Re: [Cdk-user] Get chain between ringsystems

Hi John, thank you very much for your advice. The Code works perfectly for me! Niko John M 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

Re: [Cdk-user] Get chain between ringsystems

Hi Nikolas, no idea if the Murckofragmenter can do this, but the easiest way should be to get all ring atoms using org.openscience.cdk.graph.Cycles.markRingAtomsAndBonds(mol); First you need to eat away the peripheral sustituents (recursively delete all atoms with connectivity 1 until no

Re: [Cdk-user] Get chain between ringsystems

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:

[Cdk-user] Get chain between ringsystems

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