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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