Hi John,
thank you very much for your advice. The Code works perfectly for me!
Niko
John M <[email protected]> schrieb am Di., 20. Dez. 2016 um
16:16 Uhr:
> There isn't a utility function but it's quite simple. Get the fragments as
> you are already doing, then for each fragment delete all the the cyclic
> bonds. In practise it's more efficient to build a new molecule and only
> include the acyclic bonds.
>
> Code:
> https://gist.github.com/johnmay/cd02b5e5d45dbd955a30f9e4f9d4bc39
>
> Each output molecule has all the chains in it, you may want to split these
> out using the ConnectivityChecker.
>
> John
>
> On 20 December 2016 at 12:38, Nikolas Glaser <[email protected]> wrote:
>
> Hello,
> i'm new to mailinglists so i'm not sure if my first mail is received.
> I wrote a class which uses the murckofragmenter to create fragments of
> molecules. Now I need the possibility to get the chain between to
> ringsystems as fragment.
> Is it possible to realize it with the murckofragmenter or is there another
> class in the cdk which i can use? After hours of research I could not find
> a solution.
> Does anyone have a idea how it is possible to realize?
> I am very new in the bio/cheminformatics and in using the cdk so I am
> happy for every advise!
>
> Thanks.
>
> Kind regards
> Nikolas Glaser
>
>
>
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