public override int GetHashCode()
{
unchecked
{
return((ModifiedSequence.GetHashCode() * 397) ^
(ExplicitMods != null ? ExplicitMods.GetHashCode() : 0));
}
}
public static ModifiedSequence GetFragmentSequence(ModifiedSequence modifiedSequence, IonType ionType,
int ordinal)
{
string unmodifiedSequence = modifiedSequence.GetUnmodifiedSequence();
switch (ionType)
{
case IonType.a:
case IonType.b:
case IonType.c:
return(new ModifiedSequence(unmodifiedSequence.Substring(0, ordinal),
modifiedSequence.GetModifications().Where(mod => mod.IndexAA < ordinal),
MassType.Monoisotopic));
}
int offset = unmodifiedSequence.Length - ordinal;
string fragmentSequence = unmodifiedSequence.Substring(offset);
var newModifications = modifiedSequence.GetModifications()
.Where(mod => mod.IndexAA >= offset)
.Select(mod => mod.ChangeIndexAa(mod.IndexAA - offset));
return(new ModifiedSequence(fragmentSequence, newModifications, MassType.Monoisotopic));
}
private static Molecule GetSequenceFormula(ModifiedSequence modifiedSequence, MassType massType, out double unexplainedMassShift)
{
unexplainedMassShift = 0;
var molecule = new Dictionary <string, int>();
string unmodifiedSequence = modifiedSequence.GetUnmodifiedSequence();
var modifications = modifiedSequence.GetModifications().ToLookup(mod => mod.IndexAA);
for (int i = 0; i < unmodifiedSequence.Length; i++)
{
char aminoAcid = unmodifiedSequence[i];
AddAminoAcidFormula(massType, aminoAcid, molecule, ref unexplainedMassShift);
foreach (var mod in modifications[i])
{
string formula = mod.Formula;
if (formula == null)
{
var staticMod = mod.StaticMod;
var aa = unmodifiedSequence[i];
if ((staticMod.LabelAtoms & LabelAtoms.LabelsAA) != LabelAtoms.None && AminoAcid.IsAA(aa))
{
formula = SequenceMassCalc.GetHeavyFormula(aa, staticMod.LabelAtoms);
}
}
if (formula != null)
{
var modFormula = Molecule.ParseExpression(formula);
Add(molecule, modFormula);
}
else
{
unexplainedMassShift += massType.IsMonoisotopic() ? mod.MonoisotopicMass : mod.AverageMass;
}
}
}
return(Molecule.FromDict(molecule));
}
public FragmentedMolecule ChangeModifiedSequence(ModifiedSequence modifiedSequence)
{
return(ChangeMoleculeProp(im => im.ModifiedSequence = modifiedSequence));
}
public static FragmentedMolecule GetFragmentedMolecule(SrmSettings settings, PeptideDocNode peptideDocNode,
TransitionGroupDocNode transitionGroupDocNode, TransitionDocNode transitionDocNode)
{
FragmentedMolecule fragmentedMolecule = EMPTY
.ChangePrecursorMassShift(0, settings.TransitionSettings.Prediction.PrecursorMassType)
.ChangeFragmentMassShift(0, settings.TransitionSettings.Prediction.FragmentMassType);
if (peptideDocNode == null)
{
return(fragmentedMolecule);
}
var labelType = transitionGroupDocNode == null
? IsotopeLabelType.light
: transitionGroupDocNode.TransitionGroup.LabelType;
if (peptideDocNode.IsProteomic)
{
fragmentedMolecule = fragmentedMolecule.ChangeModifiedSequence(
ModifiedSequence.GetModifiedSequence(settings, peptideDocNode, labelType));
if (transitionGroupDocNode != null)
{
fragmentedMolecule = fragmentedMolecule
.ChangePrecursorCharge(transitionGroupDocNode.PrecursorCharge);
}
if (transitionDocNode == null || transitionDocNode.IsMs1)
{
return(fragmentedMolecule);
}
var transition = transitionDocNode.Transition;
fragmentedMolecule = fragmentedMolecule
.ChangeFragmentIon(transition.IonType, transition.Ordinal)
.ChangeFragmentCharge(transition.Charge);
var transitionLosses = transitionDocNode.Losses;
if (transitionLosses != null)
{
var fragmentLosses = transitionLosses.Losses.Select(transitionLoss => transitionLoss.Loss);
fragmentedMolecule = fragmentedMolecule.ChangeFragmentLosses(fragmentLosses);
}
return(fragmentedMolecule);
}
if (transitionGroupDocNode == null)
{
return(fragmentedMolecule
.ChangePrecursorFormula(
Molecule.Parse(peptideDocNode.CustomMolecule.Formula ?? string.Empty)));
}
var customMolecule = transitionGroupDocNode.CustomMolecule;
fragmentedMolecule =
fragmentedMolecule.ChangePrecursorCharge(transitionGroupDocNode.TransitionGroup
.PrecursorCharge);
if (customMolecule.Formula != null)
{
var ionInfo = new IonInfo(customMolecule.Formula,
transitionGroupDocNode.PrecursorAdduct);
fragmentedMolecule = fragmentedMolecule
.ChangePrecursorFormula(Molecule.Parse(ionInfo.FormulaWithAdductApplied));
}
else
{
fragmentedMolecule = fragmentedMolecule.ChangePrecursorMassShift(
transitionGroupDocNode.PrecursorAdduct.MassFromMz(
transitionGroupDocNode.PrecursorMz, transitionGroupDocNode.PrecursorMzMassType),
transitionGroupDocNode.PrecursorMzMassType);
}
if (transitionDocNode == null || transitionDocNode.IsMs1)
{
return(fragmentedMolecule);
}
var customIon = transitionDocNode.Transition.CustomIon;
if (customIon.Formula != null)
{
fragmentedMolecule = fragmentedMolecule.ChangeFragmentFormula(
Molecule.Parse(customIon.FormulaWithAdductApplied));
}
else
{
fragmentedMolecule = fragmentedMolecule.ChangeFragmentMassShift(
transitionDocNode.Transition.Adduct.MassFromMz(
transitionDocNode.Mz, transitionDocNode.MzMassType),
transitionDocNode.MzMassType);
}
fragmentedMolecule = fragmentedMolecule
.ChangeFragmentCharge(transitionDocNode.Transition.Charge);
return(fragmentedMolecule);
}
public string FormatModifiedSequence(ModifiedSequence modifiedSequence)
{
return(_modifiedSequenceFormatter(modifiedSequence));
}
public static string FormatUnimodId(SrmSettings settings, IEnumerable <ModifiedSequence.Modification> mods)
{
return(ModifiedSequence.FormatUnimodIds(mods));
}
public static string FormatFullName(SrmSettings settings, IEnumerable <ModifiedSequence.Modification> mods)
{
return(string.Join(string.Empty,
mods.Select(mod => ModifiedSequence.Bracket(ModifiedSequence.FormatFullName(mod)))));
}
public static string FormatMassDelta(SrmSettings settings, IEnumerable <ModifiedSequence.Modification> mods)
{
return(ModifiedSequence.FormatMassModification(mods,
settings.TransitionSettings.Prediction.PrecursorMassType, false));
}
protected bool Equals(ModifiedSequence other)
{
return(string.Equals(_unmodifiedSequence, other._unmodifiedSequence) &&
_explicitMods.Equals(other._explicitMods) && _defaultMassType == other._defaultMassType);
}
public Modification ChangeLinkedPeptideSequence(ModifiedSequence linkedPeptideSequence)
{
return(ChangeProp(ImClone(this), im => im.LinkedPeptideSequence = linkedPeptideSequence));
}
