public void TestGeneratorSavesState()
{
IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mf1 = MolecularFormulaManipulator.GetMolecularFormula("C6H12O6", builder);
IsotopePattern ip1 = isogen.GetIsotopes(mf1);
Assert.AreEqual(1, ip1.Isotopes.Count);
IMolecularFormula mf2 = MolecularFormulaManipulator.GetMolecularFormula("C6H12O6", builder);
IsotopePattern ip2 = isogen.GetIsotopes(mf2);
Assert.AreEqual(1, ip2.Isotopes.Count);
}
public void TestCalculateIsotopesOrthinine()
{
// RESULTS ACCORDING PAGE: http://www2.sisweb.com/mstools/isotope.htm
double[] massResults = { 133.097720, 134.094750, 134.101079, 134.103990, 135.101959, 135.104430 };
double[] abundResults = { 1.00, .006, .054, 0.002, 0.004, 0.001 };
IMolecularFormula molFor = new MolecularFormula();
molFor.Add(builder.NewIsotope("C"), 5);
molFor.Add(builder.NewIsotope("H"), 13);
molFor.Add(builder.NewIsotope("N"), 2);
molFor.Add(builder.NewIsotope("O"), 2);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.0010);
IsotopePattern isoPattern = isotopeGe.GetIsotopes(molFor);
Assert.AreEqual(6, isoPattern.Isotopes.Count);
Assert.AreEqual(massResults[0], isoPattern.Isotopes[0].Mass, 0.01);
Assert.AreEqual(massResults[1], isoPattern.Isotopes[1].Mass, 0.01);
Assert.AreEqual(massResults[2], isoPattern.Isotopes[2].Mass, 0.01);
Assert.AreEqual(massResults[3], isoPattern.Isotopes[3].Mass, 0.01);
Assert.AreEqual(massResults[4], isoPattern.Isotopes[4].Mass, 0.01);
Assert.AreEqual(massResults[5], isoPattern.Isotopes[5].Mass, 0.01);
Assert.AreEqual(abundResults[0], isoPattern.Isotopes[0].Intensity, 0.01);
Assert.AreEqual(abundResults[1], isoPattern.Isotopes[1].Intensity, 0.01);
Assert.AreEqual(abundResults[2], isoPattern.Isotopes[2].Intensity, 0.01);
Assert.AreEqual(abundResults[3], isoPattern.Isotopes[3].Intensity, 0.01);
Assert.AreEqual(abundResults[4], isoPattern.Isotopes[4].Intensity, 0.01);
Assert.AreEqual(abundResults[5], isoPattern.Isotopes[5].Intensity, 0.01);
}
public void TestGetIsotopesIMolecularFormulaWithoutONE()
{
IMolecularFormula molFor = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C41H79N8O3P", builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.01);
IsotopePattern isos = isotopeGe.GetIsotopes(molFor);
Assert.AreEqual(6, isos.Isotopes.Count, 0.001);
}
[TestMethod(), Ignore()] //Non-deterministic test value is bad! This likely depends on our current isotope data which is also bad.
public void TestCalculateIsotopesC20H30Fe2P2S4Cl4()
{
IMolecularFormula molFor = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C20H30Fe2P2S4Cl4", builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.01);
IsotopePattern isos = isotopeGe.GetIsotopes(molFor);
Assert.IsTrue(isos.Isotopes.Count == 34 || isos.Isotopes.Count == 35);
}
public void TestCalculateIsotopesMn()
{
IMolecularFormula molFor = new MolecularFormula();
molFor.Add(builder.NewIsotope("Mn"), 1);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.001);
IsotopePattern isoPattern = isotopeGe.GetIsotopes(molFor);
Assert.AreEqual(1, isoPattern.Isotopes.Count);
}
public void TestGetIsotopes1()
{
var molFor = new MolecularFormula();
molFor.Add(builder.NewIsotope("Br"));
molFor.Add(builder.NewIsotope("Br"));
var isotopeGe = new IsotopePatternGenerator(0.1);
var isoPattern = isotopeGe.GetIsotopes(molFor);
Assert.AreEqual(3, isoPattern.Isotopes.Count);
}
public void TestCalculateIsotopesC10000()
{
IMolecularFormula molFor = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C10000", builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.1);
