
+ * Fixed an issue that could cause the star format parser (mmCIF, chemical
+ components dictionary) to enter an infinite loop
+ * Chemical components dictionary was extended by new chemical classes
+ introduced by PDB
+ * Fixed unit tests
+ * Improved documentation
+
Changes in Release 1.7
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2f582069ba52a1b79e281c8866d6f591c5f1942e..2cf4c283a4cbfd59833a4d76837da48948dbe9f1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -7,7 +7,7 @@ project(OpenStructure CXX C)
set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
set (OST_VERSION_MAJOR 1)
set (OST_VERSION_MINOR 7)
-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/conop/doc/cleanup.rst b/modules/conop/doc/cleanup.rst
index 35b20e5705b248a995ec61c5e06604c53df0767f..a7a49bdf6d1463fdead7fd9ad02180be4ea0bcbe 100644
--- a/modules/conop/doc/cleanup.rst
+++ b/modules/conop/doc/cleanup.rst
@@ -1,7 +1,7 @@
:mod:`conop.cleanup <ost.conop.cleanup>` -- Sanitize structures
================================================================================
-.. module:: ost.conop.ceanup
+.. module:: ost.conop.cleanup
:synopsis: Contains functions to sanitize (cleanup) structures by using
information from the compound library.
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index 47f7f6f2d369a9e446a4929ec6a914fa6aa179d4..cf97f5e23d933c68a7fa6e5419027ae5b24cf534 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -195,17 +195,18 @@ void ChemdictParser::InitTypeMap()
tm_["DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
tm_["RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
tm_["L-DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
- tm_["L-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
+ tm_["L-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
tm_["R-DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
- tm_["R-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
+ tm_["R-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
tm_["DNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
+ tm_["DNA OH 5 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
tm_["PEPTIDE-LIKE"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);
tm_["PEPTIDE LINKING"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);
- tm_["PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);
+ tm_["PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);
tm_["NON-POLYMER"]=mol::ChemClass(mol::ChemClass::NON_POLYMER);
tm_["RNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
tm_["RNA OH 5 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
- tm_["?"]=mol::ChemClass(mol::ChemClass::UNKNOWN);
+ tm_["?"]=mol::ChemClass(mol::ChemClass::UNKNOWN);
tm_["WATER"]=mol::ChemClass(mol::ChemClass::WATER);
}
diff --git a/modules/io/src/mol/star_parser.cc b/modules/io/src/mol/star_parser.cc
index 80043259b4df5fdf34ee81de6bf471696d03bc5a..214eb626c9f743a1cbbb218bede0ad7f795b2f73 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/modules/io/src/mol/star_parser.cc
@@ -550,11 +550,15 @@ void StarParser::Parse()
case 'd':
if (tline.length()>=5 && StringRef("data_", 5)==tline.substr(0, 5)) {
this->ParseData();
+ } else {
+ throw IOException("Missing 'data_' control structure");
}
break;
case 'g':
if (tline.length()>=7 && StringRef("global_", 7)==tline.substr(0, 7)) {
this->ParseGlobal();
+ } else {
+ throw IOException("Missing 'global_' control structure");
}
break;
case '#':
diff --git a/modules/io/tests/test_star_parser.cc b/modules/io/tests/test_star_parser.cc
index 6ff217b748c123770f789a2168d540be3f1ef94d..c4e40fdbda137d74293282a592884fb5aa7e8305 100644
--- a/modules/io/tests/test_star_parser.cc
+++ b/modules/io/tests/test_star_parser.cc
@@ -389,6 +389,20 @@ BOOST_AUTO_TEST_CASE(star_items_as_row)
BOOST_TEST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(star_broken_data)
+{
+ std::ifstream s("testfiles/broken_data.cif");
+ LoopTestParser star_p(s);
+ BOOST_CHECK_THROW(star_p.Parse(), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(star_broken_global)
+{
+ std::ifstream s("testfiles/broken_global.cif");
+ LoopTestParser star_p(s);
+ BOOST_CHECK_THROW(star_p.Parse(), IOException);
+}
+
BOOST_AUTO_TEST_CASE(star_missing_data)
{
std::ifstream s("testfiles/missing_data.cif");
diff --git a/modules/io/tests/testfiles/broken_data.cif b/modules/io/tests/testfiles/broken_data.cif
new file mode 100644
index 0000000000000000000000000000000000000000..2ae242255c2bd8c6e952ffee6d1815ee01f6335a
--- /dev/null
+++ b/modules/io/tests/testfiles/broken_data.cif
@@ -0,0 +1 @@
+d lines starting with a 'd' kicked the parser into an infinite loop.
