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));
}
public void DihedralAnglesConverge()
{
var targetPhi = 40.To(Unit.Degree);
var targetPsi = -10.To(Unit.Degree);
var approximatePeptide = ApproximatePeptideBuilder.FromSequence(new [] { AminoAcidName.Alanine, AminoAcidName.Alanine, AminoAcidName.Alanine }, 1);
approximatePeptide.UpdatePositions();
var startAngles = AminoAcidAngleMeasurer.MeasureAngles(approximatePeptide);
var simulationSettings = new ApproximatePeptideSimulationSettings
{
SimulationTime = 500.To(SIPrefix.Femto, Unit.Second),
TimeStep = 2.To(SIPrefix.Femto, Unit.Second),
ResetAtomVelocityAfterEachTimestep = true,
UseCompactingForce = false
};
var ramachandranPlotDistribution = new RamachandranPlotFixedDistribution(AminoAcidName.Alanine, new UnitPoint2D(targetPhi, targetPsi));
var distributionSource = new RamachandranPlotDistributionFixedSource(ramachandranPlotDistribution);
var sut = new RamachandranForceCalculator(distributionSource);
var simulator = new ApproximatePeptideFoldingSimulator(
approximatePeptide,
simulationSettings,
new CompactingForceCalculator(),
sut,
new BondForceCalculator());
var angleHistory = new List <AminoAcidAngles>();
var simulationEndedWaitHandle = new ManualResetEvent(false);
simulator.SimulationCompleted += (sender, args) => simulationEndedWaitHandle.Set();
simulator.TimestepCompleted += (sender, args) =>
{
var angles = AminoAcidAngleMeasurer.MeasureAngles(args.PeptideCopy);
var midAminoAcid = args.PeptideCopy.AminoAcids[1];
angleHistory.Add(angles[midAminoAcid]);
};
simulator.StartSimulation();
simulationEndedWaitHandle.WaitOne();
File.WriteAllLines(@"G:\Projects\HumanGenome\angles.csv",
angleHistory.Select(angle => $"{angle.Omega.In(Unit.Degree).ToString(CultureInfo.InvariantCulture)};" +
$"{angle.Phi.In(Unit.Degree).ToString(CultureInfo.InvariantCulture)};" +
$"{angle.Psi.In(Unit.Degree).ToString(CultureInfo.InvariantCulture)}"));
var finalAngles = AminoAcidAngleMeasurer.MeasureAngles(approximatePeptide);
var middleAminoAcid = approximatePeptide.AminoAcids[1];
Assert.That((finalAngles[middleAminoAcid].Phi - targetPhi).Abs(),
Is.LessThan((startAngles[middleAminoAcid].Phi - targetPhi).Abs()));
Assert.That((finalAngles[middleAminoAcid].Psi - targetPsi).Abs(),
Is.LessThan((startAngles[middleAminoAcid].Psi - targetPsi).Abs()));
}
public static ApproximatePeptideFoldingSimulator Create(ApproximatePeptide peptide,
ApproximatePeptideSimulationSettings simulationSettings,
string ramachadranDataDirectory)
{
var compactnessForceCalculator = new CompactingForceCalculator();
var ramachandranPlotDistributionSource = new RamachandranPlotGradientDistributionFileSource(ramachadranDataDirectory);
var ramachadranForceCalculator = new RamachandranForceCalculator(ramachandranPlotDistributionSource);
var bondForceCalculator = new BondForceCalculator();
return(new ApproximatePeptideFoldingSimulator(peptide,
simulationSettings,
compactnessForceCalculator,
ramachadranForceCalculator,
bondForceCalculator));
}
public ApproximatePeptideFoldingSimulator(ApproximatePeptide peptide,
ApproximatePeptideSimulationSettings simulationSettings,
CompactingForceCalculator compactnessForceCalculator,
RamachandranForceCalculator ramachandranForceCalculator,
BondForceCalculator bondForceCalculator)
{
this.simulationSettings = simulationSettings;
this.compactnessForceCalculator = compactnessForceCalculator;
this.ramachandranForceCalculator = ramachandranForceCalculator;
this.bondForceCalculator = bondForceCalculator;
Peptide = peptide;
if (peptide.AminoAcids.Count <= 3)
{
simulationSettings.UseCompactingForce = false; // Cannot be done
}
}
