Hi Jameed,
On Wed, Apr 10, 2013 at 9:07 AM, Jameed Hussain
<jameed.x.huss...@gsk.com> wrote:
>
> Just noticed this bug in the reaction functionality. I want to apply the
> following transform:
>
> [*:1]c1ccc([*:2])o1>>[*:1]c1ccc([*:2])cc1
>
> To the following reactant:
>
> Cc1ccc(CC)o1
>
> Code:
>
> In [1]: from rdkit import Chem
> In [2]: from rdkit.Chem import AllChem
]> In [3]: rxn =
> AllChem.ReactionFromSmarts('[*:1]c1ccc([*:2])o1>>[*:1]c1ccc([*:2])cc1')
>
> In [4]: ps = rxn.RunReactants( (Chem.MolFromSmiles('Cc1ccc(CC)o1')) )
>
> ---------------------------------------------------------------------------
>
> ArgumentError Traceback (most recent call last)
>
> <ipython-input-4-6b04a2899e4e> in <module>()
>
> ----> 1 ps = rxn.RunReactants( (Chem.MolFromSmiles('Cc1ccc(CC)o1')) )
>
>
>
> ArgumentError: Python argument types in
>
> ChemicalReaction.RunReactants(ChemicalReaction, Mol)
>
> did not match C++ signature:
>
> RunReactants(RDKit::ChemicalReaction*, boost::python::list)
>
> RunReactants(RDKit::ChemicalReaction*, boost::python::tuple)
>
>
>
> It appears that the RunReactants function expects two reactants and does not
> work with just one reactant - this is only the case when you specify a tuple
> as the input. If you use a list/array instead, it works fine:
You're actually not providing a tuple in the above call. In python you
have to use a comma to create a single-element tuple:
In [5]: (1)
Out[5]: 1
In [6]: (1,)
Out[6]: (1,)
To look at your example:
In [7]: rxn =
AllChem.ReactionFromSmarts('[*:1]c1ccc([*:2])o1>>[*:1]c1ccc([*:2])cc1')
In [8]: ps = rxn.RunReactants( (Chem.MolFromSmiles('Cc1ccc(CC)o1'),) )
In [9]: Chem.MolToSmiles(ps[0][0])
Out[9]: 'CCc1ccc(C)cc1'
-greg
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