[Rdkit-discuss] Substructure matching misbehaving with bridged atoms?
I've been using the substructure match with query molecules to do an R-Group decomposition. This works well, except in the case where the query molecule contains a 'bridged atom in a ring. Take this example (I've replaced the irrelevant part with a Y atom for confidentiality) FC1=CC=C(N2CC3CC2CN3S(=O)(=O)C2=CC=C([Y])C=C2)C2=CC=CC=C12 [image: image.png] Using the following as a query, you get the usual result you'd expect: *-N1CC2CC1CN2S(-*)(=O)=O [image: image.png] However, I also see when I do the match: [image: image.png] Even switching back to the R-group code from before the latest refactor seems to have this issue, like the query molecule is perceived as having the actual bridged ring, and the smaller ring bounded by the bridge atom. Am I missing an obvious setting to exclude those latter matches, as obviously the groups generated do not match reality in this case. Such as it is, I'm doing everything via a version of Pat Walters R-Group method from the older RDkit, with the list to generate SMILES coming from: match_list = test_mol.GetSubstructMatches(self.query_mol, False) ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] substructure matching
I get both to be True using version 2020.03.04
On 21 Jul 2020, at 14.08, Quoc-Tuan DO
mailto:quoctuan...@greenpharma.com>> wrote:
Hello,
I am not very familiar with smiles/smarts and find the following results quite
puzzling:
>>> patt =
>>> Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c23.c1ccc(cc1)C~C2NC~Cc3c23')
>>> mol =
>>> Chem.MolFromSmiles('COc1ccc2cc1Oc1ccc(cc1)CC1N(C)CCc3c1c1Oc4cc5C(C2)NCCc5cc4Oc1c(c3)OC')
>>> print mol.HasSubstructMatch(patt)
False
>>> mol =
>>> Chem.MolFromSmiles('COc1ccc7cc1Oc2ccc(cc2)CC3N(C)CCc4c3cc(c(c4)OC)Oc5ccc6c(c5)CCNC6C7')
>>> print mol.HasSubstructMatch(patt)
True
It seems that a presence of an extra Ph - O - Ph makes the difference but I am
not sure why. How should the smarts be to have positive results for both smiles
?
Thank you in advance for your help.
Best regards,
Quoc-Tuan
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Re: [Rdkit-discuss] substructure matching
Hi Quoc-Tuan,
I can't reproduce your observations; I get True in both cases. Which
version of RDKit are you using?
One thing to note is that you are parsing a SMARTS with MolFromSmiles. I
wouldn't recommend that in general, although it appears that in this case
RDKit is lenient enough to accept "~" in a SMILES and turn it into a
QueryBond. What happens if you use MolFromSmarts instead?
Ivan
On Tue, Jul 21, 2020 at 8:12 AM Quoc-Tuan DO
wrote:
> Hello,
>
> I am not very familiar with smiles/smarts and find the following results
> quite puzzling:
>
> >>> patt =
> Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c23.c1ccc(cc1)C~C2NC~Cc3c23')
>
> >>> mol =
> Chem.MolFromSmiles('COc1ccc2cc1Oc1ccc(cc1)CC1N(C)CCc3c1c1Oc4cc5C(C2)NCCc5cc4Oc1c(c3)OC')
>
> >>> print mol.HasSubstructMatch(patt)
>
> False
>
> >>> mol =
> Chem.MolFromSmiles('COc1ccc7cc1Oc2ccc(cc2)CC3N(C)CCc4c3cc(c(c4)OC)Oc5ccc6c(c5)CCNC6C7')
>
> >>> print mol.HasSubstructMatch(patt)
>
> True
>
> It seems that a presence of an extra Ph* - O - *Ph makes the difference
> but I am not sure why. How should the smarts be to have positive results
> for both smiles ?
>
> Thank you in advance for your help.
>
> Best regards,
>
> Quoc-Tuan
>
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>
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[Rdkit-discuss] substructure matching
Hello,
I am not very familiar with smiles/smarts and find the following results quite puzzling:
>>> patt = Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c23.c1ccc(cc1)C~C2NC~Cc3c23')
>>> mol = Chem.MolFromSmiles('COc1ccc2cc1Oc1ccc(cc1)CC1N(C)CCc3c1c1Oc4cc5C(C2)NCCc5cc4Oc1c(c3)OC')
>>> print mol.HasSubstructMatch(patt)
False
>>> mol = Chem.MolFromSmiles('COc1ccc7cc1Oc2ccc(cc2)CC3N(C)CCc4c3cc(c(c4)OC)Oc5ccc6c(c5)CCNC6C7')
>>> print mol.HasSubstructMatch(patt)
True
It seems that a presence of an extra Ph - O - Ph makes the difference but I am not sure why. How should the smarts be to have positive results for both smiles ?
Thank you in advance for your help.
Best regards,
Quoc-Tuan
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Re: [Rdkit-discuss] substructure matching
Hello,
I am not very familiar with smiles/smarts and find the following results quite puzzling:
>>> patt = Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c23.c1ccc(cc1)C~C2NC~Cc3c23')
>>> mol = Chem.MolFromSmiles('COc1ccc2cc1Oc1ccc(cc1)CC1N(C)CCc3c1c1Oc4cc5C(C2)NCCc5cc4Oc1c(c3)OC')
>>> print mol.HasSubstructMatch(patt)
False
>>> mol = Chem.MolFromSmiles('COc1ccc7cc1Oc2ccc(cc2)CC3N(C)CCc4c3cc(c(c4)OC)Oc5ccc6c(c5)CCNC6C7')
>>> print mol.HasSubstructMatch(patt)
True
It seems that a presence of an extra Ph - O - Ph makes the difference but I am not sure why. How should the smarts be to have positive results for both smiles ?
Thank you in advance for your help.
Best regards,
Quoc-Tuan
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