Hi,
If I have a five membered ring with 2 consecutive Ns and alternating single
and double bonds expressed by the smiles: N1N=CC=C1 RDKit gives me a
molecule in which every atom is aromatic. If I give it: N1=NC=CC1 it gives
me a molecule in which every atom is aliphatic. If I give it: n1nccc1 it
gives me a kekulization error. I, possibly naively, thought the forms would
be all aromatic or all aliphatic. Am I missing something or is this a bug?
>>> Chem.MolFromSmiles('N1N=CC=C1').Debug()
Atoms:
0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0
1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0
2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
Bonds:
0 0->1 order: 12 conj?: 1 aromatic?: 1
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->0 order: 12 conj?: 1 aromatic?: 1
>>> Chem.MolFromSmiles('N1=NC=CC1').Debug()
Atoms:
0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 0 chi: 0
1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 0 chi: 0
2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0
3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0
4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0
Bonds:
0 0->1 order: 2 conj?: 1 aromatic?: 0
1 1->2 order: 1 conj?: 1 aromatic?: 0
2 2->3 order: 2 conj?: 1 aromatic?: 0
3 3->4 order: 1 conj?: 0 aromatic?: 0
4 4->0 order: 1 conj?: 0 aromatic?: 0
>>> Chem.MolFromSmiles('n1nccc1').Debug()
[15:31:44] Can't kekulize mol
Yours,
Toby Wright
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