public ProvidePDBInfoOptions(string pdbId, double interfaceDefDist, bool interfaceUseVanDerWaalsRadii, double graphNeighourDistance, ResidueNodeCenterDefinition nodeCenterDef)
{
PDBId = pdbId;
ComputeRasa = true;
ComputeInterface = true;
InterfaceDefDistance = interfaceDefDist;
InterfaceUseVanDerWaalsRadii = interfaceUseVanDerWaalsRadii;
ComputeGraph = true;
GraphNeighbourDistance = graphNeighourDistance;
GraphNodeCenterDef = nodeCenterDef;
}
//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.PDBFile = file;
// graph.NeighbourDistance = neighbourDistance;
// graph.NodeCenterDefinition = centerdef;
// //Compute Nodes:
// foreach (var residue in chain.Residues)
// {
// var node = new ResidueNode(residue, graph);
// switch (centerdef)
// {
// case ResidueNodeCenterDefinition.CAlpha:
// node.SetValuesTo(residue.CAlpha);
// break;
// case ResidueNodeCenterDefinition.BalancePoint:
// node.SetValuesTo(residue.Atoms.BalancePoint());
// break;
// default:
// break;
// }
// graph.Nodes.Add(node);
// }
// 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.Distance(nodetwo);
// if (dist <= neighbourDistance)
// {
// var edge = new SimpleEdge<ResidueNode>(nodeOne, nodetwo);
// graph.Edges.Add(edge);
// }
// }
// }
// dict.Add(chain.Name, graph);
// }
// return dict;
//}
public static Dictionary <string, IDictionary <string, ProteinGraph> > Do(IEnumerable <PDBFile> files, double neighbourDistance, ResidueNodeCenterDefinition centerdef)
{
var dict = new Dictionary <string, IDictionary <string, ProteinGraph> >();
foreach (var file in files)
{
dict.Add(file.Name, Do(file, neighbourDistance, centerdef));
}
return(dict);
}
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);
}
