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 
>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 
Is this presumption correct?

From: Guillaume GODIN []
Sent: Thursday, October 05, 2017 22:59
To: Bennion, Brian <>; RDKit Discuss 
( <>
Subject: RE: UFF atom type errors


Can you provide a small sdf contains molecules that have this issue ?

thanks in advance,


Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
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De : Bennion, Brian <<>>
Envoyé : vendredi 6 octobre 2017 06:11
À : RDKit Discuss 
Objet : [Rdkit-discuss] UFF atom type errors

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?


for m in ms:
#add hydrogen atoms to the molecule before generating 3D coordinates
#start generating 3D coordinates and optimize the conformation
  if embedError == 0 :
  elif UffoptError != 0 :
       print ("UFF optimization failed, trying MMFF optimization")
  elif MMFFoptError != 0 :
       print ("MMFF optimizaiton has also failed on: ", molName)
       print ("Continuing on to next molecule")
     print("Embedding Failed for: ", molName)

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