void OEAssignAromaticFlags(OEMolBase &mol,
unsigned int model=OEAroModel::OpenEye,
bool clearflags=true, unsigned int maxpath=0,
Perceives the aromatic atoms and bonds of a molecule.
The assigned atom and bond aromaticity can be accessed by
OEBondBase.IsAromatic methods, respectively.
- The parameter that specifies that aromaticity model that are perceived by the
The default aromaticity ‘model’ is OEAroModel_OpenEye.
Other predefined aromaticity models provided by OEChem TK
OEAroModel_MDL that represent the Daylight,
Tripos, MMFF and MDL definitions, respectively.
- The parameter that specifies whether to clear the
aromaticity flags by calling OEClearAromaticFlags prior
to re-perceiving the aromaticity.
Newly created molecules that have not had their aromaticity assigned
yet can specify false, for a very small performance advantage.
- The parameter that specifies the maximum path
length to consider an aromatic cycle, or zero (the default) to specify
no upper bound on aromatic cycle length. Some formal models of
aromaticity use the value six, limiting aromaticity to six membered
rings like benzene or pyridine.
- The parameter that specifies whether or not to run a
post-processing step to consider rings with exo-double bonds as not
aromatic. This is also required by some formal models of aromaticity.