private static List <PeptideAnnotation <AminoAcidReference> > ExtractAnnotations(IList <string> lines, char chainId, Peptide peptide)
{
var helices = lines
.Where(line => ReadLineCode(line) == "HELIX")
.Select(ParseHelix)
.Where(helix => helix.FirstResidueChainId == chainId);
var annotations = new List <PeptideAnnotation <AminoAcidReference> >();
foreach (var helix in helices)
{
var annotation = new PeptideAnnotation <AminoAcidReference>(
PeptideSecondaryStructure.AlphaHelix,
peptide.AminoAcids
.Where(aa => aa.SequenceNumber >= helix.FirstResidueNumber && aa.SequenceNumber <= helix.LastResidueNumber)
.ToList());
annotations.Add(annotation);
}
var sheetStrandGroups = lines
.Where(line => ReadLineCode(line) == "SHEET")
.Select(ParseSheetStrand)
.Where(strand => strand.FirstResidueChainId == chainId)
.GroupBy(strand => strand.SheetId);
foreach (var sheetStrands in sheetStrandGroups)
{
var sheetAminoAcids = new List <AminoAcidReference>();
foreach (var strand in sheetStrands)
{
var aminoAcids = peptide.AminoAcids.Where(aa =>
aa.SequenceNumber >= strand.FirstResidueNumber &&
aa.SequenceNumber <= strand.LastResidueNumber);
sheetAminoAcids.AddRange(aminoAcids);
}
var annotation = new PeptideAnnotation <AminoAcidReference>(
PeptideSecondaryStructure.BetaSheet,
sheetAminoAcids);
annotations.Add(annotation);
}
return(annotations);
}
/// <summary>
/// Detects alpha helixes in a peptide. Does NOT add these annotations to peptide.
/// </summary>
public List <PeptideAnnotation <AminoAcidReference> > Detect(Peptide peptide)
{
var slidingWindow = new SlidingWindow <AminoAcidReference>(
peptide.AminoAcids,
x => x.SequenceNumber,
4.5,
WindowPositioningType.StartingAtPosition);
const int MinimumHelixLength = 7;
var helixAnnotations = new List <PeptideAnnotation <AminoAcidReference> >();
PeptideAnnotation <AminoAcidReference> currentAnnotation = null;
foreach (var aminoAcid in peptide.AminoAcids.OrderBy(x => x.SequenceNumber))
{
if (currentAnnotation != null && aminoAcid.SequenceNumber > currentAnnotation.AminoAcidReferences.Last().SequenceNumber)
{
if (currentAnnotation.AminoAcidReferences.Count >= MinimumHelixLength)
{
helixAnnotations.Add(currentAnnotation);
}
currentAnnotation = null;
}
slidingWindow.SetPosition(aminoAcid.SequenceNumber - 0.1); // -0.1 to avoid problems with rounding
var secondAminoAcid = slidingWindow.FirstOrDefault(x => x.SequenceNumber == aminoAcid.SequenceNumber + 1);
if (secondAminoAcid == null)
{
continue;
}
var thirdAminoAcid = slidingWindow.FirstOrDefault(x => x.SequenceNumber == aminoAcid.SequenceNumber + 2);
if (thirdAminoAcid == null)
{
continue;
}
var fourthAminoAcid = slidingWindow.FirstOrDefault(x => x.SequenceNumber == aminoAcid.SequenceNumber + 3);
if (fourthAminoAcid == null)
{
continue;
}
try
{
var firstVector = FindPositionVector(aminoAcid, secondAminoAcid);
var secondVector = FindPositionVector(aminoAcid, thirdAminoAcid);
var thirdVector = FindPositionVector(aminoAcid, fourthAminoAcid);
var isAlphaHelix = IsAlphaHelix(firstVector, secondVector, thirdVector);
if (isAlphaHelix)
{
if (currentAnnotation == null)
{
currentAnnotation = new PeptideAnnotation <AminoAcidReference>(
PeptideSecondaryStructure.AlphaHelix,
new List <AminoAcidReference> {
aminoAcid, secondAminoAcid, thirdAminoAcid, fourthAminoAcid
});
}
else
{
currentAnnotation.AminoAcidReferences.Add(fourthAminoAcid);
}
}
else
{
if (currentAnnotation != null)
{
if (currentAnnotation.AminoAcidReferences.Count >= MinimumHelixLength)
{
helixAnnotations.Add(currentAnnotation);
}
currentAnnotation = null;
}
}
}
catch (KeyNotFoundException)
{
continue;
}
}
return(helixAnnotations);
}
