Emma Schymanski

My comment stands for both the individual spectrum and library level ... many spectral libraries will likewise not come from an organism ... although some may and in this case...

I agree wholeheartedly. We should be flexible, be able to store all existing information from existing libraries (even if we don't necessarily see the use) and by allowing apppropriate optional...

We are enjoying the `wot` ;-)

I confirm the same ... ``` > ext_smiles mol view.molecule.2d(mol) Error in view.molecule.2d(mol) : java.lang.NoSuchMethodError: ``` SessionInfo: ``` > sessionInfo() R version 4.3.3 (2024-02-29 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under:...

Ok cool we thought about the depict package yesterday but weren't sure and used the inbuilt one instead. We don't think we're heavily reliant on the AWT parts... We can...

So we tried to use your depict code to visualize and that didn't work for us either :-( Any idea what I've done wrong? ``` > library(depict) > depiction() |>...

ahh `parse_smiles` not `parse.smiles` ... so we have to use the depict read-in not the rcdk read-in, that's confusing ... sorry, missed that ... ``` > cxSMILES = "O=C(*)Oc1ccc(cc1)C(C)(C)c1ccc(O*)cc1 |Sg:n:0,1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20::ht|...

@bachi55 this is a great point and it's a problem we are encountering beyond the fingerprints (look at e.g. #73 and the massfuncs branch where we are trying to capture...

I haven’t looked into this for fingerprints, but was answering some queries about them only a few days ago ;-) and some of the edge cases I pulled out for...

Noting here that we will probably need to update terms in massfuncs branch once we come to an alignment on discussions in https://github.com/cdk/cdk/pull/547