Worked it out for myself.
I needed to use:
Chem.AddHs(mol, addCoords=True)
Doh!
On Tue, Dec 14, 2021 at 5:45 PM Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> I'm seeing lots of failures when minimising molecules using
> MMFFOptimizeMolecule.
> A large proportion of seemingly valid molecules seem to fail.
> Am I doing something stupid here?
>
> Example:
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> molblock = '''
> RDKit 3D
>
> 5 4 0 0 0 0 0 0 0 0999 V2000
> 10.2630 -5.8010 25.0960 N 0 0 0 0 0 0 0 0 0 0 0 0
> 8.8220 -3.5490 23.3680 C 0 0 0 0 0 0 0 0 0 0 0 0
> 8.2100 -4.7890 24.0210 C 0 0 0 0 0 0 0 0 0 0 0 0
> 9.1000 -5.2470 25.1770 C 0 0 0 0 0 0 0 0 0 0 0 0
> 8.5860 -5.0380 26.4480 N 0 0 0 0 0 0 0 0 0 0 0 0
> 3 2 1 0
> 4 1 2 0
> 4 3 1 0
> 5 4 1 0
> M END
> '''
>
> mol = Chem.MolFromMolBlock(molblock)
> print("Processing", Chem.MolToSmiles(mol))
> molh = Chem.AddHs(mol)
> converged = AllChem.MMFFOptimizeMolecule(molh)
>
>
> Outcome:
>
> Processing CCC(=N)N
> [17:41:57]
>
> ****
> Invariant Violation
> bad direction in linearSearch
> Violation occurred on line 234 in file
> /home/conda/feedstock_root/build_artifacts/rdkit_1620892510968/work/Code/Numerics/Optimizer/BFGSOpt.h
> Failed Expression: status >= 0
> ****
>
> Traceback (most recent call last):
> File "/data/work/jku/5V6S/simple-min.py", line 23, in <module>
> converged = AllChem.MMFFOptimizeMolecule(molh)
> RuntimeError: Invariant Violation
> bad direction in linearSearch
> Violation occurred on line 234 in file
> Code/Numerics/Optimizer/BFGSOpt.h
> Failed Expression: status >= 0
> RDKIT: 2021.03.2
> BOOST: 1_74
>
>
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