/// <summary>
/// Returns true if the given element is a balanced isotopic label, where the only
/// thing changing is the isotopes of the atoms in question.
/// </summary>
private static bool IsIsotopicDiff(IEnumerable <elem_ref_t> element)
{
var dictSymToCount = element.ToDictionary(el => el.symbol, el => int.Parse(el.number));
foreach (var pair in dictSymToCount.ToArray())
{
string labelSym = pair.Key;
int labelCount = pair.Value;
char monoChar;
if (DICT_HEAVY_LABELS.TryGetValue(labelSym, out monoChar))
{
// Must be adding labeled atoms and removing unlabeled atoms
if (labelCount < 0)
{
return(false);
}
string monoSym = monoChar.ToString(CultureInfo.InvariantCulture);
int monoCount;
if (!dictSymToCount.TryGetValue(monoSym, out monoCount))
{
return(false);
}
if (labelCount + monoCount != 0)
{
return(false);
}
dictSymToCount.Remove(monoSym);
dictSymToCount.Remove(labelSym);
}
}
return(dictSymToCount.Count == 0);
}
/// <summary>
/// Check for label atoms in the given sequence matching the given aa, and create a corresponding string if found.
/// </summary>
private static bool CheckLabelAtoms(mod_t mod, char[] aas, out string labelAtomsFormula)
{
labelAtomsFormula = "";
bool hasLabelAtoms = true;
if (mod.title.StartsWith("Label"))
{
foreach (var element in mod.delta.element)
{
char elementMatch;
if (hasLabelAtoms && DICT_HEAVY_LABELS.TryGetValue(element.symbol, out elementMatch))
{
foreach (char aa in aas)
{
int numInFormula = ParseSeqMassCalcFormula(aa, elementMatch);
if (!Equals(element.number, numInFormula.ToString(CultureInfo.InvariantCulture)))
{
hasLabelAtoms = false;
break;
}
}
if (!string.IsNullOrEmpty(labelAtomsFormula))
{
labelAtomsFormula += '|';
}
var symbol = element.symbol;
var elementIndex = symbol.IndexOfAny(new[] { 'N', 'C', 'O', 'H' });
labelAtomsFormula += "LabelAtoms." + symbol[elementIndex] + symbol.Remove(elementIndex);
}
else if (element.symbol.Length == 1 && DICT_HEAVY_LABELS.ContainsValue(element.symbol[0]))
{
foreach (char aa in aas)
{
int numInFormula = ParseSeqMassCalcFormula(aa, element.symbol[0]);
if ((Int32.Parse(element.number) * -1) > numInFormula)
{
return(false);
}
}
}
}
}
if (!hasLabelAtoms || string.IsNullOrEmpty(labelAtomsFormula))
{
labelAtomsFormula = "LabelAtoms.None";
}
return(true);
}
/// <summary>
/// Create a Skyline chemical formula given a modification from the XML.
/// </summary>
private static string BuildFormula(IEnumerable <elem_ref_t> elements)
{
string positive = "";
string negative = " - ";
foreach (elem_ref_t element in elements)
{
int num = Int32.Parse(element.number);
string symbol = element.symbol;
char aa;
symbol = DICT_HEAVY_LABELS.TryGetValue(symbol, out aa) ? aa.ToString(CultureInfo.InvariantCulture) + '\'' : symbol;
if (num < 0)
{
negative += symbol + (num == -1 ? "" : (num * -1).ToString(CultureInfo.InvariantCulture));
}
else
{
positive += symbol + (num == 1 ? "" : num.ToString(CultureInfo.InvariantCulture));
}
}
string formula = positive + (negative.Length > 3 ? negative : "");
return(positive.Length > 0 ? formula : formula.Replace(" ", ""));
}