public void ForceDirectionAsExpected()
{
var approximatePeptide = new ApproximatePeptide(new []
{
new ApproximatedAminoAcid(AminoAcidName.Alanine, 1)
{
NitrogenPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, -150, -150, 0),
CarbonAlphaPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, -150, 0),
CarbonPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 0, 0)
},
new ApproximatedAminoAcid(AminoAcidName.Alanine, 2)
{
NitrogenPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 150, 0, 0),
CarbonAlphaPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 150, 0, 150),
CarbonPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 300, 0, 150)
}
});
var angles = AminoAcidAngleMeasurer.MeasureAngles(approximatePeptide);
var ramachandranPlotDistribution = new RamachandranPlotFixedDistribution(AminoAcidName.Alanine, new UnitPoint2D(Unit.Degree, -90, -20));
var distributionSource = new RamachandranPlotDistributionFixedSource(ramachandranPlotDistribution);
var sut = new RamachandranForceCalculator(distributionSource);
var forces = sut.Calculate(approximatePeptide);
var aminoAcid1Forces = forces[approximatePeptide.AminoAcids[0]];
var aminoAcid2Forces = forces[approximatePeptide.AminoAcids[1]];
Assert.That(aminoAcid1Forces.CarbonAlphaForce.In(Unit.Newton).Z, Is.LessThan(0));
Assert.That(aminoAcid1Forces.CarbonForce.Magnitude().In(Unit.Newton), Is.EqualTo(0).Within(1e-6));
Assert.That(aminoAcid2Forces.NitrogenForce.Magnitude().In(Unit.Newton), Is.EqualTo(0).Within(1e-6));
Assert.That(aminoAcid2Forces.CarbonAlphaForce.In(Unit.Newton).Y, Is.GreaterThan(0));
}
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;
}
