/// <summary>
/// Completely removes a particular isotope from this chemical formula.
/// </summary>
/// <param name="isotope">The isotope to remove</param>
/// <returns>True if the isotope was in the chemical formula and removed, false otherwise</returns>
public int Remove(Isotope isotope)
{
if (isotope == null)
{
return(0);
}
int id = isotope.UniqueId;
int count;
if (id > _largestIsotopeId || (count = _isotopes[id]) == 0)
{
// isotope not contained or is already zero, do nothing and just return false
return(0);
}
MonoisotopicMass -= isotope.AtomicMass * count;
_isotopes[id] = 0;
if (id == _largestIsotopeId)
{
// id is the largest, find the new largest
FindLargestIsotope();
}
_isFormulaDirty = _isDirty = true;
return(count);
}
/// <summary>
/// Return the number of given isotopes in this chemical fomrula
/// </summary>
/// <param name="isotope"></param>
/// <returns></returns>
public int Count(Isotope isotope)
{
if (isotope == null || isotope.UniqueId > _largestIsotopeId)
{
return(0);
}
return(_isotopes[isotope.UniqueId]);
}
public static IEnumerable <IChemicalFormula> Validate(this IEnumerable <IChemicalFormula> formulas, FilterTypes filters = FilterTypes.All)
{
bool useValence = filters.HasFlag(FilterTypes.Valence);
bool useHydrogenCarbonRatio = filters.HasFlag(FilterTypes.HydrogenCarbonRatio);
foreach (IChemicalFormula formula in formulas)
{
if (useHydrogenCarbonRatio)
{
double ratio = formula.ChemicalFormula.GetCarbonHydrogenRatio();
if (ratio < 0.5 || ratio > 2.0)
{
continue;
}
}
if (useValence)
{
int totalValence = 0;
int maxValence = 0;
int oddValences = 0;
int atomCount = 0;
int[] isotopes = formula.ChemicalFormula.GetIsotopes();
for (int i = 0; i < isotopes.Length; i++)
{
int numAtoms = isotopes[i];
if (numAtoms != 0)
{
continue;
}
Isotope isotope = PeriodicTable.GetIsotope(i);
int numValenceElectrons = isotope.ValenceElectrons;
totalValence += numValenceElectrons * numAtoms;
atomCount += numAtoms;
if (numValenceElectrons > maxValence)
{
maxValence = numValenceElectrons;
}
if (numValenceElectrons % 2 != 0)
{
oddValences += numAtoms;
}
}
if (!((totalValence % 2 == 0 || oddValences % 2 == 0) && (totalValence >= 2 * maxValence) && (totalValence >= ((2 * atomCount) - 1))))
{
continue;
}
}
yield return(formula);
}
}
/// <summary>
/// Add the principal isotope of the element to this chemical formula
/// given its chemical symbol
/// </summary>
/// <param name="symbol">The chemical symbol of the element to add</param>
/// <param name="count">The number of the element to add</param>
public void Add(string symbol, int count)
{
try
{
Isotope isotope = PeriodicTable.GetElement(symbol).PrincipalIsotope;
Add(isotope, count);
}
catch (KeyNotFoundException e)
{
throw new KeyNotFoundException(string.Format("The element symbol '{0}' is not found in the periodic table", symbol), e);
}
}
/// <summary>
/// Parses a string representation of chemical formula and adds the elements
/// to this chemical formula
/// </summary>
/// <param name="formula">the Chemical Formula to parse</param>
private void ParseString(string formula)
{
if (string.IsNullOrEmpty(formula))
{
return;
}
if (!IsValidChemicalFormula(formula))
{
throw new FormatException("Input string for chemical formula was in an incorrect format");
}
foreach (Match match in FormulaRegex.Matches(formula))
{
string chemsym = match.Groups[1].Value; // Group 1: Chemical Symbol
Element element;
if (PeriodicTable.TryGetElement(chemsym, out element))
{
Isotope isotope = element.PrincipalIsotope; // Start with the most abundant (principal) isotope
if (chemsym.Equals("D")) // Special case for Deuterium
{
isotope = element.Isotopes[2];
}
else if (match.Groups[2].Success) // Group 2 (optional): Isotope Mass Number
{
isotope = element[int.Parse(match.Groups[2].Value)];
}
int sign = match.Groups[3].Success ? // Group 3 (optional): Negative Sign
-1 :
1;
int numofelem = match.Groups[4].Success ? // Group 4 (optional): Number of Elements
int.Parse(match.Groups[4].Value) :
1;
Add(isotope, sign * numofelem);
}
else
{
throw new ArgumentException(string.Format("The chemical Symbol '{0}' does not exist in the Periodic Table", chemsym));
}
}
}
/// <summary>
/// Recalculate parameters of the chemical formula
/// </summary>
private void CleanUp()
{
int atomCount = 0;
int isotopeCount = 0;
