It's worth noting that you can write a python function to do this, but I just don't think it's possible to express it as a SMARTS.
Here's a gist showing how to identify (and highlight) the rings in a molecule which contain atoms matching particular substructure queries; https://gist.github.com/greglandrum/798f555959e04356537d63d659dd8e76 I'm going to do a blog post on this in the next day or so with more details because I think it demonstrates a couple of interesting and useful tricks,[1] but here's a quick explanation: getSharedRings() takes a molecule and a list of query molecules. It returns all rings (as atom indices) from the molecule which contain at least one of each type of "matching atom". In this case a "matching atom" is the first atom in each of the query molecules. Best -greg [1] plus it was kind of fun to think about and put together. On Wed, Jan 29, 2020 at 7:21 PM Alexis Parenty < alexis.parenty.h...@gmail.com> wrote: > 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 >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Rdkit-discuss mailing list >>>> Rdkit-discuss@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>> >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >>
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