Many thanks for your responses. Recursive smiles become cumbersome to write
when they are on fused aromatics. I was hopping I could write a simple
function that would cover all regio-isomers from any aromatics... Looks
more complicated than I thought!
Thanks,
Alexis
On Wed, 29 Jan 2020 at 13:49, Greg Landrum <greg.land...@gmail.com> wrote:
> I agree with Chris here: I don't think you can do this with dot
> disconnection and that you need to use recursive SMARTS as Chris describes.
>
> A tweak to Chris' answer: if you want the query to look for regioisomers
> around a phenyl ring you unfortunately need to actually specify the whole
> ring in order to avoid having the query match a Cl and a Br in different
> fused rings in some cases. This gets a bit unwieldy:
> Cl[c;$(c1(Cl)c(Br)cccc1),$(c1(Cl)cc(Br)ccc1),$(c1(Cl)ccc(Br)cc1)]
>
> Here's a demo:
>
> In [12]: p =
> Chem.MolFromSmarts('Cl[c;$(c1(Cl)c(Br)cccc1),$(c1(Cl)cc(Br)ccc1),$(c1(Cl)ccc(Br)cc1)]')
>
>
> In [13]: Chem.MolFromSmiles('Clc1c(Br)cccc1').HasSubstructMatch(p)
>
> Out[13]: True
>
> In [14]: Chem.MolFromSmiles('Clc1cc(Br)ccc1').HasSubstructMatch(p)
>
> Out[14]: True
>
> In [15]: Chem.MolFromSmiles('Clc1ccc(Br)cc1').HasSubstructMatch(p)
>
> Out[15]: True
>
> In [16]:
> Chem.MolFromSmiles('ClC1=CC=CC2=C1C(Br)=CC=C2').HasSubstructMatch(p)
>
> Out[16]: False
>
>
> It's harder if you want to actually retrieve the atoms that match the
> query directly using the SMARTS. Hopefully you're just looking for the
> match. :-)
>
> -greg
>
>
> On Wed, Jan 29, 2020 at 1:39 PM Chris Earnshaw <cgearns...@gmail.com>
> wrote:
>
>> Hi
>>
>> Dot-disconnected fragments are not going to work for this, as you
>> describe. You need to use recursive SMARTS (see
>> https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html section
>> 4.4). Something like:
>> Clc[$(cBr);$(ccBr);$(cccBr)]
>> should (I hope!) be a reasonable starting point.
>>
>> Chris Earnshaw
>>
>> On Wed, 29 Jan 2020 at 11:12, Alexis Parenty <
>> alexis.parenty.h...@gmail.com> wrote:
>>
>>> Hi everyone,
>>>
>>>
>>>
>>> Is there a way to get a substructure match of regioisomers using a
>>> smarts by separating the fragments with “.”:
>>>
>>>
>>>
>>> The following approach works but is too permissive since it will also
>>> match structures with a bromide or a chloride linked to a aliphatic
>>> carbon...
>>>
>>>
>>> [image: image.png]
>>>
>>>
>>>
>>> mol_smiles_structure = Chem.MolFromSmiles("Clc1cc(Br)ccc1")
>>>
>>> mol_smarts_fragment = Chem.MolFromSmarts("c1ccccc1.[Cl].[Br]")
>>>
>>> print(mol_smiles_structure.HasSubstructMatch(mol_smarts_fragment))
>>>
>>> ð True
>>>
>>>
>>>
>>>
>>>
>>> mol_smiles_structure = Chem.MolFromSmiles("ClCc1cc(Br)ccc1")
>>>
>>> print(mol_smiles_structure.HasSubstructMatch(mol_smarts_fragment))
>>>
>>> ð True
>>>
>>>
>>>
>>> If I specify that the Br and the Cl need to be attached to an aromatic
>>> to make it less permissive, it no longer match because I cannot specify
>>> that the two general aromatics [a] also belong to the benzene ring... (i,e.
>>> it tries to look for 8 aromatics instead of six...)
>>>
>>> mol_smiles_structure = Chem.MolFromSmiles("Clc1cc(Br)ccc1")
>>>
>>> mol_smarts_fragment = Chem.MolFromSmarts("c1ccccc1.[a][Cl].[a][Br]")
>>>
>>> print(mol_smiles_structure.HasSubstructMatch(mol_smarts_fragment))
>>>
>>> ð False
>>>
>>>
>>>
>>> Thanks!
>>>
>>> Alexis
>>>
>>>
>>>
>>>
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