//TO THINK: Is it reasonable to transfer Glycan to Modification the first time Glycan is read in? Which could save time.
//Use glycan index and modification index to reduce space.
public static Modification NGlycanToModification(Glycan glycan)
{
Dictionary <DissociationType, List <double> > neutralLosses = new Dictionary <DissociationType, List <double> >();
if (glycan.Ions != null)
{
List <double> lossMasses = glycan.Ions.Where(p => p.IonMass < 57000000).Select(p => (double)p.LossIonMass / 1E5).OrderBy(p => p).ToList(); //570 is a cutoff for glycan ion size 2N1H, which will generate fragment ions.
neutralLosses.Add(DissociationType.HCD, lossMasses);
neutralLosses.Add(DissociationType.CID, lossMasses);
neutralLosses.Add(DissociationType.EThcD, lossMasses);
}
Dictionary <DissociationType, List <double> > diagnosticIons = new Dictionary <DissociationType, List <double> >();
diagnosticIons.Add(DissociationType.HCD, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
diagnosticIons.Add(DissociationType.CID, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
diagnosticIons.Add(DissociationType.EThcD, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
ModificationMotif.TryGetMotif("N", out ModificationMotif finalMotif); //TO DO: only one motif can be write here.
var id = Glycan.GetKindString(glycan.Kind);
Modification modification = new Modification(
_originalId: id,
_modificationType: "N-Glycosylation",
_monoisotopicMass: (double)glycan.Mass / 1E5,
_locationRestriction: "Anywhere.",
_target: finalMotif,
_neutralLosses: neutralLosses,
_diagnosticIons: diagnosticIons
);
return(modification);
}
public static Modification OGlycanToModification(Glycan glycan)
{
//TO THINK: what the neutralLoss for O-Glyco?
Dictionary <DissociationType, List <double> > neutralLosses = new Dictionary <DissociationType, List <double> >();
if (glycan.Ions != null)
{
List <double> lossMasses = glycan.Ions.Select(p => (double)p.LossIonMass / 1E5).OrderBy(p => p).ToList();
neutralLosses.Add(DissociationType.HCD, lossMasses);
neutralLosses.Add(DissociationType.CID, lossMasses);
neutralLosses.Add(DissociationType.EThcD, lossMasses);
}
Dictionary <DissociationType, List <double> > diagnosticIons = new Dictionary <DissociationType, List <double> >();
diagnosticIons.Add(DissociationType.HCD, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
diagnosticIons.Add(DissociationType.CID, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
diagnosticIons.Add(DissociationType.EThcD, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
ModificationMotif.TryGetMotif("X", out ModificationMotif finalMotif); //TO DO: only one motif can be write here.
var id = Glycan.GetKindString(glycan.Kind);
Modification modification = new Modification(
_originalId: id,
_modificationType: "O-Glycosylation",
_monoisotopicMass: (double)glycan.Mass / 1E5,
_locationRestriction: "Anywhere.",
_target: finalMotif,
_neutralLosses: neutralLosses,
_diagnosticIons: diagnosticIons
);
return(modification);
}
private static void _GetCombinations(byte[] kind, List <byte[]> _kinds, HashSet <string> _keys)
{
if (kind.Sum(p => p) == 0)
{
return;
}
else
{
for (int i = 0; i < kind.Length; i++)
{
if (kind[i] >= 1)
{
byte[] akind = (byte[])kind.Clone();
akind[i]--;
if (akind.Sum(p => p) != 0)
{
if (!_keys.Contains(Glycan.GetKindString(akind)))
{
_keys.Add(Glycan.GetKindString(akind));
_kinds.Add((byte[])akind.Clone());
_GetCombinations(akind, _kinds, _keys);
}
}
}
}
}
}
