public void Test_Thirty_Charged_Distribution_Carbonic()
{
// Testing data generated with mMass
ChemicalFormula ca_form = new ChemicalFormula("C1290H1970N354O394S4");
double[] mass = new double[] { 962.8872757, 962.9206969, 962.9541272, 962.9875463, 963.0209669,
963.0543831, 963.0878052, 963.1212239, 963.1546426, 963.188077,
963.2214919, 963.2549111, 963.288333, 963.3217516, 963.3551663,
963.3885924, 963.4220101, 963.4554372, 963.4888482, 963.5222744,
963.5556881, 963.5891017, 963.622521, 963.6559335, 963.6893484,
963.7227599, 963.7561442, 963.7895819 };
double[] intensity = new double[] { 0.000170524, 0.000533111, 0.001558402, 0.003715026, 0.007459397,
0.013822287, 0.023144359, 0.035408395, 0.049036297, 0.062576509,
0.075865762, 0.086457957, 0.091842426, 0.09290665, 0.089605827,
0.080993753, 0.070710633, 0.058926547, 0.046819002, 0.035888922,
0.026327029, 0.018401792, 0.012303588, 0.007758151, 0.004530259,
0.002327596, 0.000773207, 0.000136591 };
ChargedIsotopicDistribution ca_ref = new ChargedIsotopicDistribution(mass, intensity, 30);
IIsotopeDistGenerator gen = new Mercury7();
ChargedIsotopicDistribution ca_mercury = gen.GenerateChargedIsotopicDistribution(ca_form, 30);
for (int i = 0; i < ca_ref.Length; i++)
{
// mMass doesn't calculate the intensity of the monoisotopic mass peak so need to offset by 4
Assert.AreEqual(ca_ref.GetMz()[i], ca_mercury.GetMz()[i + 4], 0.0001);
Assert.AreEqual(ca_ref.GetIntensity()[i], ca_mercury.GetIntensity()[i + 4], 0.01);
}
}
public void Test_Single_Charged_Distribution_Carbonic()
{
// Testing data generated with mMass
ChemicalFormula ca_form = new ChemicalFormula("C1290H1970N354O394S4");
double[] mass = new double[] { 28856.40546, 28857.40794, 28858.41098, 28859.41393, 28860.41678,
28861.41962, 28862.42237, 28863.42505, 28864.42769, 28865.4304,
28866.43308, 28867.43578, 28868.43842, 28869.44104, 28870.44363,
28871.44619, 28872.44873, 28873.45127, 28874.45379, 28875.4563,
28876.4588, 28877.46128, 28878.46374, 28879.46606, 28880.46894,
28881.471, 28882.47337, 28883.47578, 28884.47736, 28885.47777 };
double[] intensity = new double[] { 6.35739E-05, 0.000250289, 0.000837294, 0.002145702, 0.004773472,
0.009359079, 0.016488538, 0.026415142, 0.039026016, 0.052946508,
0.06681604, 0.07886135, 0.087496192, 0.091605672, 0.09087918,
0.085730901, 0.077143899, 0.066368093, 0.054709443, 0.043300049,
0.032963397, 0.024176561, 0.017106652, 0.01164814, 0.007704643,
0.004963036, 0.003030278, 0.001782571, 0.000980136, 0.000428152 };
ChargedIsotopicDistribution ca_ref = new ChargedIsotopicDistribution(mass, intensity, 1);
IIsotopeDistGenerator gen = new Mercury7();
ChargedIsotopicDistribution ca_mercury = gen.GenerateChargedIsotopicDistribution(ca_form, 1);
for (int i = 0; i < ca_ref.Length; i++)
{
// mMass doesn't calculate the intensity of the monoisotopic mass peak so need to offset by 3
Assert.AreEqual(ca_ref.GetMz()[i], ca_mercury.GetMz()[i + 3], 0.01);
Assert.AreEqual(ca_ref.GetIntensity()[i], ca_mercury.GetIntensity()[i + 3], 0.01);
}
}
public void Mercury_HexNAc()
{
IIsotopeDistGenerator gen = new Mercury7();
IsotopicDistribution hexnac_mercury = gen.GenerateIsotopicDistribution(hexnac_form);
for (int i = 0; i < hexnac_ref.Length; i++)
{
Assert.AreEqual(hexnac_ref.Masses[i], hexnac_mercury.Masses[i], 0.0001);
Assert.AreEqual(hexnac_ref.Intensities[i], hexnac_mercury.Intensities[i], 0.0001);
}
}
public void Mercury_Carbonic()
{
IIsotopeDistGenerator gen = new Mercury7();
IsotopicDistribution ca_mercury = gen.GenerateIsotopicDistribution(ca_form);
for (int i = 0; i < ca_ref.Length; i++)
{
// mMass doesn't calculate the intensity of the monoisotopic mass peak so need to offset by 4
Assert.AreEqual(ca_ref.Masses[i], ca_mercury.Masses[i + 4], 0.01);
Assert.AreEqual(ca_ref.Intensities[i], ca_mercury.Intensities[i + 4], 0.01);
}
}
private static void BenchmarkIsotopicEvelopeGeneration()
{
// Generate the formulas
var random = new Random(1);
var chemicalFormulas = new IChemicalFormula[MaxRunValue];
IElementProvider elementProvider = new MockElementProvider();
for (int i = 2; i < MaxRunValue; i++)
{
var elements = new[]
{
new EntityCardinality <IElement>(elementProvider.GetElement("H"), (int)(random.Next(i) * 7.7583)),
new EntityCardinality <IElement>(elementProvider.GetElement("C"), (int)(random.Next(i) * 4.9384)),
new EntityCardinality <IElement>(elementProvider.GetElement("N"), (int)(random.Next(i) * 1.3577)),
new EntityCardinality <IElement>(elementProvider.GetElement("O"), (int)(random.Next(i) * 1.4773)),
new EntityCardinality <IElement>(elementProvider.GetElement("S"), (int)(random.Next(i) * 0.0417)),
};
chemicalFormulas[i] = new ChemicalFormula(elements);
}
var stopwatch = new Stopwatch();
// Time UW Madison (port)
var fineGrain = new FineStructureIsotopicGenerator();
stopwatch.Reset();
stopwatch.Start();
for (int i = 2; i < MaxRunValue; i++)
{
var nice = fineGrain.GenerateIsotopicDistribution(chemicalFormulas[i], 0.2, 1E-26);
}
stopwatch.Stop();
Console.WriteLine("Elapsed time for UofW Madison Port: " + stopwatch.Elapsed);
// Time Northwestern (port)
var mercury7 = new Mercury7();
stopwatch.Reset();
stopwatch.Start();
for (int i = 2; i < MaxRunValue; i++)
{
MassSpectrometry.IIsotopicDistribution nice = mercury7.GenerateIsotopicDistribution(chemicalFormulas[i]);
}
stopwatch.Stop();
Console.WriteLine("Elapsed time for Northwestern Port: " + stopwatch.Elapsed);
}
public void Test_Single_Charged_Distribution_HexNAc()
{
ChemicalFormula hexnac_form = new ChemicalFormula("C8H13N1O5");
IIsotopeDistGenerator gen = new Mercury7();
ChargedIsotopicDistribution hexnac_mercury = gen.GenerateChargedIsotopicDistribution(hexnac_form, 1);
for (int i = 0; i < hexnac_ref.Length; i++)
{
Assert.AreEqual(hexnac_ref.GetMz()[i], hexnac_mercury.GetMz()[i], 0.0001);
Assert.AreEqual(hexnac_ref.GetIntensity()[i], hexnac_mercury.GetIntensity()[i], 0.0001);
}
}
