Issue rendering an organometallic complex SMILES

[felipe-imanishi]

We have this canonical SMILES generated by RDKIT CNc1ccccc1-c1[c-]cccc1.COc1ccc(OC)c(P(C2CCCCC2)C2CCCCC2)c1-c1c(C(C)C)cc(C(C)C)cc1C(C)C.CS(=O)(=O)O.[Pd] that fails to render in openchemlib. If we remove the negatively charged carbon (the - in the [c-], it renders but it is then incorrect.

Is there a limitation here or is this known?

The original smiles (before being canonicalized by RDKIT) CC(C)C1=CC(=C(C(=C1)C(C)C)C2=C(C=CC(=C2P(C3CCCCC3)C4CCCCC4)OC)OC)C(C)C.CNC1=CC=CC=C1C2=CC=CC=[C-]2.CS(=O)(=O)O.[Pd] does render, but because we are using rdkit as our standardization tool, it is not possible for us to use this smiles.

Thank you!

Image below is from chemdraw. It shows both smiles mentioned plotted.
The first one is for smiles CNc1ccccc1-c1[c-]cccc1.COc1ccc(OC)c(P(C2CCCCC2)C2CCCCC2)c1-c1c(C(C)C)cc(C(C)C)cc1C(C)C.CS(=O)(=O)O.[Pd] and the second one for smiles CC(C)C1=CC(=C(C(=C1)C(C)C)C2=C(C=CC(=C2P(C3CCCCC3)C4CCCCC4)OC)OC)C(C)C.CNC1=CC=CC=C1C2=CC=CC=[C-]2.CS(=O)(=O)O.[Pd].

[targos]

/cc @thsa as this is probably not specific to the JS port of OpenChemLib

[lpatiny]

The error code is 'Assignment of aromatic double bonds failed'. Currently openchemlib do not accept c1[c-]cccc1

[thsa]

this was just fixed

…

________________________________ Von: Luc Patiny ***@***.***> Gesendet: Mittwoch, 6. Juli 2022 07:02 An: cheminfo/openchemlib-js ***@***.***> Cc: Thomas Sander ***@***.***>; Mention ***@***.***> Betreff: Re: [cheminfo/openchemlib-js] Issue rendering an organometallic complex SMILES (Issue #130) The error code is 'Assignment of aromatic double bonds failed'. Currently openchemlib do not accept c1[c-]cccc1 — Reply to this email directly, view it on GitHub<https://che01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcheminfo%2Fopenchemlib-js%2Fissues%2F130%23issuecomment-1175784022&data=05%7C01%7Cthomas.sander%40idorsia.com%7Cab598fcf6ea847df84f008da5f0cc8dc%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637926805764806746%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=u9Ti%2FXbuN8%2F41pvzquYVZHqipyar7DdfiQUn7r0VtCY%3D&reserved=0>, or unsubscribe<https://che01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACNFEBQZLUPZGZVFHZ77BSDVSUHPZANCNFSM5W6AA3IQ&data=05%7C01%7Cthomas.sander%40idorsia.com%7Cab598fcf6ea847df84f008da5f0cc8dc%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637926805764806746%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=76JgYIzV8RN7NEGoAV6BGldhxlsEbJwO1xfTEHpc3uA%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***>

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[felipe-imanishi]

@targos what is the release cadence for openchemlib-js? With the fix above, I was wondering when openchemlib-js would be able to make a release to include this release https://github.com/Actelion/openchemlib/releases/tag/openchemlib-2022.7.2 from openchemlib. Thank you!

[targos]

Unfortunately I tried to update openchemlib last year and there were issues preventing the compilation. I haven't found the time to resolve them yet, so for now this is blocked on either me finding the time or someone else doing it (I'd be happy to review a pull request)

[targos]

I'll do a release as soon as #135 is merged.