/**
* add two atoms ( a + b).
*
* @param a an Atom object
* @param b an Atom object
* @return an Atom object
*/
public static final Atom add(Atom a, Atom b) {
double[] coords = new double[3];
coords[0] = a.getX() + b.getX();
coords[1] = a.getY() + b.getY();
coords[2] = a.getZ() + b.getZ();
Atom c = new AtomImpl();
c.setCoords(coords);
return c;
}
/**
* calculate distance between two atoms.
*
* @param a an Atom object
* @param b an Atom object
* @return a double
* @throws StructureException ...
*/
public static final double getDistance(Atom a, Atom b) throws StructureException {
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
double s = x * x + y * y + z * z;
double dist = Math.sqrt(s);
return dist;
}
/**
* substract two atoms ( a - b).
*
* @param a an Atom object
* @param b an Atom object
* @return an Atom object
* @throws StructureException ...
*/
public static final Atom substract(Atom a, Atom b) throws StructureException {
nullCheck(a);
nullCheck(b);
double[] coords = new double[3];
coords[0] = a.getX() - b.getX();
coords[1] = a.getY() - b.getY();
coords[2] = a.getZ() - b.getZ();
Atom c = new AtomImpl();
c.setCoords(coords);
return c;
}
/**
* Shift a vector.
*
* @param a vector a
* @param b vector b
*/
public static final void shift(Atom a, Atom b) {
Atom natom = add(a, b);
double x = natom.getX();
double y = natom.getY();
double z = natom.getZ();
a.setX(x);
a.setY(y);
a.setZ(z);
}
/**
* Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the
* centroid is already known
*
* @param atomSet array of Atoms
* @return the vector needed to shift the set of atoms to its geometric center
*/
public static final Atom getCenterVector(Atom[] atomSet, Atom centroid) {
double[] coords = new double[3];
coords[0] = 0 - centroid.getX();
coords[1] = 0 - centroid.getY();
coords[2] = 0 - centroid.getZ();
Atom shiftVec = new AtomImpl();
shiftVec.setCoords(coords);
return shiftVec;
}
/**
* return the unit vector of vector a .
*
* @param a an Atom object
* @return an Atom object
*/
public static final Atom unitVector(Atom a) {
double amount = amount(a);
Atom U = a;
double[] coords = new double[3];
coords[0] = a.getX() / amount;
coords[1] = a.getY() / amount;
coords[2] = a.getZ() / amount;
U.setCoords(coords);
return U;
}
/**
* Rotate an atom around a Matrix object.
*
* @param atom atom to be rotated
* @param m rotation matrix to be applied to the atom
*/
public static final void rotate(Atom atom, Matrix m) {
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.times(m);
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);
}
/**
* 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);
}
}
/**
* rotate a single atom aroud a rotation matrix. matrix must be a 3x3 matrix.
*
* @param atom atom to be rotated
* @param m a rotation matrix represented as a double[3][3] array
*/
public static final void rotate(Atom atom, double[][] m) {
double x = atom.getX();
double y = atom.getY();
double z = atom.getZ();
double nx = m[0][0] * x + m[0][1] * y + m[0][2] * z;
double ny = m[1][0] * x + m[1][1] * y + m[1][2] * z;
double nz = m[2][0] * x + m[2][1] * y + m[2][2] * z;
double[] coords = new double[3];
coords[0] = nx;
coords[1] = ny;
coords[2] = nz;
atom.setCoords(coords);
}
/**
* 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();
}
}
/**
* Returns the center of mass of the set of atoms.
*
* @param atomSet a set of Atoms
* @return an Atom representing the Centroid of the set of atoms
*/
public static final Atom getCentroid(Atom[] atomSet) {
double[] coords = new double[3];
coords[0] = 0;
coords[1] = 0;
coords[2] = 0;
for (int i = 0; i < atomSet.length; i++) {
Atom a = atomSet[i];
coords[0] += a.getX();
coords[1] += a.getY();
coords[2] += a.getZ();
}
int n = atomSet.length;
coords[0] = coords[0] / n;
coords[1] = coords[1] / n;
coords[2] = coords[2] / n;
Atom vec = new AtomImpl();
vec.setCoords(coords);
return vec;
}
/**
* skalar product.
*
* @param a an Atom object
* @param b an Atom object
* @return a double
*/
public static final double skalarProduct(Atom a, Atom b) {
double skalar;
skalar = a.getX() * b.getX() + a.getY() * b.getY() + a.getZ() * b.getZ();
return skalar;
}