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
MOBILE          +41 (0)79 536 1039
        Firmenich SA
        RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8

________________________________
De : Bennion, Brian <benni...@llnl.gov<mailto:benni...@llnl.gov>>
Envoyé : vendredi 6 octobre 2017 06:11
À : RDKit Discuss 
(rdkit-discuss@lists.sourceforge.net<mailto: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


**********************************************************************
DISCLAIMER
This email and any files transmitted with it, including replies and forwarded 
copies (which may contain alterations) subsequently transmitted from Firmenich, 
are confidential and solely for the use of the intended recipient. The contents 
do not represent the opinion of Firmenich except to the extent that it relates 
to their official business.
**********************************************************************
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to