public FormulaBuilder(BioMassCalc massCalc)
{
_massCalc = massCalc;
_dictAtomCounts = new Dictionary<string, int>();
}
public SequenceMassCalc(MassType type)
{
_massCalc = new BioMassCalc(type);
// Not L10N
// Mass of a proton, i.e. +1 positive charge, hydrogen atom without its electron.
// See http://antoine.frostburg.edu/chem/senese/101/atoms/index.shtml
// _massWater = _massCalc.CalculateMass("H2O");
// _massAmmonia = _massCalc.CalculateMass("NH3");
// ReSharper disable NonLocalizedString
_massDiffA = -_massCalc.CalculateMassFromFormula("CO");
_massDiffB = 0.0;
_massDiffC = _massCalc.CalculateMassFromFormula("NH3");
_massDiffY = _massCalc.CalculateMassFromFormula("H2O");
_massDiffX = _massCalc.CalculateMassFromFormula("CO2");
_massDiffZ = _massDiffY - _massCalc.CalculateMassFromFormula("NH2");
_massCleaveN = _massCalc.CalculateMassFromFormula("H");
_massCleaveC = _massCalc.CalculateMassFromFormula("OH");
// ReSharper restore NonLocalizedString
// These numbers are set intentionally smaller than any known instrument
// can measure. Filters are then applied to resulting distributions
// to get more useful numbers.
_massResolution = 0.001;
_minimumAbundance = 0.00001; // 0.001%
InitAminoAcidMasses();
}
public static string[] ParseModParts(BioMassCalc calc, string desc)
{
string parse = desc;
calc.ParseMass(ref parse);
string part1 = desc.Substring(0, desc.Length - parse.Length).Trim();
string part2 = string.Empty;
if (parse.Length > 0 && parse[0] == '-') // Not L10N
{
parse = parse.Substring(1);
part2 = parse.Trim();
calc.ParseMass(ref parse);
}
if ((part1.Length == 0 && part2.Length == 0) || parse.Length > 0)
calc.ThrowArgumentException(desc);
return new[] { part1, part2 };
}
public static void ParseModCounts(BioMassCalc calc, string desc, IDictionary<string, int> dictAtomCounts)
{
string parse = desc;
calc.ParseCounts(ref parse, dictAtomCounts, false);
if (parse.Length > 0 && parse[0] == '-') // Not L10N
{
parse = parse.Substring(1);
calc.ParseCounts(ref parse, dictAtomCounts, true);
}
if (parse.Length > 0)
calc.ThrowArgumentException(desc);
}
public static double ParseModMass(BioMassCalc calc, string desc)
{
string parse = desc;
double totalMass = calc.ParseMass(ref parse);
if (parse.Length > 0 && parse[0] == '-') // Not L10N
{
parse = parse.Substring(1);
totalMass -= calc.ParseMass(ref parse);
}
if (totalMass == 0.0 || parse.Length > 0)
calc.ThrowArgumentException(desc);
return Math.Round(totalMass, MassPrecision);
}
