public MassDistribution CalcDistribution(IsotopeAbundances isotopeAbundances)
{
var massDistribution = isotopeAbundances[Symbol];
massDistribution = massDistribution.SetAbundance(IsotopeMass, AtomPercentEnrichment);
return(massDistribution);
}
/// <summary>
/// Synchronizes the masses of an <see cref="IsotopeAbundances"/> object with
/// the masses of this <see cref="BioMassCalc"/>, ensuring compatible mass calculations
/// using the different classes. This is only allowed with a monoisotopic mass calculator.
/// </summary>
/// <param name="abundances">An existing <see cref="IsotopeAbundances"/> object to be synchronized</param>
/// <returns>An <see cref="IsotopeAbundances"/> object synchronized with this <see cref="BioMassCalc"/></returns>
public IsotopeAbundances SynchMasses(IsotopeAbundances abundances)
{
if (MassType != MassType.Monoisotopic)
{
throw new InvalidOperationException(
Resources.
BioMassCalc_SynchMasses_Fixing_isotope_abundance_masses_requires_a_monoisotopic_mass_calculator);
}
var dictFixes = new Dictionary <string, MassDistribution>();
foreach (var atomAbundance in abundances)
{
double monoMassCalc;
if (!_atomicMasses.TryGetValue(atomAbundance.Key, out monoMassCalc))
{
continue;
}
double secondMassCalc, thirdMassCalc;
_atomicMasses.TryGetValue(atomAbundance.Key + "'", out secondMassCalc); // Not L10N
_atomicMasses.TryGetValue(atomAbundance.Key + "\"", out thirdMassCalc); // Not L10N
var massDist = atomAbundance.Value;
var massDistFixed = SynchDist(massDist, monoMassCalc, secondMassCalc, thirdMassCalc);
if (!ReferenceEquals(massDist, massDistFixed))
{
dictFixes.Add(atomAbundance.Key, massDistFixed);
}
}
return(abundances.SetAbundances(dictFixes));
}
public MassDistribution CalcDistribution(IsotopeAbundances isotopeAbundances)
{
var massDistribution = isotopeAbundances[Symbol];
double mass = massDistribution.ToArray()[IsotopeIndex].Key;
massDistribution = massDistribution.SetAbundance(mass, AtomPercentEnrichment);
return(massDistribution);
}
private void DoValidate()
{
var isotopes = BioMassCalc.DEFAULT_ABUNDANCES;
var dictSymDist = _isotopeEnrichments.ToDictionary(e => e.IsotopeSymbol,
e => e.CalcDistribution(isotopes));
// Make sure all heavy symbols used in Skyline are represented.
foreach (string symbol in BioMassCalc.HeavySymbols.Where(symbol => !dictSymDist.ContainsKey(symbol)))
{
dictSymDist.Add(symbol, new IsotopeEnrichmentItem(symbol, 1.0).CalcDistribution(isotopes));
}
IsotopeAbundances = isotopes.SetAbundances(dictSymDist);
}
/// <summary>
/// Ensure that the entries for D and T are the same as the entries for H' and H".
/// </summary>
public static IsotopeAbundances AddHeavyNicknames(IsotopeAbundances isotopeAbundances)
{
var changes = new Dictionary <string, MassDistribution>();
foreach (var kvp in DICT_HEAVYSYMBOL_NICKNAMES)
{
MassDistribution massDistribution;
if (isotopeAbundances.TryGetValue(kvp.Value, out massDistribution))
{
changes.Add(kvp.Key, massDistribution);
}
}
return(isotopeAbundances.SetAbundances(changes));
}
public Settings ChangeIsotopeAbundances(IsotopeAbundances isotopeAbundances)
{
return(ChangeProp(ImClone(this), im => im.IsotopeAbundances = isotopeAbundances ?? DEFAULT.IsotopeAbundances));
}
private void DoValidate()
{
var isotopes = BioMassCalc.DEFAULT_ABUNDANCES;
var dictSymDist = _isotopeEnrichments.ToDictionary(e => e.IsotopeSymbol,
e => e.CalcDistribution(isotopes));
// Make sure all heavy symbols used in Skyline are represented.
