/// <summary>
/// Replace all of the crosslinked peptide with the mass of the crosslinker plus the mass of the linked peptide.
/// </summary>
public ModifiedSequence ReplaceCrosslinksWithMasses(SrmSettings settings, IsotopeLabelType labelType)
{
if (ExplicitMods.All(mod => null == mod.LinkedPeptideSequence))
{
return(this);
}
var newModifications = new List <Modification>(ExplicitMods.Count);
foreach (var modification in ExplicitMods)
{
if (null == modification.LinkedPeptideSequence)
{
newModifications.Add(modification);
continue;
}
var formula = modification.StaticMod.Formula;
MoleculeMassOffset moleculeMassOffset;
if (string.IsNullOrEmpty(formula))
{
moleculeMassOffset = new MoleculeMassOffset(Molecule.Empty, modification.StaticMod.MonoisotopicMass ?? 0, modification.StaticMod.AverageMass ?? 0);
}
else
{
moleculeMassOffset = new MoleculeMassOffset(Molecule.ParseExpression(formula), 0, 0);
}
moleculeMassOffset = moleculeMassOffset.Plus(modification.ExplicitMod.LinkedPeptide.GetNeutralFormula(settings, labelType));
var fragmentedMoleculeSettings = FragmentedMolecule.Settings.FromSrmSettings(settings);
moleculeMassOffset = fragmentedMoleculeSettings.ReplaceMoleculeWithMassOffset(moleculeMassOffset);
Assume.IsTrue(0 == moleculeMassOffset.Molecule.Count);
newModifications.Add(new Modification(modification.ExplicitMod, moleculeMassOffset.MonoMassOffset, moleculeMassOffset.AverageMassOffset));
}
return(new ModifiedSequence(_unmodifiedSequence, newModifications, _defaultMassType));
}
public MoleculeMassOffset ReplaceMoleculeWithMassOffset(MoleculeMassOffset moleculeMassOffset)
{
double monoMass = GetMonoMass(moleculeMassOffset.Molecule) + moleculeMassOffset.MonoMassOffset;
double averageMass = GetAverageMass(moleculeMassOffset.Molecule) + moleculeMassOffset.AverageMassOffset;
return(new MoleculeMassOffset(Molecule.Empty, monoMass, averageMass));
}
public MoleculeMassOffset SubtractLosses(MoleculeMassOffset moleculeMassOffset, TransitionLosses transitionLosses)
{
if (transitionLosses == null)
{
return(moleculeMassOffset);
}
foreach (var loss in transitionLosses.Losses)
{
moleculeMassOffset = moleculeMassOffset.Minus(FragmentedMolecule.ToMoleculeMassOffset(loss.Loss));
}
return(moleculeMassOffset);
}
public MoleculeMassOffset GetPrecursorFormula()
{
var moleculeMassOffset = new MoleculeMassOffset(GetSimplePrecursorMolecule().PrecursorFormula);
if (ExplicitMods != null)
{
foreach (var child in ExplicitMods.LinkedCrossslinks)
{
moleculeMassOffset = moleculeMassOffset.Plus(GetChildBuilder(child.Key).GetPrecursorFormula());
}
}
return(moleculeMassOffset);
}
public static TypedMass GetFragmentMassFromFormula(SrmSettings settings, MoleculeMassOffset formula)
{
var fragmentedMoleculeSettings = FragmentedMolecule.Settings.FromSrmSettings(settings);
MassType massType = settings.TransitionSettings.Prediction.FragmentMassType;
if (massType.IsMonoisotopic())
{
return(new TypedMass(fragmentedMoleculeSettings.GetMonoMass(formula.Molecule) + formula.MonoMassOffset + BioMassCalc.MassProton, MassType.MonoisotopicMassH));
}
else
{
return(new TypedMass(fragmentedMoleculeSettings.GetAverageMass(formula.Molecule) + formula.AverageMassOffset + BioMassCalc.MassProton, MassType.AverageMassH));
}
}
public static Molecule AddFragmentLosses(Molecule molecule, IList <FragmentLoss> fragmentLosses,
MassType massType, ref double unexplainedMass)
{
MoleculeMassOffset moleculeMassOffset = new MoleculeMassOffset(molecule, unexplainedMass, unexplainedMass);
foreach (var fragmentLoss in fragmentLosses)
{
moleculeMassOffset = moleculeMassOffset.Minus(ToMoleculeMassOffset(fragmentLoss));
}
if (massType.IsMonoisotopic())
{
unexplainedMass = moleculeMassOffset.MonoMassOffset;
}
else
{
unexplainedMass = moleculeMassOffset.AverageMassOffset;
}
return(moleculeMassOffset.Molecule);
}
/// <summary>
/// Returns the chemical formula for this fragment and none of its children.
/// </summary>
private MoleculeMassOffset GetSimpleFragmentFormula(ComplexFragmentIon complexFragmentIon)
{
if (complexFragmentIon.IsOrphan)
{
return(MoleculeMassOffset.EMPTY);
}
var key = Tuple.Create(complexFragmentIon.Transition.IonType, complexFragmentIon.Transition.CleavageOffset);
MoleculeMassOffset moleculeMassOffset;
if (_fragmentedMolecules.TryGetValue(key, out moleculeMassOffset))
{
return(moleculeMassOffset);
}
var fragmentedMolecule = GetSimplePrecursorMolecule().ChangeFragmentIon(complexFragmentIon.Transition.IonType, complexFragmentIon.Transition.Ordinal);
moleculeMassOffset = new MoleculeMassOffset(fragmentedMolecule.FragmentFormula, 0, 0);
_fragmentedMolecules.Add(key, moleculeMassOffset);
return(moleculeMassOffset);
}
public double GetAverageMass(MoleculeMassOffset moleculeMassOffset)
{
return(GetAverageMass(moleculeMassOffset.Molecule) + moleculeMassOffset.AverageMassOffset);
}
public double GetMonoMass(MoleculeMassOffset moleculeMassOffset)
{
return(GetMonoMass(moleculeMassOffset.Molecule) + moleculeMassOffset.MonoMassOffset);
}
