TranslateAMolecule

How can I rotate an entire Molecule?

Rotating an entire molecule, single atom or any other AtomContainer can be done with the help of BALL's TransformationProcessor:

Specify a rotation-matrix:

#include <BALL/MATHS/angle.h>
#include <BALL/COMMON/constants.h>
#include <BALL/MATHS/vector3.h>
#include <BALL/MATHS/matrix44.h>

using namespace BALL;

...
Angle angle = Angle(Constants::PI, true);
Vector3 rotationaxis(1., 0., 0.);

Matrix4x4 mat;
mat.setRotation(angle, rotationaxis); 

Then create a transformation using the rotation-matrix and apply

#include <BALL/STRUCTURE/geometricTransformations.h>

// create
TransformationProcessor transformation(mat);

// apply
molecule->apply(transformation);

Single atoms can be also be transformed by

 atom.setPosition(mat * atom.getPosition());

Note Since objects are not necessarily located in the origin, move your object under consideration into the origin, then rotate, and move back. Otherwise your object will be shifted around.

#include <BALL/STRUCTURE/geometricTransformations.h>
#include <BALL/STRUCTURE/geometricProperties.h>

...

// compute the translation vector to the origin
GeometricCenterProcessor center;
molecule->apply(center);
Vector3 toOrigin = center.getCenter().negate();

// create the translation
TranslationProcessor translation;
translation.setTranslation(toOrigin);

// translate the molecule
molecule->apply(translation);

/* 
*  rotate the molecule here as described above
*/

// move the molecule back to its original center
translation.setTranslation(toOrigin.negate());
molecule->apply(translation);

Information on how to determine a transformation between two proteins can be found here.