private Molecule GetFormula(string seq, ExplicitSequenceMods mods, out double unexplainedMass)
{
var formula = new FormulaBuilder(_massCalc);
var modMasses = GetModMasses(mods);
formula.Append(modMasses._massModCleaveNFormula, modMasses._massModCleaveNExtra);
formula.Append(modMasses._massModCleaveCFormula, modMasses._massModCleaveCExtra);
for (int i = 0, len = seq.Length; i < len; i++)
{
char c = seq[i];
formula.Append(AMINO_FORMULAS[c])
.Append(modMasses._aminoModFormulas[c], modMasses._aminoModMassesExtra[c]);
// Terminal modifications
if (i == 0)
formula.Append(modMasses._aminoNTermModFormulas[c], modMasses._aminoNTermModMassesExtra[c]);
else if (i == len - 1)
formula.Append(modMasses._aminoCTermModFormulas[c], modMasses._aminoCTermModMassesExtra[c]);
}
if (mods != null)
{
foreach (ExplicitMod mod in mods.AllMods)
{
double modUnexplainedMass;
string modFormula = GetModFormula(seq[mod.IndexAA], mod.Modification, out modUnexplainedMass);
formula.Append(modFormula, modUnexplainedMass);
}
}
formula.Append("H2O"); // N-term = H, C-term = OH // Not L10N
unexplainedMass = formula.UnexplainedMass;
// CONSIDER: More efficient translation between builder and Molecure.
// Both contain a dictionary for atom counts.
return Molecule.Parse(formula.ToString());
}
