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 RunSimulationForSequence(string pdbCode, string sequenceString, string outputFilePath)
{
var distributionDirectory = @"G:\Projects\HumanGenome\ramachadranDistributions";
var sut = new MultiLevelGrowingFoldingSimulator(distributionDirectory);
var settings = new MultiLevelGrowingFoldingSimulatorSettings
{
};
var aminoAcidSequence = sequenceString
.Select(c => c.ToAminoAcidName())
.ToList();
var peptide = sut.Simulate(aminoAcidSequence, settings);
var approximatePeptideCompleter = new ApproximatePeptideCompleter(peptide);
var completedPeptide = approximatePeptideCompleter.GetBackbone();
File.WriteAllText(outputFilePath, PdbSerializer.Serialize(pdbCode, completedPeptide));
}
