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);
}
static void Main(string[] args)
{
try
{
bool okArgs = false;
//okArgs |= (new CyclizeAssemblyFlags()).ParseArgs(args);
//okArgs |= (new AsymmetricFusionFlags()).ParseArgs(args);
okArgs |= (new CxrcxFusionFlags()).ParseArgs(args);
if (!okArgs)
{
throw new ArgumentException();
}
}
catch
{
Console.WriteLine();
Console.WriteLine("Options:");
//Console.WriteLine(AsymmetricFusionFlags.BaseFlag + AsymmetricFusionFlags.GetUsageOptions().Aggregate("\t", (a, b) => a + "\n\t" + b));
//Console.WriteLine();
Console.WriteLine(CxrcxFusionFlags.BaseFlag + CxrcxFusionFlags.GetUsageOptions().Aggregate("\t", (a, b) => a + "\n\t" + b));
//Console.WriteLine();
//Console.WriteLine("-splice_cyclize" + CyclizeAssemblyFlags.GetUsageOptions().Aggregate("\t", (a, b) => a + "\n\t" + b));
return;
}
try
{
FusionJobRunner.Run(args);
}
catch (Exception e)
{
Console.Write(e.StackTrace);
}
}
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);
}
}
}
}
