I have a molecule with radicals for which I'm trying to correct the bond
orders.
The mol block I have currently is shown below.
Ultimately it thinks the first carbon (which is supposed to have 2 explicit
hydrogens, 1 C-C bond, and 1 radical electron) has a valence of 5. So when
I try to call `SanitizeMol`, it errors out with too high a valence.
for the problematic atom 'a',
>>> a.GetNumImplicitHs()
RuntimeError: Pre-condition Violation
getNumImplicitHs() called without preceding call to
calcImplicitValence()
>>> a.GetTotalValence()
3 (odd, since this is what I want)
>>> a.UpdatePropertyCache()
ValueError: Sanitization error: Explicit valence for atom # 0 C, 5, is
greater than permitted
And when I print the mol block, it clearly thinks that first carbon as
a valence of 5.
Any suggestions how to fix this?
>>> print(Chem.MolToMolBlock(mol))
9572
RDKit 3D
15 14 0 0 0 0 0 0 0 0999 V2000
2.0411 -0.0455 -0.1061 C 0 0 0 0 0 *5* 0 0 0 0 0 0
0.8127 -0.5644 0.2519 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.3953 0.0049 -0.3294 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6511 1.4326 0.1487 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5741 -0.9060 -0.0263 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1578 0.2387 -1.1430 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9032 -0.4021 0.4366 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7154 -0.7889 1.2330 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2282 0.0219 -1.4109 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8463 1.4378 1.2242 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2197 2.0597 -0.0426 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5161 1.8651 -0.3565 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.7375 -0.9640 1.0535 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3932 -1.9131 -0.4005 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4874 -0.5194 -0.4787 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 7 1 0
2 8 1 0
3 5 1 0
3 4 1 0
3 2 1 0
4 10 1 0
5 13 1 0
6 1 1 0
9 3 1 0
11 4 1 0
12 4 1 0
14 5 1 0
15 5 1 0
M RAD 1 1 2
M END
Thanks!
-- Peter St. John
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