diff --git a/modules/io/tests/testfiles/broken_global.cif b/modules/io/tests/testfiles/broken_global.cif
new file mode 100644
index 0000000000000000000000000000000000000000..0f340e0befe0077229b53b121979181ec3c890fc
--- /dev/null
+++ b/modules/io/tests/testfiles/broken_global.cif
@@ -0,0 +1 @@
+g lines starting with a 'g' kicked the parser into an infinite loop.
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 42c073f41eccfb77f44d5d89f49ca52169496a19..16635d7025e330345dfc20109cf19fd63ffc4257 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -56,6 +56,8 @@ class QSscorer:
qs_scorer = qsscoring.QSscorer(ent_1, ent_2)
ost.LogScript('QSscore:', str(qs_scorer.global_score))
ost.LogScript('Chain mapping used:', str(qs_scorer.chain_mapping))
+ # commonly you want the QS global score as output
+ qs_score = qs_scorer.global_score
except qsscoring.QSscoreError as ex:
# default handling: report failure and set score to 0
ost.LogError('QSscore failed:', str(ex))
diff --git a/modules/mol/base/tests/CMakeLists.txt b/modules/mol/base/tests/CMakeLists.txt
index 1aa275c1adca3bbc7afed1f34b4b3518fcfa6593..0f756cd3c159d204d93c4653e513be0599ca5ac8 100644
--- a/modules/mol/base/tests/CMakeLists.txt
+++ b/modules/mol/base/tests/CMakeLists.txt
@@ -17,7 +17,7 @@ set(OST_MOL_BASE_UNIT_TESTS
)
if (USE_NUMPY)
- set(OST_MOST_BASE_UNIT_TESTS "${OST_MOST_BASE_UNIT_TESTS}" test_numpy.py)
+ list(APPEND OST_MOL_BASE_UNIT_TESTS test_numpy.py)
endif (USE_NUMPY)
ost_unittest(MODULE mol SOURCES "${OST_MOL_BASE_UNIT_TESTS}")
diff --git a/modules/mol/base/tests/test_numpy.py b/modules/mol/base/tests/test_numpy.py
index 217ed89dd7adb6380b6fea22719e49f310b2c2cb..27061a234cc96d72ceaeec28ffad6ab18ca44d0a 100644
--- a/modules/mol/base/tests/test_numpy.py
+++ b/modules/mol/base/tests/test_numpy.py
@@ -5,6 +5,7 @@ if __name__== '__main__':
sys.path.insert(0,"../../../../stage/lib/openstructure/")
import ost
+from ost import geom, mol
if ost.WITH_NUMPY:
has_numpy=True
@@ -16,10 +17,10 @@ else:
has_numpy=False
def v2v(v):
- return ost.geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
+ return geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
def dd(v1,v2):
- return ost.geom.Distance(v1,v2)<1e-8
+ return geom.Distance(v1,v2)<1e-8
class TestNumpy(unittest.TestCase):
def setUp(self):
@@ -28,46 +29,46 @@ class TestNumpy(unittest.TestCase):
def test_(self):
if not has_numpy:
return
- entity=ost.mol.CreateEntity()
+ entity=mol.CreateEntity()
ed=entity.EditXCS()
ch=ed.InsertChain("X")
