ptosco 1957baadb0 - 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

2013-10-01 23:16:15 +02:00

..

CMakeLists.txt

- I have made MMFF atom typing more robust since I realized that

2013-09-16 12:08:02 +02:00

rdForceFields.cpp

more mmff api consistency

2013-09-29 07:58:34 +02:00

test_list.py

- I have made MMFF atom typing more robust since I realized that

2013-09-16 12:08:02 +02:00

testHelpers.py

- replaced the call to sanitizeMMFFMol() in the MMFFMolProperties

2013-10-01 23:16:15 +02:00