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 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 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 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 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>
/// 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);
}
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);
}
public SingleStructureRandomGeneratorTest()
{
Console.Out.WriteLine("Instantiating MoleculeListViewer");
Console.Out.WriteLine("Instantiating SingleStructureRandomGenerator");
ssrg = new SingleStructureRandomGenerator();
Console.Out.WriteLine("Assining unbonded set of atoms");
AtomContainer ac = GetBunchOfUnbondedAtoms();
mf = MolecularFormulaManipulator.GetString(MolecularFormulaManipulator.GetMolecularFormula(ac));
Console.Out.WriteLine("Molecular Formula is: " + mf);
ssrg.SetAtomContainer(ac);
}
public static void Script8_3()
{
var parser = new SmilesParser();
var hAdder = CDKHydrogenAdder.GetInstance();
var methanol = parser.ParseSmiles("CO");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(methanol);
hAdder.AddImplicitHydrogens(methanol);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(methanol);
var dimethoxymethane = parser.ParseSmiles("COC");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(dimethoxymethane);
hAdder.AddImplicitHydrogens(dimethoxymethane);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(dimethoxymethane);
var water = parser.ParseSmiles("O");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(water);
hAdder.AddImplicitHydrogens(water);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(water);
var reaction = new Reaction();
reaction.Reactants.Add(methanol, 2.0D);
reaction.Products.Add(dimethoxymethane);
reaction.Products.Add(water);
Console.WriteLine("Reactants:");
foreach (var reactant in reaction.Reactants)
{
var formula = MolecularFormulaManipulator.GetMolecularFormula(reactant);
Console.WriteLine(MolecularFormulaManipulator.GetString(formula));
}
Console.WriteLine("Products: ");
foreach (var product in reaction.Products)
{
var formula = MolecularFormulaManipulator.GetMolecularFormula(product);
Console.WriteLine(MolecularFormulaManipulator.GetString(formula));
}
}
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 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 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 TestSelectingMF()
{
var is_ = new IsotopePatternSimilarity();
IsotopePattern spExp = new IsotopePattern(new[]
{
new IsotopeContainer(156.07770, 1),
new IsotopeContainer(157.07503, 0.0101),
new IsotopeContainer(157.08059, 0.074),
new IsotopeContainer(158.08135, 0.0024),
});
spExp.MonoIsotope = spExp.Isotopes[0];
spExp.Charge = 1;
double score = 0;
string mfString = "";
string[] listMF = { "C4H8N6O", "C2H12N4O4", "C3H12N2O5", "C6H10N3O2", "CH10N5O4", "C4H14NO5" };
for (int i = 0; i < listMF.Length; i++)
{
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula(listMF[i], builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.01);
IsotopePattern patternIsoPredicted = isotopeGe.GetIsotopes(formula);
IsotopePattern patternIsoNormalize = IsotopePatternManipulator.Normalize(patternIsoPredicted);
double tempScore = is_.Compare(spExp, patternIsoNormalize);
if (score < tempScore)
{
mfString = MolecularFormulaManipulator.GetString(formula);
score = tempScore;
}
}
Assert.AreEqual("C6H10N3O2", mfString);
}
[TestCategory("VerySlowTest")] // structgen is slow... a single method here currently takes ~6 seconds
public void TestDoCrossover_IAtomContainer()
{
IChemObjectSet <IAtomContainer> som;
var filename = "NCDK.Data.Smiles.c10h16isomers.smi";
using (var ins = ResourceLoader.GetAsStream(filename))
using (SMILESReader reader = new SMILESReader(ins))
{
som = reader.Read(CDK.Builder.NewAtomContainerSet());
Assert.AreEqual(99, som.Count, "We must have read 99 structures");
}
// Comment out next line to enable time seed random.
RandomNumbersTool.RandomSeed = 0L;
CrossoverMachine cm = new CrossoverMachine();
string correctFormula = "C10H16";
int errorcount = 0;
for (int i = 0; i < som.Count; i++)
{
int[] hydrogencount1 = new int[4];
foreach (var atom in som[i].Atoms)
{
hydrogencount1[atom.ImplicitHydrogenCount.Value]++;
}
for (int k = i + 1; k < som.Count; k++)
{
try
{
var result = cm.DoCrossover(som[i], som[k]);
int[] hydrogencount2 = new int[4];
foreach (var atom in som[k].Atoms)
{
hydrogencount2[atom.ImplicitHydrogenCount.Value]++;
}
Assert.AreEqual(2, result.Count, "Result size must be 2");
for (int l = 0; l < 2; l++)
{
IAtomContainer ac = result[l];
Assert.IsTrue(ConnectivityChecker.IsConnected(ac), "Result must be connected");
Assert.AreEqual(
MolecularFormulaManipulator.GetString(MolecularFormulaManipulator.GetMolecularFormula(ac)),
correctFormula,
"Molecular formula must be the same as" + "of the input");
int[] hydrogencountresult = new int[4];
int hcounttotal = 0;
foreach (var atom in result[l].Atoms)
{
hydrogencountresult[atom.ImplicitHydrogenCount.Value]++;
hcounttotal += atom.ImplicitHydrogenCount.Value;
}
if (hydrogencount1[0] == hydrogencount2[0])
{
Assert.AreEqual(
hydrogencount1[0], hydrogencountresult[0],
"Hydrogen count of the result must" + " be same as of input");
}
if (hydrogencount1[1] == hydrogencount2[1])
{
Assert.AreEqual(
hydrogencount1[1], hydrogencountresult[1],
"Hydrogen count of the result must" + " be same as of input");
}
if (hydrogencount1[2] == hydrogencount2[2])
{
Assert.AreEqual(
hydrogencount1[2], hydrogencountresult[2],
"Hydrogen count of the result must" + " be same as of input");
}
if (hydrogencount1[3] == hydrogencount2[3])
{
Assert.AreEqual(
hydrogencount1[3], hydrogencountresult[3],
"Hydrogen count of the result must" + " be same as of input");
}
Assert.AreEqual(16, hcounttotal);
}
}
catch (CDKException)
{
errorcount++;
}
}
}
Assert.IsTrue(errorcount < 300, "We tolerate up to 300 errors");
}