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 static void DecodeComposition(string composition, Dictionary <string, ChemElement> elements, out int[] counts,
out string[] comp, out double[] monoMasses, out double[] averageMasses)
{
string[] matches = composition.Split(new[] { " " }, StringSplitOptions.RemoveEmptyEntries);
counts = new int[matches.Length];
comp = new string[matches.Length];
monoMasses = new double[matches.Length];
averageMasses = new double[matches.Length];
Regex pattern2 = new Regex("\\(([-]*[0-9]+)\\)");
Regex pattern3 = new Regex("[0-9]+");
for (int i = 0; i < matches.Length; i++)
{
string key;
if (pattern2.IsMatch(matches[i]))
{
Match match = pattern2.Match(matches[i]);
string temp = match.Value;
key = matches[i].Replace(temp, "");
counts[i] = Convert.ToInt32(temp.Replace("(", "").Replace(")", "").Trim());
}
else
{
key = matches[i];
counts[i] = 1;
}
if (elements.ContainsKey(key))
{
ChemElement element = elements[key];
comp[i] = element.Symbol;
monoMasses[i] = element.MonoIsotopicMass;
averageMasses[i] = element.AtomicWeight;
}
else if (pattern3.IsMatch(key))
{
Match match = pattern3.Match(key);
string key2 = key.Replace(match.Value, "");
if (elements.ContainsKey(key2 + "x"))
{
ChemElement element = elements[key2 + "x"];
monoMasses[i] = element.MonoIsotopicMass;
averageMasses[i] = element.AtomicWeight;
comp[i] = element.Symbol;
}
else
{
throw new Exception();
}
}
else
{
throw new Exception();
}
}
}
private static int GetElementIndexByName(string label, IList <ChemElement> chemElements)
{
for (int i = 0; i < chemElements.Count; i++)
{
ChemElement element = chemElements[i];
if (element.Symbol.Equals(label))
{
return(i);
}
}
throw new Exception("Never get here.");
}
public double[][] GetIsotopeDistribution(double massPrecision)
{
if (AtomType.Length == 0)
{
return(new[] { new double[] { 0 }, new double[] { 1 } });
}
ChemElement element = ChemElement.Elements[AtomType[0]];
double[][] distrib = element.GetIsotopeDistribution(AtomCount[0]);
for (int i = 1; i < AtomType.Length; i++)
{
element = ChemElement.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.EndsWith("x"))
{
throw new Exception("Never get here.");
}
label = label.Substring(0, label.Length - 1);
ce.NaturalVersion = GetElementIndexByName(label, chemElements);
}
public bool ContainsOnly(string[] elems)
{
HashSet <int> types = new HashSet <int>();
string[] symbols = ChemElement.GetSymbols();
foreach (string elem in elems)
{
int ind = ArrayUtils.IndexOf(symbols, elem);
if (ind < 0)
{
throw new Exception("Element is not contained: " + elem);
}
types.Add(ind);
}
foreach (int atomType in AtomType)
{
if (!types.Contains(atomType))
{
return(false);
}
}
return(true);
}
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.EndsWith("x")){
throw new Exception("Never get here.");
}
label = label.Substring(0, label.Length - 1);
ce.NaturalVersion = GetElementIndexByName(label, chemElements);
}
