/// <summary>
/// Add the given multiple of mf into to.
/// </summary>
/// <param name="to"></param>
/// <param name="mf"></param>
/// <param name="multiple"></param>
private void Add(MolecularFormula to, MolecularFormula mf, int multiple)
{
foreach (String s in mf.elementCounts.Keys)
{
to.Add(s, ((int)mf.elementCounts[s]) * multiple);
}
}
/// <summary>
/// Add the given multiple of formulaToAdd into targetFormula
/// </summary>
/// <param name="targetFormula"></param>
/// <param name="formulaToAdd"></param>
/// <param name="multiple"></param>
private void Add(MolecularFormula targetFormula, MolecularFormula formulaToAdd, int multiple)
{
foreach (var item in formulaToAdd.elementCounts)
{
targetFormula.Add(item.Key, item.Value * multiple);
}
}
public MolecularFormula GetAveragineFormula(double mz, int chargeState)
{
var monoIsotopicMass = mz * chargeState - chargeState * decon2LSMercuryDistribution.ChargeCarrierMass;
var empiricalFormula = averagineFormulaCreator.GenerateAveragineFormula(monoIsotopicMass);
return(MolecularFormula.Parse(empiricalFormula));
}
public MolecularFormula GetAveragineFormula(double mz, int chargeState)
{
double monoIsotopicMass = mz * chargeState - chargeState * hornParameters.CCMass;
string empiricalFormula = avergineFormulaCreator.GenerateAveragineFormula(monoIsotopicMass, hornParameters.AveragineFormula, hornParameters.TagFormula);
return(MolecularFormula.Parse(empiricalFormula));
}
public void CreateDistribution(double mass, int chargeState, double resolution)
{
string empiricalFormula = avergineFormulaCreator.GenerateAveragineFormula(mass, hornParameters.AveragineFormula, hornParameters.TagFormula);
this.molecularFormula = MolecularFormula.Parse(empiricalFormula);
this.resolution = resolution;
this.chargeState = chargeState;
CreateDistribution(this.molecularFormula);
}
public void CreateDistribution(double mass, int chargeState, double resolution)
{
var empiricalFormula = averagineFormulaCreator.GenerateAveragineFormula(mass);
MolecularFormula = MolecularFormula.Parse(empiricalFormula);
Resolution = resolution;
ChargeState = chargeState;
CreateDistribution(MolecularFormula);
}
public void Add(String part, MolecularFormula mf)
{
if (part == null)
{
throw new ArgumentNullException("part");
}
if (mf == null)
{
throw new ArgumentNullException("mf");
}
partFormulas.Add(part, mf);
}
public void Set(String part, MolecularFormula mf)
{
if (part == null)
{
throw new ArgumentNullException("part");
}
if (mf == null)
{
throw new ArgumentNullException("mf");
}
this.partFormulas.Remove(part);
this.Add(part, mf);
}
public MolecularFormula Add(MolecularFormula mf, int multiple, bool permitNegativeMultiple)
{
if (multiple < 0 && !permitNegativeMultiple)
{
throw new ArgumentOutOfRangeException("multiple", multiple, "Multiple must be >= 0");
}
var newFormula = new MolecularFormula(this);
newFormula.name = null;
newFormula.formulaString = null;
Add(newFormula, mf, multiple);
return(newFormula);
}
public static MolecularFormula Parse(string formula, string name, bool allowNegatives)
{
if (formula == null)
{
throw new ArgumentNullException(nameof(formula));
}
var match = parsingRegex.Match(formula);
if (!match.Success)
{
throw new ApplicationException("Formula can not be parsed");
}
var mf = new MolecularFormula();
var matched = match.Groups["element"].Captures.Count;
//Console.WriteLine("Num Groups {0}", matched);
// Iterate through the matched groups, updating element counts
for (var i = 0; i < matched; i++)
{
var element = match.Groups["element"].Captures[i].Value;
var count = match.Groups["count"].Captures[i].Value;
//Console.WriteLine("Element {0}, Count {1}", element, count);
// If the symbol is unknown, throw an exception.
