Hi Peter,
Without seeing how you're building the molecule this one is a bit tricky to
help with.
If I start with a standard molecule and just adjust the valence count
things are fine:
In [22]: m = Chem.MolFromSmiles('CNC(C)C')
In [23]: m.GetAtomWithIdx(0).SetNumRadicalElectrons(1)
In [24]: mh = Chem.AddHs(m)
In [25]: print(Chem.MolToMolBlock(mh))
RDKit 2D
16 15 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 4 0 0 0 0 0 0
1.5000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.2500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9510 -2.0490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5490 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.5000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0972 -0.7912 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0861 1.3808 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0000 -2.5981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3481 -2.7990 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3314 -1.5474 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7010 -3.3481 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8481 0.2010 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2990 -1.8481 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9630 0.8317 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
3 5 1 0
1 6 1 0
1 7 1 0
1 8 1 0
2 9 1 0
3 10 1 0
4 11 1 0
4 12 1 0
4 13 1 0
5 14 1 0
5 15 1 0
5 16 1 0
M RAD 1 1 2
M END
In [26]: Chem.SanitizeMol(mh)
Out[26]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
In [27]: Chem.SanitizeMol(m)
Out[27]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
How are you constructing the molecule with the radical?
Best,
-greg
On Wed, Nov 14, 2018 at 7:36 PM Peter St. John <[email protected]>
wrote:
> 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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