Hello Changge,
By default, RDKit throws away hydrogens. If you add explicit hydrogens to
mol using AddHs(), it should work. Just add the line
mol = Chem.AddHs(mol)
Ling
On Thu, Jan 19, 2017 at 9:49 AM, Changge Ji <chicago...@gmail.com> wrote:
> Dear All,
>
> I'm a new to rdkit.
>
> I fount that the molecule 'c1ccccc1' don't fit to the smarts
> 'c1cc([#1,F,Cl,I])ccc1'
>
> -------------------------------------------------------
> mol = Chem.MolFromSmiles('c1ccccc1')
> fap = FragmentMatcher.FragmentMatcher()
> smarts = 'c1cc([#1,F,Cl,I])ccc1'
> fap.Init(smarts)
> tp = fap.HasMatch(mol)
>
> result : tp = 0
> -----------------------------------------------------
>
> It seems that it is due to the explict H atom in smarts.
>
> How can I make my smarts work?
>
> Thank you for your help.
>
>
>
>
> Best,
>
>
> ------------------------------
> Changge
>
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