Thanks. Yes, I figured that out and am handling this mapping
"externally", but was wondering whether there was an easier way. But
handling externally is fine.
Tim
On 28/09/2016 19:00, John M wrote:
Sure, just use the method of iAtomContainer?
IMoleculeSet fragments =
ConnectivityChecker.partitionIntoMolecules(iAtomContainer);
int idx =
iAtomContainer.getAtomNumber(fragments.getAtomContainer(0).getAtom(0));
On 28 September 2016 at 11:16, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Hi,
I'm needing to extract the biggest fragment from a molecule (e.g.
exclude salts) and then perform an operation on the biggest. To do
this I'm using ConnectivityChecker.
IMoleculeSet fragments =
ConnectivityChecker.partitionIntoMolecules(iAtomContainer);
But I need to be able to map the atom numbers in the fragment back
to the atom numbers in the original. Is there an easy way to
achieve this?
(note, I'm having to use the 1.4 API for this).
Tim
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