public string MolFormula => GetMolecularFormula(NativeMol); // get mol formula
/// <summary>
/// GetMolecularFormula
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static string GetMolecularFormula(IAtomContainer mol)
{
IMolecularFormula moleculeFormula = MolecularFormulaManipulator.getMolecularFormula(mol);
String formula = MolecularFormulaManipulator.getString(moleculeFormula);
return(formula);
}
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 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 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 TestDefaultValidFalse()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C2H4", builder);
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
/// <summary>
/// Extract from a set of MolecularFormula the minimal occurrence of each element found and
/// put the element and occurrence in a new IMolecularFormula.
/// </summary>
/// <param name="mfSet">The set of molecularFormules to inspect</param>
/// <returns>A IMolecularFormula containing the minimal occurrence of the elements</returns>
/// <seealso cref="GetMaxOccurrenceElements(IMolecularFormulaSet)"/>
public static IMolecularFormula GetMinOccurrenceElements(IMolecularFormulaSet mfSet)
{
var molecularFormula = mfSet.Builder.NewMolecularFormula();
foreach (var mf in mfSet)
{
foreach (var isotope in mf.Isotopes)
{
var element = isotope.Element;
int occur_new = MolecularFormulaManipulator.GetElementCount(mf, element);
if (!MolecularFormulaManipulator.ContainsElement(molecularFormula, element))
{
molecularFormula.Add(mfSet.Builder.NewIsotope(element), occur_new);
}
else
{
int occur_old = MolecularFormulaManipulator.GetElementCount(molecularFormula, element);
if (occur_new < occur_old)
{
MolecularFormulaManipulator.RemoveElement(molecularFormula, element);
molecularFormula.Add(mfSet.Builder.NewIsotope(element), occur_new);
}
}
}
}
return(molecularFormula);
}
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]));
}
[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 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);
}
public void Test2()
{
RDBERule rule = new RDBERule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C4H8O3S1", builder);
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestValidate_IMolecularFormula_Double()
{
RDBERule rule = new RDBERule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C2H4", builder);
Assert.IsTrue(rule.Validate(formula, 2.0));
}
public void TestAnticipatedIonState_2()
{
RDBERule rule = new RDBERule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("NH4", builder);
Assert.AreEqual(0.0, rule.Validate(formula), 0.0001);
}
public void TestGetRDBEValue_IMolecularFormula()
{
RDBERule rule = new RDBERule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C2H4", builder);
Assert.AreEqual(1.0, rule.GetRDBEValue(formula)[0], 0.0001);
}
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]));
}
/// <summary>
/// Constructor of the <see cref="IsotopeContainer"/> object setting a <see cref="IMolecularFormula"/> object and intensity value.
/// </summary>
/// <param name="formula">The formula of this container</param>
/// <param name="intensity">The intensity of this container</param>
public IsotopeContainer(IMolecularFormula formula, double intensity)
{
forms.Add(formula);
if (formula != null)
{
Mass = MolecularFormulaManipulator.GetTotalExactMass(formula);
}
Intensity = intensity;
}
/// <summary>
/// Get all combinatorial chemical isotopes given a structure.
