public void TestRemove_IMolecularFormulaSet_IMolecularFormula_IMolecularFormula()
{
var formulaMin = new MolecularFormula();
formulaMin.Add(builder.NewIsotope("C"), 1);
formulaMin.Add(builder.NewIsotope("H"), 1);
formulaMin.Add(builder.NewIsotope("O"), 1);
var formulaMax = new MolecularFormula();
formulaMax.Add(builder.NewIsotope("C"), 4);
formulaMax.Add(builder.NewIsotope("H"), 12);
formulaMax.Add(builder.NewIsotope("N"), 2);
var mf1 = new MolecularFormula();
mf1.Add(builder.NewIsotope("C"), 3);
mf1.Add(builder.NewIsotope("H"), 10);
mf1.Add(builder.NewIsotope("N"), 1);
var formulaSet = new MolecularFormulaSet {
mf1
};
var newMFSet = MolecularFormulaSetManipulator.Remove(formulaSet, formulaMin, formulaMax);
Assert.IsNull(newMFSet);
}
public override void TestValidate_IMolecularFormula()
{
var formula = new MolecularFormula();
formula.Add(ifac.GetMajorIsotope("C"), 5);
formula.Add(ifac.GetMajorIsotope("H"), 13);
formula.Add(ifac.GetMajorIsotope("N"), 2);
formula.Add(ifac.GetMajorIsotope("O"), 2);
formula.Charge = 0;
// experimental results
var spectrum = new List <double[]>
{
new double[] { 133.0977, 100.00 },
new double[] { 134.09475, 0.6 },
new double[] { 134.1010, 5.4 }
};
var rule = new IsotopePatternRule();
var parameters = new object[2];
parameters[0] = spectrum;
parameters[1] = 0.001;
rule.Parameters = parameters;
Assert.AreEqual(0.9433, rule.Validate(formula), 0.001);
}
public void TestRemove_IMolecularFormulaSet_MolecularFormulaRange()
{
var formulaRange = new MolecularFormulaRange();
formulaRange.AddIsotope(builder.NewIsotope("C"), 0, 4);
formulaRange.AddIsotope(builder.NewIsotope("H"), 0, 12);
formulaRange.AddIsotope(builder.NewIsotope("N"), 0, 2);
var mf2 = new MolecularFormula();
mf2.Add(builder.NewIsotope("C"), 1);
mf2.Add(builder.NewIsotope("H"), 11);
mf2.Add(builder.NewIsotope("N"), 1);
var mf1 = new MolecularFormula();
mf1.Add(builder.NewIsotope("C"), 3);
mf1.Add(builder.NewIsotope("H"), 10);
var formulaSet = new MolecularFormulaSet
{
mf1,
mf2
};
var newMFSet = MolecularFormulaSetManipulator.Remove(formulaSet, formulaRange);
/* the mf2 is excluded from the limits. It doesn't contain N */
Assert.AreEqual(2, newMFSet.Count());
}
public void TestRemove_1()
{
var formulaMin = new MolecularFormula();
formulaMin.Add(builder.NewIsotope("C"), 1);
formulaMin.Add(builder.NewIsotope("H"), 1);
formulaMin.Add(builder.NewIsotope("N"), 1);
var formulaMax = new MolecularFormula();
formulaMax.Add(builder.NewIsotope("C"), 4);
formulaMax.Add(builder.NewIsotope("H"), 12);
formulaMax.Add(builder.NewIsotope("N"), 2);
var mf1 = new MolecularFormula();
mf1.Add(builder.NewIsotope("C"), 3);
mf1.Add(builder.NewIsotope("H"), 10);
mf1.Add(builder.NewIsotope("N"), 1);
var mf2 = new MolecularFormula();
mf2.Add(builder.NewIsotope("C"), 1);
mf2.Add(builder.NewIsotope("H"), 1);
mf2.Add(builder.NewIsotope("N"), 1);
var mf3 = new MolecularFormula();
mf3.Add(builder.NewIsotope("C"), 4);
mf3.Add(builder.NewIsotope("H"), 12);
mf3.Add(builder.NewIsotope("N"), 2);
var mf4 = new MolecularFormula();
mf4.Add(builder.NewIsotope("C"), 7);
mf4.Add(builder.NewIsotope("H"), 10);
mf4.Add(builder.NewIsotope("N"), 1);
var formulaSet = new MolecularFormulaSet
{
mf1,
mf2,
mf3,
mf4
};
var newMFSet = MolecularFormulaSetManipulator.Remove(formulaSet, formulaMin, formulaMax);
/* the mf4 is excluded from the limits */
Assert.AreEqual(3, newMFSet.Count());
Assert.AreEqual(MolecularFormulaManipulator.GetString(mf1),
MolecularFormulaManipulator.GetString(newMFSet[0]));
Assert.AreEqual(MolecularFormulaManipulator.GetString(mf2),
