Dear All,
I'm generating analogs from a parent compound. An unfortunate side effect
is the generation of various highly strained rings among other compounds.
I'm developing filters to deal with any unwanted generated compounds, but
I'm having difficulty with strained ring systems.
Attached are some examples in mol2 format: https://ufile.io/bdmcp
For this problem I'm thinking of using an energy/bond approach:
ff = AllChem.UFFGetMoleculeForceField(mol)
energy_per_bond = ff.CalcEnergy()/len(mol.GetBonds())
If energy/bond is above a certain value it gets filtered out. Do you think
this is the best solution? Is there a way of viewing each bonds energy
(with increasing amount of bonds an unstable bond might not be filtered)?
Do you have any suggestions on alternate ways of doing this?
Thank you for the help, it is very much appreciated! :)
- James
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