problem with IUPAC name generator

Hey,





Here is the SMILES of a chemical formula:





O=C1\C(=C\C2=CC=CC=C2)S(=O)C3=C1C=CC=C3





and here is the generated name:





(2Z)-2-(phenylmethylidene)-2,3-dihydro-1$l^{4}-benzothiophene-1,3-dione





What's the 1$|^ ??

1$l^{4} is an ascii representation of what could be written in unicode as: 1λ⁴. λ is used in IUPAC names to signify a non-standard valence.





In this case, atom number 1 in benzothiophene (the sulfur atom) has a non-standard valence of 4 (instead of the standard valence 2 for sulfur).





It might be a good idea to generate unicode output by default, possibly with an option to generate ascii. Feel free to let us know what would be best for you.

Hey,





It would be a good idea to have an option for ascii or unicode output.


you can consider too that to have an working trivial name generator. My experience is that the trivial name generator make in 99% the same name as the IUPAC name.


In the case above could be named as thioauron sulphoxide.

We will switch to unicode by default in the next release, with an option for ascii. Note that the Tools/IUPAC Name plugin in the GUI already displays lambdas as symbols in the current version. (How did you generate the name?)





Concerning trivial name, we do plan to support them more. About this specific example, I did not find references for "auron" (in pubchem and google); a few for thioauron, all in german texts.

I realize this is an old, old topic, but I noticed that the output is still ASCII using the caret system, at least in the JChem web services. Was there ever an option for unicode added?

Craig

The λ is now used in unicode output (which is the default) since Marvin/JChem 5.11 (which version are you using?). The generated name is:

(2Z)-2-(phenylmethylidene)-2,3-dihydro-1λ⁴-benzothiophene-1,3-dione.

I'm asking the JChem webservices team to comment on whether they force an ASCII output by default.

Hi Craig,

What kind of client are you using for accessing the web services? 

It is working with javascript client for the current version:
https://plexus.chemaxon.com/table/sample/unicode_test/details/1 (see Names and identifiers box)

We can enforce the utf-8 encoding in responses with mime type parameters, or we an help you with the client settings if you provide more information.

Regards,
Peter 

Sorry to waste your time.. I am using an old database and I swore I had recalculated the IUPAC name, but when I run  a script to recalculate it is indeed using unicode.

Thanks,

Craig

No problem, good to hear it's working for you now!