Thank you Greg you made my day!
For future references, "not hydrogen" is [!#1]
(not [!#0])
Il giorno lun 30 gen 2023 alle ore 17:47 Greg Landrum <
greg.land...@gmail.com> ha scritto:
> 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
>>
>
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