Hello, On the other hand, a chemical structure database with 100% naming correctness - from where do I get one of these marvels - with or without tools and AI? ;-)
Best, Markus On Sat, Jul 29, 2023 at 12:32 PM Christoph Steinbeck < christoph.steinb...@uni-jena.de> wrote: > Hi Yong, > > I wanted to say that STOUT only generates correct IUPAC names in 90% of > the cases. Like many deep-learning-based applications, it dreams up the > rest. Those wrong ones will usually still be relatively close to the > correct ones, so it depends on your application whether STOUT is helpful > for you. > If, for example, you are a chemist (which you aren’t, I read this :), but > let’s assume you are) and you want to name a few compounds for a paper, > then STOUT is helpful, and you can correct its occasional mistakes and > still have a much easier life. > If, however, you want to name 10k compounds in your database, then you > cannot live with <100% naming success. > If you need 100%, you need to switch to an algorithmic tool like Marvin's > name generator, referenced in our paper. > I hope that makes sense. > > Kind regards, > > Chris > > — > Prof. Dr. Christoph Steinbeck > Vice President for Digitalisation of the Friedrich-Schiller-University Jena > > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Team Assistant: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > > > On 28. Jul 2023, at 17:36, Yong Gao <y...@blueprintmedicines.com> wrote: > > > > Thank you, Chris. > > Tried a couple of smiles strings with STOUT. They seem to work. I’m not > a chemist, but does non-deterministic suggest not unique? > > Yong From: Christoph Steinbeck <christoph.steinb...@uni-jena.de> > > Date: Friday, July 28, 2023 at 4:19 AM > > To: Yong Gao <y...@blueprintmedicines.com> > > Cc: "cdk-user@lists.sourceforge.net" <cdk-user@lists.sourceforge.net> > > Subject: Re: [Cdk-user] IUPAC name generation > > [EXTERNAL SENDER] > > You can try our STOUT > > https://github.com/Kohulan/Smiles-TO-iUpac-Translator > > https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00512-4 > > but be aware that this deep learning tool is not deterministic and makes > occasional mistakes. > > If your structures are not too complicated, you can use Egon‘s tip of > cross checking with OPSIN. > > If, of course, you want to name large amounts of structures in an > unsupervised manner, you need a deterministic tool. > > Kind regards, > > Chris > > — > > Prof. Dr. Christoph Steinbeck > > Vice President for Digitalisation of the Friedrich-Schiller-University > Jena > > > > Analytical Chemistry - Cheminformatics and Chemometrics > > Friedrich-Schiller-University Jena, Germany > > Phone Secretariat: +49-3641-948171 > > http://cheminf.uni-jena.de > > http://orcid.org/0000-0001-6966-0814 > > > > What is man but that lofty spirit - that sense of enterprise. > > ... Kirk, "I, Mudd," stardate 4513.3.. > > > > > > Am 27.07.2023 um 17:33 schrieb Yong Gao <y...@blueprintmedicines.com>: > > Hi, > > Has anyone successfully generated IUPAC names from a smiles string? I > see some code in the legacy module, but did not see a way to do it. Also, > any suggestions for doing this with some other open source software? > > Thanks, > > Yong > > CONFIDENTIALITY NOTICE: This electronic mail transmission may contain > privileged, confidential and/or sensitive information and is intended only > for the review of the party to whom it is addressed and for the stated > purpose. Unauthorized use or disclosure is strictly prohibited. If you > have received this transmission in error, please notify > eupriv...@blueprintmedicines.com if you're in the EU or > priv...@blueprintmedicines.com for all other locations. Then immediately > delete the transmission without reading its contents. > > _______________________________________________ > > Cdk-user mailing list > > Cdk-user@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > > CONFIDENTIALITY NOTICE: This electronic mail transmission may contain > privileged, confidential and/or sensitive information and is intended only > for the review of the party to whom it is addressed and for the stated > purpose. Unauthorized use or disclosure is strictly prohibited. If you > have received this transmission in error, please notify > eupriv...@blueprintmedicines.com if you're in the EU or > priv...@blueprintmedicines.com for all other locations. Then immediately > delete the transmission without reading its contents. > > > > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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