Program: 16293
Project: 16293
Buggy source:
private void solve(){
  initialize();
  Vector3d trans=new Vector3d(subunits.getCentroid());
  trans.negate();
  List<Point3d[]> traces=subunits.getTraces();
  Point3d[] x=CalcPoint.clonePoint3dArray(traces.get(0));
  CalcPoint.translate(new Point3d(trans),x);
  Point3d[] y=CalcPoint.clonePoint3dArray(traces.get(1));
  CalcPoint.translate(new Point3d(trans),y);
  Matrix4d transformation=SuperPositions.superposeAndTransformAtOrigin(y,x);
  AxisAngle4d axisAngle=new AxisAngle4d();
  axisAngle.set(transformation);
  Vector3d axis=new Vector3d(axisAngle.x,axisAngle.y,axisAngle.z);
  if (axis.lengthSquared() < 1.0E-6) {
    axisAngle.x=0;
    axisAngle.y=0;
    axisAngle.z=1;
    axisAngle.angle=0;
  }
 else {
    axis.normalize();
    axisAngle.x=axis.x;
    axisAngle.y=axis.y;
    axisAngle.z=axis.z;
  }
  double angleThresholdRadians=Math.toRadians(parameters.getAngleThreshold());
  double deltaAngle=Math.abs(Math.PI - axisAngle.angle);
  if (deltaAngle > angleThresholdRadians) {
    rotations.setC1(subunits.getSubunitCount());
    return;
  }
  addEOperation();
  int fold=2;
  combineWithTranslation(transformation);
  List<Integer> permutation=Arrays.asList(1,0);
  QuatSymmetryScores scores=QuatSuperpositionScorer.calcScores(subunits,transformation,permutation);
  scores.setRmsdCenters(0.0);
  if (scores.getRmsd() > parameters.getRmsdThreshold() || deltaAngle > angleThresholdRadians) {
    rotations.setC1(subunits.getSubunitCount());
    return;
  }
  Rotation symmetryOperation=createSymmetryOperation(permutation,transformation,axisAngle,fold,scores);
  rotations.addRotation(symmetryOperation);
}

Fixed version (ground truth):
private void solve(){
  initialize();
  Vector3d trans=new Vector3d(subunits.getCentroid());
  trans.negate();
  List<Point3d[]> traces=subunits.getTraces();
  Point3d[] x=CalcPoint.clonePoint3dArray(traces.get(0));
  CalcPoint.translate(new Point3d(trans),x);
  Point3d[] y=CalcPoint.clonePoint3dArray(traces.get(1));
  CalcPoint.translate(new Point3d(trans),y);
  Quat4d quat=UnitQuaternions.relativeOrientation(x,y);
  AxisAngle4d axisAngle=new AxisAngle4d();
  Matrix4d transformation=new Matrix4d();
  transformation.set(quat);
  axisAngle.set(quat);
  Vector3d axis=new Vector3d(axisAngle.x,axisAngle.y,axisAngle.z);
  if (axis.lengthSquared() < 1.0E-6) {
    axisAngle.x=0;
    axisAngle.y=0;
    axisAngle.z=1;
    axisAngle.angle=0;
  }
 else {
    axis.normalize();
    axisAngle.x=axis.x;
    axisAngle.y=axis.y;
    axisAngle.z=axis.z;
  }
  CalcPoint.transform(transformation,y);
  double angleThresholdRadians=Math.toRadians(parameters.getAngleThreshold());
  double deltaAngle=Math.abs(Math.PI - axisAngle.angle);
  if (deltaAngle > angleThresholdRadians) {
    rotations.setC1(subunits.getSubunitCount());
    return;
  }
  addEOperation();
  int fold=2;
  combineWithTranslation(transformation);
  List<Integer> permutation=Arrays.asList(1,0);
  QuatSymmetryScores scores=QuatSuperpositionScorer.calcScores(subunits,transformation,permutation);
  scores.setRmsdCenters(0.0);
  if (scores.getRmsd() > parameters.getRmsdThreshold() || deltaAngle > angleThresholdRadians) {
    rotations.setC1(subunits.getSubunitCount());
    return;
  }
  Rotation symmetryOperation=createSymmetryOperation(permutation,transformation,axisAngle,fold,scores);
  rotations.addRotation(symmetryOperation);
}