private static PDBFile pdbReadCore(StreamReader reader)
{
var pdb = new PDBFile();
var currentAA = new Residue(pdb);
var currentChain = new Chain();
var currentResidue = "";
var chain = "";
string line = "";
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith("ATOM"))
{
var chaintemp = line.Substring(21, 1);
if (!chaintemp.Equals(chain))
{
chain = chaintemp;
currentChain = new Chain();
currentChain.Name = chain;
currentChain.PDB = pdb;
pdb.Chains.Add(currentChain);
}
var residue = line.Substring(22, 5).Trim();
if (!residue.Equals(currentResidue))
{
currentResidue = residue;
currentAA = new Residue(pdb);
currentChain.Residues.AddLast(currentAA);
currentAA.Code = line.Substring(17, 3);
currentAA.Id = residue;
currentAA.Chain = chain;
}
var atom = new Atom();
atom.Residue = currentAA;
atom.Id = line.Substring(6, 5);
atom.Name = line.Substring(12, 4).Trim();
atom.Element = line.Substring(76, 2).Trim();
atom.TemperatureFactor = double.Parse(line.Substring(60, 6), CultureInfo.InvariantCulture);
//check for CAlpha
if (atom.Name.Contains("CA"))
{
currentAA.CAlpha = atom;
}
atom.X = double.Parse(line.Substring(30, 8), CultureInfo.InvariantCulture);
atom.Y = double.Parse(line.Substring(38, 8), CultureInfo.InvariantCulture);
atom.Z = double.Parse(line.Substring(46, 8), CultureInfo.InvariantCulture);
//pdb.Atoms.AddLast(atom);
currentAA.Atoms.AddLast(atom);
}
else if (line.StartsWith("HEADER"))
{
pdb.Name = line.Substring(62, 4);
}
}
return(pdb);
}
public static Dictionary <string, ProteinGraph> Do(PDBFile file, double neighbourDistance, ResidueNodeCenterDefinition centerdef)
{
var dict = new Dictionary <string, ProteinGraph>();
foreach (var chain in file.Chains)
{
var graph = new ProteinGraph();
graph.Data = new ProteinGraphData();
graph.Data.PDBFile = file;
graph.Data.NeighbourDistance = neighbourDistance;
graph.Data.NodeCenterDefinition = centerdef;
//Compute Nodes:
foreach (var residue in chain.Residues)
{
if (residue.CAlpha != null)
{
var node = graph.CreateNode();
node.Data = new ResidueNodeData(residue);
node.Data.IsCore = residue.IsCore;
node.Data.ZScore = residue.ZScore;
switch (centerdef)
{
case ResidueNodeCenterDefinition.CAlpha:
node.Data.SetValuesTo(residue.CAlpha);
break;
case ResidueNodeCenterDefinition.BalancePoint:
node.Data.SetValuesTo(residue.Atoms.BalancePoint());
break;
default:
break;
}
}
}
var nodeList = graph.Nodes.ToList();
//compute edges:
for (int i = 0; i < nodeList.Count - 1; i++)
{
for (int k = i + 1; k < nodeList.Count; k++)
{
var nodeOne = nodeList[i];
var nodetwo = nodeList[k];
var dist = nodeOne.Data.Distance(nodetwo.Data);
if (dist <= neighbourDistance)
{
var edge = graph.CreateEdge(nodeOne, nodetwo);
edge.Data = new SimpleEdgeData();
}
}
}
dict.Add(chain.Name, graph);
}
return(dict);
}
public Dictionary <string, Dictionary <Residue, bool> > Predict(PDBFile file, IDictionary <string, ProteinGraph> graphs)
{
if (TrainingPDBs.Any(pdb => pdb.Equals(file.Name)))
{
Log.Post("This PDB was used to train this predictor.");
}
return(PredictionFunc(file, graphs));
}
private Dictionary <string, Dictionary <Residue, bool> > doPrediction(PDBFile file, IDictionary <string, ProteinGraph> graphs)
{
var dict = new Dictionary <string, Dictionary <Residue, bool> >();
var Feature = new AverageHydrophobicityFeature();
var req = new RequestRasa(file);
req.RequestInDefaultContext();
var rasa = req.Rasavalues;
//Threshold = 0.5;
//foreach (var graph in graphs)
//{
// Feature.Compute(graph.Value);
// var valdict = new Dictionary<ResidueNode, double[]>();
// var edgeScores = new double[2, 2] { { 1.2, 0.6 }, { 0.6, 1.0 } };
// foreach (var node in graph.Value.Nodes)
// {
// var val = (Feature.ValueOf(node.Data.Residue) * rasa[node.Data.Residue]) / Max;
// valdict.Add(node, new double[2] { val, 1 - val });
// }
