Merge branch 'develop' into lDDT-SCHWED-3127

CHANGELOG.txt

+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
 --------------------------------------------------------------------------------
 

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)

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 '#':

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");

modules/io/tests/testfiles/broken_data.cif

+d lines starting with a 'd' kicked the parser into an infinite loop.

modules/io/tests/testfiles/broken_global.cif

+g lines starting with a 'g' kicked the parser into an infinite loop.

modules/mol/base/doc/entity.rst

@@ -732,6 +732,7 @@ The Handle Classes
   
     The atom's occupancy in the range 0 to 1. Read/write. Also available as 
     :meth:`GetOccupancy`, :meth:`SetOccupancy`.
+
     :type: float
     
   .. attribute:: b_factor
@@ -1199,7 +1200,8 @@ The View Classes
   .. method:: GetBondCount()
 
     Get number of bonds
-    :rtype: int
+
+    :rtype: :class:`int`
 
   .. method:: GetBondList()