Re: [OpenBabel-scripting] modify coordinates of a molecule

[Noel O'B. <bao...@gm...>]

Hello Xavier,

Pybel does not allow assignment of coordinate values (the next version
will raise an error when you try, instead of failing silently). To set
the coordinates you need to use the SetVector() method of the
underlying OBAtom, e.g.

>>> mol = pybel.readstring("smi", "CCC")
>>> mol.make3D()
>>> mol.atoms[0].coords
(0.9762193757974641, -0.018350366821008612, 0.0057426618097852662)
>>> a = mol.atoms[0].OBAtom
>>> a.SetVector(1,2,3)
>>> mol.atoms[0].coords
(1.0, 2.0, 3.0)
>>>

Perhaps I will add setting coordinates as a feature in a future
version of Pybel?

- Noel

2009/2/18 Xavier Prat-Resina <xav...@gm...>:
> Hi,
>
> I'm trying to change the coordinates of a molecule using
> the coordinates from another file:
>
> gaussbel = pybel.readfile("g03", "myfile.g03").next()
> molbel   = pybel.readfile("mol", "myfile.mol").next()
>
> If I try to change the coordinates directly:
> molbel.atoms[0].coords[0] = gaussbel.atoms[0].coords[0]
> it gives
> TypeError: 'tuple' object does not support item assignment
>
> I can loop over atoms:
>
> for atom in molbel:
>     (assign x,y,z)
>     atom.coords = numpy.array([x,y,z], "float64")
>
> but then, how can I update the molbel molecule with the new atom.coords?
>
> I know I'm missing something very simple.
> Sorry for such naive questions :)
>
> Xavier
>
> --
> Xavier Prat-Resina
> Research Associate
> Journal of Chemical Education and University of Wisconsin
> 209 N. Brooks St. Madison, WI  53715-1116
>
> Tel: 608 8901702 // Fax: 608 2627145
> e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
> http://x.prat.resina.googlepages.com
>
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