- 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
add sa score
Fixes #112
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
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
Merge branch 'O3DAlign_29Sept2013'
remove USR and USRCAT implementation
Fixes #116
Merge pull request #125 from sriniker/master

Documentation of similarity maps and scikit-learn