IsotopePattern isos = isotopeGe.GetIsotopes(molFor);
Assert.AreEqual(44, isos.Isotopes.Count);
for (int i = 0; i < isos.Isotopes.Count; i++)
{
Assert.IsTrue(isos.Isotopes[i].Mass > 120085);
}
}
public void TestMultipleFormulasForAMass()
{
var mf = MolecularFormulaManipulator.GetMolecularFormula("C6Cl2", builder);
var isogen = new IsotopePatternGenerator(0.1)
.SetMinIntensity(0.01)
.SetMinResolution(0.01)
.SetStoreFormulas(true);
var pattern = isogen.GetIsotopes(mf);
var isotopes = pattern.Isotopes;
Assert.AreEqual(1, isotopes[0].Formulas.Count);
Assert.AreEqual(1, isotopes[1].Formulas.Count);
Assert.AreEqual(2, isotopes[2].Formulas.Count);
Assert.AreEqual(2, isotopes[3].Formulas.Count);
Assert.AreEqual(3, isotopes[4].Formulas.Count);
}
public void TestGetIsotopesIMolecularFormulaDeprotonate()
{
IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mf1 = MolecularFormulaManipulator.GetMolecularFormula("C6H12O6", builder);
MolecularFormulaManipulator.AdjustProtonation(mf1, -1);
IsotopePattern ip1 = isogen.GetIsotopes(mf1);
Assert.AreEqual(1, ip1.Isotopes.Count);
isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mf2 = MolecularFormulaManipulator.GetMolecularFormula("C6H11O6", builder);
IsotopePattern ip2 = isogen.GetIsotopes(mf2);
Assert.AreEqual(1, ip2.Isotopes.Count);
Assert.AreEqual(ip1.Isotopes[0].Mass, ip2.Isotopes[0].Mass, 0.001);
}
public void TestExperiment()
{
var spExp = new IsotopePattern(new[]
{
new IsotopeContainer(762.6006, 124118304),
new IsotopeContainer(763.6033, 57558840),
new IsotopeContainer(764.6064, 15432262),
});
spExp.MonoIsotope = spExp.Isotopes[0];
spExp.Charge = 1.0;
var formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C42H85NO8P", CDK.Builder);
var isotopeGe = new IsotopePatternGenerator(0.01);
var patternIsoPredicted = isotopeGe.GetIsotopes(formula);
var is_ = new IsotopePatternSimilarity();
var score = is_.Compare(spExp, patternIsoPredicted);
Assert.AreEqual(0.97, score, .01);
}
public void TestGetIsotopesIMolecularFormulaCharged()
{
IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mfPositive = MolecularFormulaManipulator.GetMolecularFormula("C6H11O6Na", builder);
mfPositive.Charge = 1;
IsotopePattern ip1 = isogen.GetIsotopes(mfPositive);
Assert.AreEqual(1, ip1.Isotopes.Count);
isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mfNeutral = MolecularFormulaManipulator.GetMolecularFormula("C6H12O6Na", builder);
mfNeutral.Charge = 0;
IsotopePattern ip2 = isogen.GetIsotopes(mfNeutral);
Assert.AreEqual(1, ip2.Isotopes.Count);
Assert.AreNotEqual(ip1.Isotopes[0].Mass, ip2.Isotopes[0].Mass);
}
public void TestCompareIsotopePatternIsotopePattern()
{
var is_ = new IsotopePatternSimilarity();
IsotopePattern spExp = new IsotopePattern(new[]
{
new IsotopeContainer(156.07770, 1),
new IsotopeContainer(157.07503, 0.0004),
new IsotopeContainer(157.08059, 0.0003),
new IsotopeContainer(158.08135, 0.002),
});
spExp.MonoIsotope = spExp.Isotopes[0];
var formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C6H10N3O2", builder);
var isotopeGe = new IsotopePatternGenerator(0.1);
var patternIsoPredicted = isotopeGe.GetIsotopes(formula);
var patternIsoNormalize = IsotopePatternManipulator.Normalize(patternIsoPredicted);
var score = is_.Compare(spExp, patternIsoNormalize);
Assert.AreNotSame(0.0, score);
}
public void TestCalculateIsotopesnCarbono()
{
// RESULTS ACCORDING PAGE: http://www2.sisweb.com/mstools/isotope.htm
double[] massResults = { 120.000000, 121.003360, 122.006709 };