// The multiple defaults to 1 if not found. So CHHCHH is C2 H4.
var multiple = 1;
if (count != "")
{
try
{
multiple = int.Parse(count);
if (multiple < 0 && !allowNegatives)
{
throw new ApplicationException("Negative multiple " + multiple + " for element " +
element + " is not allowed.");
}
}
// This can never actually happen, because the regex makes sure that
// only integer values which can be parsed make it to this stage
catch (Exception ex)
{
throw new ApplicationException("The multiple for element " + element + ", " + count + ", was not parseable", ex);
}
}
mf.Add(element, multiple);
}
mf.formulaString = formula;
mf.name = name;
return(mf);
}
public void Add(string part, MolecularFormula mf)
{
if (part == null)
{
throw new ArgumentNullException(nameof(part));
}
if (mf == null)
{
throw new ArgumentNullException(nameof(mf));
}
// This will raise an exception if partFormulas already contains the part string
partFormulas.Add(part, mf);
}
public void CreateDistribution(MolecularFormula molecularFormula)
{
Check.Require(molecularFormula != null, "Molecular formula has not been defined.");
this.molecularFormula = molecularFormula;
this.data = new XYData(); //clears any old data
this.elementTable = molecularFormula.ToElementTable();
this.decon2LSMercuryDistribution = new DeconToolsV2.clsMercuryIsotopeDistribution();
this.decon2LSMercuryDistribution.Resolution = this.resolution;
this.decon2LSMercuryDistribution.ChargeState = (short)this.chargeState;
System.Drawing.PointF[] drawingpoints = this.decon2LSMercuryDistribution.CalculateDistribution(this.elementTable);
this.data = XYData.ConvertDrawingPoints(drawingpoints);
}
public void CreateDistribution(MolecularFormula molecularFormula)
{
Check.Require(molecularFormula != null, "Molecular formula has not been defined.");
MolecularFormula = molecularFormula;
Data = new XYData(); //clears any old data
var deconToolsMolFormula = ProcessingTasks.Deconvoluters.HornDeconvolutor.ThrashV1.ElementalFormulas.MolecularFormula.ConvertFromString(molecularFormula.ToFormulaString());
decon2LSMercuryDistribution = new ProcessingTasks.Deconvoluters.HornDeconvolutor.ThrashV1.Mercury.MercuryIsotopeDistribution();
decon2LSMercuryDistribution.CalculateDistribution(ChargeState, Resolution, deconToolsMolFormula, out var x, out var y, 0, out _, out _);
Data = new XYData()
{
Xvalues = x.ToArray(), Yvalues = y.ToArray()
};
}
public void Set(string part, MolecularFormula mf)
{
if (part == null)
{
throw new ArgumentNullException(nameof(part));
}
if (mf == null)
{
throw new ArgumentNullException(nameof(mf));
}
if (partFormulas.ContainsKey(part))
{
partFormulas.Remove(part);
}
Add(part, mf);
}
public MolecularFormula Translate(string input, string partRegex)
{
try
{
var regex = new Regex(partRegex);
var formula = new MolecularFormula();
var matches = regex.Matches(input);
foreach (Match match in matches)
{
if (!partFormulas.TryGetValue(match.Value, out var partFormula))
{
throw new ApplicationException("Formula for part " + match.Value + " is unknown.");
}
formula = formula.Add(partFormula, 1);
}
return(formula);
}
catch (Exception e)
{
throw new ApplicationException("Translation of " + input + " failed. " + e.Message, e);
}
}
public MolecularFormula Translate(String input, String partRegex)
{
try
{
var regex = new Regex(partRegex);
var formula = new MolecularFormula();
var matches = regex.Matches(input);
foreach (Match match in matches)
{
var partFormula = (MolecularFormula)this.partFormulas[match.Value];
if (partFormula == null)
{
throw new ApplicationException("Formula for part " + match.Value + " is unknown.");
}
formula = formula.Add(partFormula, 1);
}
return(formula);
}
catch (Exception e)
{
throw new ApplicationException("Translation of " + input + " failed. " + e.Message, e);
}
}
/// <summary>
/// Clones the formula.
/// </summary>
/// <param name="formula"></param>
private MolecularFormula(MolecularFormula formula)
{
this.name = formula.name;
this.formulaString = formula.formulaString;
this.elementCounts = new Hashtable(formula.elementCounts);
}
/// <summary>
/// Create a new MolecularFormula by adding the given formula (times the given multiple)
/// to this formula.
/// </summary>
/// <param name="mf"></param>
/// <param name="multiple"></param>
/// <returns></returns>
public MolecularFormula Add(MolecularFormula mf, int multiple)
{
return(Add(mf, multiple, false));
}
/// <summary>
/// Clones the formula.
/// </summary>
/// <param name="formula"></param>
private MolecularFormula(MolecularFormula formula)
{
name = formula.name;
formulaString = formula.formulaString;
elementCounts = new Dictionary <string, int>(formula.elementCounts);
}
