Hi Matthew,
On Fri, Jan 30, 2015 at 11:06 PM, Matthew Lardy <mla...@gmail.com> wrote:
>
> I am having an issue using the Smarts based Reaction transformations in
> RDKit. This is a weird transformation, but I wanted to replace any or all
> of the protons on an aromatic ring with an F.
>
> The original transformation that I tried was:
> ccc>>cc(F)c
>
> But that didn't work. So then I tried a couple of other transformations:
>
> [c:1][c:2][c:3]>>[c:1][c:2]([F])[c:3]
>
> That failed (as these things generally were failing):
> >>> ps = rxn.RunReactants(mol1)
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> Boost.Python.ArgumentError: Python argument types in
> ChemicalReaction.RunReactants(ChemicalReaction, Mol)
> did not match C++ signature:
> RunReactants(class RDKit::ChemicalReaction *, class
> boost::python::list)
> RunReactants(class RDKit::ChemicalReaction *, class
> boost::python::tuple)
>
>
The hint to what is going on is in the error message: you called the
RunReactants method with a Mol (the ChemicalReaction in the argument list
is the "self" argument) and it was expecting either a list or a tuple.
Here's a version that works:
In [8]: rxn =
AllChem.ReactionFromSmarts('[c:1][c:2][c:3]>>[c:1][c:2]([F])[c:3]')
In [9]: m = Chem.MolFromSmiles('c1ccccc1')
In [10]: ps = rxn.RunReactants((m,))
In [11]: len(ps)
Out[11]: 12
In [12]: Chem.MolToSmiles(ps[0][0])
Out[12]: 'Fc1ccccc1'
Note that this still doesn't really do what you want, because it's encoded
to add an F to an aromatic carbon. Here's an example that shows that:
In [15]: m = Chem.MolFromSmiles('c1ccc(C)cc1')
In [16]: ps = rxn.RunReactants((m,))
In [17]: len(ps)
Out[17]: 12
In [18]: set([Chem.MolToSmiles(x[0],True) for x in ps])
Out[18]: {'Cc1(F)ccccc1', 'Cc1ccc(F)cc1', 'Cc1cccc(F)c1', 'Cc1ccccc1F'}
Note the first product: the F was also added to the carbon with the methyl
group.
We can fix that by specifying that the reacting carbon must have an H
attached:
In [22]: rxn =
AllChem.ReactionFromSmarts('[c:1][cH:2][c:3]>>[c:1][c:2]([F])[c:3]')
In [23]: ps = rxn.RunReactants((m,))
In [24]: len(ps)
Out[24]: 10
In [25]: set([Chem.MolToSmiles(x[0],True) for x in ps])
Out[25]: {'Cc1ccc(F)cc1', 'Cc1cccc(F)c1', 'Cc1ccccc1F'}
There's still the question of why so many products are being produced. Look
at Out[24], why do we get 10 different products?
The answer is the symmetry in the query describing the reactant. Everywhere
this query can match, it matches twice - frontwards and backwards. So
instead of five products, three of which are unique, we get ten.
This can be handled by recognizing that [c:1] and [c:3] are not actually
involved in the reaction, they are just there to define the environment of
[c:2]. We can do the same thing with a recursive SMARTS:
In [30]: rxn = AllChem.ReactionFromSmarts('[cH&$(c(c)c):2]>>[c:2][F]')
In [31]: ps = rxn.RunReactants((m,))
In [32]: len(ps)
Out[32]: 5
In [33]: set([Chem.MolToSmiles(x[0],True) for x in ps])
Out[33]: {'Cc1ccc(F)cc1', 'Cc1cccc(F)c1', 'Cc1ccccc1F'}
Hope this helps,
-greg
> Then I got desperate:
>
> [#6:1][#6:2]([#1])[#6:3].[H][#9:4]>>[#6:1][#6:2]([#9:4])[#6:3]
>
> Any mention of an explicit H caused issues, so then I dropped it and
> re-ran things again.
>
> No luck. I should mention that I am using the pre-built python RDKit
> wrappers for windows, and if I use the java wrappers on linux I get
> different errors but the same outcome.
>
> I should add, that the molecule that I read (and the molecule for HF) were
> both loaded without issue.
>
> Anyone else try to do something like this?
>
> Matthew
>
>
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