public ProteinAlignerResult(
LinearTransformation3D transformation,
UnitValue averagePositionError,
bool isTransformationValid)
{
Transformation = transformation;
AveragePositionError = averagePositionError;
IsTransformationValid = isTransformationValid;
}
private ProteinAlignerResult AlignUsingPositionPairs(List <Point3D> sequence1, List <Point3D> sequence2)
{
var validIndices = sequence1
.PairwiseOperation(sequence2, (p1, p2) => p1 != null && p2 != null)
.Select((isValid, idx) => new { IsValid = isValid, Index = idx })
.Where(x => x.IsValid)
.Select(x => x.Index)
.ToList();
if (validIndices.Count < 2)
{
throw new ArgumentException("Too little position information (too many null-points) for alignment of sequences");
}
var sequence2PositionArray = new double[validIndices.Count, 4];
for (int validIdx = 0; validIdx < validIndices.Count; validIdx++)
{
var idx = validIndices[validIdx];
sequence2PositionArray[validIdx, 0] = 1;
sequence2PositionArray[validIdx, 1] = sequence2[idx].X;
sequence2PositionArray[validIdx, 2] = sequence2[idx].Y;
sequence2PositionArray[validIdx, 3] = sequence2[idx].Z;
}
var sequence1X = validIndices.Select(idx => sequence1[idx].X).ToArray();
var sequence1Y = validIndices.Select(idx => sequence1[idx].Y).ToArray();
var sequence1Z = validIndices.Select(idx => sequence1[idx].Z).ToArray();
var betaX = LinearRegression(sequence2PositionArray, sequence1X);
var betaY = LinearRegression(sequence2PositionArray, sequence1Y);
var betaZ = LinearRegression(sequence2PositionArray, sequence1Z);
var rotationMatrix = new Matrix3X3();
rotationMatrix.Set(new[, ]
{
{ betaX[1], betaX[2], betaX[3] },
{ betaY[1], betaY[2], betaY[3] },
{ betaZ[1], betaZ[2], betaZ[3] }
});
var transformation = new LinearTransformation3D(
new Vector3D(betaX[0], betaY[0], betaZ[0]),
rotationMatrix);
var averagePositionError = validIndices
.Select(idx => sequence1[idx].DistanceTo(transformation.Apply(sequence2[idx])))
.Average()
.To(SIPrefix.Pico, Unit.Meter);
var isRotationMatrixValid = (rotationMatrix[0, 0].Square() + rotationMatrix[1, 0].Square() + rotationMatrix[2, 0].Square()).IsBetween(0.9, 1.1) &&
(rotationMatrix[0, 1].Square() + rotationMatrix[1, 1].Square() + rotationMatrix[2, 1].Square()).IsBetween(0.9, 1.1) &&
(rotationMatrix[0, 2].Square() + rotationMatrix[1, 2].Square() + rotationMatrix[2, 2].Square()).IsBetween(0.9, 1.1);
return(new ProteinAlignerResult(transformation, averagePositionError, isRotationMatrixValid));
}
