Awesome, thanks! On Thu, 30 Jan 2020 at 11:01, Greg Landrum <greg.land...@gmail.com> wrote:
> 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 >>>> >>>
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
