On 05/19/2011 02:00 PM, David Lonie wrote:
> Hi Fabien,
>
> On Thu, May 19, 2011 at 5:09 AM, Archambault Fabien
> <fabien.archamba...@nanotimes.fr> wrote:
>> I believe hte function I have to use is Avogadro.Navigate.rotate
>> Its help is:
>> rotate( (GLWidget)arg1, (object)arg2, (float)arg3, (float)arg4,
>> (float)arg5) -> None :
>> Rotate about center by deltaX, deltaY, and deltaZ in the x, y and z
>> axes A generalization of the rotate() and tilt() methods.
> That method will rotate the camera, not the molecule. To rotate the
> molecule itself, you will need to manually set each atom's position
> using the Molecule.pos() and Molecule.setPos() functions (I think that
> is the correct python syntax?).
>
> There is a tutorial extension that shows how to rotate selected atoms
> around an arbitrary vector -- it is in C++, but should offer some help
> as to how a rotation can be performed. The source code can be found in
> libavogadro/examples/thirdPartyExtensions/04-RotateSelection/rotateselectionextension.cpp
> of the avogadro master branch.
>
> The function that actually performs the rotation is here:
>
> https://github.com/cryos/avogadro/blob/master/libavogadro/examples/thirdPartyExtensions/04-RotateSelection/rotateselectionextension.cpp#L107
>
> The key bits are:
>
> Eigen::AngleAxis<double> rot (angle * DEG_TO_RAD, axis.normalized());
>
> This essentially constructs a rotation matrix 'rot' using the
> Eigen::AngleAxis transform from an angle and axis vector.
>
> Then it's a matter of iterating through the atoms and applying the rotation:
>
> for (int i = 0; i< selected.size(); i++) {
> atom = qobject_cast<Atom*>(selected.at(i));
> // you'll probably want 'atom = mymolecule.atoms().at(i)' in your app
> // instead of the above line
> coord = *atom->pos(); // extract coordinate
> coord -= offset; // Optional: offset the rotation axis
> coord = rot * coord; // Apply rotation
> coord += offset; // reset offset
> atom->setPos(coord); // Set new coordinate
> }
>
> Hope this helps,
>
> Dave
Hi,
thanks for this reply.
I did not notice that it was for the camera. This explains the widget...
I tried to look at the code but I do not "speak" C++ so I believe I will
have a hard time to understand... The main problem, for me, is that the
class setPos does not exists in the python binding.
Here are all the available classes for the atom object (in python) :
for atom in mol.atoms:
print atom.
atom.__class__ atom.__init__ atom.__sizeof__
atom.forceVector atom.pos
atom.__delattr__ atom.__module__ atom.__str__
atom.formalCharge atom.residue
atom.__dict__ atom.__new__ atom.__subclasshook__
atom.id atom.residueId
atom.__doc__ atom.__reduce__ atom.__weakref__
atom.index atom.type
atom.__format__ atom.__reduce_ex__ atom.atomicNumber
atom.isHydrogen atom.update
atom.__getattribute__ atom.__repr__ atom.bond
atom.neighbors atom.valence
atom.__hash__ atom.__setattr__ atom.bonds
atom.partialCharge
The pos works but not the setPos.
My trial is on a water molecule (h2o.xyz):
$ python
>>> import Avogadro as a
>>> mol = a.MoleculeFile.readMolecule('h2o.xyz')
>>> 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]
>>>
Perhaps this is somewhere else?
I also tried something I believed it should work but it did not move the
atoms:
>>> mol.center
array([-0.34436667, 2.90174 , 2.57850333])
>>> mol.translate(-mol.center)
>>> mol.center
array([ 5.55111512e-17, -1.48029737e-16, 4.44089210e-16])
>>> for atom in mol.atoms:
... print atom.pos
...
[ 0.34805667 -0.16669 0.06057667]
[-0.54278333 -0.60289 0.08765667]
[ 0.19472667 0.76958 -0.14823333]
>>>
The center seems to have moved but no atoms really moved...
If someone knows how to use python bindings in Avogadro and done some
tutorials it should be nice.
Fabien
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