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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