public static Atom getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
throws StructureException {
Atom[] a1 = getAlignedAtoms1(afpChain, ca1);
Atom[] a2 = getAlignedAtoms2(afpChain, ca2);
SVDSuperimposer svd = new SVDSuperimposer(a1, a2);
return svd.getTranslation();
}
@Override
public double calculate(
MultipleAlignment reference,
AFPChain align,
Atom[] ca1,
Atom[] ca2,
Map<String, Object> metaData) {
try {
List<Atom[]> structures = new ArrayList<Atom[]>(2);
structures.add(ca1);
structures.add(ca2);
int[][] optAln = reference.getAlignmentMatrix(structures);
// Create new arrays for the subset of atoms in the alignment.
Atom[] ca1aligned = new Atom[reference.size()];
Atom[] ca2aligned = new Atom[reference.size()];
int pos = 0;
for (int i = 0; i < optAln[0].length; i++) {
ca1aligned[pos] = ca1[optAln[0][pos]];
ca2aligned[pos] = (Atom) ca2[optAln[1][pos]].clone();
pos++;
}
// Superimpose
SVDSuperimposer svd = new SVDSuperimposer(ca1aligned, ca2aligned);
Matrix matrix = svd.getRotation();
Atom shift = svd.getTranslation();
for (Atom a : ca2aligned) {
Calc.rotate(a, matrix);
Calc.shift(a, shift);
}
return SVDSuperimposer.getTMScore(ca1aligned, ca2aligned, ca1.length, ca2.length);
} catch (StructureException e) {
e.printStackTrace();
return Double.NaN;
}
}