/// <summary>
/// Adds molecular formula into a list.
/// </summary>
/// <param name="formulas">The molecular fomula collection.</param>
/// <param name="value">A molecular formula instance to add.</param>
/// <param name="count">The count of the value.</param>
/// <param name="another">Another optional molecular formula instance to add.</param>
/// <param name="countForAnother">The count of another.</param>
/// <param name="other">The optional third molecular formula instance to add</param>
/// <param name="countForLast">The count of the third molecular formula instance to add.</param>
public static void Add(this ICollection <MolecularFormula> formulas, MolecularFormula value, int count, MolecularFormula another = null, int countForAnother = 1, MolecularFormula other = null, int countForLast = 1)
{
if (formulas is null)
{
return;
}
if (value != null)
{
for (var i = 0; i < count; i++)
{
formulas.Add(value);
}
}
if (another != null)
{
for (var i = 0; i < countForAnother; i++)
{
formulas.Add(another);
}
}
if (other != null)
{
for (var i = 0; i < countForLast; i++)
{
formulas.Add(other);
}
}
}
public clsAveragine(clsAveragine a)
{
_useTag = a._useTag;
_tagMass = a._tagMass;
_averagineFormula = new MolecularFormula(a._averagineFormula);
_tagFormula = a._tagFormula;
}
public void TestParseFormulaNew()
{
string formula = "C4.9384 H7.7583 N1.3577 O1.4773 S0.0417";
//string formula = "Ct H7.7583 N1.3577 O1.4773 S0.0417";
var elements = new clsElementIsotopes();
//var molecule = new MolecularFormula(formula, elements);
var molecule = new MolecularFormula();
molecule.SetMolecularFormula(formula, elements);
var results = molecule.ElementalComposition;
var carbon = results[0];
var hydrogen = results[1];
var nitrogen = results[2];
var oxygen = results[3];
var sulfur = results[4];
Assert.AreEqual(carbon.Index, 5);
Assert.AreEqual(carbon.NumCopies, 4.9384);
Assert.AreEqual(hydrogen.Index, 0);
Assert.AreEqual(hydrogen.NumCopies, 7.7583);
Assert.AreEqual(nitrogen.Index, 6);
Assert.AreEqual(nitrogen.NumCopies, 1.3577);
Assert.AreEqual(oxygen.Index, 7);
Assert.AreEqual(oxygen.NumCopies, 1.4773);
Assert.AreEqual(sulfur.Index, 15);
Assert.AreEqual(sulfur.NumCopies, 0.0417);
}
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 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_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 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 override int GetHashCode()
{
unchecked
{
var hashCode = CID;
hashCode = (hashCode * 397) ^ (MolecularFormula != null ? MolecularFormula.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (InChIKey != null ? InChIKey.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ ExactMass.GetHashCode();
return(hashCode);
}
}
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 TestIsTheSame_IIsotope_IIsotope()
{
MolecularFormula mf = new MolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope anotherCarb = Builder.NewIsotope("C");
IIsotope h = Builder.NewIsotope("H");
carb.ExactMass = 12.0;
anotherCarb.ExactMass = 12.0;
h.ExactMass = 1.0;
carb.Abundance = 34.0;
anotherCarb.Abundance = 34.0;
h.Abundance = 99.0;
Assert.IsTrue(MolecularFormula.IsTheSame(carb, carb));
Assert.IsTrue(MolecularFormula.IsTheSame(carb, anotherCarb));
Assert.IsFalse(MolecularFormula.IsTheSame(carb, h));
}
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 CalculateMasses(MolecularFormula formula)
{
MonoMw = 0;
AverageMw = 0;
var numElementsFound = formula.NumElements;
for (var j = 0; j < numElementsFound; j++)
{
var elementIndex = formula.ElementalComposition[j].Index;
