public string GetEmpiricalFormulaForPeptideSequence(string peptideSequence, bool includeAmineHydrogenAndFreeAcid = true, bool cysteinesAreModified = false)
{
peptideSequence = CleanUpPeptideSequence(peptideSequence);
var sequenceIsValid = ValidateSequence(peptideSequence);
if (!sequenceIsValid)
{
return(string.Empty);
}
var outputEmpiricalFormula = "";
foreach (var aminoAcid in peptideSequence)
{
var aminoAcidFormula = GetEmpiricalFormulaForAminoAcidResidue(aminoAcid);
outputEmpiricalFormula = EmpiricalFormulaUtilities.AddFormula(outputEmpiricalFormula, aminoAcidFormula);
if (cysteinesAreModified && aminoAcid == 'C')
{
outputEmpiricalFormula = EmpiricalFormulaUtilities.AddFormula(outputEmpiricalFormula, "H3C2NO");
}
}
if (includeAmineHydrogenAndFreeAcid)
{
var nterminalHydrogen = "H";
var cterminalFreeAcid = "OH";
outputEmpiricalFormula = EmpiricalFormulaUtilities.AddFormula(outputEmpiricalFormula, nterminalHydrogen);
outputEmpiricalFormula = EmpiricalFormulaUtilities.AddFormula(outputEmpiricalFormula, cterminalFreeAcid);
}
return(outputEmpiricalFormula);
}
public Dictionary <string, int> ParseEmpiricalFormulaString(string empiricalFormula)
{
return(EmpiricalFormulaUtilities.ParseEmpiricalFormulaString(empiricalFormula));
}