public void VolumeAsExpected()
{
var aa1 = new ApproximatedAminoAcid(AminoAcidName.Alanine, 1);
var aa2 = new ApproximatedAminoAcid(AminoAcidName.Alanine, 2);
var aa3 = new ApproximatedAminoAcid(AminoAcidName.Alanine, 3);
var peptide = new ApproximatePeptide(new List <ApproximatedAminoAcid> {
aa1, aa2, aa3
});
// Set positions
aa1.NitrogenPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 0, 0);
aa1.CarbonAlphaPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 1, 0, 0);
aa1.CarbonPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 1, 1, 0);
aa2.NitrogenPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 1, 0);
aa2.CarbonAlphaPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 1, 1);
aa2.CarbonPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 1, 1, 1);
aa3.NitrogenPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 1, 0, 1);
aa3.CarbonAlphaPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 0, 1);
aa3.CarbonPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0.5, 0.5, 0.5);
var result = CompactnessMeasurer.Measure(peptide);
var volume = result.Volume.Value;
var picoMultiplier = SIPrefix.Pico.GetMultiplier();
var cubicPicoMultiplier = picoMultiplier * picoMultiplier * picoMultiplier;
Assert.That(volume / cubicPicoMultiplier, Is.EqualTo(1).Within(1e-6));
}
private void RunSimulation(CancellationToken cancellationToken)
{
var simulationTime = simulationSettings.SimulationTime;
var dT = simulationSettings.TimeStep;
for (CurrentTime = 0.To(Unit.Second); CurrentTime < simulationTime; CurrentTime += dT)
{
cancellationToken.ThrowIfCancellationRequested();
var compactnessForces = simulationSettings.UseCompactingForce
? compactnessForceCalculator.Calculate(CompactnessMeasurer.Measure(Peptide))
: new Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces>();
var ramachandranForces = simulationSettings.UseRamachandranForce
? ramachandranForceCalculator.Calculate(Peptide)
: new Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces>();
var bondForces = bondForceCalculator.Calculate(Peptide);
foreach (var aminoAcid in Peptide.AminoAcids)
{
var resultingForce = new ApproximateAminoAcidForces();
if (compactnessForces.ContainsKey(aminoAcid))
{
var compactnessForce = compactnessForces[aminoAcid];
resultingForce += compactnessForce;
}
if (ramachandranForces.ContainsKey(aminoAcid))
{
var ramachandranForce = ramachandranForces[aminoAcid];
resultingForce += ramachandranForce;
}
if (bondForces.ContainsKey(aminoAcid))
{
var bondForce = bondForces[aminoAcid];
resultingForce += bondForce;
}
ApplyForce(aminoAcid, resultingForce, dT, simulationSettings.ReservoirTemperature);
}
OnSimulationTimestepComplete(new SimulationTimestepCompleteEventArgs(CurrentTime, Peptide));
}
SimulationCompleted?.Invoke(this, EventArgs.Empty);
IsSimulating = false;
}