double monoMass = 0.0;
double avgMass = 0.0;
HashSet <int> elements = new HashSet <int>();
// Loop over every possible isotope in this formula
for (int i = 0; i <= _largestIsotopeId; i++)
{
int count = _isotopes[i];
// Skip zero isotopes
if (count == 0)
{
continue;
}
Isotope isotope = PeriodicTable.GetIsotope(i);
Element element = isotope.Element;
elements.Add(element.AtomicNumber);
isotopeCount++;
atomCount += count;
monoMass += count * isotope.AtomicMass;
avgMass += count * element.AverageMass;
}
// Set the instance variables to their new values
_elementCount = elements.Count;
MonoisotopicMass = monoMass;
_averageMass = avgMass;
_isotopeCount = isotopeCount;
_atomCount = atomCount;
// Mark as clean
_isDirty = false;
}
/// <summary>
/// Add an isotope to this chemical formula
/// </summary>
/// <param name="isotope">The isotope to add</param>
/// <param name="count">The number of the isotope to add</param>
public void Add(Isotope isotope, int count)
{
if (isotope == null || count == 0)
{
return;
}
MonoisotopicMass += isotope.AtomicMass * count;
_isFormulaDirty = _isDirty = true;
int id = isotope.UniqueId;
if (id > _largestIsotopeId)
{
// Isotope doesn't exist, set the count (faster than the += below)
_largestIsotopeId = id;
if (id >= _isotopes.Length)
{
// resize array if it is too small
Array.Resize(ref _isotopes, id + 1);
}
_isotopes[id] = count;
return;
}
_isotopes[id] += count;
// Force update of the largest isotope
// if the largest isotope got cleared
if (_isotopes[_largestIsotopeId] == 0)
{
FindLargestIsotope();
}
}
/// <summary>
/// Add an isotope to this element
/// </summary>
/// <param name="atomicNumber">The atomic number of the isotope</param>
/// <param name="atomicMass">The atomic mass of the isotope </param>
/// <param name="abundance">The natural relative abundance of the isotope</param>
/// <returns>The created isotopes that is added to this element</returns>
internal Isotope AddIsotope(int atomicNumber, double atomicMass, float abundance)
{
var isotope = new Isotope(this, atomicNumber, atomicMass, abundance);
if (Isotopes.ContainsKey(atomicNumber))
{
return(isotope);
}
Isotopes.Add(atomicNumber, isotope);
TotalAbundance += abundance;
_totalMass += abundance * atomicMass;
AverageMass = _totalMass / TotalAbundance;
if (PrincipalIsotope != null && !(abundance > PrincipalIsotope.RelativeAbundance))
{
return(isotope);
}
if (PrincipalIsotope != null)
{
PrincipalIsotope.IsPrincipalIsotope = false;
}
PrincipalIsotope = isotope;
PrincipalIsotope.IsPrincipalIsotope = true;
return(isotope);
}
/// <summary>
/// Replaces one isotope with another.
/// Replacement happens on a 1 to 1 basis, i.e., if you remove 5 you will add 5
/// </summary>
/// <param name="isotopeToRemove">The isotope to remove</param>
/// <param name="isotopToAdd">The isotope to add</param>
public void Replace(Isotope isotopeToRemove, Isotope isotopToAdd)
{
int numberRemoved = Remove(isotopeToRemove);
Add(isotopToAdd, numberRemoved);
}
public void AddConstraint(Isotope isotope, Range <int> range)
{
AddConstraint(isotope, range.Minimum, range.Maximum);
}
public void RemoveConstraint(Isotope isotope)
{
MinimumFormula.Remove(isotope);
MaximumFormula.Remove(isotope);
}
/// <summary>
/// Load a xml file containing elemental and isotopic data into the periodic table
/// </summary>
public static void Load(string filePath)
{
_elements.Clear();
Element element = null;
_isotopes = new Isotope[500];
BiggestIsotopeNumber = -1;
using (XmlReader reader = XmlReader.Create(filePath))
{
while (reader.Read())
{
if (!reader.IsStartElement())
{
continue;
}
switch (reader.Name)
{
case "Element":
string name = reader["Name"];
string symbol = reader["Symbol"];
int atomicnumber = int.Parse(reader["AtomicNumber"]);
int valenceElectrons = int.Parse(reader["ValenceElectrons"]);
element = new Element(name, symbol, atomicnumber, valenceElectrons);
AddElement(element);
break;
case "Isotope":
string unqiueId = reader["Id"];
string a = reader["Mass"];
double mass = double.Parse(reader["Mass"], CultureInfo.CurrentCulture);
int massNumber = int.Parse(reader["MassNumber"]);
float abundance = float.Parse(reader["Abundance"], CultureInfo.CurrentCulture);
if (abundance > 0 && element != null)
{
Isotope isotope = element.AddIsotope(massNumber, mass, abundance);
