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Generate low energy 3D conformer with python

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Generate low energy 3D conformer with python

phuongdo
Hello, I have some 2D sdf structure and I need to generate 3D conformer, but when I used OBBuilder class, it generated a 3D conformer with high energy. I used ForceField to lower the energy but it seem not to get there yet. Here is my script:

import pybel
import openbabel

conv = openbabel.OBConversion()
mol = openbabel.OBMol()
conv.SetInAndOutFormats("sdf","sdf")
conv.ReadFile(mol,"4.sdf")
builder = openbabel.OBBuilder()
builder.Build(mol)
conv.Convert()

ff = openbabel.OBForceField.FindForceField("mmff94")
ff.Setup(mol)
print ff.Energy()
ff.WeightedRotorSearch(200,25)
print ff.Energy()
ff.UpdateCoordinates(mol)
conv.WriteFile(mol,"4b.sdf")

I tried to use SystematicRotorSearch() but it took long time for molecule with 5 rotatable bonds.
Please comment how to modify it.

Best wishes,
Phuong Do
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