/// <summary>
/// Parses a chemical formula expressed as "[{atom}[count][spaces]]*",
/// e.g. "C6H11ON", where supported atoms are H, O, N, C, S or P, etc.
/// returning the total mass for the formula.
///
/// The parser removes atoms and counts until it encounters a character
/// it does not understand as being part of the chemical formula.
/// The remainder is returned in the desc parameter.
///
/// This parser will stop at the first minus sign. If you need to parse
/// an expression that might contain a minus sign, use <see cref="ParseMassExpression"/>.
/// </summary>
/// <param name="desc">Input description, and remaining string after parsing</param>
/// <returns>Total mass of formula parsed</returns>
public double ParseMass(ref string desc)
{
double totalMass = 0.0;
desc = desc.Trim();
Molecule mol;
Adduct adduct;
string neutralFormula;
if (IonInfo.IsFormulaWithAdduct(desc, out mol, out adduct, out neutralFormula))
{
totalMass += mol.Sum(p => p.Value * GetMass(p.Key));
desc = string.Empty; // Signal that we parsed the whole thing
return(totalMass);
}
while (desc.Length > 0)
{
string sym = NextSymbol(desc);
double massAtom = GetMass(sym);
// Stop if unrecognized atom found.
if (massAtom == 0)
{
// CONSIDER: Throw with a useful message?
break;
}
desc = desc.Substring(sym.Length);
int endCount = 0;
while (endCount < desc.Length && Char.IsDigit(desc[endCount]))
{
endCount++;
}
long count = 1;
if (endCount > 0)
{
if (!long.TryParse(desc.Substring(0, endCount), out count))
{
count = long.MaxValue; // We know at this point that it should parse, so it's probably just too big
}
}
totalMass += massAtom * count;
desc = desc.Substring(endCount).TrimStart();
}
return(totalMass);
}
/// <summary>
/// Parses a chemical formula expressed as "[{atom}[count][spaces]]*",
/// e.g. "C6H11ON", where supported atoms are H, O, N, C, S or P, etc.
/// returning the total mass for the formula.
///
/// The parser removes atoms and counts until it encounters a character
/// it does not understand as being part of the chemical formula.
/// The remainder is returned in the desc parameter.
///
/// This parser will stop at the first minus sign. If you need to parse
/// an expression that might contain a minus sign, use <see cref="ParseMassExpression"/>.
/// </summary>
/// <param name="desc">Input description, and remaining string after parsing</param>
/// <param name="molReturn">Optional dictionary for returning the atoms and counts</param>
/// <returns>Total mass of formula parsed</returns>
public double ParseMass(ref string desc, Dictionary <string, int> molReturn = null)
{
double totalMass = 0.0;
desc = desc.Trim();
Molecule mol;
Adduct adduct;
string neutralFormula;
Dictionary <string, int> dict = null;
if (IonInfo.IsFormulaWithAdduct(desc, out mol, out adduct, out neutralFormula))
{
totalMass += mol.Sum(p => p.Value * GetMass(p.Key));
desc = string.Empty; // Signal that we parsed the whole thing
if (molReturn != null)
{
dict = mol.Dictionary.ToDictionary(kvp => kvp.Key, kvp => kvp.Value);
}
}
else
{
if (molReturn != null)
{
dict = new Dictionary <string, int>();
}
while (desc.Length > 0)
{
string sym = NextSymbol(desc);
double massAtom = GetMass(sym);
// Stop if unrecognized atom found.
if (massAtom == 0)
{
// CONSIDER: Throw with a useful message?
break;
}
desc = desc.Substring(sym.Length);
int endCount = 0;
while (endCount < desc.Length && Char.IsDigit(desc[endCount]))
{
endCount++;
}
var count = 1;
if (endCount > 0)
{
if (!int.TryParse(desc.Substring(0, endCount), out count))
{
count = int.MaxValue; // We know at this point that it should parse, so it's probably just too big
}
}
totalMass += massAtom * count;
if (dict != null)
{
if (dict.TryGetValue(sym, out var oldCount))
{
dict[sym] = count + oldCount;
}
else
{
dict.Add(sym, count);
}
}
desc = desc.Substring(endCount).TrimStart();
}
}
if (molReturn != null)
{
foreach (var kvp in dict)
{
var sym = kvp.Key;
var count = kvp.Value;
if (molReturn.TryGetValue(sym, out var oldCount))
{
molReturn[sym] = count + oldCount;
}
else
{
molReturn.Add(sym, count);
}
}
}
return(totalMass);
}
