public void TestDefaultValidFalse()
{
IRule rule = new MMElementRule();
var formula = new MolecularFormula();
formula.Add(builder.NewIsotope("C"), 2);
formula.Add(builder.NewIsotope("H"), 200);
Assert.AreEqual(0.0, rule.Validate(formula), 0.0001);
}
public void TestNewIsotope_String_int()
{
IChemObjectBuilder builder = RootObject.Builder;
IIsotope isotope = builder.NewIsotope("C", 13);
Assert.IsNotNull(isotope);
}
public void TestNewIsotope_IElement()
{
IChemObjectBuilder builder = RootObject.Builder;
IIsotope isotope = builder.NewIsotope(ChemicalElement.R);
Assert.IsNotNull(isotope);
}
public void TestNewIsotope_int_String_int_Double_double()
{
IChemObjectBuilder builder = RootObject.Builder;
IIsotope isotope = builder.NewIsotope("C", 13, 1.0, 1.0);
Assert.IsNotNull(isotope);
}
public void TestSetParameters()
{
IRule rule = new ElementRule();
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(builder.NewIsotope("C"), 1, 10);
mfRange.AddIsotope(builder.NewIsotope("H"), 1, 10);
rule.Parameters = new object[] { mfRange };
var objects = rule.Parameters;
Assert.AreEqual(1, objects.Count);
MolecularFormulaRange mfRange2 = (MolecularFormulaRange)objects[0];
Assert.AreEqual(mfRange.Count, mfRange2.Count);
Assert.AreEqual(mfRange.GetIsotopeCountMin(new Isotope("C")), mfRange2.GetIsotopeCountMin(new Isotope("C")));
Assert.AreEqual(mfRange.GetIsotopeCountMax(new Isotope("C")), mfRange2.GetIsotopeCountMax(new Isotope("C")));
}
/// <summary>
/// Initiate the MolecularFormulaExpand with the maximum and minimum occurrence of the Elements.
/// In this case all elements of the periodic table are loaded.
/// </summary>
/// <param name="builder"></param>
private void EnsureDefaultOccurElements(IChemObjectBuilder builder)
{
if (mfRange == null)
{
string[] elements = new string[] { "C", "H", "O", "N", "Si", "P", "S", "F", "Cl", "Br", "I", "Sn", "B", "Pb",
"Tl", "Ba", "In", "Pd", "Pt", "Os", "Ag", "Zr", "Se", "Zn", "Cu", "Ni", "Co", "Fe", "Cr", "Ti",
"Ca", "K", "Al", "Mg", "Na", "Ce", "Hg", "Au", "Ir", "Re", "W", "Ta", "Hf", "Lu", "Yb", "Tm", "Er",
"Ho", "Dy", "Tb", "Gd", "Eu", "Sm", "Pm", "Nd", "Pr", "La", "Cs", "Xe", "Te", "Sb", "Cd", "Rh",
"Ru", "Tc", "Mo", "Nb", "Y", "Sr", "Rb", "Kr", "As", "Ge", "Ga", "Mn", "V", "Sc", "Ar", "Ne", "Be",
"Li", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu" };
mfRange = new MolecularFormulaRange();
foreach (var element in elements)
{
mfRange.AddIsotope(builder.NewIsotope(element), 0, 50);
}
}
}
public void TestDefaultValidFalse()
{
IRule rule = new ToleranceRangeRule();
var formula = new MolecularFormula();
IIsotope carb = builder.NewIsotope("C");
carb.ExactMass = 12.00;
IIsotope cl = builder.NewIsotope("Cl");
cl.ExactMass = 34.96885268;
formula.Add(carb);
formula.Add(cl);
Assert.AreEqual(0.0, rule.Validate(formula), 0.0001);
}
private IIsotope CreateIsotopeOfElement(string currentElement, XElement element)
{
var isotope = builder.NewIsotope(currentElement);
XAttribute att = null;
try
{
att = element.Attribute("id");
if (att != null)
{
isotope.Id = att.Value;
}
att = element.Attribute("number");
if (att != null)
{
isotope.MassNumber = int.Parse(att.Value, NumberFormatInfo.InvariantInfo);
}
att = element.Attribute("elementType");
if (att != null)
{
isotope.Symbol = att.Value;
