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);
}
}
}
}
static void RunJobAngleCXRCX(object obj)
{
JobStartParamsCXRCX start = (JobStartParamsCXRCX)obj;
int count = 0;
// Get a bunch of fusions with the h**o-oligomer axes positioned such that after transformation by the symmetry definition's first coordinate system transformation,
// the axes overlap the first and second repeating unit axes
SymmetryBuilder builder = start.Symmetry;
CoordinateSystem coordinateSystem1 = builder.GetPrincipalCoordinateSystem(start.UnitId1);
CoordinateSystem coordinateSystem2 = builder.GetPrincipalCoordinateSystem(start.UnitId2);
Structure cnAsymmetricUnit1 = new Structure(start.Cx1);
Structure cnAsymmetricUnit2 = new Structure(start.Cx2);
Structure spacer = new Structure(start.Repeat);
Line principalAxis1 = Line.CreateFromPointAndDirection(coordinateSystem1.Translation, coordinateSystem1.UnitX); // The rosetta symdefs axes are along X of each transformed coordinate system, but something not requiring foreknowledge would be nice.
Line principalAxis2 = Line.CreateFromPointAndDirection(coordinateSystem2.Translation, coordinateSystem2.UnitX); // The rosetta symdefs axes are along X of each transformed coordinate system, but something not requiring foreknowledge would be nice.
//Quaternion premultiply = Quaternion.Inverse(coordinateSystem1.Transform.Rotation);
//principalAxis1.Direction = Vector3.Transform(principalAxis1.Direction, premultiply);
//principalAxis2.Direction = Vector3.Transform(principalAxis2.Direction, premultiply);
//principalAxis1.Point = Vector3.Transform(principalAxis1.Point, premultiply);
//principalAxis2.Point = Vector3.Transform(principalAxis2.Point, premultiply);
//AxisRealignment axisAlignmentUtility = AxisRealignment.Create((float) start.AngleDegrees, principalAxis1, principalAxis2);
TwoAxisRealignment axisAlignmentUtility = AxisRealignmentFactory.Create(builder.GetArchitecture(), start.UnitId1, start.UnitId2);
for (int chainIndexCn1 = 0; chainIndexCn1 < cnAsymmetricUnit1.Count; chainIndexCn1++)
{
for (int chainIndexCn2 = 0; chainIndexCn2 < cnAsymmetricUnit2.Count; chainIndexCn2++)
{
for (int chainIndexSpacer = 0; chainIndexSpacer < spacer.Count; chainIndexSpacer++)
{
List <Model> outputs = Fuse.SymmetricFusionGenerator.CnSnCn(
(IStructure)cnAsymmetricUnit1.DeepCopy(),
(IStructure)cnAsymmetricUnit2.DeepCopy(),
new IStructure[] { (IStructure)spacer.DeepCopy() },
new int[] { chainIndexCn1 },
new int[] { chainIndexCn2 },
new int[][] { new int[] { chainIndexSpacer } },
builder, start.UnitId1, start.UnitId2);
int writtenOutCount = 0;
foreach (Model output in outputs)
{
// Output files
lock (lockFileIO)
{
string prefixFullStructure = String.Format("CXRCX_{0}_{1}_{2}_{3}_{4}", start.OutputPrefix, start.PdbCodeBundle1, start.PdbCodeRepeat, start.PdbCodeBundle2, count++);
string prefixAsymmetricUnit = "ASU_" + prefixFullStructure;
PdbQuick.Save(prefixFullStructure + ".pdb", output.Structure);
PdbQuick.Save(prefixAsymmetricUnit + ".pdb", output.AsymmetricUnit);
// Determine which residues should be designable: include residues whose contacts have been removed and
// those with new contacts between previously separate substructures, but not existing interface residues
Selection designable = new Selection(output.Selections[SymmetricFusionGenerator.AaSelectionAsuDesignable]);
// Save a resfile identifying the designable residues
Resfile resfileDesignable = new Resfile();
resfileDesignable.SetDesignOperation(output.AsymmetricUnit, designable, ResfileDesignOperation.NOTAA, new char[] { 'W', 'M', 'P', 'C' });
File.AppendAllLines(prefixAsymmetricUnit + ".resfile", resfileDesignable.GetFileText());
}
writtenOutCount++;
}
}
}
}
start.Counter.IncrementComplete();
Console.WriteLine("Completed triplet [Bundle {0}]:[Repeat {1}]:[Bundle {2}], {3:F2} degrees, {4:F2}% ({5}/{6})", start.PdbCodeBundle1, start.PdbCodeRepeat, start.PdbCodeBundle2, start.AngleDegrees, start.Counter.PercentComplete, start.Counter.Complete, start.Counter.Total);
_threadCountSemaphore.Release();
}
