Yeah, those atom types that you are seeing are the names of the UFF atom
types that the RDKit assigns.
If an atom has a hybridization/charge-state that's not recognized, you'll
get those parameterization errors.

If you're aware of a better way to handle this (or a way to sensibly guess
parameters), please let me know.

-greg


On Fri, Oct 6, 2017 at 8:52 PM, Bennion, Brian <benni...@llnl.gov> wrote:

> CHEMBL1796997 is Helium and the same molecule that throws the first
> UFFTYPER warnings.  Originally I had searched my  sdf file only for He1 and
> found no hits.
>
> From the original Goddard paper in 1992, there is only He4+4 atomtype
> described explicitly.  I can reason based on the error that RDKIT is
> classifying He as He1 and then as He for which there is no formal UFF atom
> type.
>
> Is this presumption correct?
>
>
>
> Brian
>
> *From:* Guillaume GODIN [mailto:guillaume.go...@firmenich.com]
> *Sent:* Thursday, October 05, 2017 22:59
> *To:* Bennion, Brian <benni...@llnl.gov>; RDKit Discuss (
> rdkit-discuss@lists.sourceforge.net) <rdkit-discuss@lists.sourceforge.net>
> *Subject:* RE: UFF atom type errors
>
>
>
> Hello,
>
>
>
> Can you provide a small sdf contains molecules that have this issue ?
>
>
>
> thanks in advance,
>
>
>
> BR,
>
>
>
>
>
> *Dr. Guillaume GODIN*
>
> Principal Scientist
>
> Chemoinformatic & Datamining
>
> Innovation
>
> CORPORATE R&D DIVISION
>
> DIRECT LINE +41 (0)22 780 3645 <+41%2022%20780%2036%2045>
>
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>
>         Firmenich SA
>
>         RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
>
> ------------------------------
>
> *De :* Bennion, Brian <benni...@llnl.gov>
> *Envoyé :* vendredi 6 octobre 2017 06:11
> *À :* RDKit Discuss (rdkit-discuss@lists.sourceforge.net)
> *Objet :* [Rdkit-discuss] UFF atom type errors
>
>
>
> Hello,
>
> As part of my workflow, I am attempting to generate a starting 3D
> structure from a 2D representation loaded from an sdf file.
>
> On certain structures I receive the following UFF errors when attempting
> to minimize the structure.
>
>
>
> [20:50:43] UFFTYPER: Unrecognized atom type: He1 (0)
>
> [20:50:43] UFFTYPER: Unrecognized atom type: He (0)
>
> [20:50:45] UFFTYPER: Unrecognized atom type: B_1 (0)
>
> [20:50:45] UFFTYPER: Unrecognized atom type: B_1 (7)
>
> [20:50:45] UFFTYPER: Unrecognized atom type: B_1 (0)
>
> [20:50:45] UFFTYPER: Unrecognized atom type: B_1 (7)
>
>
>
> I have searched for these atom labels in my 2D sdf file and they don’t
> exist.  So I am not sure how the uff code in rdkit is finding these types.
>
> The relevant code is shown below, in case I am doing something incorrectly.
>
> Any thoughts or suggestions to help me find my mistakes?
>
>
>
> Brian
>
>
>
>
>
> for m in ms:
>
> #add hydrogen atoms to the molecule before generating 3D coordinates
>
>   mHs=Chem.AddHs(m)
>
> #start generating 3D coordinates and optimize the conformation
>
>   embedError=AllChem.EmbedMolecule(mHs,useRandomCoords=True)
>
>   if embedError == 0 :
>
>      UffoptError=AllChem.UFFOptimizeMolecule(mHs,3000)
>
>   elif UffoptError != 0 :
>
>        print ("UFF optimization failed, trying MMFF optimization")
>
>        MMFFoptError=AllChem.MMFFOptimizeMolecule(mHs,3000)
>
>   elif MMFFoptError != 0 :
>
>        print ("MMFF optimizaiton has also failed on: ", molName)
>
>        print ("Continuing on to next molecule")
>
>        continue
>
>   else:
>
>      print("Embedding Failed for: ", molName)
>
>      continue
>
>
>
>
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