Egon Willighagen wrote:
On 11/1/07, Rajarshi Guha <rguha@indiana.edu> wrote:
  
But what about molecules like polycyclic aromatics? Would the new
update mean that they would not be detected as aromatic? If so, that
would not be very nice form a modeling point of view :(
    

The old code makes as many right guesses as wrong guesses... so, I
would be more happy if the user would explicitly state what he wants
to be aromatic.

Egon

  
I am sorry I hadn't responded to this email earlier. I guess this approach is the most clean from design point of view but results in lot of aromatic compounds not being recognized and thus making other code unusable. As you might guess now I am having troubles with the new CDKHueckelAromaticityDetector and Toxtree code, where plenty of tests are failing.  Is there any workaround to detect polycyclic aromatic? If not, is it possible to retain both old HueckelAromaticityDetector and the new one?
It is not very likely that an ordinary user is going to redraw each structure in a huge database to explicitly specify aromaticity.

Best regards,
Nina