public void TestHighMass()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
IIsotope s = ifac.GetMajorIsotope("S");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 350, 400);
mfRange.AddIsotope(h, 620, 650);
mfRange.AddIsotope(o, 100, 150);
mfRange.AddIsotope(n, 100, 150);
mfRange.AddIsotope(s, 0, 10);
double minMass = 8445.573784 - 0.00001;
double maxMass = 8445.573784 + 0.00001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C374H623N103O116S", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void TestCompoundWith7Elements()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
IIsotope s = ifac.GetMajorIsotope("S");
IIsotope p = ifac.GetMajorIsotope("P");
IIsotope cl = ifac.GetMajorIsotope("Cl");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 7, 9);
mfRange.AddIsotope(h, 8, 10);
mfRange.AddIsotope(o, 1, 3);
mfRange.AddIsotope(n, 0, 2);
mfRange.AddIsotope(s, 0, 2);
mfRange.AddIsotope(p, 0, 2);
mfRange.AddIsotope(cl, 2, 4);
double minMass = 318.915719 - 0.0001;
double maxMass = 318.915719 + 0.0001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C8H9Cl3NO2PS", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void TestMiddleMass()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 50);
mfRange.AddIsotope(h, 0, 100);
mfRange.AddIsotope(o, 0, 30);
mfRange.AddIsotope(n, 0, 10);
double minMass = 698.25879 - 0.0001;
double maxMass = 698.25879 + 0.0001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C37H38N4O10", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void TestDifferentIsotopes()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
var carbons = ifac.GetIsotopes("C");
IIsotope c13 = carbons.ElementAt(5); // 13
IIsotope h = ifac.GetMajorIsotope("H");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 11);
mfRange.AddIsotope(c13, 0, 10);
mfRange.AddIsotope(h, 0, 10);
double minMass = 54.04193 - 0.001;
double maxMass = 54.04193 + 0.001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
IMolecularFormula trueFormula = new MolecularFormula(); // C3CH5
trueFormula.Add(c, 3);
trueFormula.Add(c13, 1);
trueFormula.Add(h, 5);
Assert.AreEqual(trueFormula.IsotopesCount, mfSet[0].IsotopesCount);
Assert.AreEqual(trueFormula.GetCount(c), mfSet[0].GetCount(c));
Assert.AreEqual(trueFormula.GetCount(c13), mfSet[0].GetCount(c13));
}
public void TestFixedElementCounts()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 7, 7);
mfRange.AddIsotope(h, 15, 15);
mfRange.AddIsotope(o, 4, 4);
mfRange.AddIsotope(n, 2, 2);
double massMin = 10d;
double massMax = 1000d;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, massMin, massMax, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C7H15N2O4", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void TestMaxCounts()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 3, 7);
mfRange.AddIsotope(h, 3, 7);
mfRange.AddIsotope(o, 3, 7);
mfRange.AddIsotope(n, 3, 7);
// The maximal formula MF=C7H7O7N7 MW=301.0406955954
double minMass = 250;
double maxMass = 400;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
// Check that all element counts in the formula are <= 7
foreach (var f in mfSet)
{
foreach (var i in f.Isotopes)
{
int count = f.GetCount(i);
Assert.IsTrue(count <= 7);
}
}
}
public void TestMinCounts()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 5, 20);
mfRange.AddIsotope(h, 5, 20);
mfRange.AddIsotope(o, 5, 20);
mfRange.AddIsotope(n, 5, 20);
// The minimal formula MF=C5H5O5N5 MW=215.0290682825
double minMass = 100;
double maxMass = 250;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
// Check that all element counts in the formula are >= 5
foreach (var f in mfSet)
{
foreach (var i in f.Isotopes)
{
int count = f.GetCount(i);
Assert.IsTrue(count >= 5);
}
}
}
public void TestFormulaFoundInRange2()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 1, 50);
mfRange.AddIsotope(h, 1, 100);
mfRange.AddIsotope(o, 1, 50);
mfRange.AddIsotope(n, 1, 50);
double minMass = 187;
double maxMass = 189;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.AreEqual(528, mfSet.Count);
bool found = false;
foreach (var formula in mfSet)
{
string mf = MolecularFormulaManipulator.GetString(formula);
if (mf.Equals("C11H10NO2"))
{
found = true;
break;
}
}
Assert.IsTrue(found, "The molecular formula C11H10NO2 should be found");
}
public void Main()
{
#region
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
IIsotope p = ifac.GetMajorIsotope("P");
IIsotope s = ifac.GetMajorIsotope("S");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 50);
mfRange.AddIsotope(h, 0, 100);
mfRange.AddIsotope(o, 0, 50);
mfRange.AddIsotope(n, 0, 50);
mfRange.AddIsotope(p, 0, 10);
mfRange.AddIsotope(s, 0, 10);
var builder = Silent.ChemObjectBuilder.Instance;
double minMass = 133.003;
double maxMass = 133.005;
