Apparently, the atom IDs returned by TorsionIter are off by one (you
need to add to each of them to get the correct atom ID - I'll file a
bug report I think about this). Hence the segfault when you tried to
access a non-existent atom (or non existent torsion...).
Noel
2008/10/13 Thomas Greve Kristensen <tg...@da...>:
> Hi,
>
> thanks for the help, but I still not sure how to do this. My problem is that
> I can extract the atom ids from TorsionIter, and wtih those I can extract
> the atoms, which I need for getting and setting torsions, but the enclosed
> script results in a segmentation fault.
>
> Is this due to a broken TorsionIter or is it me who are misunderstanding
> something?
>
> Thanks for all your help,
>
> Thomas
>
>
>
>
> On Oct 11, 2008, at 5:15 PM, Noel O'Boyle wrote:
>
>> OBMolTorsionIter may not be working correctly. Apart from that, see
>> OBMol::SetTorsion and OBMol::GetTorsion in the C++ documentation
>> (openbabel.org/api)
>>
>> 2008/10/11 Thomas Greve Kristensen <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 :(
>>>
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>
>
>
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