/// <summary>
/// Aligns <paramref name="peptide2"/> with <paramref name="peptide1"/>
/// </summary>
/// <returns>
/// Linear transformation that maps <paramref name="peptide2"/> positions
/// to best alignment with <paramref name="peptide1"/>
/// </returns>
public ProteinAlignerResult Align(Peptide peptide1, Peptide peptide2)
{
// TODO: Select sequences where missing amino acids are filled in (using sequence numbers)
var sequence1AminoAcids = peptide1.AminoAcids.Select(aa => aa.Name).ToList();
var sequence2AminoAcids = peptide2.AminoAcids.Select(aa => aa.Name).ToList();
var logicalAlignment = SequenceAligner.Align(sequence1AminoAcids, sequence2AminoAcids);
var sequence1CarbonAlphaPositions = logicalAlignment.AlignedPairs
.Select(alignedPair => alignedPair.Item1Index)
.Select(aminoAcidIdx => peptide1.AminoAcids[aminoAcidIdx].GetAtomFromName("CA"))
.Select(carbonAlpha => carbonAlpha?.Position?.In(SIPrefix.Pico, Unit.Meter))
.ToList();
var sequence2CarbonAlphaPositions = logicalAlignment.AlignedPairs
.Select(alignedPair => alignedPair.Item2Index)
.Select(aminoAcidIdx => peptide2.AminoAcids[aminoAcidIdx].GetAtomFromName("CA"))
.Select(carbonAlpha => carbonAlpha?.Position?.In(SIPrefix.Pico, Unit.Meter))
.ToList();
return(AlignUsingPositionPairs(sequence1CarbonAlphaPositions, sequence2CarbonAlphaPositions));
}
public void Debug()
{
var aligner = new ProteinAligner();
var sequence1 = new List <AminoAcidName>
{
AminoAcidName.Alanine,
AminoAcidName.Glutamine,
AminoAcidName.Glycine,
AminoAcidName.Isoleucine
};
var sequence2 = new List <AminoAcidName>
{
AminoAcidName.Histidine,
AminoAcidName.Glycine,
AminoAcidName.Isoleucine,
AminoAcidName.Proline,
AminoAcidName.Methionine
};
var alignmentResult = SequenceAligner.Align(sequence1, sequence2);
Assert.That(alignmentResult, Is.Not.Null);
}