MolecularFormulaGenerator mfg = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = mfg.GetAllFormulas();
#endregion
}
public void TestUseFullEnumerationWhenNoHydrogen()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 50);
mfRange.AddIsotope(o, 0, 30);
mfRange.AddIsotope(n, 0, 10);
MolecularFormulaGenerator generator = new MolecularFormulaGenerator(builder, 1023.000, 1023.002, mfRange);
Assert.IsTrue(generator.formulaGenerator is FullEnumerationFormulaGenerator, "generator implementation should be instance of FullEnumerationFormulaGenerator");
}
public void TestUseFullEnumerationWhenExceedIntegerSpace()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 20);
mfRange.AddIsotope(h, 0, 30);
mfRange.AddIsotope(o, 0, 15);
mfRange.AddIsotope(n, 0, 10);
MolecularFormulaGenerator generator = new MolecularFormulaGenerator(builder, 1300000, 1300000.1, mfRange);
Assert.IsTrue(generator.formulaGenerator is FullEnumerationFormulaGenerator, "generator implementation should be instance of FullEnumerationFormulaGenerator");
}
public void TestCarbons()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 100000);
double minMass = 120000.0 - 1;
double maxMass = 120000.0 + 1;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C10000", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void TestUseRoundRobinWheneverPossible()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 20);
mfRange.AddIsotope(h, 0, 30);
mfRange.AddIsotope(o, 0, 15);
mfRange.AddIsotope(n, 0, 10);
MolecularFormulaGenerator generator = new MolecularFormulaGenerator(builder, 230.002, 230.004, mfRange);
Assert.IsTrue(generator.formulaGenerator is RoundRobinFormulaGenerator, "generator implementation should be instance of RoundRobinFormulaGenerator");
}
public void TestCancel()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
IIsotope p = ifac.GetMajorIsotope("P");
IIsotope s = ifac.GetMajorIsotope("S");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 1000);
mfRange.AddIsotope(h, 0, 1000);
mfRange.AddIsotope(o, 0, 1000);
mfRange.AddIsotope(n, 0, 1000);
mfRange.AddIsotope(p, 0, 1000);
mfRange.AddIsotope(s, 0, 1000);
double minMass = 100000.0;
double maxMass = 100000.001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
var cancelThread = new ThreadStart(() => {
Thread.Sleep(5);
gen.Cancel();
});
new Thread(cancelThread).Start();
Thread.Sleep(10);
// We will get stuck in the next method call until the cancel thread
// calls the Cancel() method
gen.GetAllFormulas();
// Next GetNextFormula() call should return null
IMolecularFormula f = gen.GetNextFormula();
Assert.IsNull(f);
}
public void TestWater()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
IIsotope p = ifac.GetMajorIsotope("P");
IIsotope s = ifac.GetMajorIsotope("S");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 10);
mfRange.AddIsotope(h, 0, 10);
mfRange.AddIsotope(o, 0, 10);
mfRange.AddIsotope(n, 0, 10);
mfRange.AddIsotope(p, 0, 10);
mfRange.AddIsotope(s, 0, 10);
double minMass = 1;
double maxMass = 20;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
bool found = false;
foreach (IMolecularFormula formula in mfSet)
{
string mf = MolecularFormulaManipulator.GetString(formula);
if (mf.Equals("H2O"))
{
found = true;
break;
}
}
Assert.IsTrue(found, "The molecular formula H2O should be found");
}
public void TestGetFinishedPercentage()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 10);
mfRange.AddIsotope(h, 0, 10);
mfRange.AddIsotope(o, 0, 10);
mfRange.AddIsotope(n, 0, 10);
double minMass = 100.0;
double maxMass = 100.05;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
double finishedPerc, lastFinishedPerc = 0d;
// The initial value must be 0
finishedPerc = gen.GetFinishedPercentage();
Assert.AreEqual(0d, finishedPerc, 0.0001);
// The value must increase after each generated formula
while (gen.GetNextFormula() != null)
{
finishedPerc = gen.GetFinishedPercentage();
Assert.IsTrue(finishedPerc > lastFinishedPerc);
lastFinishedPerc = finishedPerc;
}
// The final value must be 1
finishedPerc = gen.GetFinishedPercentage();
Assert.AreEqual(1d, finishedPerc, 0.0001);
}
public void TestGetNextFormula()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 10);
mfRange.AddIsotope(h, 0, 10);
mfRange.AddIsotope(o, 0, 10);
mfRange.AddIsotope(n, 0, 10);
double minMass = 100.0;
double maxMass = 100.05;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormula f = gen.GetNextFormula();
Assert.IsNotNull(f);
}
public void TestMassRangeTooLow()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 100, 200);
mfRange.AddIsotope(h, 100, 200);
mfRange.AddIsotope(o, 100, 200);
mfRange.AddIsotope(n, 100, 200);
double massMin = 50d;
double massMax = 100d;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, massMin, massMax, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(0, mfSet.Count);
}