}
}
catch (FormatException exception)
{
Trace.TraceError($"Value of isotope {att.Name} is not as expected.");
Debug.WriteLine(exception);
}
// we set the natural abundance to 0, since the default is -1, but
// some isotope entries have no entry for this field, so the values
// stays at -1
isotope.Abundance = 0;
return(isotope);
}
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 TestAddIsotope_IIsotope_int_int()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(builder.NewIsotope("C"), 0, 10);
mfRange.AddIsotope(builder.NewIsotope("H"), 0, 10);
Assert.AreEqual(2, mfRange.Count);
}
public void TestGetMaxOccurrenceElements_IMolecularFormulaSet()
{
var mf1 = new MolecularFormula(); /* C4H12NO4 */
mf1.Add(builder.NewIsotope("C"), 4);
mf1.Add(builder.NewIsotope("H"), 12);
mf1.Add(builder.NewIsotope("N"), 1);
mf1.Add(builder.NewIsotope("O"), 4);
var mf2 = new MolecularFormula(); /* C7H20N4O2 */
mf2.Add(builder.NewIsotope("C"), 7);
mf2.Add(builder.NewIsotope("H"), 20);
mf2.Add(builder.NewIsotope("N"), 4);
mf2.Add(builder.NewIsotope("O"), 2);
var mf3 = new MolecularFormula(); /* C9H5O7 */
mf3.Add(builder.NewIsotope("C"), 9);
mf3.Add(builder.NewIsotope("H"), 5);
mf3.Add(builder.NewIsotope("O"), 7);
IMolecularFormulaSet mfSet = new MolecularFormulaSet
{
mf1,
mf2,
mf3
};
var molecularFormula = MolecularFormulaSetManipulator.GetMaxOccurrenceElements(mfSet);
/* Result: C9H20N4O7 */
Assert.AreEqual(40, MolecularFormulaManipulator.GetAtomCount(molecularFormula));
Assert.AreEqual(4, molecularFormula.Isotopes.Count());
Assert.AreEqual(9, molecularFormula.GetCount(builder.NewIsotope("C")));
Assert.AreEqual(20, molecularFormula.GetCount(builder.NewIsotope("H")));
Assert.AreEqual(4, molecularFormula.GetCount(builder.NewIsotope("N")));
Assert.AreEqual(7, molecularFormula.GetCount(builder.NewIsotope("O")));
}
public void TestGetRange_IMolecularFormulaSet()
{
var mf1 = new MolecularFormula(); /* C4H12NO4 */
mf1.Add(builder.NewIsotope("C"), 4);
mf1.Add(builder.NewIsotope("H"), 12);
mf1.Add(builder.NewIsotope("N"), 1);
mf1.Add(builder.NewIsotope("O"), 4);
var mf2 = new MolecularFormula(); /* C7H20N4O2 */
mf2.Add(builder.NewIsotope("C"), 7);
mf2.Add(builder.NewIsotope("H"), 20);
mf2.Add(builder.NewIsotope("N"), 4);
mf2.Add(builder.NewIsotope("O"), 2);
var mf3 = new MolecularFormula(); /* C9H5O7 */
mf3.Add(builder.NewIsotope("C"), 9);
mf3.Add(builder.NewIsotope("H"), 5);
mf3.Add(builder.NewIsotope("O"), 7);
var mfSet = new MolecularFormulaSet
{
mf1,
mf2,
mf3
};
MolecularFormulaRange mfRange = MolecularFormulaRangeManipulator.GetRange(mfSet);
/* Result: C4-9H5-20N0-4O2-7 */
Assert.AreEqual(4, mfRange.GetIsotopes().Count());
Assert.AreEqual(4, mfRange.GetIsotopeCountMin(builder.NewIsotope("C")));
Assert.AreEqual(9, mfRange.GetIsotopeCountMax(builder.NewIsotope("C")));
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(builder.NewIsotope("H")));
Assert.AreEqual(20, mfRange.GetIsotopeCountMax(builder.NewIsotope("H")));
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(builder.NewIsotope("N")));
Assert.AreEqual(4, mfRange.GetIsotopeCountMax(builder.NewIsotope("N")));
Assert.AreEqual(2, mfRange.GetIsotopeCountMin(builder.NewIsotope("O")));
Assert.AreEqual(7, mfRange.GetIsotopeCountMax(builder.NewIsotope("O")));
}