if (unqiueId != null)
{
int uniqueId = int.Parse(unqiueId);
if (uniqueId > BiggestIsotopeNumber)
{
BiggestIsotopeNumber = uniqueId;
}
isotope.UniqueId = uniqueId;
_isotopes[uniqueId] = isotope;
}
else
{
isotope.UniqueId = BiggestIsotopeNumber;
_isotopes[BiggestIsotopeNumber++] = isotope;
}
}
break;
}
}
}
if (_isotopes.Length > BiggestIsotopeNumber)
{
Array.Resize(ref _isotopes, BiggestIsotopeNumber + 1);
}
}
/// <summary>
/// Add an isotope to this element
/// </summary>
/// <param name="atomicNumber">The atomic number of the isotope</param>
/// <param name="atomicMass">The atomic mass of the isotope </param>
/// <param name="abundance">The natural relative abundance of the isotope</param>
/// <returns>The created isotopes that is added to this element</returns>
internal Isotope AddIsotope(int atomicNumber, double atomicMass, float abundance)
{
var isotope = new Isotope(this, atomicNumber, atomicMass, abundance);
if (!Isotopes.ContainsKey(atomicNumber))
{
Isotopes.Add(atomicNumber, isotope);
TotalAbundance += abundance;
_totalMass += abundance * atomicMass;
AverageMass = _totalMass / TotalAbundance;
if (PrincipalIsotope == null || abundance > PrincipalIsotope.RelativeAbundance)
{
if (PrincipalIsotope != null)
{
PrincipalIsotope.IsPrincipalIsotope = false;
}
PrincipalIsotope = isotope;
PrincipalIsotope.IsPrincipalIsotope = true;
}
}
return isotope;
}
public void RemoveConstraint(Isotope isotope)
{
MinimumFormula.Remove(isotope);
MaximumFormula.Remove(isotope);
}
public void AddConstraint(Isotope isotope, int min, int max)
{
MinimumFormula.Add(isotope, min);
MaximumFormula.Add(isotope, max);
}
/// <summary>
/// Remove a isotope from this chemical formula
/// </summary>
/// <param name="isotope">The isotope to remove</param>
/// <param name="count">The number of isotopes to remove</param>
public void Remove(Isotope isotope, int count)
{
Add(isotope, -count);
}
public void RemoveConstraint(Isotope isotope)
{
_minFormula.Remove(isotope);
_maxFormula.Remove(isotope);
}
/// <summary>
/// Checks if the isotope is present in this chemical formula
/// </summary>
/// <param name="isotope">The isotope to look for</param>
/// <returns>True if there is a non-negative number of the isotope in this formula</returns>
public bool Contains(Isotope isotope)
{
return(Count(isotope) != 0);
}
public void AddConstraint(Isotope isotope, int min, int max)
{
_minFormula.Add(isotope, min);
_maxFormula.Add(isotope, max);
}
public int Count(string symbol, int atomicNumber)
{
Isotope isotope = PeriodicTable.GetElement(symbol)[atomicNumber];
return(Count(isotope));
}
public void AddConstraint(Isotope isotope, Range<int> range)
{
AddConstraint(isotope, range.Minimum, range.Maximum);
}
/// <summary>
/// Produces the Hill Notation of the chemical formula
/// </summary>
public string GetHillNotation(string delimiter = "")
{
string carbonPart = string.Empty;
string hydrogenPart = string.Empty;
List <string> otherParts = new List <string>();
StringBuilder sb = new StringBuilder(4);
bool nonNullDelimiter = !string.IsNullOrEmpty(delimiter);
for (int i = 0; i <= _largestIsotopeId; i++)
{
int count = _isotopes[i];
if (count == 0)
{
continue;
}
Isotope isotope = PeriodicTable.GetIsotope(i);
sb.Clear();
sb.Append(isotope.AtomicSymbol);
if (!isotope.IsPrincipalIsotope)
{
sb.Append('{');
sb.Append(isotope.MassNumber);
sb.Append('}');
}
if (count != 1)
{
sb.Append(count);
}
switch (isotope.AtomicSymbol)
{
case "C":
if (nonNullDelimiter && !string.IsNullOrEmpty(carbonPart))
{
carbonPart += delimiter;
}
carbonPart += sb.ToString();
break;
case "D":
case "H":
if (nonNullDelimiter && !string.IsNullOrEmpty(hydrogenPart))
{
hydrogenPart += delimiter;
}
hydrogenPart += sb.ToString();
break;
default:
otherParts.Add(sb.ToString());
break;
}
}
if (string.IsNullOrEmpty(carbonPart))
{
// No carbons, so just add the hydrogen to the list and sort alphabetically
if (!string.IsNullOrEmpty(hydrogenPart))
{
otherParts.Add(hydrogenPart);
}
otherParts.Sort();
}
else
{
otherParts.Sort();
if (!string.IsNullOrEmpty(hydrogenPart))
{
otherParts.Insert(0, hydrogenPart);
}
otherParts.Insert(0, carbonPart);
}
return(string.Join(delimiter, otherParts));
}
public void AddConstraint(Isotope isotope, int min, int max)
{
MinimumFormula.Add(isotope, min);
MaximumFormula.Add(isotope, max);
}
