Paolo Tosco 633c7f8807 Fixes MMFF94 aromaticity perception and ChemicalForceFields.MMFFHasAllMoleculeParams() (#1007) ...

* - calcImplicitValence() and setNumExplicitHs() are now called after
  all aromaticity flags have been set

* - ChemicalForceFields.MMFFHasAllMoleculeParams() now operates on a copy of the molecule
  such that atom and bond aromaticity are not altered by the check
- test11 was added to GraphMol/ForceFieldHelpers/Wrap/testHelpers.py to check
  for the two bugs fixed by this PR

* - modified the prototype of MMFFHasAllMoleculeParams() to take a const ROMol&
  and make a copy of that within the function body
- removed unnecessary imports from testHelpers.py
- replaced EmbedMolecule() with a quicker test

* - WIP

* - now the issue seems to be properly fixed, as the implicit valence
  made explicit does not sum up anymore to the already explicit valence

2016-08-18 11:48:47 +02:00

..

CrystalFF

another batch of warnings squashed

2016-03-30 13:44:21 +02:00

MMFF

Fixes MMFF94 aromaticity perception and ChemicalForceFields.MMFFHasAllMoleculeParams() (#1007)

2016-08-18 11:48:47 +02:00

UFF

- fixed a bug in getUFFAngleBendParams()

2016-04-08 00:07:00 +01:00

Wrap

Fixes MMFF94 aromaticity perception and ChemicalForceFields.MMFFHasAllMoleculeParams() (#1007)

2016-08-18 11:48:47 +02:00

CMakeLists.txt

ETKDG implementation

2015-10-20 13:51:43 +02:00