var atomicity = (int)formula.ElementalComposition[j].NumCopies;
if (atomicity == 0)
{
continue;
}
//int numIsotopes = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].NumberOfIsotopes;
var monoMw = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[0].Mass;
var avgMw = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].AverageMass;
MonoMw += atomicity * monoMw;
AverageMw += atomicity * avgMw;
}
}
public void CalcVariancesAndMassRange(int charge, MolecularFormula formula)
{
MassVariance = 0;
var numElementsFound = formula.NumElements;
for (var elementNum = 0; elementNum < numElementsFound; elementNum++)
{
var elementIndex = formula.ElementalComposition[elementNum].Index;
var atomicity = (int)formula.ElementalComposition[elementNum].NumCopies;
var elementalVariance = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].MassVariance;
MassVariance += elementalVariance * atomicity;
}
if (charge == 0)
{
_massRange = (int)(Math.Sqrt(1 + MassVariance) * 10);
}
else
{
_massRange = (int)(Math.Sqrt(1 + MassVariance) * 10.0 / charge);
}
/* +/- 5 sd's : Multiply charged */
/* Set to nearest (upper) power of 2 */
for (var i = 1024; i > 0; i /= 2)
{
if (i < _massRange)
{
_massRange = i * 2;
i = 0;
}
}
if (_massRange <= 0)
{
_massRange = 1;
}
}
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);
}
public static IMolecularFormula GetMolecularFormula(IAtomContainer atomContainer)
{
var formula = new MolecularFormula();
var charge = 0;
var hydrogen = new Atom("H");
foreach (var iAtom in atomContainer.atoms().ToWindowsEnumerable<IAtom>())
{
formula.addIsotope(iAtom);
charge += iAtom.getFormalCharge().intValue();
var implicitHydrogenCount = iAtom.getImplicitHydrogenCount();
var implicitHydrogenCountValue = implicitHydrogenCount != null ? implicitHydrogenCount.intValue() : (int?) null;
if (implicitHydrogenCountValue.HasValue && implicitHydrogenCountValue.Value > 0)
{
formula.addIsotope(hydrogen, implicitHydrogenCountValue.Value);
}
}
formula.setCharge(new Integer(charge));
return formula;
}
public void TestMolecularFormula()
{
var s = "NonExist";
Assert.IsNull(MolecularFormula.TryParse(s));
s = "H2CO3";
var m = MolecularFormula.Parse(s);
Assert.AreEqual(s.Length, m.ToString().Length);
s = m.ToString();
Assert.IsTrue(s.Contains("CO"));
Assert.AreEqual(6, m.Count);
Assert.AreEqual(0, m.IndexOf("H"));
Assert.AreEqual(-1, m.IndexOf("H", 2));
Assert.AreEqual(1, m.IndexOf(ChemicalElement.C));
Assert.AreEqual(1, m.IndexOf(ChemicalElement.C, 1));
Assert.AreEqual(1, m.GetCount("C"));
Assert.AreEqual(3, m.GetCount(ChemicalElement.O));
Assert.IsFalse(m.IsIon);
m = MolecularFormula.Parse(s);
Assert.AreEqual(s, m.ToString());
Assert.AreEqual(6, m.Count);
m = new MolecularFormula(m.Items);
Assert.AreEqual(s, m.ToString());
s = "SO₄²ˉ";
m = MolecularFormula.Parse(s);
Assert.AreEqual(s, m.ToString());
Assert.IsTrue(m.IsIon);
Assert.AreEqual(-2, m.ChargeNumber);
m = MolecularFormula.Parse("R-COOH");
Assert.AreEqual(2, m.GetCount(ChemicalElement.C));
Assert.AreEqual(2, m.GetCount(ChemicalElement.O));
Assert.AreEqual(4, m.GetCount(ChemicalElement.H));
m = ChemicalElement.Fe * 2 + 3 * ChemicalElement.O;
Assert.AreEqual(2, m.GetCount("Fe"));
Assert.AreEqual(3, m.GetCount(ChemicalElement.O));
m = ChemicalElement.C + ChemicalElement.O;
Assert.AreEqual(1, m.GetCount("C"));
Assert.AreEqual(1, m.GetCount(ChemicalElement.O));
m += ChemicalElement.O;
Assert.AreEqual(1, m.GetCount("C"));
Assert.AreEqual(2, m.GetCount(ChemicalElement.O));
m = ChemicalElement.H + m;
Assert.AreEqual(1, m.GetCount("H"));
Assert.AreEqual(4, m.Count);
m = ChemicalElement.H * 2 + ChemicalElement.O;
