Hi!
I'm running at an issue with implicit hydrogens on aromatic heteroatoms. I
am feeding the following sdf into a mol object:
Mrv16c5 10021719092D
28 31 0 0 0 0 999 V2000
-2.9000 0.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1871 0.6228 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0063 0.2957 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7486 0.6354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4657 0.2118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5599 0.9164 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9000 -0.6228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1829 -1.0380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4657 -0.6228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6214 0.6228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6731 1.4574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1405 1.6335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8646 0.5976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3860 0.8367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0384 0.6731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3469 1.2687 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7257 0.0818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8641 1.5161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6861 1.4322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5477 -0.0021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1829 -1.8683 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-3.6297 1.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2085 -0.1656 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.6214 -1.0463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3385 0.1992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3385 -0.6311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3469 1.8600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9042 1.8683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 2 2 0 0 0 0
6 3 1 0 0 0 0
7 1 1 0 0 0 0
8 7 1 0 0 0 0
9 8 2 0 0 0 0
10 1 2 0 0 0 0
11 4 2 0 0 0 0
12 11 1 0 0 0 0
13 15 1 0 0 0 0
14 6 1 0 0 0 0
15 19 1 0 0 0 0
16 13 2 0 0 0 0
17 14 2 0 0 0 0
18 14 1 0 0 0 0
19 18 2 0 0 0 0
20 17 1 0 0 0 0
21 8 1 0 0 0 0
22 10 1 0 0 0 0
23 13 1 0 0 0 0
24 7 2 0 0 0 0
25 10 1 0 0 0 0
26 25 2 0 0 0 0
27 22 1 0 0 0 0
28 22 1 0 0 0 0
24 26 1 0 0 0 0
9 5 1 0 0 0 0
6 12 2 0 0 0 0
20 15 2 0 0 0 0
M END
$$$$
The nitrogen in the heterocycle should have 1 implicit hydrogen on it, and
when I look at it after initially creating the mol object, it does. I want
to convert it to aromatic form, so I am calling rdmolops.SetAromatize(mol).
Once I do this however, it seems that the implicit hydrogen on the nitrogen
is removed, which then causes an error to be thrown if I ever try to
convert it back to kekule form or do any kind of sanitization. Maybe my
understanding of aromaticity is wrong, but shouldn't the hydrogen be on the
nitrogen regardless of whether or not it is considered to be in an aromatic
form?
I could be misunderstanding rdkit's aromaticity models, but for my
purposes, I want to be able to convert the mol to either kekule or aromatic
form depending on some configuration settings. Is there a way to manipulate
the hydogrens on an atom in this case?
Thanks!
Chris
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