Merge hotfix-1.3.1 into develop

CHANGELOG.txt

@@ -26,6 +26,9 @@ Changes In Release 1.3.0
   * Update directory layout of OST to be more conformant with the site-package
     system of Python: Instead of storing the modules in lib{64}/ost/ost, they
     are now in lib{64}/python{{VERSION}}/site-packages/ost
+  * Added molck, the molecular checker. A small command-line tool to clean PDB 
+    files, e.g. remove atoms with zero occupancy, "virtual atoms", hydrogens 
+    etc.
 
 Changes In Release 1.2.3
 --------------------------------------------------------------------------------

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 3)
-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/base/src/boost_filesystem_helper.hh

@@ -37,6 +37,16 @@ String BFPathToString(const boost::filesystem::path& path)
 #endif
 }
 
+inline String BFPathStem(const boost::filesystem::path& path) {
+#if BOOST_FILESYSTEM_VERSION<103400
+  String name = BFPathToString(path);
+  size_t n = name.rfind('.');
+  return name.substr(0, n);
+#else
+  return path.stem();
+#endif
+}
+
 }
 
 

modules/mol/base/pymod/export_entity_view.cc

@@ -215,4 +215,6 @@ void export_EntityView()
   class_<EntityViewList>("EntityViewList", init<>())
     .def(vector_indexing_suite<EntityViewList>())
   ;
+  to_python_converter<std::pair<EntityView, EntityView>,
+                      PairToTupleConverter<EntityView, EntityView> >();
 }

modules/mol/base/src/editor_base.cc

@@ -208,9 +208,13 @@ void EditorBase::RenumberAllResidues(int start, bool keep_spacing)
   ent_.Impl()->RenumberAllResidues(start, keep_spacing);
 }
 
-void EditorBase::RenumberChain(const String& name, int start, bool keep_spacing)
+void EditorBase::RenumberChain(const ChainHandle& chain, int start, bool keep_spacing)
 {
-  ent_.Impl()->RenumberChain(name, start, keep_spacing);
+  CheckHandleValidity(chain);
+  if(chain.GetEntity()!=ent_){
+    throw Error("Chain does not belong to the editors entity!");
+  }
+  chain.Impl()->RenumberAllResidues(start, keep_spacing);
 }
 
 void EditorBase::RenameAtom(AtomHandle atom, const String& new_name)

modules/mol/base/src/editor_base.hh

@@ -293,7 +293,7 @@ public:
   /// \param keep_spacing
   ///           If set to false, residues will continously be renumbered ongoing from start.
   ///           Otherwise the spacings between the residues are kept.
-  void RenumberChain(const String& name, int start, bool keep_spacing);
+  void RenumberChain(const ChainHandle& chain, int start, bool keep_spacing);
     
   /// \brief Get edit mode of editor
   EditMode GetMode() const {return mode_;}

modules/seq/alg/src/impl/align_impl.hh

@@ -98,6 +98,15 @@ inline void DLLEXPORT StoreStrAsAln(String& aln_str1, String& aln_str2,
   AlignmentHandle aln=CreateAlignment();
   aln.AddSequence(CreateSequence(s1.GetName(), aln_str1));
   aln.AddSequence(CreateSequence(s2.GetName(), aln_str2));  
+
+  if (s1.GetAttachedView()) {
+    aln.AttachView(0, s1.GetAttachedView());
+  }
+
+  if (s2.GetAttachedView()) {
+    aln.AttachView(1, s2.GetAttachedView());
+  }
+
   aln.SetSequenceOffset(0, i);
   aln.SetSequenceOffset(1, j);
   alignments.push_back(aln);

modules/seq/base/pymod/export_sequence.cc

@@ -80,6 +80,9 @@ ConstSequenceList do_slice_a(ConstSequenceList& t, slice sl)
 {
   return do_slice<ConstSequenceList>(t, sl);
 }
+String aln_to_str(const AlignmentHandle& aln) {
+  return aln.ToString();
+}
 
 SequenceList do_slice_b(SequenceList& t, slice sl)
 {
@@ -334,9 +337,6 @@ void export_sequence()
   class_<SeqListIter>("SeqListIter", no_init)
     .def("next", &SeqListIter::next)
   ;
-  to_python_converter<std::pair<mol::EntityView, mol::EntityView>, 
-                      PairToTupleConverter<mol::EntityView, mol::EntityView> >();
-  
   class_<AlignmentHandle>("AlignmentHandle", init<>())
     .def("GetCount", &AlignmentHandle::GetCount)
     .add_property("sequence_count", &AlignmentHandle::GetCount)
@@ -345,10 +345,13 @@ void export_sequence()
     .def("GetResidueIndex", &AlignmentHandle::GetResidueIndex)
     .def("GetResidue", &AlignmentHandle::GetResidue)
     .def("AddSequence", &AlignmentHandle::AddSequence)
+    .def("GetMatchingBackboneViews", &AlignmentHandle::GetMatchingBackboneViews,
+         (arg("idx_a")=0, arg("idx_b")=1))
     .def("FindSequence", &AlignmentHandle::FindSequence)
     .def("FindSequenceIndex", &AlignmentHandle::FindSequenceIndex)
     .def("Copy", &AlignmentHandle::Copy)
-    .def("ToString", &AlignmentHandle::ToString)
+    .def("ToString", &AlignmentHandle::ToString, (arg("width")=80))
+    .def("__str__", aln_to_str)
     .def("GetLength", &AlignmentHandle::GetLength)
     .def("__len__", &AlignmentHandle::GetLength)
     .def("GetSequences", &AlignmentHandle::GetSequences)

modules/seq/base/src/sequence_op.cc

@@ -41,7 +41,9 @@ SequenceHandle SequenceFromChain(const String& name,
        e=residues.end(); i!=e; ++i) {
     sequence+=(*i).GetOneLetterCode();
   }
-  return CreateSequence(name, sequence);
+  SequenceHandle s = CreateSequence(name, sequence);
+  s.AttachView(chain.Select(""));
+  return s;
 }
 
 
@@ -54,7 +56,9 @@ SequenceHandle SequenceFromChain(const String& name,
        e=chain.GetResidueList().end(); i!=e; ++i) {
     sequence+=(*i).GetOneLetterCode();
   }
-  return CreateSequence(name, sequence);
+  SequenceHandle s = CreateSequence(name, sequence);
+  s.AttachView(chain.Select(""));
+  return s;
 } 
  
 }}

tools/molck/main.cc

@@ -370,7 +370,7 @@ int main(int argc, char *argv[])
     }
     if (write_to_file) {
       fs::path input_file_path(files[i]);
-      fs::path input_filename = input_file_path.stem();
+      fs::path input_filename = BFPathStem(input_file_path);
  
 
       String input_filename_string=BFPathToString(input_filename);