Hi Jason,
The MMFF94 force field uses a different aromaticity model from the
RDKit; to restore the traditional RDKit aromaticity model you may
useChem.SetAromaticity():
from cresset import flare
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles("Cc1cccc(Oc2cnc(=O)[nH]c2)c1")
m1 = Chem.AddHs(m)
m2 = Chem.Mol(m1)
AllChem.EmbedMolecule(m2);
m2.GetSubstructMatches(Chem.MolFromSmarts('a'))
((1,), (2,), (3,), (4,), (5,), (7,), (8,), (9,), (10,), (12,), (13,), (14,))
AllChem.MMFFOptimizeMolecule(m2);
m2.GetSubstructMatches(Chem.MolFromSmarts('a'))
((1,), (2,), (3,), (4,), (5,), (14,))
Chem.SetAromaticity(m2)
m2.GetSubstructMatches(Chem.MolFromSmarts('a'))
((1,), (2,), (3,), (4,), (5,), (7,), (8,), (9,), (10,), (12,), (13,), (14,))
Cheers,
p.
On 02/05/19 20:31, Jason Biggs wrote:
I noticed that I'm getting a different substructure match depending on
whether I have called the MMFF optimization. This is reproducible in
python with
>> m = Chem.MolFromSmiles("Cc1cccc(Oc2cnc(=O)[nH]c2)c1")
>> m1 = Chem.AddHs(m)
>> m2 = Chem.Mol(m1)
>> AllChem.EmbedMolecule(m2);
>> m2.GetSubstructMatches(Chem.MolFromSmarts('a'))
((1,), (2,), (3,), (4,), (5,), (7,), (8,), (9,), (10,), (12,), (13,), (14,))
>> AllChem.MMFFOptimizeMolecule(m2);
>> m2.GetSubstructMatches(Chem.MolFromSmarts('a'))
((1,), (2,), (3,), (4,), (5,), (14,))
Is this expected behavior? I notice in the C++ code that the
constructor for RDKit::MMFF::MMFFMolProperties will
call MolOps::Kekulize, so maybe this is expected. For my application
it's undesirable, and I can work around it by creating a copy of my
ROMol and generating the MMFFMolProperties object using that copy
(which can then be discarded). Is there a better workaround?
Jason Biggs
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