numbering of molecule is enabled?

[biotech7]

Hi, team: I want to number a series of molecules , is OPSIN capable of this task？ thanks！

[dan2097]

I suspect the answer is no. Given an IUPAC name, OPSIN can output the label(s) associated with each atom, but there are some caveats with this. The labels are dependent on the nomenclature used in the chemical name rather than just the structure, and these labels aren't neccesarily unique e.g. in say ethylbenzene, there are two atoms that would be labelled 1 and two that would be labelled 2.

[biotech7]

Thanks for detailed explanation. it solved my doubts. By the way, is there any client tool to label/number a molecule or render a labeled molecule? i tried Epam Indigo(by which render a labeled molecule to client) and ketcher standalone, but all failed to find this function.

[dan2097]

The CDK's depiction functionality has the ability to render a labelled molecule, it can be tried by changing "No Annotation" on https://www.simolecule.com/cdkdepict/depict.html

For example, using the SMILES labelling that is normally used for atom mapping can give you this

EDIT: The code behind that depiction service is https://github.com/cdk/depict

[biotech7]

Thanks Daniel ! It is really useful. I has run it and it worked well with many amazing functions. The next only thing to do is how to intergrate this lib into my Java platform. I'll try it later.