[OpenBabel-scripting] Rotable bonds

[Thomas G. K. <tg...@da...>]

Hi all,

I'm trying to rotate parts of a molecule around a rotable bond, but I
can't seem to figure out how to do this from python.
My experiments try to rotate the bonds of a ligand to see how the energy
landscape changes. My goal is to experiment with energy minimization
algorithms.

I appreciate all the help I can get...

Thomas G. Kristensen
(phd student, Aarhus University, Denmark)

p.s: This is how far I've gotten so far:

#!/usr/bin/env python
"""
A (hopefully) small test that will reviel how easy
it is to calculate the energy of a molecule using
the open babel python swig bindings.
"""
import pybel
import openbabel

forcefield = openbabel.OBForceField.FindForceField("MMFF94")

if __name__ == "__main__":
    for mol in pybel.readfile("mol2", "ligands.mol2"):
      obmol = mol.OBMol
      forcefield.Setup(obmol)
      print forcefield.Energy()

      for bond in openbabel.OBMolBondIter(obmol):
        print bond.IsRotor() # I cant ask this object to rotate :(

      for torsion in openbabel.OBMolTorsionIter(obmol):
        print torsion # Is not an object, can not be manipulated :(