public async Task <ActionResult> Index(string lastEditedMoleculeId)
{
var filter = new MoleculeFilter();
// Get values from database.
var molecules = await _moleculeService.GetAllAsync(filter);
var substances = await _substanceService.GetAllAsync(new SubstanceFilter());
IList <MoleculeViewModel> moleculeViewModels = new List <MoleculeViewModel>();
// Create list of molecules for view.
foreach (var molecule in molecules)
{
var model = new MoleculeViewModel(molecule, null);
if (molecule.SubstanceIdString != null)
{
var substance = await _moleculeService.GetSubstanceForMoleculeAsync(molecule.SubstanceIdString);
// Set name of substance for molecule.
model.SubstanceValue = substance.Name;
}
moleculeViewModels.Add(model);
}
// Create view model for Index view.
var moleculeViewModelIndex = new MoleculeViewModelIndex(moleculeViewModels, substances);
// Set value to where to scroll to.
moleculeViewModelIndex.LastEditedMoleculeId = lastEditedMoleculeId;
return(View(moleculeViewModelIndex));
}
public async Task <ActionResult> CreateOrEdit(string id)
{
var substances = await _substanceService.GetAllAsync(new SubstanceFilter());
MoleculeViewModel model;
// Get MoleculeViewModel according to whether is edit or create.
if (!string.IsNullOrEmpty(id))
{
// Edit
var molecule = await _moleculeService.GetByIdAsync(id);
if (molecule == null)
{
Log.Error($"An unexpected error occurred while getting id. No entity with id {id} could be found.");
throw new ArgumentNullException(string.Format(Resources.Resources.Error_NoEntityWithIdFound, id));
}
model = new MoleculeViewModel(molecule, substances);
}
else
{
// Create
model = new MoleculeViewModel(null, substances);
}
return(View(model));
}
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 async Task <ActionResult> CreateOrEdit(MoleculeViewModel model)
{
var validationResult = new ValidationResultList();
if (ModelState.IsValid)
{
try
{
var molecule = new Molecule();
// Map view model to entity.
model.MapViewModelToEntity(molecule);
// Edit or create
if (molecule.Id != null)
{
// Edit
// Only update if molecule name doesn't already exist.
validationResult = await _moleculeService.UpdateAsync(molecule);
}
else
{
// Create
// Only insert if molecule name doesn't already exist.
validationResult = await _moleculeService.InsertAsync(molecule);
model.Id = molecule.Id;
}
}
catch (Exception e)
{
Log.Error($"An unexpected error occurred while inserting or editing: {e}");
throw new ArgumentException(Resources.Resources.Error_UnexpectedError);
}
}
// Show validation result, if validation error occurred while
// inserting or if ModelState is invalid.
if (validationResult.HasErrors || !ModelState.IsValid)
{
AddValidationResultsToModelStateErrors(validationResult.Errors);
// Set substances to display in drop down.
var substances = await _substanceService.GetAllAsync(new SubstanceFilter());
model.Substances = substances;
Log.Info("Show CreateOrEdit");
return(View(nameof(CreateOrEdit), model));
}
Log.Info("Redirect to Index");
return(RedirectToAction(nameof(Index), new { lastEditedMoleculeId = model.Id }));
}
