private static ProteinGraph TrimGraph(PDBFile pdbFile, ProteinGraph proteinGraph)
{
var trimmedGraph = new ProteinGraph();
Dictionary <GWNode <ResidueNodeData, SimpleEdgeData, ProteinGraphData>, GWNode <ResidueNodeData, SimpleEdgeData, ProteinGraphData> > dict = new Dictionary <GWNode <ResidueNodeData, SimpleEdgeData, ProteinGraphData>, GWNode <ResidueNodeData, SimpleEdgeData, ProteinGraphData> >();
foreach (var node in proteinGraph.Nodes)
{
if (!node.Data.IsCore)
{
var newNode = trimmedGraph.CreateNode();
newNode.Data = node.Data;
dict.Add(node, newNode);
}
else
{
}
}
foreach (var edge in proteinGraph.Edges)
{
if (!edge.Head.Data.IsCore && !edge.Foot.Data.IsCore)
{
var newEdge = trimmedGraph.CreateEdge(dict[edge.Head], dict[edge.Foot]);
newEdge.Data = edge.Data;
}
}
return(trimmedGraph);
}
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 void Compute(ProteinGraph graph)
{
Graph = graph;
foreach (var node in graph.Nodes)
{
var totalHydrophobicity = Hydrophobicity.GetHydrophobicity(node.Data.Residue.Code);
foreach (var neighbour in node.Neighbours)
{
totalHydrophobicity += Hydrophobicity.GetHydrophobicity(neighbour.Data.Residue.Code);
}
totalHydrophobicity /= (node.Neighbours.Count() + 1);
logic.Values.Add(node.Data.Residue, (totalHydrophobicity + maxEntry) / (2 * maxEntry));
}
}
public void Compute(ProteinGraph graph, IDictionary <Residue, double> rasaValues)
{
Graph = graph;
foreach (var node in graph.Nodes)
{
var rasasum = rasaValues[node.Data.Residue];
var totalHydrophobicity = Hydrophobicity.GetHydrophobicity(node.Data.Residue.Code) * rasaValues[node.Data.Residue];
foreach (var neighbour in node.Neighbours)
{
rasasum += rasaValues[neighbour.Data.Residue];
totalHydrophobicity += Hydrophobicity.GetHydrophobicity(neighbour.Data.Residue.Code) * rasaValues[neighbour.Data.Residue];
}
totalHydrophobicity /= rasasum;
logic.Values.Add(node.Data.Residue, (totalHydrophobicity + maxEntry) / (2 * maxEntry));
}
}
/// <summary>
/// Proteins constructor
/// </summary>
public Proteins()
: base()
{
// enable object tracking :
Parameters.TrackObjects = true;
Parameters.MsaaLevel = 8;
// uncomment to enable debug graphics device:
// (MS Platform SDK must be installed)
// Parameters.UseDebugDevice = true;
// add services :
AddService(new SpriteBatch(this), false, false, 0, 0);
AddService(new DebugStrings(this), true, true, 9999, 9999);
AddService(new DebugRender(this), true, true, 9998, 9998);
AddService(new GraphSystem(this), true, true, 9997, 9997);
AddService(new GreatCircleCamera(this), true, true, 9996, 9996);
AddService(new UserInterface(this, "stencil"), true, true, 10000, 10000);
// add here additional services :
// load configuration for each service :
LoadConfiguration();
// make configuration saved on exit :
Exiting += Game_Exiting;
nodeSelected = false;
selectedNodeIndex = 0;
// hotNodes = new List<int>();
coldNodes = new List<int>();
protGraph = new ProteinGraph();
timer = 0;
timer2 = 0;
delay = 500;
delay2 = 3000;
//COLORS FOR HIGHLIGHT / цвета для активных
nodeHighlightColorNeg = new Color(221,0,41) ;
nodeHighlightColorPos = new Color(0,221,180) ;
}
public ResidueNode(Residue residue, ProteinGraph graph)
{
Graph = graph;
Residue = residue;
}
public static GWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData> CreateGraph(this ProteinGraph graph, IDictionary <ResidueNodeData, double[]> nodescores, IDictionary <SimpleEdgeData, double[, ]> edgescores)
{
var clonegraph = new GWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData>();
foreach (var node in graph.Nodes)
{
var clone = clonegraph.CreateNode();
clone.Data = new CRFNodeData()
{
Id = node.Data.Residue.Id, Scores = nodescores[node.Data]
};
clonegraph.Nodes.Add(clone);
}
foreach (var edge in graph.Edges)
{
var newEdge = new GWEdge <ICRFNodeData, ICRFEdgeData, ICRFGraphData>(clonegraph.Nodes.First(n => n.Data.Id.Equals(edge.Head.Data.Residue.Id)),
clonegraph.Nodes.First(n => n.Data.Id.Equals(edge.Foot.Data.Residue.Id)));
newEdge.Data = new CRFEdgeData();
newEdge.Data.Scores = edgescores[edge.Data];
clonegraph.Edges.Add(newEdge);
}
return(clonegraph);
}
private static GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> SetReferenceLabel(ProteinGraph trimmedGraph)
{
var nameWithChain = RandomlySelectedPDBFile.Substring(fileFolder.Length + 1, 6);
var interfacesList = new List <string>();
using (var reader = new StreamReader(InterfaceDefLocation))
{
var line = "";
while ((line = reader.ReadLine()) != null)
{
var nuss = nameWithChain;
if (line.StartsWith(nameWithChain))
{
interfacesList.Add(line.Substring(7));
}
}
}
foreach (var interfaceEntry in interfacesList)
{
var node = trimmedGraph.Nodes.FirstOrDefault(n => n.Data.Residue.Id.Equals(interfaceEntry));
if (node != null)
{
node.Data.ReferenceLabel = 1;
}
}
//test
if (GraphVisualization)
{
var graph3D = trimmedGraph.Wrap3D(nd => new Node3DWrap <ResidueNodeData>(nd.Data)
{
ReferenceLabel = nd.Data.ReferenceLabel, X = nd.Data.X, Y = nd.Data.Y, Z = nd.Data.Z
});
new ShowGraph3D(graph3D).Request(RequestRunType.Background);
Thread.Sleep(120000);
}
var crfGraph = trimmedGraph.Convert <ResidueNodeData, CRFNodeData, SimpleEdgeData, CRFEdgeData,
ProteinGraphData, CRFGraphData>(nd => new CRFNodeData(nd.Data.Residue.Id)
{
X = nd.Data.X, Y = nd.Data.Y, Z = nd.Data.Z, ReferenceLabel = nd.Data.ReferenceLabel, Characteristics = new double[] { nd.Data.ZScore }
}, ed => new CRFEdgeData(),
gd => new CRFGraphData());
//crfGraph.SaveAsJSON("testGraph.txt");
crfGraph.Data.ReferenceLabeling = new int[crfGraph.Nodes.Count()];
foreach (var node in crfGraph.Nodes)
{
crfGraph.Data.ReferenceLabeling[node.GraphId] = node.Data.ReferenceLabel;
}
if (GraphVisualization == true)
{
var graph3D = crfGraph.Wrap3D(nd => new Node3DWrap <CRFNodeData>(nd.Data)
{
ReferenceLabel = nd.Data.ReferenceLabel, X = nd.Data.X, Y = nd.Data.Y, Z = nd.Data.Z
}, (ed) => new Edge3DWrap <CRFEdgeData>(ed.Data)
{
Weight = 1.0
});
new ShowGraph3D(graph3D).Request();
}
return(crfGraph);
}
