static void RunJobAngleCXCX(object start)
{
JobStartParamsCXCX startParams = (JobStartParamsCXCX)start;
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 = startParams.Symmetry;
CoordinateSystem coordinateSystem1 = builder.GetPrincipalCoordinateSystem(startParams.UnitId1);
CoordinateSystem coordinateSystem2 = builder.GetPrincipalCoordinateSystem(startParams.UnitId2);
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);
TwoAxisRealignment axisAlignmentUtility = TwoAxisRealignment.Create((float)startParams.AngleDegrees, principalAxis1, principalAxis2);
List <FusionDesignInfo> fusions = Fuse.SymmetricFusionGenerator.CnCn(startParams.Cx1, startParams.Cx2, startParams.ChainCount1, startParams.ChainCount2, startParams.AngleDegrees, axisAlignmentUtility);
int writtenOutCount = 0;
foreach (FusionDesignInfo fusion in fusions)
{
// Create the pdb chains as per the symmetry builder and find whether any of these copies clashes
bool fullSystemClashes = false;
List <Chain> outputChains = new List <Chain>();
if (builder is PxSymmetryBuilder)
{
TwoAxisFusionDesignInfo twoAxisFusion = (TwoAxisFusionDesignInfo)fusion;
PxSymmetryBuilder pxBuilder = (PxSymmetryBuilder)builder;
pxBuilder.Scale = Line.GetDistance(twoAxisFusion.Axis1, twoAxisFusion.Axis2.Point) / Line.GetDistance(principalAxis1, principalAxis2.Point);
//pxBuilder.Scale = 2 * Line.GetDistance(twoAxisFusion.Axis2, twoAxisFusion.Axis1.Point);
}
CoordinateSystem[] coordinateSystems = builder.GetCoordinateSystems(startParams.UnitId1);
for (int i = 0; i < coordinateSystems.Length; i++)
{
outputChains.Add(new Chain(fusion.Peptide));
outputChains[i].Transform(coordinateSystems[i].Transform);
if (i > 0 && Clash.AnyContact(outputChains[0], outputChains[i], Clash.ContactType.MainchainMainchainClash))
{
fullSystemClashes = true;
break;
}
}
#if DEBUG
IChain[] originalChains = fusion.PdbOutputChains;
#endif
fusion.PdbOutputChains = outputChains.ToArray();
if (fullSystemClashes || writtenOutCount >= startParams.TopX)
{
continue;
}
lock (lockFileIO)
{
// Output files
string identifier = String.Format("CXCX_{0}_{1}_{2}_{3}", startParams.OutputPrefix, startParams.PdbCodeBundle1, startParams.PdbCodeBundle2, 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_CXCX.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);
#if DEBUG
PdbQuick.Save(identifier + "_2axis.pdb", originalChains);
#endif
}
}
Console.WriteLine("Completed triplet [Bundle {0}]:[Bundle {1}], {2:F2} degrees, {3:F2}% ({4}/{5})", startParams.PdbCodeBundle1, startParams.PdbCodeBundle2, startParams.AngleDegrees, startParams.Counter.PercentComplete, startParams.Counter.Complete, startParams.Counter.Total);
startParams.Counter.IncrementComplete();
_threadCountSemaphore.Release();
}
static void StartJobsAngleCXCX(CxcxFusionFlags 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();
ThreadSafeJobCounter sharedCounter = new ThreadSafeJobCounter();
sharedCounter.Total = filesOligomer1.Count * filesOligomer2.Count;
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 pdbCode1 = PdbQuick.CodeFromFilePath(fileOligomer1);
IChain peptide1 = PdbQuick.ChainFromFileOrCode(fileOligomer1);
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 pdbCode2 = PdbQuick.CodeFromFilePath(fileOligomer2);
IChain peptide2 = PdbQuick.ChainFromFileOrCode(fileOligomer2);
peptide2.Translate(new Vector3(0, 0, 20 - Rmsd.GetBackboneCentroid(peptide2).Z));
if (peptide1 == null || peptide2 == null)
{
Console.WriteLine("Pdb parsing failed for one of [{0}, {1}]", fileOligomer1, fileOligomer2);
continue;
}
JobStartParamsCXCX startParams = new JobStartParamsCXCX();
// 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 = pdbCode1;
startParams.PdbCodeBundle2 = pdbCode2;
startParams.Cx1 = peptide1;
startParams.Cx2 = peptide2;
startParams.AngleDegrees = angleDegrees;
startParams.Counter = sharedCounter; // Shared counter across queued jobs
Debug.Assert(startParams.Validate(), "JobStartParamsCXRCX validation failure");
_threadCountSemaphore.WaitOne();
sharedCounter.IncrementQueued();
Thread thread = new Thread(new ParameterizedThreadStart(RunJobAngleCXCX));
thread.Start(startParams);
Console.WriteLine("Queuing triplet [Bundle {0}]:[Bundle {1}], {2:F2} degrees, {3:F2} % ({4}/{5})", pdbCode1, pdbCode2, angleDegrees, startParams.Counter.PercentQueued, startParams.Counter.Queued, startParams.Counter.Total);
}
}
}