/// </summary>
/// <param name="molFor">The IMolecularFormula to start</param>
/// <returns>A IsotopePattern object containing the different combinations</returns>
public IsotopePattern GetIsotopes(IMolecularFormula molFor)
{
if (builder == null)
{
try
{
isoFactory = CDK.IsotopeFactory;
builder = molFor.Builder;
}
catch (Exception e)
{
Console.WriteLine(e.StackTrace);
}
}
var mf = MolecularFormulaManipulator.GetString(molFor, true);
var molecularFormula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula(mf, builder);
IsotopePattern abundance_Mass = null;
foreach (var isos in molecularFormula.Isotopes)
{
var elementSymbol = isos.Symbol;
var atomCount = molecularFormula.GetCount(isos);
// Generate possible isotope containers for the current atom's
// these will then me 'multiplied' with the existing patten
var additional = new List <IsotopeContainer>();
foreach (var isotope in isoFactory.GetIsotopes(elementSymbol))
{
double mass = isotope.ExactMass.Value;
double abundance = isotope.Abundance.Value;
if (abundance <= 0.000000001)
{
continue;
}
IsotopeContainer container = new IsotopeContainer(mass, abundance);
if (storeFormula)
{
container.Formula = AsFormula(isotope);
}
additional.Add(container);
}
for (int i = 0; i < atomCount; i++)
{
abundance_Mass = CalculateAbundanceAndMass(abundance_Mass, additional);
}
}
var isoP = IsotopePatternManipulator.SortAndNormalizedByIntensity(abundance_Mass);
isoP = CleanAbundance(isoP, minIntensity);
var isoPattern = IsotopePatternManipulator.SortByMass(isoP);
return(isoPattern);
}
public void TestCalculate_IronOxide()
{
var material = CDK.Builder.NewSubstance();
material.Add(MolecularFormulaManipulator.GetAtomContainer("Fe3O4", material.Builder));
var value = Descriptor.Calculate(material);
Assert.IsNotNull(value);
Assert.AreEqual(4, value.Value);
}
public void TestDefaultValidTrue()
{
IRule rule = new RDBERule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C1H4", builder);
formula.Charge = 0;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestC45H75NO15()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C45H75NO15", builder);
formula.Charge = 0;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestDoubleCharge()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula("C22H34N2S2", builder);
formula.Charge = 2;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestWithCo()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula("C43H50CoN4O16", builder);
formula.Charge = 0;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestB()
{
RDBERule rule = new RDBERule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C6H9BNO2", builder);
formula.Charge = 1;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestWithFe()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula("C40H46FeN6O8S2", builder);
formula.Charge = 2;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestNominalMass()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula("C25H53NO7P", builder);
formula.Charge = 1;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
static void Main(string[] args)
{
IAtomContainer mol1 = Chem.MolFromSmiles("[C:1]([C:5]1[CH:10]=[CH:9][C:8]([OH:11])=[CH:7][CH:6]=1)([CH3:4])([CH3:3])[CH3:2]");
IMolecularFormula form1 = MolecularFormulaManipulator.GetMolecularFormula(mol1);
Console.WriteLine(MolecularFormulaManipulator.GetString(form1));
IAtomContainer mol2 = Chem.MolFromFile("/Users/john/My Documents/1,3-diisopropenylbenzene.mol");
var form2 = MolecularFormulaManipulator.GetMolecularFormula(mol2);
Console.WriteLine(MolecularFormulaManipulator.GetString(form2));
}
public string MolFormula => GetMolecularFormula(NativeMol); // get mol formula
/// <summary>
/// GetMolecularFormula
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static string GetMolecularFormula(IAtomContainer mol)
{
if (mol == null)
{
return("");
}
IMolecularFormula moleculeFormula = MolecularFormulaManipulator.GetMolecularFormula(mol);
String formula = MolecularFormulaManipulator.GetString(moleculeFormula);
return(formula);
}
private void AddDistinctFormula(IsotopeContainer container, IMolecularFormula mf)
{
foreach (var curr in container.Formulas)
{
if (MolecularFormulaManipulator.Compare(curr, mf))
{
return;
}
}
container.AddFormula(mf);
}
/// <summary>
/// In the minimal IMolecularFormula must contain all those IElement found in the
/// minimal IMolecularFormula.
/// </summary>
/// <param name="formulaMax">A IMolecularFormula which contains the maximal representation of the Elements</param>
/// <param name="formulaMin">A IMolecularFormula which contains the minimal representation of the Elements</param>
/// <returns>True, if the correlation is valid</returns>
private static bool ValidCorrelation(IMolecularFormula formulaMin, IMolecularFormula formulaMax)
{
foreach (var element in MolecularFormulaManipulator.Elements(formulaMin))
{
if (!MolecularFormulaManipulator.ContainsElement(formulaMax, element))
{
return(false);
}
}
return(true);
}
/// <summary>
/// True, if the IMolecularFormulaSet contains the given IMolecularFormula but not
/// as object. It compare according contains the same number and type of Isotopes.
/// It is not based on compare objects.
/// </summary>
/// <param name="formulaSet">The IMolecularFormulaSet</param>
/// <param name="formula">The IMolecularFormula this IMolecularFormulaSet is searched for</param>
/// <returns>True, if the IMolecularFormulaSet contains the given formula</returns>
/// <seealso cref="System.Collections.Generic.ICollection{T}.Contains(T)"/>
public static bool Contains(IMolecularFormulaSet formulaSet, IMolecularFormula formula)
{
foreach (var fm in formulaSet)
{
if (MolecularFormulaManipulator.Compare(fm, formula))
{
return(true);
}
}
return(false);
}