var col = new List <MolecularFormula>
{
{ m, 2, ChemicalElement.Na }
};
Assert.AreEqual(3, col.Count);
Console.WriteLine(MolecularFormula.ToString(col));
Assert.IsTrue(MolecularFormula.ToString(col).Length > 6);
col.RemoveAt(2);
Assert.IsTrue(MolecularFormula.ConservationOfMass(
new List <MolecularFormula>
{
4 * ChemicalElement.H,
ChemicalElement.O * 2
},
col));
Assert.IsFalse(MolecularFormula.ConservationOfMass(
new List <MolecularFormula>
{
ChemicalElement.C + ChemicalElement.O * 2
},
new List <MolecularFormula>
{
ChemicalElement.Na,
ChemicalElement.Cl
}));
Assert.IsFalse(MolecularFormula.ConservationOfMass(
new List <MolecularFormula>
{
new MolecularFormula(new List <MolecularFormula.Item>
{
new MolecularFormula.Item(ChemicalElement.Cl)
}, -1)
},
new List <MolecularFormula>
{
new MolecularFormula(ChemicalElement.Cl)
}));
}
public void CalcFrequencies(int charge, int numPoints, MolecularFormula formula)
{
int i;
int j, k;
double real, imag, freq, x, theta, r, tempr;
var numElementsInEntity = formula.NumElements;
/* Calculate first half of Frequency Domain (+)masses */
for (i = 1; i <= numPoints / 2; i++)
{
freq = (double)(i - 1) / _massRange;
r = 1;
theta = 0;
for (j = 0; j < numElementsInEntity; j++)
{
var elementIndex = formula.ElementalComposition[j].Index;
var atomicity = (int)formula.ElementalComposition[j].NumCopies;
var numIsotopes = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].NumberOfIsotopes;
var averageMass = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].AverageMass;
real = imag = 0.0;
for (k = 0; k < numIsotopes; k++)
{
double wrapFreq = 0;
var isotopeAbundance =
ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[k].Probability;
if (numIsotopes > 1)
{
wrapFreq =
ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[k].Mass /
charge - averageMass / charge;
if (wrapFreq < 0)
{
wrapFreq += _massRange;
}
}
x = 2 * Pi * wrapFreq * freq;
real += isotopeAbundance * Math.Cos(x);
imag += isotopeAbundance * Math.Sin(x);
}
/* Convert to polar coordinates, r then theta */
tempr = Math.Sqrt(real * real + imag * imag);
r *= Math.Pow(tempr, atomicity);
if (real > 0)
{
theta += atomicity * Math.Atan(imag / real);
}
else if (real < 0)
{
theta += atomicity * (Math.Atan(imag / real) + Pi);
}
else if (imag > 0)
{
theta += atomicity * Pi / 2;
}
else
{
theta += atomicity * -Pi / 2;
}
}
/* Convert back to real:imag coordinates and store */
_frequencyData[i - 1] = new Complex(r * Math.Cos(theta), r * Math.Sin(theta));
} /* end for(i) */
/* Calculate second half of Frequency Domain (-)masses */
for (i = numPoints / 2 + 1; i <= numPoints; i++)
{
freq = (double)(i - numPoints - 1) / _massRange;
r = 1;
theta = 0;
for (j = 0; j < numElementsInEntity; j++)
{
var elementIndex = formula.ElementalComposition[j].Index;
var atomicity = (int)formula.ElementalComposition[j].NumCopies;
var numIsotopes = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].NumberOfIsotopes;
var averageMass = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].AverageMass;
real = imag = 0;
for (k = 0; k < numIsotopes; k++)
{
double wrapFreq = 0;
var isotopeAbundance =
ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[k].Probability;
if (numIsotopes > 1)
{
wrapFreq =
ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[k].Mass /
charge - averageMass / charge;
if (wrapFreq < 0)
{
wrapFreq += _massRange;
}
}
x = 2 * Pi * wrapFreq * freq;
real += isotopeAbundance * Math.Cos(x);
imag += isotopeAbundance * Math.Sin(x);
}
/* Convert to polar coordinates, r then theta */
tempr = Math.Sqrt(real * real + imag * imag);
