That's great. (You can tell I have been elsewhere for several years!). I've now switched to Python for about 4-5 years and wondered if there was demand. At heart CML is a structured ontology/knowledge graph and it doesn't matter whether it's Java or Python (or possibly JS), and whether it's XML or JSON or YAML. Or LISP :-) And is there anything missing? We did surfaces and fragments and uncertainty - don't know if there are other specialist domains.
P. On Thu, Jul 31, 2025 at 3:00 PM Geoffrey Hutchison < [email protected]> wrote: > There’s already a chemical JSON, inspired by CML. It’s used by Avogadro > and has support in OpenBabel. Several computational packages also support > it. > > https://github.com/OpenChemistry/chemicaljson > https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0241-z > > If you have suggestions or ideas on extending it, please submit them. It’s > intended to be extendable, particularly through key/value properties. > > Best, > Geoff > On Jul 31, 2025 at 8:40 AM -0400, Egon Willighagen < > [email protected]>, wrote: > > I am fine with Java (and can use the CDK and other Java tools in Python). > > But CML (Core) in JSON and/or JSON-LD and/or YAML could be interesting. > > Egon > > On Tue, 29 Jul 2025 at 16:17, Peter Murray-Rust via Blueobelisk-discuss < > [email protected]> wrote: > >> Is there a need (or desire) for a Python implementation of CML? (Or does >> it already exist?) . Given today's tools (such as Cursor) it should be >> fairly easy to implement the current schema and CML-XOM in Python. In >> particular if there are conformance tests in Java or other languages that's >> a strong way to implement a parallel version. >> >> P >> >> -- >> Peter Murray-Rust >> Founder ContentMine.org >> and >> Reader Emeritus in Molecular Informatics >> Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK >> _______________________________________________ >> Blueobelisk-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss >> > > > -- > -- > E.L. Willighagen > Department of Translational Genomics > NUTRIM Institute of Nutrition and Translational Research in Metabolism > Maastricht University > Blog: https://chem-bla-ics.linkedchemistry.info/ > Mastodon: https://social.edu.nl/@egonw > PubList: https://orcid.org/0000-0001-7542-0286 > _______________________________________________ > Blueobelisk-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > > -- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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