Hi James,
There's not currently any way to get the contributions to the overall
energy from a force field.
Here's one approach to approximate what you're trying to do:
from rdkit import Chem
from rdkit.Chem import AllChem
def fragmentAndGetEnergies(mol,sma='[r]-[!r;!#1]'):
pattern = Chem.MolFromSmarts(sma)
m.GetSubstructMatches(pattern)
bonds = [m.GetBondBetweenAtoms(x[0],x[1]).GetIdx() for x in matches]
splitmol = AllChem.FragmentOnBonds(m,bonds)
frags = Chem.GetMolFrags(splitmol,asMols=True)
res = []
for frag in frags:
ff = AllChem.UFFGetMoleculeForceField(frag)
res.append((Chem.MolToSmiles(frag,True),ff.CalcEnergy()))
return res
m = Chem.AddHs(Chem.MolFromSmiles('c1cccn1CCC1=CC1'))
AllChem.EmbedMolecule(m,AllChem.ETKDG())
vs = fragmentAndGetEnergies(m)
for smi,energy in vs:
print(smi,energy)
The function splits molecules into pieces by breaking single bonds between
rings and non-ring atoms and then calculates the energies of those pieces.
This generates warnings from the UFF code since it doesn't have parameters
for the dummy atoms that FragmentOnBonds() inserts. I think this is
probably ok, but you may want to investigate changing those dummies to
hydrogens (and adjusting the corresponding bond lengths).
Best,
-greg
On Sat, Apr 15, 2017 at 5:11 PM, James Johnson <totalboron...@gmail.com>
wrote:
> 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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