private readonly double _airFrictionConstant; //a constant of air friction applied to masses
public RopeSimulation( //a long long constructor with 11 parameters starts here
int numOfMasses, //1. the number of masses
double m, //2. weight of each mass
double springConstant, //3. how stiff the springs are
double springLength, //4. the length that a spring does not exert any force
double springFrictionConstant, //5. inner friction constant of spring
Vector gravitation, //6. gravitational acceleration
double airFrictionConstant, //11. height of the ground (y position)
Vector position
)
{
_gravitation = gravitation;
_airFrictionConstant = airFrictionConstant;
for (int i = 0; i < numOfMasses; i++)
{
Masses.Add(new Mass(m)
{
Pos = position
});
}
_ropeConnectionPos1 = position;
_ropeConnectionPos2 = position;
var index = 1;
while (index < Masses.Count)
{
_springs.Add(new Spring(Masses[index - 1], Masses[index], springConstant, springLength, springFrictionConstant));
index++;
}
}
public IsotopicDistribution(ChemicalFormula formula, double fineResolution, double minProbability, double molecularWeightResolution)
{
ValidateFormulaForIsotopologueComputation(formula);
double monoisotopicMass = formula.MonoisotopicMass;
var a = GetNewFineAndMergeResolutions(monoisotopicMass, fineResolution);
fineResolution = a.Item1;
double _mergeFineResolution = a.Item2;
List <List <Composition> > elementalComposition = new List <List <Composition> >();
// Get all the unique elements that might have isotopes
foreach (var elementAndCount in formula.elements)
{
int count = elementAndCount.Value;
List <Composition> isotopeComposition = new List <Composition>();
foreach (Isotope isotope in elementAndCount.Key.Isotopes.OrderBy(iso => iso.AtomicMass))
{
Composition c = new Composition
{
Atoms = count,
MolecularWeight = isotope.AtomicMass,
Power = isotope.AtomicMass,
Probability = isotope.RelativeAbundance
};
isotopeComposition.Add(c);
}
elementalComposition.Add(isotopeComposition);
}
foreach (List <Composition> compositions in elementalComposition)
{
double sumProb = compositions.Sum(t => t.Probability);
foreach (Composition composition in compositions)
{
composition.Probability /= sumProb;
composition.LogProbability = Math.Log(composition.Probability);
composition.Power = Math.Floor(composition.MolecularWeight / molecularWeightResolution + 0.5);
}
}
CalculateFineGrain(elementalComposition, molecularWeightResolution, _mergeFineResolution, fineResolution, minProbability);
double additionalMass = 0;
foreach (var isotopeAndCount in formula.isotopes)
{
additionalMass += isotopeAndCount.Key.AtomicMass * isotopeAndCount.Value;
}
for (int i = 0; i < Masses.Count(); i++)
{
masses[i] += additionalMass;
}
}
private void ImportDataFromFile()
{
var data = File.ReadAllLines(dataFilePath);
Masses.AddRange(data.Select(int.Parse).ToArray());
}