subject:"\[Cdk\-user\] Merge molecules"

Re: [Cdk-user] Merge molecules

2016-11-26 Thread John M

Ahh okay, merge via MCS. Yes you'll need to do that on your own, UniversalIsomorphismTester should help or perhaps something in the SMSD - but as you know NP-Complete so not generally something you want to be doing. John

Re: [Cdk-user] Merge molecules

2016-11-26 Thread Tim Dudgeon

Yes, I think we are talking about different things. My use case can be described as having inputs of toluene and nitrobenzene. They share a benzene ring as common subgraph. The merged output would be nitrotoluene. But because of symmetry there are multiple ways to match the subgraph so the

Re: [Cdk-user] Merge molecules

2016-11-26 Thread John M

My mistake, the method add() already does what you need... just can be more efficient. IAtomContainer a; IAtomContainer b; a.add(b); John On 26 November 2016 at 16:56, John M wrote: > No convenience method, curiously addAtom() does a unique check (so that's >