private void OnCreatePredictor(CreatePredictor request)
{
var req = new GetPDBs(ReadFileLines.Do(request.ViewModel.TrainingPDBsFile));
req.RequestInDefaultContext();
var files = req.Files;
var graphs = CreateProteinGraph.Do(files, request.ViewModel.InterfaceDist, request.ViewModel.GraphNodeDefinition);
var requestI = new RequestInterface(files, request.ViewModel.InterfaceDist, request.ViewModel.UseVanDerWaalsRadiiIface);
requestI.RequestInDefaultContext();
var interfaces = requestI.Interface;
switch (request.ViewModel.PredictionType)
{
case PredictorTypes.RasaAverageHydrophobicityPredictor:
var predictor = new RasaAverageHydrophobicityPredictor(request.ViewModel);
predictor.Train(request.ViewModel, files, interfaces, graphs);
//store Predictor
using (var writer = new StreamWriter(BaseDirectory + predictor.Name + RasaAverageHydrophobicityPredictorFileEnding))
{
var serializer = new XmlSerializer(typeof(RasaAverageHydrophobicityPredictor));
serializer.Serialize(writer, predictor);
}
predictors.Add(predictor);
this.DoRequest(new Created <IHas <IPredictionLogic> >(predictor));
break;
case PredictorTypes.RasaAverageHydrophobicityCRFPredictor:
var predictor2 = new RasaAverageHydrophobicityCRFPredictor(request.ViewModel);
predictor2.Train(request.ViewModel, files, interfaces, graphs);
//store Predictor
using (var writer = new StreamWriter(BaseDirectory + predictor2.Name + RasaAverageHydrophobicityCRFPredictorFileEnding))
{
var serializer = new XmlSerializer(typeof(RasaAverageHydrophobicityCRFPredictor));
serializer.Serialize(writer, predictor2);
}
predictors.Add(predictor2);
this.DoRequest(new Created <IHas <IPredictionLogic> >(predictor2));
break;
default:
break;
}
}
private void OnProvidePDBInfo(ProvidePDBInfo obj)
{
var options = obj.Options;
var pdbId = options.PDBId;
var pdbinfo = default(PDBInfo);
var req = new GetPDBs(pdbId.ToIEnumerable());
req.RequestInDefaultContext();
var file = req.Files.FirstOrDefault();
if (req.Files.NotNullOrEmpty())
{
pdbinfo = new PDBInfo(file);
}
if (options.ComputeRasa)
{
var reqR = new RequestRasa(file);
reqR.RequestInDefaultContext();
var rasa = reqR.Rasavalues;
}
if (options.ComputeInterface)
{
var request = new RequestInterface(pdbinfo.PDBFile.ToIEnumerable(), options.InterfaceDefDistance, options.InterfaceUseVanDerWaalsRadii);
request.RequestInDefaultContext();
pdbinfo.Interface.Clear();
foreach (var residue in pdbinfo.PDBFile.Residues)
{
pdbinfo.Interface.Add(residue, request.Interface[pdbinfo.PDBFile.Name][residue]);
}
}
if (options.ComputeGraph)
{
pdbinfo.Graphs = CreateProteinGraph.Do(pdbinfo.PDBFile, options.GraphNeighbourDistance, options.GraphNodeCenterDef);
if (!(pdbinfo.Interface.Count == 0))
{
foreach (var pgraph in pdbinfo.Graphs)
{
pgraph.Value.Nodes.Where(n => pdbinfo.Interface[n.Data.Residue]).Each((node) => node.Data.IsRefInterface = true);
}
}
}
obj.PDBInfo = pdbinfo;
}
private void OnGetPDB(GetPDBs obj)
{
foreach (var pdbname in obj.PDBNames)
{
PDBFile pdb;
pdb = filesCache.FirstOrDefault(file => file.Name.Equals(pdbname));
if (pdb != null)
{
obj.Files.Add(pdb);
continue;
}
var pdbfile = Directory.GetFiles(BaseDirectory).FirstOrDefault(file => file.Contains(pdbname + ".pdb"));
if (pdbfile != null)
{
pdb = PDBExt.Parse(pdbfile);
obj.Files.Add(pdb);
filesCache.Add(pdb);
continue;
}
new DownLoadPDB(pdbname.ToIEnumerable()).RequestInDefaultContext();
pdbfile = Directory.GetFiles(BaseDirectory).FirstOrDefault(file => file.Contains(pdbname + ".pdb"));
if (pdbfile == null)
{
new NotifyUser("couldnt get pdb " + pdbname);
Log.Post("couldnt get pdb " + pdbname);
}
else
{
pdb = PDBExt.Parse(pdbfile);
obj.Files.Add(pdb);
filesCache.Add(pdb);
}
}
}
