Re: [Cdk-devel] Next step of the atom type refactoring: Removal of the HueckelAromaticityDetector from trunk/

[Nina J. <ni...@ac...>]

Egon Willighagen wrote:
> On 11/1/07, Rajarshi Guha <rg...@in...> 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