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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