r *= Math.Pow(tempr, atomicity);
if (real > 0)
{
theta += atomicity * Math.Atan(imag / real);
}
else if (real < 0)
{
theta += atomicity * (Math.Atan(imag / real) + Pi);
}
else if (imag > 0)
{
theta += atomicity * Pi / 2;
}
else
{
theta -= atomicity * Pi / 2;
}
} /* end for(j) */
/* Convert back to real:imag coordinates and store */
_frequencyData[i - 1] = new Complex(r * Math.Cos(theta), r * Math.Sin(theta));
} /* end of for(i) */
}
/// <summary>
/// Calculate the isotope distribution
/// </summary>
/// <param name="charge"></param>
/// <param name="resolution"></param>
/// <param name="formula"></param>
/// <param name="x">mz values of isotopic profile that are above the threshold</param>
/// <param name="y">intensity values of isotopic profile that are above the threshold</param>
/// <param name="threshold"></param>
/// <param name="isotopeMzs">peak top mz's for the peaks of the isotopic profile</param>
/// <param name="isotopeIntensities">peak top intensities's for the peaks of the isotopic profile</param>
/// <param name="debug"></param>
public void CalculateDistribution(int charge, double resolution, MolecularFormula formula, out List <double> x,
out List <double> y, double threshold, out List <double> isotopeMzs, out List <double> isotopeIntensities,
bool debug = false)
{
/* Calculate mono and average mass */
CalculateMasses(formula);
if (debug)
{
Console.Error.WriteLine("MonoMW =" + MonoMw + " AverageMW =" + AverageMw);
}
/* Calculate mass range to use based on molecular variance */
CalcVariancesAndMassRange(charge, formula);
if (debug)
{
Console.Error.WriteLine("Variance =" + MassVariance + " Mass Range =" + _massRange);
}
_minMz = AverageMw / charge + (ChargeCarrierMass - MercuryCache.ElectronMass) - _massRange * 1.0 / 2;
_maxMz = _minMz + _massRange;
PointsPerAmu = MercurySize / _massRange; /* Use maximum of 2048 real, 2048 imag points */
// calculate Ap_subscript to from requested Res
double aPSubscript;
if (charge == 0)
{
aPSubscript = AverageMw / resolution * MercurySize * 2.0 / _massRange;
}
else
{
aPSubscript = AverageMw / (resolution * Math.Abs(charge)) * MercurySize * 2.0 / _massRange;
}
/* Allocate memory for Axis arrays */
var numPoints = _massRange * PointsPerAmu;
_frequencyData = new Complex[numPoints];
if (charge == 0)
{
charge = 1;
}
if (debug)
{
Console.Error.WriteLine("MINMZ = " + _minMz + " MAXMZ = " + _maxMz);
Console.Error.WriteLine("Num Points per AMU = " + PointsPerAmu);
}
CalcFrequencies(charge, numPoints, formula);
/* Apodize data */
double apResolution = 1; /* Resolution used in apodization. Not used yet */
Apodize(numPoints, apResolution, aPSubscript);
Fourier.Inverse(_frequencyData, FourierOptions.NumericalRecipes);
// myers changes this line to Realft(FreqData,NumPoints,-1);
/*
* [gord] 'OutputData' fills 'x', 'y'
* [gord] x = mz values of isotopic profile that are above the threshold
* [gord] y = intensity values of isotopic profile that are above the threshold
* [gord] isotopeMzs = peak top mz's for the peaks of the isotopic profile
* [gord] isotopeIntensities = peak top intensities's for the peaks of the isotopic profile
*/
OutputData(numPoints, charge, out x, out y, threshold, out isotopeMzs, out isotopeIntensities);
//NormalizeToPercentIons(vect_y);
}
public void TestMolecularFormula()
{
IMolecularFormula mf = new MolecularFormula();
Assert.IsNotNull(mf);
}
private void reportFormula(StringBuilder sb, MolecularFormula formula)
{
sb.Append(formula.ToFormulaString());
sb.Append("\n");
}
/// <summary>
/// calculates the fit score for a peak against a molecular formula.
