Explicit valence for atom # 37 C greater than permitted

[kexul]

Hi, I'm parametrising CHEMBL3127463 by ProtoCaller with the following code:

lig = Ligand('CC(C)CC(=O)Nc1cc(-c2ccc(C(N)=O)cc2C(=O)O)cc(C2CC(C)(c3ccccc3)c3cc(C(=N)N)ccc3N2)c1', protonated=False, minimise=True)
lig.protonate()
lig.parametrise()

which threw an error:

  File "/data/FEP/prepare/ProtoCaller/Ensemble/Ligand.py", line 183, in protonate
    molecule = _rdkit.AssignBondOrdersFromTemplate(self.molecule, molecule, assign_charge=False)
  File "/data/FEP/prepare/ProtoCaller/Wrappers/rdkitwrapper.py", line 296, in AssignBondOrdersFromTemplate
    _Chem.SanitizeMol(mol)
rdkit.Chem.rdchem.AtomValenceException: Explicit valence for atom # 37 C greater than permitte

[kexul]

After protonated by openbabel, the C turned to C+, which might not be correct. Before: After:

[kexul]

After some digging, I found that Dimorphite-DL may be a good alternative to openbabel , which provide a reasonable protonated result.

[msuruzhon]

It does seem that this issue is related to Open Babel, it would be worth reproducing it outside of ProtoCaller in the newest Open Babel version and if the problem still persists, you should probably submit an issue there.

In any case, I added some basic (experimental!) checks to spot unphysical charges and fix them, so your example should work now. I pushed the update to the development branch, so you can get the update when the conda package is built.

Edit: Dimorphite-DL seems interesting, I will consider adding it to ProtoCaller.

[kexul]

Reproduced with the newest version of openbabel, I'll file an issue there.

As always, thanks for your work!

[kexul]

Hi @msuruzhon , use latest version of openbabel from conda should fix this, see https://github.com/openbabel/openbabel/issues/2353