/**
* Returns a list of list of subunit ids that form an "orbit", i.e. they are transformed into each
* other during a rotation around the principal symmetry axis (z-axis)
*
* @return
*/
private List<List<Integer>> calcOrbits() {
int n = subunits.getSubunitCount();
List<List<Integer>> orbits = new ArrayList<List<Integer>>();
for (int i = 0; i < n; i++) {
orbits.add(Collections.singletonList(i));
}
return orbits;
}
public HelixAxisAligner(QuatSymmetryResults results) {
this.subunits = results.getSubunits();
this.helixLayers = results.getHelixLayers();
if (subunits == null) {
throw new IllegalArgumentException("HelixAxisTransformation: Subunits are null");
} else if (helixLayers == null) {
throw new IllegalArgumentException("HelixAxisTransformation: HelixLayers is null");
} else if (subunits.getSubunitCount() == 0) {
throw new IllegalArgumentException("HelixAxisTransformation: Subunits is empty");
} else if (helixLayers.size() == 0) {
throw new IllegalArgumentException("HelixAxisTransformation: HelixLayers is empty");
}
}
private double[] getSubunitZDepth() {
int n = subunits.getSubunitCount();
double[] depth = new double[n];
Point3d probe = new Point3d();
// transform subunit centers into z-aligned position and calculate
// z-coordinates (depth) along the z-axis.
for (int i = 0; i < n; i++) {
Point3d p = subunits.getCenters().get(i);
probe.set(p);
transformationMatrix.transform(probe);
depth[i] = probe.z;
}
return depth;
}
