Incorrect rendering of SMARTS

[tsufz]

Hi,
The depiction of SMARTS is broken. For example record MSBNK-HBM4EU-HB002824.

CDK depicts the SMART correctly:

*NC1=NC(=NC(=N1)Cl)N* |$R1;;;;;;;;;;R2;;$| R1 = [C3H5 | C3H7 ] R2 = [C2H3|C2H5]

But the content list wrongly depicts the R indicators:

And the record does not load.

Yours
Tobias

[sneumann]

Thanks for the report and especially the screenshots. We will have to consider changing some software components for the CxSMILES. Is that correct @michaelwenk ?
Yours,
Steffen

[michaelwenk]

@tsufz

I did some changes to enable the parsing of extended SMILES.
Here are two examples of how it currently looks in development mode:

This fix will be available with the next official MassBank3 release.

[sneumann]

Just for reference here the CDK depict versions. Interesting, the annotation strings are not part of the images generated by the online service. After some pondering I also understood how to read the annotation in the Dimethanamid case.
Could it become an issue if different renderers conjure different numbering R1, R2, ... for the * ?
Yours, Steffen

https://www.simolecule.com/cdkdepict/depict/bot/svg?smi=*NC1%3DNC(%3DNC(%3DN1)Cl)N*%20%7C%24R1%3B%3B%3B%3B%3B%3B%3B%3B%3B%3BR2%3B%3B%24%7C%20R1%20%3D%20%5BC3H5%20%7C%20C3H7%20%5D%20R2%20%3D%20%5BC2H3%7CC2H5%5D&w=-1&h=-1&abbr=on&hdisp=S&zoom=1.3&annotate=none&r=0

and

https://www.simolecule.com/cdkdepict/depict/bot/svg?smi=C(*)C1%3DC(*)SC(%3DC1N(C(*)(C(*))C(*)OC(*))C(%3DO)C(*)Cl)C(*)%20*%3D%5BOH%20(n%3D1)%20%26%20H%20(n%3D7)%5D&w=-1&h=-1&abbr=on&hdisp=S&zoom=1.3&annotate=none&r=0