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aiidalab / aiidalab-widgets-base

Reusable widgets for AiiDAlab applications
MIT License
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Problematic SMILES #519

Open danielhollas opened 9 months ago

danielhollas commented 9 months ago

List of SMILES which currently do not work in SmilesWidget. Feel free to reopen the issue if you come up with new ones!

  1. [H][C]1C2=CC=CC3=C2C(C4=C1C=CC5=C4C6=C(C7=C([C]([H])C8=CC=CC9=CC=CC7=C98)C=C%10)C%10=CC=C6C=C5)=CC=C3
danielhollas commented 8 months ago

I briefly looked into it and this SMILES will be harder to fix, none of the various RDkit options I tried worked.

Next step is to try to tease out a concrete Error coming from RDkit. If we do not manage to figure this out, I'll open an issue on RDKit itself.

fabioacl commented 1 month ago

I used RDKit to generate the following SMILES from a CDXML file:

Cc1cccc(C)c1-c1c2ccccc2c(C2=c3ccc4n3[Zn]35n6c(ccc6C(c6c7ccccc7c(-c7c(C)cccc7C)c7ccccc67)=c6ccc(n63)=Cc3ccc2n35)C=4)c2ccccc12

I checked whether it was a problem with the SMILES but it works using Mathematica.

image

cpignedoli commented 1 month ago

@danielhollas this also fails in the SMILES widget, do you think it is related to the same problem you mentioned before?

danielhollas commented 1 month ago

@cpignedoli hard to say without taking a closer look. Note that I will be away on holiday until 20th so will not have a look until then.

It would be helpful if you could provide a more concrete RDKit error. Note that when using SmilesWidget, you need to run it from within a plain notebook interface, since Appmode hides errors by default.

cpignedoli commented 1 month ago

@danielhollas I will ask @fabioacl to document the rdkit error, will be ready for after your holidays :)