Indeed - Andrew's approach is all you can do at the moment. I've often thought it would be a useful option to add, and just a one or two line change to the C++ (just skip the part where the "organic subset" is treated as special).
Regarding SMARTS, given that "CC" is also a valid SMARTS that would match the SMILES "CC", it sounds like you want a bespoke conversion solution. But either way, it's not available as an option. Regards, Noel On Wed, 22 Feb 2023 at 11:06, Thomas <odioidenti...@gmail.com> wrote: > Thank you Andrew, your script does the job. > > Apparently, this was the original behaviour of OB back in 2011, then it > has been preferred to write H as atoms instead ( > https://sourceforge.net/p/openbabel/mailman/message/26960761/). > > I would include your script under GPL license if you don't mind. > Thank you > > Il giorno mer 22 feb 2023 alle ore 11:12 Andrew Dalke < > da...@dalkescientific.com> ha scritto: > >> On Feb 21, 2023, at 19:23, Thomas <odioidenti...@gmail.com> wrote: >> > Is it possible to get SMILES with explicit hydrogens as a "property" of >> another atom? >> > For example from the SMILES "CC" I'd like to get '[CH3][CH3]' instead >> of '[H]C(C([H])([H])[H])([H])[H]' >> >> I don't see a direct way to do it. >> >> I wrote to_H_smiles() at >> https://paste.sr.ht/~dalke/8f51a0df8b37585010ca38b54a337f4efbec8667 >> which I think does what you want. >> >> In short, I add an atom class to each atom, generate the SMILES with the >> 'a' option to include the atom class. As a side-effect, this also include >> the H3 terms you're looking for. I then post-process the output SMILES to >> adjust the atom classes, either to remove them (if the original atom didn't >> have an atom class) or to use the original input value. >> >> > Furthermore, is it possible to generate SMARTS? For example from "CC" >> I'd like to get '[#6]-[#6]' >> >> I don't know of one, though that doesn't mean there isn't one. >> >> >> Andrew >> da...@dalkescientific.com >> >> >> _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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