// var edgedict = new Dictionary<SimpleEdge<ResidueNode>, double[,]>();
// foreach (var edge in graph.Value.Edges)
// {
// edgedict.Add(edge, edgeScores);
// }
// var predDict = new Dictionary<Residue, bool>();
// dict.Add(graph.Key, predDict);
// var crfGraph = graph.Value.CreateGraph(valdict, edgedict);
// //var options = new MarginalizeByResamplingOptions(2, 200);
// //foreach (var node in crfNodes)
// //{
// // var probs = MarginalizeByResampling.Do(crfNodes, node, options);
// // predDict.Add(graph.Value.Nodes.First(nd => nd.Residue.Id.Equals(node.Id)).Residue, probs[0] >= Threshold);
// //}
// var result = SimpleSampling.Do(crfGraph, 2000);
// foreach (var node in crfGraph.Nodes)
// {
// var score1 = result[new Assign() { Node = node, Label = 0 }];
// var score2 = result[new Assign() { Node = node, Label = 1 }];
// var prob = score2 / (score1 + score2);
// predDict.Add(graph.Value.Nodes.First(nd => nd.Data.Residue.Id.Equals(node.Data.Id)).Residue, prob >= Threshold);
// }
//}
return(dict);
}
private Dictionary <string, Dictionary <Residue, bool> > doPrediction(PDBFile file, IDictionary <string, ProteinGraph> graphs)
{
var dict = new Dictionary <string, Dictionary <Residue, bool> >();
var Feature = new AverageHydrophobicityFeature();
var req = new RequestRasa(file);
req.RequestInDefaultContext();
var rasa = req.Rasavalues;
foreach (var graph in graphs)
{
Feature.Compute(graph.Value);
var predDict = new Dictionary <Residue, bool>();
dict.Add(graph.Key, predDict);
foreach (var node in graph.Value.Nodes)
{
predDict.Add(node.Data.Residue, (Feature.ValueOf(node.Data.Residue) * rasa[node.Data.Residue]) / Max >= Threshold);
}
}
return(dict);
}
public RequestRasa(PDBFile file)
{
File = file;
Rasavalues = new Dictionary <Residue, double>();
}
public DoPrediction(PDBFile file, IDictionary <string, ProteinGraph> graphs)
{
File = file;
Graphs = graphs;
}
public static Dictionary <string, Dictionary <Residue, bool> > Predict(this IHas <IPredictionLogic> logicHolder, PDBFile file, IDictionary <string, ProteinGraph> graphs)
{
return(logicHolder.Logic.Predict(file, graphs));
}
public ComputeInterface(PDBFile pdb, double distance, bool useVanDerWaalsRadii)
{
Distance = distance;
UseVanDerWaalsRadii = useVanDerWaalsRadii;
PDB = pdb;
}
public static Dictionary <string, LinkedList <Residue> > Do(PDBFile pdb, double distance, bool useVanDerWaalsRadii)
{
var iface = new Dictionary <string, LinkedList <Residue> >();
for (int i = 0; i < pdb.Chains.Count; i++)
{
var chain1 = pdb.Chains[i];
iface.Add(chain1.Name, new LinkedList <Residue>());
}
for (int i = 0; i < pdb.Chains.Count; i++)
{
var chain1 = pdb.Chains[i];
var otherchains = pdb.Chains.ToList();
otherchains.Remove(chain1);
var allotheratoms = otherchains.SelectMany(chain => chain.Atoms);
foreach (var residue in chain1.Residues)
{
if (iface[chain1.Name].Contains(residue))
{
continue;
}
bool isInterface = false;
foreach (var atom in residue.Atoms)
{
foreach (var otherchain in otherchains)
{
foreach (var atomPartner in otherchain.Atoms)
{
if (isInterface)
{
break;
}
if (useVanDerWaalsRadii)
{
if (atom.Distance(atomPartner) <=
+VanDerWaalsRadii.GetRadius(atom.Element)
+ VanDerWaalsRadii.GetRadius(atomPartner.Element) + distance)
{
isInterface = true;
if (!iface[otherchain.Name].Contains(atomPartner.Residue))
{
iface[otherchain.Name].Add(atomPartner.Residue);
}
}
}
else
{
if (atom.Distance(atomPartner) <= distance)
{
isInterface = true;
if (!iface[otherchain.Name].Contains(atomPartner.Residue))
{
iface[otherchain.Name].Add(atomPartner.Residue);
}
}
}
}
}
if (isInterface)
{
iface[chain1.Name].Add(residue);
}
}
}
}
return(iface);
}
public PDBInfo(PDBFile file)
{
file1 = file;
file.Chains.Each(chain => ShowChain.Add(chain.Name, true));
}
public Residue(PDBFile pdb)
{
PDB = pdb;
}