MolecularFormulaManipulator.GetString(newMFSet[1]));
Assert.AreEqual(MolecularFormulaManipulator.GetString(mf3),
MolecularFormulaManipulator.GetString(newMFSet[2]));
}
public void TestReactionSchemeWithFormula()
{
var writer = new StringWriter();
var scheme1 = builder.NewReactionScheme();
scheme1.Id = "rs0";
var reaction = builder.NewReaction();
reaction.Id = "r1";
var moleculeA = reaction.Builder.NewAtomContainer();
moleculeA.Id = "A";
var formula = new MolecularFormula();
formula.Add(reaction.Builder.NewIsotope("C"), 10);
formula.Add(reaction.Builder.NewIsotope("H"), 15);
formula.Add(reaction.Builder.NewIsotope("N"), 2);
formula.Add(reaction.Builder.NewIsotope("O"), 1);
moleculeA.SetProperty(CDKPropertyName.Formula, formula);
var moleculeB = reaction.Builder.NewAtomContainer();
moleculeB.Id = "B";
reaction.Reactants.Add(moleculeA);
reaction.Products.Add(moleculeB);
scheme1.Add(reaction);
var reaction2 = reaction.Builder.NewReaction();
reaction2.Id = "r2";
var moleculeC = reaction.Builder.NewAtomContainer();
moleculeC.Id = "C";
reaction2.Reactants.Add(moleculeB);
reaction2.Products.Add(moleculeC);
scheme1.Add(reaction2);
using (var cmlWriter = new CMLWriter(writer))
{
cmlWriter.Write(scheme1);
}
var cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<reactionScheme id=\"rs0") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"r1") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"r2") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"A") != -1);
Assert.IsTrue(cmlContent.IndexOf("<formula concise=") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"B") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"C") != -1);
}
public void TestDefaultValidTrue()
{
IRule rule = new MMElementRule();
var formula = new MolecularFormula();
formula.Add(builder.NewIsotope("C"), 2);
formula.Add(builder.NewIsotope("H"), 6);
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestDefaultValidFalseSetParam()
{
IRule rule = new ChargeRule();
var formula = new MolecularFormula();
formula.Add(builder.NewIsotope("C"), 2);
formula.Add(builder.NewIsotope("H"), 200);
formula.Charge = 1;
rule.Parameters = new object[] { -1.0 };
Assert.AreEqual(0.0, rule.Validate(formula), 0.0001);
}
public virtual void TestValidate_IMolecularFormula()
{
var rule = GetRule();
IMolecularFormula mf = new MolecularFormula();
mf.Add(new Isotope("C", 13));
mf.Add(new Isotope("H", 2), 4);
rule.Validate(mf);
// can it handle an empty MF?
rule.Validate(new MolecularFormula());
}
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);
}
public void TestDefaultValidFalseSetParam()
{
IRule rule = new ElementRule();
var formula = new MolecularFormula();
formula.Add(builder.NewIsotope("C"), 2);
formula.Add(builder.NewIsotope("H"), 6);
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(builder.NewIsotope("C"), 1, 2);
mfRange.AddIsotope(builder.NewIsotope("H"), 1, 2);
rule.Parameters = new object[] { mfRange };
Assert.AreEqual(0.0, rule.Validate(formula), 0.0001);
}
public void TestGetMaximalFormula_MolecularFormulaRange_IChemObjectBuilder()
{
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);
IMolecularFormula formula = MolecularFormulaRangeManipulator.GetMaximalFormula(mfRange, builder);
/* Result: C4-9H5-20N0-4O2-7 */
Assert.AreEqual(4, mfRange.GetIsotopes().Count());
Assert.AreEqual(formula.GetCount(builder.NewIsotope("C")),
mfRange.GetIsotopeCountMax(builder.NewIsotope("C")));
Assert.AreEqual(formula.GetCount(builder.NewIsotope("H")),
mfRange.GetIsotopeCountMax(builder.NewIsotope("H")));
Assert.AreEqual(formula.GetCount(builder.NewIsotope("N")),
