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);
}