foreach (string symbol in BioMassCalc.HeavySymbols.Where(symbol => !dictSymDist.ContainsKey(symbol)))
{
dictSymDist.Add(symbol, new IsotopeEnrichmentItem(symbol, 1.0).CalcDistribution(isotopes));
}
IsotopeAbundances = isotopes.SetAbundances(dictSymDist);
}
public MassDistribution CalcDistribution(IsotopeAbundances isotopeAbundances)
{
var massDistribution = isotopeAbundances[Symbol];
double mass = massDistribution.ToArray()[IsotopeIndex].Key;
massDistribution = massDistribution.SetAbundance(mass, AtomPercentEnrichment);
return massDistribution;
}
/// <summary>
/// Synchronizes the masses of an <see cref="IsotopeAbundances"/> object with
/// the masses of this <see cref="BioMassCalc"/>, ensuring compatible mass calculations
/// using the different classes. This is only allowed with a monoisotopic mass calculator.
/// </summary>
/// <param name="abundances">An existing <see cref="IsotopeAbundances"/> object to be synchronized</param>
/// <returns>An <see cref="IsotopeAbundances"/> object synchronized with this <see cref="BioMassCalc"/></returns>
public IsotopeAbundances SynchMasses(IsotopeAbundances abundances)
{
if (MassType != MassType.Monoisotopic)
throw new InvalidOperationException(
Resources.
BioMassCalc_SynchMasses_Fixing_isotope_abundance_masses_requires_a_monoisotopic_mass_calculator);
var dictFixes = new Dictionary<string, MassDistribution>();
foreach (var atomAbundance in abundances)
{
double monoMassCalc;
if (!_atomicMasses.TryGetValue(atomAbundance.Key, out monoMassCalc))
continue;
double secondMassCalc, thirdMassCalc;
_atomicMasses.TryGetValue(atomAbundance.Key + "'", out secondMassCalc); // Not L10N
_atomicMasses.TryGetValue(atomAbundance.Key + "\"", out thirdMassCalc); // Not L10N
var massDist = atomAbundance.Value;
var massDistFixed = SynchDist(massDist, monoMassCalc, secondMassCalc, thirdMassCalc);
if (!ReferenceEquals(massDist, massDistFixed))
dictFixes.Add(atomAbundance.Key, massDistFixed);
}
return abundances.SetAbundances(dictFixes);
}
// ReSharper disable once ParameterTypeCanBeEnumerable.Local
private MassDistribution GetMzDistribution(Molecule molecule, int charge, IsotopeAbundances abundances, double unexplainedMass, bool isMassH)
{
// Low resolution to get back only peaks at Dalton (i.e. neutron) boundaries
var md = new MassDistribution(_massResolution, _minimumAbundance);
var result = md;
foreach (var element in molecule)
{
result = result.Add(md.Add(abundances[element.Key]).Multiply(element.Value));
}
return result.OffsetAndDivide(unexplainedMass + charge* (isMassH ? BioMassCalc.MassProton : -BioMassCalc.MassElectron), charge);
}
public MassDistribution GetMZDistributionFromFormula(string formula, int charge, IsotopeAbundances abundances)
{
Molecule molecule = Molecule.Parse(formula);
return GetMzDistribution(molecule, charge, abundances, 0, false);
}
public MassDistribution GetMzDistribution(string seq, int charge, IsotopeAbundances abundances, ExplicitSequenceMods mods)
{
double unexplainedMass;
Molecule molecule = GetFormula(seq, mods, out unexplainedMass);
return GetMzDistribution(molecule, charge, abundances, unexplainedMass, true);
}
public MassDistribution GetMzDistribution(string seq, int charge, IsotopeAbundances abundances)
{
return GetMzDistribution(seq, charge, abundances, null);
}
public MassDistribution GetMZDistributionFromFormula(string formula, int charge, IsotopeAbundances abundances)
{
return _massCalcBase.GetMZDistributionFromFormula(formula, charge, abundances);
}
public MassDistribution GetMzDistribution(string seq, int charge, IsotopeAbundances abundances)
{
return _massCalcBase.GetMzDistribution(seq, charge, abundances, _mods);
}
public AminoAcidFormulas SetIsotopeAbundances(IsotopeAbundances newAbundances)
{
var result = Clone();
result.IsotopeAbundances = newAbundances;
return result;
}