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Varied sanitise rejection with hydrogen representation #418

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johnmay opened this issue Jan 29, 2015 · 1 comment
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Varied sanitise rejection with hydrogen representation #418

johnmay opened this issue Jan 29, 2015 · 1 comment
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@johnmay
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johnmay commented Jan 29, 2015

Performing sanitise on the two SMILES below results in the first raising the following exception (expected) and the second one not.

Explicit valence for atom # 34 N, 5, is greater than permitted

The second SMILES is representing the same compound but as Kekulé, with explicit hydrogens, and different ordering .

CC(C)CN(CC(O)C(Cc1ccccc1)NC(=O)OC1CCOC1)S(=O)(=O)c1ccc(cc1)[NH2]=N a
[H]O[C@]([H])(C([H])([H])N(C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])S(=O)(=O)C1=C([H])C([H])=C(C([H])=C1[H])N([H])([H])=N)[C@@]([H])(N([H])C(=O)O[C@]2([H])C([H])([H])OC([H])([H])C2([H])[H])C([H])([H])C3=C([H])C([H])=C([H])C([H])=C3[H] b
@greglandrum
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A simpler reproducible:

In [5]: m = Chem.MolFromSmiles('[H]N([H])([H])[H]')

In [6]: m.Debug()
Atoms:
    0 7 N chg: 0  deg: 0 exp: 0 imp: 3 hyb: 4 arom?: 0 chi: 0
Bonds:

In [8]: m = Chem.MolFromSmiles('[2H]N([2H])([2H])[2H]')
[11:53:29] Explicit valence for atom # 1 N, 4, is greater than permitted

Yep, that's a bug. Thanks for reporting it.

@greglandrum greglandrum added this to the 2015_03_1 milestone Jan 29, 2015
@greglandrum greglandrum self-assigned this Jan 29, 2015
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