/// </summary>
/// <param name="peakData"> variable which stores the data itself</param>
/// <param name="chargeState"> charge state at which we want to compute the peak.</param>
/// <param name="peak"> peak for which we want to compute the fit function.</param>
/// <param name="formula">stores the formula we want to fit.</param>
/// <param name="deleteIntensityThreshold">intensity of least isotope to delete.</param>
/// <param name="minTheoreticalIntensityForScore">minimum intensity of point to consider for scoring purposes.</param>
/// <param name="debug">if debugging output is enabled</param>
public double GetFitScore(PeakData peakData, int chargeState, ThrashV1Peak peak, MolecularFormula formula,
double deleteIntensityThreshold, double minTheoreticalIntensityForScore, bool debug = false)
{
if (chargeState <= 0)
{
Console.WriteLine("Negative value for charge state. " + chargeState);
Environment.Exit(1);
}
if (debug)
{
Console.WriteLine("Getting isotope distribution for formula = " + formula + " mz = " + peak.Mz +
" charge = " + chargeState);
}
var resolution = peak.Mz / peak.FWHM;
IsotopeDistribution.ChargeCarrierMass = ChargeCarrierMass;
IsotopeDistribution.ApType = ApodizationType.Gaussian;
TheoreticalDistIntensities.Clear();
TheoreticalDistMzs.Clear();
IsotopeDistribution.CalculateDistribution(chargeState, resolution, formula, out TheoreticalDistMzs,
out TheoreticalDistIntensities, deleteIntensityThreshold, out IsotopeMzs, out IsotopeIntensities, debug);
var delta = peak.Mz - IsotopeDistribution.MaxPeakMz;
if (debug)
{
Console.WriteLine("Going for first fit");
}
int pointsUsed;
return(FitScore(peakData, chargeState, peak, delta, minTheoreticalIntensityForScore, out pointsUsed,
debug));
}
/**
* Gets the neutral losses which are stored in a file.
*
* @return the neutral losses
*/
private void ReadInNeutralLosses()
{
neutralLoss = new Dictionary<double, NeutralLoss>();
const string lossesString = "Ion Mode Exact DM Topological fragment Elemental Composition H-Difference Furthest Distance Atom to start Hydrogen Connected to Start Atom Substance Class Identifier\n"
+ "+ - 18.01056 OH H2O -1 3 O 1 Non-specific (OH)\n"
+ "+ 46.00548 COOH HCOOH -1 3 O 0 Aliphatic Acids, Amino Acid Conjugates …\n"
+ "+ - 17.02655 NH2 NH3 -1 3 N 2 not sure\n"
+ "+ - 27.01090 CN HCN -1 3 N 0 Alkaloids\n"
+ "+ - 30.01056 COH CH2O -1 3 O 0 Methoxylated aromatic compounds\n"
+ "#+ - 27.99491 COH CO 1 3 O 0 Flavonoids, Coumarins, Chromones ….\n"
+ "#+ - 43.98983 COOH CO2 1 3 O 0 Aromatic acids, Lactones \n"
+ "#- 79.95681 SO3H SO3 1 3 S 0 0 -sulfated compounds\n"
+ "#+ - 162.05282 C6H11O5 C6H10O5 1 6 O 0 Glucosides";
var lines = lossesString.Split('\n');
//Read File Line By Line, skipping header
foreach (var lineArray in lines.Skip(1).Where(l => !l.StartsWith("#")).Select(l => l.Split('\t')))
{
int mode;
switch (lineArray[0])
{
case "+ -":
mode = 0;
break;
case "-":
mode = -1;
break;
default:
mode = 1;
break;
}
var mfT = new MolecularFormula();
var mfE = new MolecularFormula();
var nl = new NeutralLoss(MolecularFormulaManipulator.getMolecularFormula(lineArray[3], mfE), MolecularFormulaManipulator.getMolecularFormula(lineArray[2], mfT), mode, Integer.parseInt(lineArray[4]), Integer.parseInt(lineArray[5]), lineArray[6], Integer.parseInt(lineArray[7]));
var deltaM = Double.Parse(lineArray[1], CultureInfo.InvariantCulture);
neutralLoss[deltaM] = nl;
}
}
