public GlycanComposition(GlycanComposition other)
{
//Components are not reference types, and so they will be copied by value
this.ElementalComposition = new Dictionary<string, int>(other.ElementalComposition);
this.MolecularComposition = new Dictionary<string, int>(other.MolecularComposition);
this.MassWeight = other.MassWeight;
this.AdductAmount = other.AdductAmount;
this.AdductReplaces = other.AdductReplaces;
this.Annotation = other.Annotation;
}
/// <summary>
/// Incorporate the components of a GlycanComposition object into
/// this glycopeptide.
/// </summary>
/// <param name="glycanComposition"></param>
public void AttachGlycan(GlycanComposition glycanComposition)
{
this.MassWeight += glycanComposition.MassWeight - WaterMass - glycanComposition.AdductMass;
this.GlycosylationCount++;
foreach (KeyValuePair<string, int> kvp in glycanComposition.ElementalComposition)
{
if (!ElementalComposition.ContainsKey(kvp.Key))
{
ElementalComposition[kvp.Key] = kvp.Value;
}
else
{
ElementalComposition[kvp.Key] += kvp.Value;
}
}
foreach (KeyValuePair<string, int> kvp in glycanComposition.MolecularComposition)
{
if (!MolecularComposition.ContainsKey(kvp.Key))
{
MolecularComposition[kvp.Key] = kvp.Value;
}
else
{
MolecularComposition[kvp.Key] += kvp.Value;
}
}
if (MolecularComposition.ContainsKey("Water"))
{
MolecularComposition["Water"] -= 1;
}
else
{
Console.WriteLine(JsonConvert.SerializeObject(this));
throw new Exception("No water found to remove!");
}
if (ElementalComposition.ContainsKey("O"))
{
ElementalComposition["O"] -= 1;
ElementalComposition["H"] -= 2;
}
//Adduct information is a singleton despite there being multiple glycans per peptide.
//Is this actually correct chemically?
this.AdductReplaces = glycanComposition.AdductReplaces;
this.AdductAmount = glycanComposition.AdductAmount;
}
/// <summary>
/// Combination Cosntructor
/// </summary>
/// <param name="glycanComposition"></param>
/// <param name="peptide"></param>
public GlycopeptideComposition(GlycanComposition glycanComposition, MSDigestPeptide peptide)
: base(glycanComposition)
{
this.PeptideSequence = peptide.Sequence;
this.PeptideModification = peptide.Modifications;
this.StartAA = peptide.StartAA;
this.EndAA = peptide.EndAA;
this.GlycosylationCount = peptide.NumGlycosylations;
this.MassWeight += peptide.Mass - WaterMass - glycanComposition.AdductMass;
MolecularComposition["Water"] -= 1;
if (ElementalComposition.ContainsKey("O"))
{
ElementalComposition["O"] -= 1;
ElementalComposition["H"] -= 2;
}
this.ProteinID = peptide.ProteinID;
AdductAmount = 0;
AdductReplaces = "";
}
