diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index c5ae5d2a49de307843bd31c986b7bab853c880dd..8891b9639dcdac2c2c38132c8028cd0836951e91 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,29 @@
+Changes In Release 1.3.1
+--------------------------------------------------------------------------------
+
+ * Export missing default argument for AligmentHandle.ToString
+ * Automatically attach entity view in SequenceFromChain
+ * Export GetMatchingBackboneViews to Python
+ * Fix compilation with boost 1.33.1
+ * Allow renumbering of single chain
+
+Changes In Release 1.3.0
+--------------------------------------------------------------------------------
+
+ * Scene background can now be set to a gradient or an image
+ * Better Handling of HSV colors
+ * Table: direct access to columns tab['x'] is also available as tab.x
+ * Table: Export to ConTeXt and HTML tables
+ * Table: Barplot interface
+ * The BLAST binding supports newer versions of BLAST
+ * Bindings for CAD score
+ * 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
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index cfbd59e3ac4f1e437bd2ecc6abb889d45a6a7898..f4ce4d675a556308f5b1031c3f4446050d9a15eb 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 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)
diff --git a/modules/base/src/boost_filesystem_helper.hh b/modules/base/src/boost_filesystem_helper.hh
index 5418253fd7553f7f715e8259d1f6f08615080ca1..450ffa94deaef5b230c11cd0129e3a5422549fda 100644
--- a/modules/base/src/boost_filesystem_helper.hh
+++ b/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
+}
+
}
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index aae903f7d276721545a60af51cd1ed0dff227263..e204bbd2e7c190fc42b4d931a4e9a584577a4719 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -249,6 +249,7 @@ void export_Editors()
.def("ReorderResidues",&EditorBase::ReorderResidues)
.def("ReorderAllResidues",&EditorBase::ReorderAllResidues)
.def("RenumberAllResidues",&EditorBase::RenumberAllResidues)
+ .def("RenumberChain",&EditorBase::RenumberChain)
;
void (XCSEditor::*apply_transform1)(const geom::Mat4&) = &XCSEditor::ApplyTransform;
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index 0ae2b8a09c026a6c70bf28cc113467f4fc09589a..fd97572869e6f935b0a3ab7b7b6226f8d850dcd9 100644
--- a/modules/mol/base/pymod/export_entity_view.cc
+++ b/modules/mol/base/pymod/export_entity_view.cc
@@ -215,6 +215,6 @@ void export_EntityView()
class_<EntityViewList>("EntityViewList", init<>())
.def(vector_indexing_suite<EntityViewList>())
;
- to_python_converter<std::pair<EntityView, EntityView>,
+ to_python_converter<std::pair<EntityView, EntityView>,
PairToTupleConverter<EntityView, EntityView> >();
}
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index ff19cddff9f8aaab6cd5910db047f1a5cc4f8ef5..9e8729d9374391321f511f8e17e1bef79b81d327 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -208,6 +208,15 @@ void EditorBase::RenumberAllResidues(int start, bool keep_spacing)
ent_.Impl()->RenumberAllResidues(start, keep_spacing);
}
+void EditorBase::RenumberChain(const ChainHandle& chain, int start, bool 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)
{
CheckHandleValidity(atom);
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 7d6f6d65a2e9761e1cebdd4b014589e5a0174cd0..05d82ddb0682e12737b629947f010947cb009842 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -277,6 +277,23 @@ public:
/// If set to false, residues will continously be renumbered ongoing from start.
/// Otherwise the spacings between the residues are kept.
void RenumberAllResidues(int start, bool keep_spacing);
+
+
+
+ /// \brief renumber residues of one chain
+ ///
+ /// \param name
+ /// All residues of this chain will be renumbered according to the
+ /// parameters start and keep_spacing
+ ///
+ /// \param start
+ /// Residues of given chain will be renumbered, whereas the first
+ /// residue gets the residue number start.
+ ///
+ /// \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 ChainHandle& chain, int start, bool keep_spacing);
/// \brief Get edit mode of editor
EditMode GetMode() const {return mode_;}
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 75f289aaba84c7f15de01cbf2a11350770d36c23..6cdf081cd35740fa1f4a543ef341e37f3e0974f6 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -345,7 +345,7 @@ void export_sequence()
.def("GetResidueIndex", &AlignmentHandle::GetResidueIndex)
.def("GetResidue", &AlignmentHandle::GetResidue)
.def("AddSequence", &AlignmentHandle::AddSequence)
- .def("GetMatchingBackboneViews", &AlignmentHandle::GetMatchingBackboneViews,
+ .def("GetMatchingBackboneViews", &AlignmentHandle::GetMatchingBackboneViews,
(arg("idx_a")=0, arg("idx_b")=1))
.def("FindSequence", &AlignmentHandle::FindSequence)
.def("FindSequenceIndex", &AlignmentHandle::FindSequenceIndex)
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index dab69250c67ce2022bc66555b0179c8386ef577e..6b896ac68313eb65e8ed10c75040f6bdd2bfa3c2 100644
--- a/tools/molck/main.cc
+++ b/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);