private void ProposeMoleculeWithCommonFormula(Peptide peptide)
{
// Examine any provided formulas (including parent molecule and/or precursor ions) and find common basis
ProposedMolecule = peptide.CustomMolecule;
var precursorsWithFormulas = _precursorRawDetails.Where(d => !string.IsNullOrEmpty(d._formulaUnlabeled)).ToList();
var parentFormula = peptide.CustomMolecule.UnlabeledFormula;
var commonFormula = string.IsNullOrEmpty(parentFormula)
? BioMassCalc.MONOISOTOPIC.FindFormulaIntersectionUnlabeled(
precursorsWithFormulas.Select(p => p._formulaUnlabeled))
: parentFormula;
// Check for consistent and correctly declared precursor formula+adduct
var precursorsWithFormulasAndAdducts = precursorsWithFormulas.Where(d => !Adduct.IsNullOrEmpty(d._nominalAdduct)).ToList();
if (precursorsWithFormulasAndAdducts.Any() &&
precursorsWithFormulas.All(
d => d._formulaUnlabeled.Equals(precursorsWithFormulasAndAdducts[0]._formulaUnlabeled)))
{
commonFormula = precursorsWithFormulasAndAdducts[0]._formulaUnlabeled;
}
if (!string.IsNullOrEmpty(commonFormula))
{
var parentComposition = Molecule.ParseExpression(commonFormula);
// Check for children proposing to label more atoms than parent provides, adjust parent as needed
foreach (var precursor in _precursorRawDetails.Where(d => d._labels != null))
{
foreach (var kvpIsotopeCount in precursor._labels)
{
var unlabeled = BioMassCalc.GetMonoisotopicSymbol(kvpIsotopeCount.Key);
int parentCount;
parentComposition.TryGetValue(unlabeled, out parentCount);
if (kvpIsotopeCount.Value > parentCount)
{
// Child proposes to label more of an atom than the parent possesses (seen in the wild) - update the parent
commonFormula =
Molecule.AdjustElementCount(commonFormula, unlabeled, kvpIsotopeCount.Value - parentCount);
parentComposition = Molecule.ParseExpression(commonFormula);
}
}
}
if (!Equals(peptide.CustomMolecule.Formula, commonFormula))
{
ProposedMolecule = new CustomMolecule(commonFormula, peptide.CustomMolecule.Name);
}
}
}