protected override void Run()
{
var agent = new Algorithms.Deterministic(settings);
BFSNode seedNode = new BFSNode(Seed, 0);
QueueBFS.Enqueue(seedNode);
while (QueueBFS.Count != 0)
{
var popNode = QueueBFS.Dequeue();
Console.WriteLine("{0},{1}", popNode.getSMILE(), popNode.getDepth());
// Console.Write(".");
if (popNode.getDepth() < MAX_DEPTH)
{
var newNodes = popNode.getChildren(agent);
foreach (var node in newNodes)
{
var nodeSMILE = node.getSMILE();
if (!allNode.Contains(nodeSMILE))
{
nodeInfoWriter.WriteLine("{0},{1}", nodeSMILE, node.getDepth());
// var nodeDir = _runDirectory + "/interNode/depth" + node.getDepth() + "/node" + nodeCnt;
// Directory.CreateDirectory(nodeDir);
// Settings.filer.Save(nodeDir + "/node" + nodeCnt + ".xml", node.getCand());
allNode.Add(nodeSMILE);
QueueBFS.Enqueue(node);
nodeCnt++;
var terminalLinker = node.getFinalCand(agent);
foreach (var linker in terminalLinker)
{
var mol = OBFunctions.designgraphtomol(linker.graph);
var candSMILE = OBFunctions.moltoSMILES(mol);
if (!allFinalCand.Contains(candSMILE))
{
// var linkerDir = _runDirectory + "/finalNode/depth" + node.getDepth() + "/linker" + candCnt;
// Directory.CreateDirectory(linkerDir);
//
// var coeff = Path.Combine(linkerDir, "linker" + candCnt + ".coeff");
// var lmpdat = Path.Combine(linkerDir, "linker" + candCnt + ".lmpdat");
allFinalCand.Add(candSMILE);
// // Set up UFF and run lammps
// Converter.moltoUFF(mol, coeff, lmpdat, false, 100);
// Settings.filer.Save(linkerDir + "/linker" + candCnt + ".xml", linker.graph);
candInfoWriter.WriteLine("{0},{1}", candSMILE, node.getDepth());
candCnt++;
}
}
}
}
}
}
nodeInfoWriter.Close();
candInfoWriter.Close();
}
public BFSNode[] getChildren(Deterministic agent)
{
var opts = AbstractAlgorithm.GetAvailableOptions(Cand);
var nodes = new BFSNode[opts.Count];
for (var i = 0; i < nodes.Length; i++)
{
var child = agent.CopyAndApplyOption(opts[i], Cand, true);
nodes[i] = new BFSNode(child, Depth + 1);
}
return(nodes);
}