On 05/19/2011 04:32 PM, Geoffrey Hutchison wrote:
> On May 19, 2011, at 8:54 AM, Archambault Fabien wrote:
>
>> None.None(Atom, numpy.ndarray)
>> did not match C++ signature:
>> None(Avogadro::Atom {lvalue}, Eigen::Matrix<double, 3, 1, 2, 3, 1>)
> The problem seems to be that the conversion between numpy and the vector
> library Eigen isn't working. I'm not sure if there's a good solution to that
> directly.
>
> OTOH, you can always use mol.OBMol to get an OBMol, use the Open Babel or
> Pybel libraries to change the coordinates, and then update the Avogadro
> molecule.
>
> http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html
> http://openbabel.org/docs/dev/UseTheLibrary/PythonExamples.html
>
> I can't say I've used the Avogadro python integration much, but I'll see what
> I can do with the Eigen bindings.
>
> Hope that helps,
> -Geoff
Hi again,
thanks for the tip about the openbabel but I was not yet able to use it
correctly but I am now able to modify the position of the atoms as I
need so I believe I will be soon able to rotate as I need (just a matter
of matrices).
Here is the trick I was using array but in fact it is a ndarray from
numpy. So:
>>> import Avogadro as a
>>> import numpy as np
>>> mol = a.MoleculeFile.readMolecule('h2o.xyz')
>>> zero = np.ndarray((3,), buffer=np.array([0.,0.,0.]), dtype=float)
>>> for atom in mol.atoms:
... print atom.pos
...
[ 0.00369 2.73505 2.63908]
[-0.88715 2.29885 2.66616]
[-0.14964 3.67132 2.43027]
>>> for atom in mol.atoms:
... atom.pos = zero
...
>>> for atom in mol.atoms:
... print atom.pos
...
[ 0. 0. 0.]
[ 0. 0. 0.]
[ 0. 0. 0.]
>>>
This was not that hard! I should have thought at those ndarrays...
Thanks for the help again!
Fabien
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