Re: [Cdk-devel] aromaticity detection in GasteigerPEPEPartialCharges

[Rajarshi G. <rg...@in...>]

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This brings up the topic of caching - can we cache the fact that  
aromaticity has been detected or needs to be redetected?

This would avoid the whole issue of passing around aromaticity flags.  
Anything that needs to use aromaticity would check the flag, and if  
not set, would redetect the aromaticity.

I suppose the tricky part is how and when would this be propagated.  
As a first approximation any method that modifies atoms or bonds  
(addBond, addAtom) would set the flag to NOT_DETECTED and it would  
only be set to DETECTED by the CDKAromaticityDetector

Also, I thought HueckelAromaticityDetector was deprecated?

On Feb 26, 2008, at 6:49 PM, Stefan Kuhn wrote:

> Dear co-developers,
> the class GasteigerPEPEPartialCharges uses  
> HueckelAromaticityDetector like
> this:
> if(HueckelAromaticityDetector.detectAromaticity(ac))
> Am I correct to think that this means aromaticity detection is done  
> each time?
> If so, I suggest:
> 1) To have a detectAromaticity flag and if this is set, to replace  
> the above
> mentioned call with a loop checking if any aromaticity flag is in the
> atomcontainer on bonds or atoms
> AromaticityDetection is also done on AtomContainers from an acSet  
> which is
> generated like this:
> IAtomContainerSet iSet = gR.getAllStructures(ac);
> Does this mean aromaticity is "propagated" to the new AtomContainers?
> If yes, I suggest
> 2) The same as in 1) for these AtomContainers.
> The PartialPiChargeDescriptor would also have the flag, which could  
> lead to
> another boost in descriptor calculation time.
> Stefan
>
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Rajarshi Guha  <rg...@in...>
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