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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