BRICSBuild not reconstructing original molecule.. #5297
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Hi @DanielGoede sorry I'm so slow to reply to this.
Since your molecule produces 6 fragments, you would have to go all the way to a maxDepth of 5 in order to find the input molecule. This will take quite a while and generate a bunch of molecules (I didn't let it run to completion, so I'm not sure how many). If you want to check that the fragmentation does in fact return the original molecule, you need to either start with a smaller input structure or be prepared to wait. :-) |
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I am trying to learn more about the BRICS implementation in rdkit, but running into a peculiarity.
I can fragment a molecule easily, but when I try to re-assemble it, the enumerated molecules
either (a) don't use all of the available fragments, or (b) use the same fragments over and over.
For example:
Is there a way to ensure that the original molecule is reconstructed in this process? I would like to be
able to manipulate this process for core hopping by changing the new scaffolds to match the fragmentation labels
on the old core and reconstruct as close as possible, but can't seem to make it work...
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