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;
}
public void Do(RequestInterface request)
{
foreach (var pdb in request.PDBs)
{
var Iface = new Dictionary <Residue, bool>();
pdb.Residues.Each(r => Iface.Add(r, false));
var filename = Location + pdb.Name + "_" + request.Distance + "_" + request.UseVanDerWaalsRadii + "." + FileEnding;
if (Directory.GetFiles(Location).Contains(filename))
{
using (var reader = new StreamReader(filename))
{
string line = "";
while ((line = reader.ReadLine()) != null)
{
var residue = pdb.Residues.First(res => (res.Chain + "_" + res.Id).Equals(line));
Iface[residue] = true;
}
}
}
else
{
var comprequest = new ComputeInterface(pdb, request.Distance, request.UseVanDerWaalsRadii);
comprequest.RequestInDefaultContext();
var result = comprequest.Result;
using (var writer = new StreamWriter(Location + pdb.Name + "_" + request.Distance + "_" + request.UseVanDerWaalsRadii + "." + FileEnding))
{
foreach (var entry in result)
{
foreach (var residue in entry.Value)
{
writer.WriteLine(residue.Chain + "_" + residue.Id);
Iface[residue] = true;
}
}
}
}
request.Interface.Add(pdb.Name, Iface);
}
}
