public static double CalculateProteoformMass(string sequence, List <Ptm> ptm_combination)
{
if (Sweet.lollipop.theoretical_database.aaIsotopeMassList == null)
{
Sweet.lollipop.theoretical_database.populate_aa_mass_dictionary();
}
if (!Sweet.lollipop.use_average_mass)
{
double proteoformMass = 18.010565; // start with water
char[] aminoAcids = sequence.ToCharArray();
List <double> aaMasses = new List <double>();
for (int i = 0; i < sequence.Length; i++)
{
if (Sweet.lollipop.theoretical_database.aaIsotopeMassList.ContainsKey(aminoAcids[i]))
{
aaMasses.Add(Sweet.lollipop.theoretical_database.aaIsotopeMassList[aminoAcids[i]]);
}
}
return(proteoformMass + aaMasses.Sum() +
ptm_combination.Sum(p => Math.Round((double)p.modification.MonoisotopicMass, 5)));
}
//if most abundant mass, calculate iso distrubution, set modified/unmodified masses to most abundant.
var formula = new Proteomics.AminoAcidPolymer.Peptide(sequence).GetChemicalFormula();
// append mod formulas
foreach (var mod in ptm_combination)
{
var modCf = mod.modification.ChemicalFormula;
if (modCf != null)
{
formula.Add(modCf);
}
}
//Calculate isotopic distribution of the full peptide
//var dist = IsotopicDistribution.GetDistribution(formula, 0.1, 1e-12);
//double[] masses = dist.Masses.ToArray();
//double[] intensities = dist.Intensities.ToArray();
//double max = intensities.Max();
//int modeMassIndex = Array.IndexOf(intensities, max);
//return masses[modeMassIndex];
return(formula.AverageMass);
}
public ChemicalFormula GetChemicalFormula()
{
var formula = new Proteomics.AminoAcidPolymer.Peptide(sequence).GetChemicalFormula();
// append mod formulas
foreach (var mod in ptm_list)
{
var modCf = mod.modification.ChemicalFormula;
if (modCf != null)
{
formula.Add(modCf);
}
else
{
return(null);
}
}
return(formula);
}