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?
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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
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________________________________
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
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