#1322 Should AtomTypeManipulator.configure() set aromatic information

cdk-1.0.x
open
nobody
None
1
6 days ago
2014-01-13
John May
No

Stephan found this when debugging in the LogP code.

percieveAtomTypesAndConfigureAtoms() will set the aromatic flags based on atom-types. Now we have multiple aromatic models this means information is removed. Configure unset does the job correctly but should atom types and aromaticity be this tightly linked?

Discussion

  • IMHO, that would be incorrect, because the CDK atom types do not have a concept of aromaticity.