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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