Re: [Rdkit-discuss] Problems minimising

2021-12-14 Thread Tim Dudgeon 
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  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 
> 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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[Rdkit-discuss] Problems minimising

2021-12-14 Thread Tim Dudgeon 
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 
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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