- implemented Open3DALIGN-like alignment functionality (from both
  C++ and Python)
- added relevant C++/Python tests
this passes all tests
- replaced  the call to sanitizeMMFFMol() in the MMFFMolProperties
  constructor (which is overkill, if the molecule had already been
  sanitized) with a call to MolOps::Kekulize(). Thus it is not
  necessary to call Kekulize() either from Python or from C++,
  and no changes are required to the scripts/source codes
  previously used for UFF
- removed the code which throws an exception asking to reload the
  molecule with sanitize=false since it is not necessary:
  only one test in the MMFF validation suite fails if the
  molecule is aromatized and then re-kekulized (CIKSEU10), and
  it represents a case where the position of double bonds in
  a conjugated, non-aromatic system makes a difference for atom
  type assignments, which in general is a nonsense. This is not
  due to a bug in the code, but rather depends on MMFF atom
  typing rules. Hence, I kept the sanitize=false and the call to
  sanitizeMMFFMol() in testMMFFForceField.cpp, but I would not
  generalize this requirement to "normal" molecules, because it
  is really not necessary, since you do not have a reference
  kekulization to refer to in the real world.
- updated Docs/Book/GettingStartedInPython.rst accordingly
- updated tests accordingly
- propagated the changes in the master branch to the O3A branch
Merge pull request #110 from ptosco/master

Removed special sanitization/kekulization requirements for MMFF
Merge pull request #111 from ptosco/O3DAlign_29Sept2013

- propagated the changes in the master branch to the O3A branch
Update GettingStartedInPython.rst

Description of similarity maps added.
Update GettingStartedInPython.rst

Description of similarity maps
figures for documentation
Update GettingStartedInPython.rst

similarity maps for descriptors
figures for documentation
Update Cookbook.rst

scikit-learn and similarity maps for models
efficiency patch for the sa score code from Nick Firth
Changes to the various bulk similarity functions for #119; not closing yet since there may still be other places that need to be updated
Fixed GitHub Issue #114
https://github.com/rdkit/rdkit/issues/114
Removed some superfluous changes (was including SmilesParse for
visual testing, extra whitespace etc.)
add support for tversky similarity to cartridge
Merge pull request #122 from malteseunderdog/master

Fixes #114
Fixes #118
some small cleanups