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);
}
}
}
static void RunJobAsymmetricPair(object start)
{
JobStartParamsAsymmetricPair startParams = (JobStartParamsAsymmetricPair)start;
int count = 0;
IEnumerable <FusionDesignInfo> fusions = Fuse.Fusion2.GetSplices(startParams.PeptideN, startParams.RangeN, startParams.PeptideC, startParams.RangeC, (int)startParams.TopX);
lock (lockFileIO)
{
foreach (FusionDesignInfo fusion in fusions)
{
// Output files
string identifier = String.Format("PAIR_{0}_{1}_{2}_{3}", startParams.OutputPrefix, startParams.PdbCodeN, startParams.PdbCodeC, count++);
// -resfile
Resfile resfile = new Resfile();
fusion.DesignablePositions.ToList().ForEach(item => resfile.SetNotAminoAcids(0, item, "MW")); // Set the designable residues, disallowing Met and Trp entirely
fusion.ImmutablePositions.ToList().ForEach(item => resfile.SetNativeRotamer(0, item)); // Set the immutable positions, overriding any designable ones if they conflict
File.AppendAllLines(identifier + ".resfile", resfile.GetFileText());
// -scores
File.AppendAllText("scores_CXR.txt", String.Format("{0} {1:F2}\n", identifier, fusion.Score));
// -forward folding fixed-backbone ranges
File.AppendAllText(identifier + ".fixed_ranges", String.Format("fixedbb_range1={0}-{1} fixedbb_range2={2}-{3}", 1, fusion.IdentityRanges[0].End + 1, fusion.IdentityRanges[1].Start + 1, fusion.Peptide.Count));
// -pdbs
PdbQuick.Save(identifier + "_monomer.pdb", new IChain[] { fusion.Peptide });
PdbQuick.Save(identifier + "_multichain.pdb", fusion.PdbOutputChains);
}
}
Console.WriteLine("Completed triplet [N-term {0}]:[C-term {1}], {2:F2}% ({3}/{4})", startParams.PdbCodeN, startParams.PdbCodeC, (float)startParams.Counter.Complete / startParams.Counter.Total * 100, startParams.Counter.Complete, startParams.Counter.Total);
startParams.Counter.IncrementComplete();
_threadCountSemaphore.Release();
}
