Hi, Alexis,
Why don’t you output the molecule as “Smiles” format since the “Smarts” you
wanted to output was really a molecule.
And it is possible to remove the dummy atom via mol object. For example:
In [26]: x = Chem.MolFromSmiles('CC*')
In [27]: x.GetSubstructMatch(Chem.MolFromSmiles('*'))
Out[27]: (2,)
In [28]: mw = Chem.RWMol(x)
In [29]: mw.RemoveAtom(2)
In [30]: Chem.MolToSmiles(mw)
Out[30]: 'CC'
But I don’t know whether it can handle SMARTS. Hope that it is helpful for you.
Hongbin Yang
> On 14 Jul 2017, at 4:59 PM, Alexis Parenty <alexis.parenty.h...@gmail.com>
> wrote:
>
> <>Dear Rdkiters,
>
>
>
> I sometimes get smarts from mol in atomic number notation such as:
>
> [#6]-[#7+]1=[#6]2-[#6]3:[#7]:[#6]:[#6]:[#6]:[#6]:3-[#6]3:[#6]:[#6]:[#6]:[#6]:[#6]:3-[#7]-2-[#6]-[#6]-1
>
>
>
> Is there a way to force the method Chem.MolToSmarts(mol) to output a smarts
> using alphabetic letters instead of atomic numbers?
>
> The reason I am asking is because I need to remove dummy atoms [*] from
> smarts using string manipulation and I would rather use only one method.
> Unless I can do that from the mol object?
>
>
>
> Many thanks,
>
>
>
> Alexis
>
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