Hi Paolo,
Thanks, this is an interesting feature - may come useful one day!
I found a different solution - via torsion constraints:
mp = ChemicalForceFields.MMFFGetMoleculeProperties(mol)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(mol, mp)
sp=Chem.MolFromSmarts(c1ccsc1!@c) #thiophene
Dear Michal,
please find attached a small script which accomplishes what you describe
by a different approach, i.e. it minimizes only the methyl group in
2-methylthiophene while keeping the rest fixed, effectively pushing it
back in plane. Would that work for you?
Best,
Paolo
On 04/15/2015
Hello,
I'm trying to manipulate out-of-plane bends of substituents attached to
aromatic rings. Obviously, they should lie in the plane of the ring, but
sometimes (after constrained optimization) they come slightly out of plane
and there doesn't seem to be a way to push/rotate them back to the ring
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