double[] abundResults = { 1.00, .108, 0.005 };
IMolecularFormula molFor = new MolecularFormula();
molFor.Add(builder.NewIsotope("C"), 10);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.0010);
IsotopePattern isoPattern = isotopeGe.GetIsotopes(molFor);
Assert.AreEqual(3, isoPattern.Isotopes.Count);
Assert.AreEqual(massResults[0], isoPattern.Isotopes[0].Mass, 0.01);
Assert.AreEqual(massResults[1], isoPattern.Isotopes[1].Mass, 0.01);
Assert.AreEqual(massResults[2], isoPattern.Isotopes[2].Mass, 0.01);
Assert.AreEqual(abundResults[0], isoPattern.Isotopes[0].Intensity, 0.01);
Assert.AreEqual(abundResults[1], isoPattern.Isotopes[1].Intensity, 0.01);
Assert.AreEqual(abundResults[2], isoPattern.Isotopes[2].Intensity, 0.01);
}
public void TestCalculateIsotopesAllBromine()
{
// RESULTS ACCORDING PAGE: http://www2.sisweb.com/mstools/isotope.htm
double[] massResults = { 157.836669, 159.834630, 161.832580 };
double[] abundResults = { .512, 1.00, .487 };
IMolecularFormula molFor = new MolecularFormula();
molFor.Add(builder.NewIsotope("Br"));
molFor.Add(builder.NewIsotope("Br"));
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.1);
IsotopePattern isoPattern = isotopeGe.GetIsotopes(molFor);
Assert.AreEqual(3, isoPattern.Isotopes.Count);
Assert.AreEqual(massResults[0], isoPattern.Isotopes[0].Mass, 0.01);
Assert.AreEqual(massResults[1], isoPattern.Isotopes[1].Mass, 0.01);
Assert.AreEqual(massResults[2], isoPattern.Isotopes[2].Mass, 0.01);
Assert.AreEqual(abundResults[0], isoPattern.Isotopes[0].Intensity, 0.01);
Assert.AreEqual(abundResults[1], isoPattern.Isotopes[1].Intensity, 0.01);
Assert.AreEqual(abundResults[2], isoPattern.Isotopes[2].Intensity, 0.01);
}
public void TestCalculateIsotopesIodemethylidyne()
{
// RESULTS ACCORDING PAGE: http://www2.sisweb.com/mstools/isotope.htm
var massResults = new[] { 138.904480, 139.907839 };
var abundResults = new[] { 1.00, .011 };
var molFor = new MolecularFormula();
molFor.Add(builder.NewIsotope("C"));
molFor.Add(builder.NewIsotope("I"));
Assert.AreEqual(2, molFor.IsotopesCount);
var isotopeGe = new IsotopePatternGenerator(.01);
var isoPattern = isotopeGe.GetIsotopes(molFor);
Assert.AreEqual(2, isoPattern.Isotopes.Count);
Assert.AreEqual(massResults[0], isoPattern.Isotopes[0].Mass, 0.01);
Assert.AreEqual(massResults[1], isoPattern.Isotopes[1].Mass, 0.01);
Assert.AreEqual(abundResults[0], isoPattern.Isotopes[0].Intensity, 0.01);
Assert.AreEqual(abundResults[1], isoPattern.Isotopes[1].Intensity, 0.01);
}
public void TestSelectingMF()
{
var is_ = new IsotopePatternSimilarity();
IsotopePattern spExp = new IsotopePattern(new[]
{
new IsotopeContainer(156.07770, 1),
new IsotopeContainer(157.07503, 0.0101),
new IsotopeContainer(157.08059, 0.074),
new IsotopeContainer(158.08135, 0.0024),
});
spExp.MonoIsotope = spExp.Isotopes[0];
spExp.Charge = 1;
double score = 0;
string mfString = "";
string[] listMF = { "C4H8N6O", "C2H12N4O4", "C3H12N2O5", "C6H10N3O2", "CH10N5O4", "C4H14NO5" };
for (int i = 0; i < listMF.Length; i++)
{
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula(listMF[i], builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.01);
IsotopePattern patternIsoPredicted = isotopeGe.GetIsotopes(formula);
IsotopePattern patternIsoNormalize = IsotopePatternManipulator.Normalize(patternIsoPredicted);
double tempScore = is_.Compare(spExp, patternIsoNormalize);
if (score < tempScore)
{
mfString = MolecularFormulaManipulator.GetString(formula);
score = tempScore;
}
}
Assert.AreEqual("C6H10N3O2", mfString);
}