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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