re=ed.AppendResidue(ch,"ALA")
- a0=ed.InsertAtom(re,"A",ost.geom.Vec3(0,0,0))
+ a0=ed.InsertAtom(re,"A",geom.Vec3(0,0,0))
self.assertEqual(a0.GetIndex(),0)
- a1=ed.InsertAtom(re,"B",ost.geom.Vec3(1,0,0))
+ a1=ed.InsertAtom(re,"B",geom.Vec3(1,0,0))
self.assertEqual(a1.GetIndex(),1)
- a2=ed.InsertAtom(re,"C",ost.geom.Vec3(2,0,0))
+ a2=ed.InsertAtom(re,"C",geom.Vec3(2,0,0))
self.assertEqual(a2.GetIndex(),2)
- a3=ed.InsertAtom(re,"D",ost.geom.Vec3(3,0,0))
+ a3=ed.InsertAtom(re,"D",geom.Vec3(3,0,0))
self.assertEqual(a3.GetIndex(),3)
- self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,0,0)))
- self.assertTrue(dd(a1.pos,ost.geom.Vec3(1,0,0)))
- self.assertTrue(dd(a2.pos,ost.geom.Vec3(2,0,0)))
- self.assertTrue(dd(a3.pos,ost.geom.Vec3(3,0,0)))
+ self.assertTrue(dd(a0.pos,geom.Vec3(0,0,0)))
+ self.assertTrue(dd(a1.pos,geom.Vec3(1,0,0)))
+ self.assertTrue(dd(a2.pos,geom.Vec3(2,0,0)))
+ self.assertTrue(dd(a3.pos,geom.Vec3(3,0,0)))
ed.SetAtomTransformedPos(entity.GetAtomList(),
numpy.array([[0,1,0],[0,2,0],[0,3,0],[0,4,0]], dtype=numpy.float32))
- self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,1,0)))
- self.assertTrue(dd(a1.pos,ost.geom.Vec3(0,2,0)))
- self.assertTrue(dd(a2.pos,ost.geom.Vec3(0,3,0)))
- self.assertTrue(dd(a3.pos,ost.geom.Vec3(0,4,0)))
+ self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
+ self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
+ self.assertTrue(dd(a2.pos,geom.Vec3(0,3,0)))
+ self.assertTrue(dd(a3.pos,geom.Vec3(0,4,0)))
na=entity.positions
- self.assertTrue(dd(v2v(na[0]),ost.geom.Vec3(0,1,0)))
- self.assertTrue(dd(v2v(na[1]),ost.geom.Vec3(0,2,0)))
- self.assertTrue(dd(v2v(na[2]),ost.geom.Vec3(0,3,0)))
- self.assertTrue(dd(v2v(na[3]),ost.geom.Vec3(0,4,0)))
+ self.assertTrue(dd(v2v(na[0]),geom.Vec3(0,1,0)))
+ self.assertTrue(dd(v2v(na[1]),geom.Vec3(0,2,0)))
+ self.assertTrue(dd(v2v(na[2]),geom.Vec3(0,3,0)))
+ self.assertTrue(dd(v2v(na[3]),geom.Vec3(0,4,0)))
ed.SetAtomTransformedPos([3,99,2],
numpy.array([[0,0,-3],[-1,-1,-1],[0,0,-2]], dtype=numpy.float32))
- self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,1,0)))
- self.assertTrue(dd(a1.pos,ost.geom.Vec3(0,2,0)))
- self.assertTrue(dd(a2.pos,ost.geom.Vec3(0,0,-2)))
- self.assertTrue(dd(a3.pos,ost.geom.Vec3(0,0,-3)))
+ self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
+ self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
+ self.assertTrue(dd(a2.pos,geom.Vec3(0,0,-2)))
+ self.assertTrue(dd(a3.pos,geom.Vec3(0,0,-3)))
if __name__== '__main__':
unittest.main()