public MainWindow()
{
InitializeComponent();
var filename = @"G:\Projects\HumanGenome\Protein-PDBs\2mgo.pdb";
//var filename = @"G:\Projects\HumanGenome\AminoseqFiles\CFTR.aminoseq";
ApproximatePeptide approximatePeptide;
Peptide peptide;
if (filename.ToLowerInvariant().EndsWith(".pdb"))
{
peptide = PeptideLoader.Load(filename);
peptide.Molecule.MarkBackbone(peptide.MoleculeReference);
peptide.Molecule.PositionAtoms(peptide.MoleculeReference.FirstAtomId, peptide.MoleculeReference.LastAtomId);
approximatePeptide = ApproximatePeptideBuilder.FromPeptide(peptide);
}
else
{
approximatePeptide = ApproximatePeptideBuilder.FromSequence(new string('A', 8), 1);
//approximatePeptide = ApproximatePeptideBuilder.FromSequence(File.ReadAllLines(filename).Aggregate((a,b) => a + b));
approximatePeptide.UpdatePositions();
peptide = new ApproximatePeptideCompleter(approximatePeptide).GetFullPeptide();
}
var simulationSettings = new ApproximatePeptideSimulationSettings
{
TimeStep = 2.To(SIPrefix.Femto, Unit.Second),
SimulationTime = 10.To(SIPrefix.Nano, Unit.Second),
ResetAtomVelocityAfterEachTimestep = false,
UseCompactingForce = true,
UseRamachandranForce = true
};
var ramachadranDataDirectory = @"G:\Projects\HumanGenome\ramachadranDistributions";
var ramachandranPlotDistributionSource = new RamachandranPlotGradientDistributionFileSource(ramachadranDataDirectory);
//var ramachandranPlotDistributionSource = new RamachandranPlotDistributionFixedSource(
// new RamachandranPlotFixedDistribution(AminoAcidName.Alanine, new UnitPoint2D(-57.To(Unit.Degree), -47.To(Unit.Degree))));
//var simulationRunner = ApproximatePeptideFoldingSimulatorFactory.Create(
// approximatePeptide, simulationSettings, ramachadranDataDirectory);
var simulationRunner = new ApproximatePeptideFoldingSimulator(approximatePeptide,
simulationSettings,
new CompactingForceCalculator(),
new RamachandranForceCalculator(ramachandranPlotDistributionSource),
new BondForceCalculator());
//var simulationRunner = new MoleculeDynamicsSimulator(peptide.Molecule, new List<CustomAtomForce>(),
// new MoleculeDynamicsSimulationSettings
// {
// TimeStep = 2.To(SIPrefix.Femto, Unit.Second),
// SimulationTime = 10.To(SIPrefix.Pico, Unit.Second)
// });
MoleculeViewModel = new MoleculeViewModel();
//MoleculeViewModel.DrawAtoms(AtomExtractor.FromApproximatePeptide(approximatePeptide));
MoleculeViewModel.DrawAtoms(AtomExtractor.FromMolecule(peptide.Molecule));
simulationRunner.TimestepCompleted += (sender, args) => Application.Current.Dispatcher.BeginInvoke(new Action(() => MoleculeViewModel.DrawAtoms(args.Atoms)));
SimulationViewModel = new SimulationViewModel(simulationRunner);
}
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 void ApproximatePeptideIsFoldedToKnownStableState(string pdbFilePath)
{
var pdbReadResult = PdbReader.ReadFile(pdbFilePath);
var peptide = pdbReadResult.Models.First().Chains.First();
var approximatePeptide = ApproximatePeptideBuilder.FromPeptide(peptide);
var simulationSettings = new ApproximatePeptideSimulationSettings
{
SimulationTime = 10.To(SIPrefix.Pico, Unit.Second),
TimeStep = 2.To(SIPrefix.Femto, Unit.Second)
};
var ramachadranDataDirectory = @"G:\Projects\HumanGenome\ramachadranDistributions";
var simulator = ApproximatePeptideFoldingSimulatorFactory.Create(
approximatePeptide, simulationSettings, ramachadranDataDirectory);
simulator.TimestepCompleted += Simulator_TimestepCompleted;
simulator.SimulationCompleted += Simulator_SimulationCompleted;
simulationWaitHandle.Reset();
simulator.StartSimulation();
simulationWaitHandle.WaitOne();
Assert.Pass();
}