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 StartJobsAngleCXRCX(CxrcxFusionFlags options)
{
SymmetryBuilder symmetry = SymmetryBuilderFactory.CreateFromSymmetryName(options.Architecture);
List <string> filesOligomer1 = GetPdbFiles(Directory.GetCurrentDirectory(), options.OligomerRegex1).ToList();
List <string> filesOligomer2 = GetPdbFiles(Directory.GetCurrentDirectory(), options.OligomerRegex2).ToList();
List <string> filesRepeat = GetPdbFiles(Directory.GetCurrentDirectory(), options.RepeatRegex).ToList();
ThreadSafeJobCounter sharedCounter = new ThreadSafeJobCounter();
sharedCounter.Total = filesOligomer1.Count * filesOligomer2.Count * filesRepeat.Count;
Console.WriteLine("Using the following spacer repeat proteins:");
filesRepeat.ForEach(file => Console.WriteLine(file));
Console.WriteLine("\nUsing the following files for h**o-oligomer 1:");
filesOligomer1.ForEach(file => Console.WriteLine(file));
Console.WriteLine("\nUsing the following files for h**o-oligomer 2:");
filesOligomer2.ForEach(file => Console.WriteLine(file));
float angleDegrees = (float)VectorMath.GetAngleDegrees(symmetry.GetPrincipalCoordinateSystem(options.UnitId1).UnitX, Vector3.Zero, symmetry.GetPrincipalCoordinateSystem(options.UnitId2).UnitX);
Console.WriteLine("Angle for {0}:{1}:{2} calculated to: {3:F4}", options.Architecture, options.UnitId1, options.UnitId2, angleDegrees);
// Parse oligomer 1 and offset it to positive Z
foreach (string fileOligomer1 in filesOligomer1)
{
string pdbCodeOligomer1 = PdbQuick.CodeFromFilePath(fileOligomer1);
IChain peptide1 = PdbQuick.ChainFromFileOrCode(fileOligomer1);
if (peptide1 == null)
{
Console.WriteLine("Pdb parsing failed for {0}", fileOligomer1);
continue;
}
peptide1.Translate(new Vector3(0, 0, 20 - Rmsd.GetBackboneCentroid(peptide1).Z));
// Parse oligomer 2 and offset it to positive Z
foreach (string fileOligomer2 in filesOligomer2)
{
string pdbCodeOligomer2 = PdbQuick.CodeFromFilePath(fileOligomer2);
IChain peptide2 = PdbQuick.ChainFromFileOrCode(fileOligomer2);
if (peptide2 == null)
{
Console.WriteLine("Pdb parsing failed for {0}", fileOligomer2);
continue;
}
peptide2.Translate(new Vector3(0, 0, 20 - Rmsd.GetBackboneCentroid(peptide2).Z));
// Parse the repeat and offset it to positive Z
foreach (string fileRepeat in filesRepeat)
{
IChain repeat = PdbQuick.ChainFromFileOrCode(fileRepeat);
string pdbCodeRepeat = PdbQuick.CodeFromFilePath(fileRepeat);
if (repeat == null)
{
Console.WriteLine("Pdb parsing failed for {0}", repeat);
continue;
}
repeat.Translate(new Vector3(0, 0, 20 - Rmsd.GetBackboneCentroid(repeat).Z));
JobStartParamsCXRCX startParams = new JobStartParamsCXRCX();
// things taken directly from user options
startParams.OutputPrefix = options.Architecture + "-" + options.UnitId1 + "-" + options.UnitId2;
startParams.UnitId1 = options.UnitId1;
startParams.UnitId2 = options.UnitId2;
startParams.ChainCount1 = options.Oligomerization1;
startParams.ChainCount2 = options.Oligomerization2;
startParams.TopX = options.TopX;
// everything else:
startParams.Symmetry = SymmetryBuilderFactory.CreateFromSymmetryName(options.Architecture);
startParams.PdbCodeBundle1 = pdbCodeOligomer1;
startParams.PdbCodeBundle2 = pdbCodeOligomer2;
startParams.PdbCodeRepeat = pdbCodeRepeat;
startParams.Cx1 = peptide1;
startParams.Cx2 = peptide2;
startParams.Repeat = repeat;
startParams.AngleDegrees = angleDegrees;
startParams.Counter = sharedCounter; // Shared counter across queued jobs
Debug.Assert(startParams.Validate(), "JobStartParamsCXRCX validation failure");
// Wait for free threads
_threadCountSemaphore.WaitOne();
sharedCounter.IncrementQueued();
// Start the job
Thread thread = new Thread(new ParameterizedThreadStart(RunJobAngleCXRCX));
thread.Start(startParams);
Console.WriteLine("Queuing triplet [Bundle {0}]:[Repeat {1}]:[Bundle {2}], {3:F2} degrees, {4:F2} % ({5}/{6})", pdbCodeOligomer1, pdbCodeRepeat, pdbCodeOligomer2, angleDegrees, startParams.Counter.PercentQueued, startParams.Counter.Queued, startParams.Counter.Total);
}
}
}
}