/**
* Rotate a group object.
*
* @param group a group to be rotated
* @param m a Matrix object representing the translation matrix
*/
public static final void rotate(Group group, Matrix m) {
AtomIterator iter = new AtomIterator(group);
while (iter.hasNext()) {
Atom atom = (Atom) iter.next();
rotate(atom, m);
}
}
/**
* Rotate a structure object.
*
* @param structure the structure to be rotated
* @param m rotation matrix to be applied
*/
public static final void rotate(Structure structure, Matrix m) {
AtomIterator iter = new AtomIterator(structure);
while (iter.hasNext()) {
Atom atom = (Atom) iter.next();
rotate(atom, m);
}
}
/**
* Rotate a structure.
*
* @param structure a Structure object
* @param rotationmatrix an array (3x3) of double representing the rotation matrix.
* @throws StructureException ...
*/
public static final void rotate(Structure structure, double[][] rotationmatrix)
throws StructureException {
double[][] m = rotationmatrix;
if (m.length != 3) {
throw new StructureException("matrix does not have size 3x3 !");
}
AtomIterator iter = new AtomIterator(structure);
while (iter.hasNext()) {
Atom atom = (Atom) iter.next();
Calc.rotate(atom, rotationmatrix);
}
}
/**
* Shift a Group with a vector.
*
* @param group a group object
* @param a an Atom object representing a shift vector
*/
public static final void shift(Group group, Atom a) {
AtomIterator iter = new AtomIterator(group);
while (iter.hasNext()) {
Atom atom = null;
atom = (Atom) iter.next();
Atom natom = add(atom, a);
double x = natom.getX();
double y = natom.getY();
double z = natom.getZ();
atom.setX(x);
atom.setY(y);
atom.setZ(z);
}
}
/**
* calculate structure + Matrix coodinates ...
*
* @param s the structure to operate on
* @param matrix a Matrix object
*/
public static final void plus(Structure s, Matrix matrix) {
AtomIterator iter = new AtomIterator(s);
Atom oldAtom = null;
Atom rotOldAtom = null;
while (iter.hasNext()) {
Atom atom = null;
atom = (Atom) iter.next();
try {
if (oldAtom != null) {
// System.out.println("before " +getDistance(oldAtom,atom));
}
} catch (Exception e) {
e.printStackTrace();
}
oldAtom = (Atom) atom.clone();
double x = atom.getX();
double y = atom.getY();
double z = atom.getZ();
double[][] ad = new double[][] {{x, y, z}};
Matrix am = new Matrix(ad);
Matrix na = am.plus(matrix);
double[] coords = new double[3];
coords[0] = na.get(0, 0);
coords[1] = na.get(0, 1);
coords[2] = na.get(0, 2);
atom.setCoords(coords);
try {
if (rotOldAtom != null) {
// System.out.println("after " + getDistance(rotOldAtom,atom));
}
} catch (Exception e) {
e.printStackTrace();
}
rotOldAtom = (Atom) atom.clone();
}
}