public void TestGetAllFormulas()
{
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, 10);
mfRange.AddIsotope(h, 0, 10);
mfRange.AddIsotope(o, 0, 10);
mfRange.AddIsotope(n, 0, 10);
double minMass = 100.0;
double maxMass = 100.05;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreNotEqual(0, mfSet.Count);
}
public void TestGetIsotopeCount()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
Assert.AreEqual(0, mfRange.Count);
}
public void TestMolecularFormulaRange()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
Assert.IsNotNull(mfRange);
}
/// <summary>
/// Returns an iterator over all decompositons of this mass range
/// </summary>
/// <param name="from">lowest mass to decompose</param>
/// <param name="to">(inclusive) largest mass to decompose</param>
/// <param name="boundaries">defines lowerbounds and upperbounds for the number of elements</param>
internal DecompIterator DecomposeIterator(double from, double to, MolecularFormulaRange boundaries)
{
Init();
if (to < 0d || from < 0d)
{
throw new ArgumentException("Expect positive mass for decomposition: [" + from + ", " + to + "]");
}
if (to < from)
{
throw new ArgumentException("Negative range given: [" + from + ", " + to + "]");
}
int[] minValues = new int[weights.Count];
int[] boundsarray = new int[weights.Count];
double cfrom = from, cto = to;
Arrays.Fill(boundsarray, int.MaxValue);
if (boundaries != null)
{
for (int i = 0; i < boundsarray.Length; i++)
{
IIsotope el = weights[i].GetOwner();
int max = boundaries.GetIsotopeCountMax(el);
int min = boundaries.GetIsotopeCountMin(el);
if (min >= 0 || max >= 0)
{
boundsarray[i] = max - min;
minValues[i] = min;
if (minValues[i] > 0)
{
double reduceWeightBy = weights[i].GetMass() * min;
cfrom -= reduceWeightBy;
cto -= reduceWeightBy;
}
}
}
}
int[] minmax = new int[2];
IntegerBound(cfrom, cto, minmax);
int deviation = minmax[1] - minmax[0];
//calculate the required ERTs
if ((1 << (ERTs.Length - 1)) <= deviation)
{
CalcERT(deviation);
}
{
int[][][] ERTs = this.ERTs;
//take ERT with required deviation
int[][] currentERT;
if (deviation == 0)
{
currentERT = ERTs[0];
}
else
{
currentERT = ERTs[32 - Ints.NumberOfLeadingZeros(deviation)];
}
return(new DecompIterator(currentERT, minmax[0], minmax[1], from, to, minValues, boundsarray, weights));
}
}
/// <summary>
/// Initiate the MolecularFormulaGenerator.
/// </summary>
/// <param name="minMass">Lower boundary of the target mass range</param>
/// <param name="maxMass">Upper boundary of the target mass range</param>
/// <param name="mfRange">A range of elemental compositions defining the search space</param>
/// <exception cref="ArgumentOutOfRangeException">In case some of the isotopes in mfRange has undefined exact mass or in case illegal parameters are provided (e.g., negative mass values or empty MolecularFormulaRange)</exception>
/// <seealso cref="MolecularFormulaRange"/>
public FullEnumerationFormulaGenerator(IChemObjectBuilder builder,
double minMass, double maxMass,
MolecularFormulaRange mfRange)
{
Trace.TraceInformation("Initiate MolecularFormulaGenerator, mass range " + minMass + "-" + maxMass);
// Check parameter values
if (minMass < 0.0)
{
throw (new ArgumentOutOfRangeException(nameof(minMass), "The minimum and maximum mass values must be >=0"));
}
if (maxMass < 0.0)
{
throw (new ArgumentOutOfRangeException(nameof(maxMass), "The minimum and maximum mass values must be >=0"));
}
if ((minMass > maxMass))
{
throw (new ArgumentException("Minimum mass must be <= maximum mass"));
}
if ((mfRange == null) || (mfRange.GetIsotopes().Count() == 0))
{
throw (new ArgumentException("The MolecularFormulaRange parameter must be non-null and must contain at least one isotope"));
}
// Save the parameters
this.builder = builder;
this.minMass = minMass;
this.maxMass = maxMass;
// Sort the elements by mass in ascending order. That speeds up
// the search.
var isotopesSet = new SortedSet <IIsotope>(
new IIsotopeSorterByMass());
foreach (IIsotope isotope in mfRange.GetIsotopes())
{
// Check if exact mass of each isotope is set
if (isotope.ExactMass == null)
{
throw new ArgumentException($"The exact mass value of isotope {isotope} is not set");
}
isotopesSet.Add(isotope);
}
isotopes = isotopesSet.ToArray();
// Save the element counts from the provided MolecularFormulaRange
minCounts = new int[isotopes.Length];
maxCounts = new int[isotopes.Length];
for (int i = 0; i < isotopes.Length; i++)
{
minCounts[i] = mfRange.GetIsotopeCountMin(isotopes[i]);
maxCounts[i] = mfRange.GetIsotopeCountMax(isotopes[i]);
// Update the maximum count according to the mass limit
int maxCountAccordingToMass = (int)Math.Floor(maxMass
/ isotopes[i].ExactMass.Value);
if (maxCounts[i] > maxCountAccordingToMass)
{
maxCounts[i] = maxCountAccordingToMass;
}
}
// Set the current counters to minimal values, initially
currentCounts = Arrays.CopyOf(minCounts, minCounts.Length);
}
