public static double[][] Convolute(double[][] distrib1, double[][] distrib2, double massPrecision, double weightCutoff)
{
double[] masses1 = distrib1[0];
double[] masses2 = distrib2[0];
double[] weights1 = distrib1[1];
double[] weights2 = distrib2[1];
double[] masses = new double[masses1.Length * masses2.Length];
double[] weights = new double[masses1.Length * masses2.Length];
int count = 0;
for (int i = 0; i < masses1.Length; i++)
{
for (int j = 0; j < masses2.Length; j++)
{
masses[count] = masses1[i] + masses2[j];
weights[count] = weights1[i] * weights2[j];
count++;
}
}
int[] o = ArrayUtils.Order(masses);
masses = ArrayUtils.SubArray(masses, o);
weights = ArrayUtils.SubArray(weights, o);
double[][] x = ChemElement.FilterMasses(masses, weights, massPrecision);
masses = x[0];
weights = x[1];
if (!double.IsNaN(weightCutoff))
{
x = ChemElement.FilterWeights(masses, weights, weightCutoff);
masses = x[0];
weights = x[1];
}
return(new[] { masses, weights });
}
public Molecule GetUnlabeledVersion()
{
Dictionary <int, int> w = new Dictionary <int, int>();
for (int i = 0; i < AtomType.Length; i++)
{
w.Add(AtomType[i], AtomCount[i]);
}
foreach (int t in AtomType)
{
ChemElement el = ChemElements.Elements[t];
if (el.IsIsotopicLabel)
{
int c = w[t];
w.Remove(t);
int n = el.NaturalVersion;
if (!w.ContainsKey(n))
{
w.Add(n, 0);
}
w[n] += c;
}
}
int[] newTypes = w.Keys.ToArray();
Array.Sort(newTypes);
int[] newCounts = new int[newTypes.Length];
for (int i = 0; i < newCounts.Length; i++)
{
newCounts[i] = w[newTypes[i]];
}
return(new Molecule(newTypes, newCounts));
}
public double[][] GetIsotopeDistribution(double massPrecision)
{
if (AtomType.Length == 0)
{
return(new[] { new double[] { 0 }, new double[] { 1 } });
}
ChemElement element = ChemElements.Elements[AtomType[0]];
double[][] distrib = element.GetIsotopeDistribution(AtomCount[0]);
for (int i = 1; i < AtomType.Length; i++)
{
element = ChemElements.Elements[AtomType[i]];
distrib = Convolute(distrib, element.GetIsotopeDistribution(AtomCount[i]), massPrecision, 1e-6);
}
return(distrib);
}
public double[][] GetIsotopeDistributionAlteredDeuterium(double deltaDeuterium, double massPrecision)
{
if (AtomType.Length == 0)
{
return(new[] { new double[] { 0 }, new double[] { 1 } });
}
ChemElement element = ChemElements.Elements[AtomType[0]];
double[][] distrib = element.IsHydrogen()
? element.GetIsotopeDistributionAlteredIsotopeContribution(AtomCount[0], 1, deltaDeuterium)
: element.GetIsotopeDistribution(AtomCount[0]);
for (int i = 1; i < AtomType.Length; i++)
{
element = ChemElements.Elements[AtomType[i]];
distrib = Convolute(distrib, element.GetIsotopeDistribution(AtomCount[i]), massPrecision, 1e-6);
}
return(distrib);
}
private static void SetNaturalVersion(ChemElement ce, IList<ChemElement> chemElements)
{
string label = ce.Symbol;
if (label.Equals("D")){
ce.NaturalVersion = GetElementIndexByName("H", chemElements);
return;
}
if (label.Equals("T")){
ce.NaturalVersion = GetElementIndexByName("H", chemElements);
return;
}
if (label.Equals("Fey")){
ce.NaturalVersion = GetElementIndexByName("Fe", chemElements);
return;
}
if (label.Equals("Oy")){
ce.NaturalVersion = GetElementIndexByName("O", chemElements);
return;
}
if (label.Equals("Sy")){
ce.NaturalVersion = GetElementIndexByName("S", chemElements);
return;
}
if (!label.EndsWith("x")){
throw new Exception("Never get here.");
}
label = label.Substring(0, label.Length - 1);
ce.NaturalVersion = GetElementIndexByName(label, chemElements);
}