Thomas - Check out https://www.rdkit.org/docs/RDKit_Book.html#smarts-reference. It's always hard to make a SMARTS expression that works for both implicit hydrogen and explicit hydrogen ROMols. I think that you probably want:
[#6d1] Which will match any carbon with non-hydrogen degree one, including terminal methyls, and also =C and ≡C. If you also want the neighbor: [!#0][#6d1] If you want terminal methyls only: [!#0][#6H3] Good luck! dan nealschneider | senior staff developer *he/him/his* [image: Schrödinger, Inc.] <https://schrodinger.com/> On Mon, Jan 30, 2023 at 8:48 AM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Thomas, > > * in SMARTS just means "any atom". > [!H], for historical reasons, means "and atom without a single Hydrogen" > (i.e. it matches CH2 and CH3, but not CH) > You want [!#0], that is "not hydrogen" > > -greg > > > On Mon, Jan 30, 2023 at 5:40 PM Thomas <odioidenti...@gmail.com> wrote: > >> I thought that the wildcard * would match any atom except hydrogen, but >> that's true unless hydrogens are explicit in the molecule.... >> >> I have some patterns in the form of SMILES with wildcards and implicit >> hydrogens. For example C* means "terminal carbons" only. >> (" * " stands for any atom except hydrogen) >> >> I want to transform this SMILES in SMARTS, if I just write: >> >> smarts = rdkit.MolFromSmarts('*C') >> >> the smarts I get matches any C with AT LEAST one non-hydrogen bond (not >> EXACTLY one). >> >> If I add explicit hydrogens to the smarts (and to the molecules to be >> tested) >> >> smartsH = rdkit.AddHs(smarts) >> rdkit.MolToSmiles(smartsH) >> '*C([H])([H])[H]' >> >> I get this pattern where the wildcard matches ANY atom including hydrogen >> (it matches with the single carbon atom). >> >> Basically I am trying to get the SMARTS *C[H3] starting from the >> respective SMILES *C. Is there a way? >> >> I've already tried to replace the * with a [!H] (NOT hydrogen) with no >> luck. >> Thanks to anyone :) >> Thomas >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
