Re: [Cdk-devel] AllRingsFinder and marking ring bonds

[John M. <joh...@gm...>]

Possible, but I would try and avoid the flags/properties completely. One large collection is much better then many small collections. As tools are setting these flags all over the place the current design requires you reset the flag before you anything else (PathTools.resetFlags) - this is really just annoying. A lot of existing tools also use the flags to mark their intermediate states, this is bad as you're leaking implementation details into the domain objects. If you really want to provide that information it should explicitly be part of the API signature - and use an encapsulated data structure.

It could be added but there are much better ways to do it. Again, RingSearch is extremely fast (< 200 ms for ~30,000 structures from ChEBI) and provides this exact information.

J

On 20 Jun 2013, at 22:50, Rajarshi Guha <raj...@gm...> wrote:

> Hi, it seems that after a call to AllRingsFinder atoms are flagged as ring atoms or non-ring atoms. But this is not the case for bonds. Is this meant to be the case?
> 
> -- 
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
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