Hi,
I don't really know what's going on here, but you could try [#5!B] for you
SMARTS.
#5 to match any boron, and !B to disallow non-aromatic.
Matt
On 18 Feb 2014, at 16:05, Elizabeth Wylie <ewyli...@gmail.com> wrote:
> Hello All,
>
> I have a series of 'aromatic' compounds in SMILES provided from a large
> database. These may or may not be nonsensical compounds, but I'm running into
> issues finding SMARTS expressions that can match an aromatic boron atom.
>
> example:
> In [1]: from rdkit import Chem
>
> In [2]: s = "Cb1c2sccc2cnn#1"
>
>
>
> In [3]: m = Chem.MolFromSmiles(s)
>
>
>
> In [4]: t = Chem.MolFromSmarts('B')
>
>
>
> In [5]: m.HasSubstructMatch(t)
>
>
> Out[5]: False
>
> In [6]: t = Chem.MolFromSmarts('[b]')
>
>
> [09:54:18] SMARTS Parse Error: syntax error for input: [b]
>
> In [7]: m.Debug()
> Atoms:
> 0 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
> 1 5 B chg: 0 deg: 3 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0
> 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0
> 3 16 S chg: 0 deg: 2 exp: 2 imp: 0 hyb: 3 arom?: 1 chi: 0
> 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
> 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
> 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0
> 7 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
> 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0
> 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0
> Bonds:
> 0 0->1 order: 1 conj?: 0 aromatic?: 0
> 1 1->2 order: 12 conj?: 1 aromatic?: 1
> 2 2->3 order: 12 conj?: 1 aromatic?: 1
> 3 3->4 order: 12 conj?: 1 aromatic?: 1
> 4 4->5 order: 12 conj?: 1 aromatic?: 1
> 5 5->6 order: 12 conj?: 1 aromatic?: 1
> 6 6->7 order: 12 conj?: 1 aromatic?: 1
> 7 7->8 order: 12 conj?: 1 aromatic?: 1
> 8 8->9 order: 12 conj?: 1 aromatic?: 1
> 9 9->1 order: 3 conj?: 1 aromatic?: 1
> 10 6->2 order: 12 conj?: 1 aromatic?: 1
>
>
> I understand that the lowercase aromatic notation for boron is not accepted
> in Daylight, but the SMILES parser in RDKit does not seem to have any issues
> with it within the molecule. Is there a different SMARTS expression that I'm
> missing that would match these boron atoms?
>
> This seems like inconsistent behavior given the example below where an
> aromatic form matches a non-aromatic SMARTS:
>
> In [12]: s =
> 'c1c[se]c(C2CN(c3ccccc3)N=C2c2ccc(C3=NN(c4ccccc4)CC3c3ccc[se]3)s2)c1'
>
> In [13]: m = Chem.MolFromSmiles(s)
>
>
> In [14]: m
> Out[14]: <rdkit.Chem.rdchem.Mol at 0x28f90c0>
>
> In [15]: t = Chem.MolFromSmarts('[Se]')
>
> In [16]: m.HasSubstructMatch(t)
> Out[16]: True
>
>
> Thanks
>
> Liz Wylie
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