This replaces the awkward FindCompound(... by=) which would return
a single arbitrary compound.

This allows preferentially picking a non-obsolete compound
in FindCompound by="smiles/inchi"

Simon found issues when reading and writing CONECT statements
in PDB io and provided code to fix it. yay

Reading: OpenStructure did not read CONECT statements at all. By default,
it still doesnt. Many PDB files out there don't provide these
statements and we really don't want to rely on them. We rather want
to assign connectivity based on the chemical component dictionary from
the PDB. However, a valid use case are novel compounds that are not
in the component dictionary. Reading connect statements can now be
enabled in the pdb reader through the IOProfile. This may give issues
in processing after reading. OpenStructure implements processors that
are responsible for connectivity. Now that we build some of the
connectivity already at the reading stage, this might cause trouble.
To remedy most of the nightmares that can come out of that, the
processors can now optionally skip connectivities between Hetatoms.

Writing: That was a plain bug when writing CONECT statements for
bond orders > 1.

That's the Python modules we generate with boost.python. 2to3 misses them

This commit doesn't make OpenStructure work with Python 3. The goal of this
commit was to perform an automated port of the Python code and make it compile.
The performed steps:

- Edited CMakeLists.txt to search for Python with 3.6 as min version 3.6 is the
  Python version shipped by default with Ubuntu 18.04 LTS
- Add version 3.6 to cmake_support/FindPython.cmake
- Adapt setup_boost macro in cmake_support/OST.cmake to prefer versioned
  libraries and not first check for boost_python.so. In the example of
  Ubuntu 18.04, libboost_python.so is specific for Python 2 but
  libboost_python3.so is the one we want.
- apply the following command: 2to3-2.7 -n -w <OST_DIR>
- adapt base/pymod/wrap_base.cc, gui/pymod/wrap_gui.cc and
  gui/pymod/export_message_widget.cc as PyString functionalities do not exist
  anymore in the Python 3 interpreter (replaced by PyUnicode)
- adapt gui/src/python_shell/python_interpreter_worker.hh to resolve issue
  discussed in https://stackoverflow.com/questions/23068700/embedding-python3-in-qt-5
  Long story short: Qt does a typedef for "slots" which causes trouble with
  other headers that are pulled in from the Python interpreter

wrong branch, big sorry

This reverts commit e77d08a6.

This reverts commit bf46ad1a.

Conflicts:
	modules/conop/src/compound.hh
	modules/conop/src/compound_lib.cc

setting it to false by default was creating too much downstream
trouble. the proper fix for not having to waste any CPU cycles
assigning torsions (which are barely ever looked at) would be to
have GetPhiTorsion/GetPsiTorsion/GetOmegaTorsion return temporary
Dihedral objects with the same interface than TorsionHandle.
These would be created on the fly.

The order of destruction of static objects, e.g. singletons is
arbitrary and can not be relied upon. For some versions of
Python, the singletons are destroyed after Python has shutdown.
When objects stored in the singletons have been created in Python,
a segfault is produced when they are destroyed, since the destructor
assumes a Python interpreter exists. To work around that, we register
atexit handlers to remove all references to Python objects. That's
required for the IOProfileRegistry and Conopology singletons.

The order of destruction of static objects, e.g. singletons is
arbitrary and can not be relied upon. For some versions of
Python, the singletons are destroyed after Python has shutdown.
When objects stored in the singletons have been created in Python,
a segfault is produced when they are destroyed, since the destructor
assumes a Python interpreter exists. To work around that, we register
atexit handlers to remove all references to Python objects. That's
required for the IOProfileRegistry and Conopology singletons.

not tested yet.

Unit tests are working, except the ones relying on the
HeuristicProcessor, which is currently only a stub.

RuleBased conop is an experimental new interface for processing
structures in the conop module. The class exposes a single method
Process with takes care of the complete conop procedure. There are
still a few methods missing, they will be added shortly.

fixed some DLLEXPORTs for exceptions
based ost:Error on std::runtime_error (avoids string member in ost::Error)

Mainly Marco's work

BZDNG-336;adding creation date and version of OST used to create compound lib to compound lib;adding API to retrieve this information, calls: GetOSTVersionUsed() and GetCreationDate()