diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 242aa5daf1e72d50ecf1d753bafcb65488d6e86f..720b4ff22b90294f17ab075473c78882fb7af1dd 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -4,6 +4,17 @@ Changes in Release 1.4
* Feasibility check set to off by default, atoms in compounds are now
connected by the Builder irrespective of the distance between them
* Speed improvement for bracketed within selections up to a factor of 20
+ * refactored and streamlined the conop interface. The builder classes
+ have been replaced by processors (HeuristicProcessor, RuleBasedProcessor)
+
+Changes In Release 1.3.3
+--------------------------------------------------------------------------------
+
+ * fix context menu/main menu for newer Qt versions
+ * CreateEntityFromView remembers chemical type (BZDNG-430)
+ * fix gfx.PrimList.SetLineWidth
+ * Fix remote=true for MMCIF loader (BZDNG-449)
+ * made CreateViewFromAtoms more flexible (BZDNG-408)
Changes In Release 1.3.2
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 34244717a2e4676c37d1499e6c175e53dd3930f4..3cdb0fba0c88e8b217f5ae8e9b7deaa856934702 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 2)
+set (OST_VERSION_PATCH 3)
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/doc/install.rst b/modules/doc/install.rst
index b92727bed28fe9e9885ac5f940f8b92ab3a768b5..3392798c24a18b191f8be7941c367a913ee8998b 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -74,11 +74,12 @@ The above command will clone OpenStructure into the directory called `directory-
Some versions of curl have have trouble with the certificate of the
OpenStructure git server and fail to clone the repository. To work around
- this, disable the SSL certificate verification with the following command:
+ this, disable the SSL certificate verification by setting the following
+ environment variable:
.. code-block:: bash
-
- git config --global http.sslVerify false
+
+ export GIT_SSL_NO_VERIFY=1
Picking the right branch
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 7fcf429230c8eeddcd1a5873286d0312a056c239..e2e6330adf18847dcc8d94bb4954e5df8ab5366b 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -299,11 +299,9 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
if remote:
- output_dir = tempfile.gettempdir()
- if __GetModelFromPDB(filename, output_dir):
- filename = os.path.join(output_dir, 'pdb%s.ent.gz' % filename)
- else:
- raise IOError('Can not load PDB %s from www.pdb.org'%filename)
+ from ost.io.remote import RemoteGet
+ tmp_file =RemoteGet(filename, from_repo='cif')
+ filename = tmp_file.name
try:
ent = mol.CreateEntity()
diff --git a/modules/io/pymod/remote.py b/modules/io/pymod/remote.py
index 102cf680711ffafaeb98aab2c5f6a0aff082044d..aeb9bee0503b054bfc74007023826f554816bd54 100644
--- a/modules/io/pymod/remote.py
+++ b/modules/io/pymod/remote.py
@@ -50,7 +50,10 @@ class RemoteRepository:
try:
connection = urllib2.urlopen(remote_url)
- status = connection.getcode()
+ if hasattr(connection, 'code'):
+ status = connection.code
+ else:
+ status = connection.getcode()
except urllib2.HTTPError, e:
status = e.code
msg = 'Could not load %s from %s (status code %d)'
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index a65e95457400b5ee4806c49e4bf0dc666ba398ad..909f41d711b987afccd82319cbe10575ed7dca5f 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -30,7 +30,6 @@
#include <ost/export_helper/pair_to_tuple_conv.hh>
#include <ost/export_helper/vec_to_list_conv.hh>
-
using namespace boost::python;
using namespace ost;
@@ -110,8 +109,6 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
export_entity_to_density();
#endif
-
-
def("LocalDistDiffTest", lddt_a, (arg("sequence_separation")=0,arg("local_lddt_property_string")=""));
def("LocalDistDiffTest", lddt_c, (arg("local_lddt_property_string")=""));
def("LocalDistDiffTest", lddt_b, (arg("ref_index")=0, arg("mdl_index")=1));
@@ -166,7 +163,6 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
def("PrintGlobalRDMap",&mol::alg::PrintGlobalRDMap);
def("PrintResidueRDMap",&mol::alg::PrintResidueRDMap);
-
class_<mol::alg::PDBize>("PDBize",
init<int>(arg("min_polymer_size")=10))
.def("Add", &mol::alg::PDBize::Add,
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index 866a33e1b1734859a8f818044d908687cf0f4395..2422c154ad6a9f6e764a824264066b550807d9b3 100644
--- a/modules/mol/base/pymod/export_entity_view.cc
+++ b/modules/mol/base/pymod/export_entity_view.cc
@@ -36,7 +36,7 @@ using namespace ost::mol;
namespace {
template<class T>
-std::vector<T> from_list(const list& seq)
+std::vector<T> from_list(const object& seq)
{
std::vector<T> nrvo;
for (int i = 0; i < len(seq); ++i) {
@@ -62,9 +62,12 @@ StringMethod find_chain_str=&EntityView::FindChain;
QSMethod select_string=&EntityView::Select;
QueryMethod select_query=&EntityView::Select;
-EntityView create_view(const list& seq)
+EntityView create_view(const object& seq)
{
- if(len(seq)==0) return EntityView();
+
+ if(len(seq)==0) {
+ return EntityView();
+ }
extract<AtomHandle> get_handle(seq[0]);
if(get_handle.check()) {
return CreateViewFromAtomList(from_list<AtomHandle>(seq));
@@ -209,6 +212,7 @@ void export_EntityView()
def("Intersection", &Intersection);
def("CreateViewFromAtoms", create_view);
+ def("CreateViewFromAtomList", create_view);
def("CreateEntityFromView", &CreateEntityFromView,
arg("handle")=EntityHandle());
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 2ec5b8694668d91c207679a99de9c0b2a80157f9..c6acf1a6af3438e68c8e32c858ed3a31aa303114 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -69,6 +69,7 @@ ResidueImplPtr ChainImpl::AppendResidue(const ResidueImplPtr& res, bool deep)
dst_res->SetSecStructure(res->GetSecStructure());
dst_res->SetChemClass(res->GetChemClass());
dst_res->SetProtein(res->IsProtein());
+ dst_res->SetChemType(res->GetChemType());
dst_res->SetIsLigand(res->IsLigand());
if(deep)
{