static void StartJobsAsymmetricPair(AsymmetricFusionFlags options)
{
List <string> files1 = GetPdbFiles("./", options.PeptideRegex1).ToList();
List <string> files2 = GetPdbFiles("./", options.PeptideRegex2).ToList();
ThreadSafeJobCounter sharedCounter = new ThreadSafeJobCounter();
sharedCounter.Total = files1.Count * files2.Count;
Console.WriteLine("\nUsing the following files for unit 1:");
files1.ForEach(file => Console.WriteLine(file));
Console.WriteLine("\nUsing the following files for unit 2:");
files2.ForEach(file => Console.WriteLine(file));
// Parse n-peptide and offset it to positive Z
foreach (string file1 in files1)
{
string pdbCode1 = PdbQuick.CodeFromFilePath(file1);
IChain peptide1 = PdbQuick.ChainFromFileOrCode(file1);
peptide1.Translate(-Rmsd.GetBackboneCentroid(peptide1));
// Parse c-peptide and offset it to positive Z
foreach (string file2 in files2)
{
string pdbCode2 = PdbQuick.CodeFromFilePath(file2);
IChain peptide2 = PdbQuick.ChainFromFileOrCode(file2);
peptide2.Translate(-Rmsd.GetBackboneCentroid(peptide2));
if (peptide1 == null || peptide2 == null)
{
Console.WriteLine("Pdb parsing failed for one of [{0}, {1}]", file1, file2);
continue;
}
JobStartParamsAsymmetricPair startParams = new JobStartParamsAsymmetricPair();
startParams.OutputPrefix = "PAIR";
startParams.PdbCodeN = pdbCode1;
startParams.PdbCodeC = pdbCode2;
startParams.PeptideN = peptide1;
startParams.PeptideC = peptide2;
startParams.RangeN = options.Range1 != null ? (Range)options.Range1 : new Range(0, peptide1.Count - 1);
startParams.RangeC = options.Range2 != null ? (Range)options.Range2 : new Range(0, peptide2.Count - 1);
startParams.TopX = options.TopX;
startParams.Counter = sharedCounter; // Shared counter across queued jobs
Debug.Assert(startParams.Validate(), "JobStartParamsAsymmetricPair validation failure");
_threadCountSemaphore.WaitOne();
sharedCounter.IncrementQueued();
Console.WriteLine("Queuing triplet [Bundle {0}]:[Bundle {1}], {2:F2} % ({3}/{4})", pdbCode1, pdbCode2, startParams.Counter.PercentQueued, startParams.Counter.Queued, startParams.Counter.Total);
Thread thread = new Thread(new ParameterizedThreadStart(RunJobAsymmetricPair));
thread.Start(startParams);
}
}
}
public static bool Run(string[] args)
{
switch (args.FirstOrDefault())
{
case CxrcxFusionFlags.BaseFlag:
{
CxrcxFusionFlags options = new CxrcxFusionFlags();
if (options.ParseArgs(args))
{
StartJobsAngleCXRCX(options);
}
else
{
return(false);
}
}
break;
case CxcxFusionFlags.BaseFlag:
{
CxcxFusionFlags options = new CxcxFusionFlags();
if (options.ParseArgs(args))
{
StartJobsAngleCXCX(options);
}
else
{
return(false);
}
}
break;
case AsymmetricFusionFlags.BaseFlag:
{
AsymmetricFusionFlags options = new AsymmetricFusionFlags();
if (options.ParseArgs(args))
{
StartJobsAsymmetricPair(options);
}
else
{
return(false);
}
}
break;
default: return(false);
}
return(true);
}
