rdkit/rdkit — pull request #110 by ptosco (2013-10-01 21:20:52+00:00)
Title: Removed special sanitization/kekulization requirements for MMFF

- 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