Untested, but try "mol.GetData(ob.ConformerData)". I note that the value of
ConformerData is 4 not 1.
- Noel
On Tue, 4 Feb 2020 at 00:10, Shiring, Stephen B <sshir...@purdue.edu> wrote:
> Hi all,
>
>
>
> I’m writing a Python script to screen a bunch of molecules, and for part
> of that I would like to read in and optimize a geometry using OpenBabel’s
> ForceField methods subjected to a couple constraints. I would like to
> obtain the resulting forces for each atom from the optimization to use as
> an initial cut off. Avagadro will print out force arrows during an
> optimization and I see in the API documentation that functions exist to
> obtain the forces, however, I keep getting an error when I try to implement
> this. For reference, I am using OpenBabel 2.4.1 installed through conda.
>
>
>
> Using the openbabel module with
>
> --
>
> conv = openbabel.OBConversion()
>
> conv.SetInAndOutFormats('xyz','xyz')
>
>
>
> mol = openbabel.OBMol()
>
> conv.ReadFile(mol,'my_molecule.xyz’)
>
>
>
> constraints = openbabel.OBFFConstraints()
>
> constraints.AddAtomConstraint(1)
>
> constraints.AddAtomConstraint(2)
>
>
>
> forcefield = openbabel.OBForceField.FindForceField("UFF")
>
> forcefield.Setup(mol, constraints)
>
> forcefield.SetConstraints(constraints)
>
>
>
> forcefield.ConjugateGradients(500)
>
> forcefield.GetCoordinates(mol)
>
>
>
> data = openbabel.toConformerData(mol.GetData(1))
>
> f = data.GetForces()
>
>
>
> --
>
>
>
> I get this error:
>
> --
>
> terminate called after throwing an instance of 'std::bad_alloc'
>
> what(): std::bad_alloc
>
> Aborted
>
> --
>
>
>
> Can anyone shed any light on this and possibly point me in the right
> direction?
>
>
>
> Thanks for your time,
>
>
> Stephen
>
>
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