mfRange.GetIsotopeCountMax(builder.NewIsotope("N")));
Assert.AreEqual(formula.GetCount(builder.NewIsotope("O")),
mfRange.GetIsotopeCountMax(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")));
}
public void TestContains_IMolecularFormulaSet_IMolecularFormula()
{
var mf1 = new MolecularFormula();
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 mf3 = new MolecularFormula();
mf3.Add(builder.NewIsotope("C"), 9);
mf3.Add(builder.NewIsotope("H"), 5);
mf3.Add(builder.NewIsotope("O"), 7);
var formulaSet = new MolecularFormulaSet
{
mf1,
mf3
};
var mf2 = new MolecularFormula();
mf2.Add(builder.NewIsotope("C"), 4);
mf2.Add(builder.NewIsotope("H"), 12);
mf2.Add(builder.NewIsotope("N"), 1);
mf2.Add(builder.NewIsotope("O"), 4);
var mf4 = new MolecularFormula();
mf4.Add(builder.NewIsotope("C"), 4);
var hyd = builder.NewIsotope("H");
hyd.ExactMass = 2.0032342;
mf4.Add(hyd, 12);
mf4.Add(builder.NewIsotope("N"), 1);
mf4.Add(builder.NewIsotope("O"), 4);
Assert.IsTrue(MolecularFormulaSetManipulator.Contains(formulaSet, mf2));
Assert.IsFalse(MolecularFormulaSetManipulator.Contains(formulaSet, mf4));
}
public void TestDefaultValidFalse_SetParam()
{
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);
object[] parameters = new object[2];
parameters[0] = 46.0; // real -> 46.96885268
parameters[1] = 0.00005;
rule.Parameters = parameters;
Assert.AreEqual(0.0, rule.Validate(formula), 0.0001);
}
public void TestRemove_3()
{
var formulaMin = new MolecularFormula();
formulaMin.Add(builder.NewIsotope("C"), 1);
formulaMin.Add(builder.NewIsotope("H"), 1);
formulaMin.Add(builder.NewIsotope("N"), 1);
var formulaMax = new MolecularFormula();
formulaMax.Add(builder.NewIsotope("C"), 4);
formulaMax.Add(builder.NewIsotope("H"), 12);
formulaMax.Add(builder.NewIsotope("N"), 2);
var mf1 = new MolecularFormula();
mf1.Add(builder.NewIsotope("C"), 3);
mf1.Add(builder.NewIsotope("H"), 10);
mf1.Add(builder.NewIsotope("N"), 1);
var mf2 = new MolecularFormula();
mf2.Add(builder.NewIsotope("C"), 1);
mf2.Add(builder.NewIsotope("H"), 1);
mf2.Add(builder.NewIsotope("O"), 1);
var formulaSet = new MolecularFormulaSet
{
mf1,
mf2
};
var newMFSet = MolecularFormulaSetManipulator.Remove(formulaSet, formulaMin, formulaMax);
/* the mf2 is excluded from the limits. It doesn't contain N */
Assert.AreEqual(1, newMFSet.Count());
Assert.AreEqual(MolecularFormulaManipulator.GetString(mf1),
MolecularFormulaManipulator.GetString(newMFSet[0]));
}
public void TestGetMinOccurrenceElements_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
};
var molecularFormula = MolecularFormulaSetManipulator.GetMinOccurrenceElements(mfSet);
/* Result: C4H5NO2 */
Assert.AreEqual(12, MolecularFormulaManipulator.GetAtomCount(molecularFormula));
Assert.AreEqual(4, molecularFormula.Isotopes.Count());
Assert.AreEqual(4, molecularFormula.GetCount(builder.NewIsotope("C")));
Assert.AreEqual(5, molecularFormula.GetCount(builder.NewIsotope("H")));
Assert.AreEqual(1, molecularFormula.GetCount(builder.NewIsotope("N")));
Assert.AreEqual(2, molecularFormula.GetCount(builder.NewIsotope("O")));
}
public void TestValidBromine()
{
var spectrum = new List <double[]>
{
new double[] { 157.8367, 51.399 },
new double[] { 159.8346, 100.00 },
new double[] { 161.8326, 48.639 }
};
var rule = new IsotopePatternRule();
var parameters = new object[2];
parameters[0] = spectrum;
parameters[1] = 0.001;
rule.Parameters = parameters;
var formula = new MolecularFormula();
formula.Add(ifac.GetMajorIsotope("C"), 2);
formula.Add(ifac.GetMajorIsotope("Br"), 2);
formula.Charge = 0;
Assert.AreEqual(0.0, rule.Validate(formula), 0.0001);
}