public void SetSymmetry(SymmetryBuilder symmetry)
{
Trace.Assert(symmetry.EnabledUnits != null && symmetry.EnabledUnits.Length > 0);
// Replace intermediate pattern-flow stages, but neither _in or _out, so as to maintain
// connectivity with other objects
CoordinateSystems = symmetry.EnabledUnits.SelectMany(unitId => symmetry.GetCoordinateSystems(unitId)).ToArray();
}
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();
}
public override CoordinateSystem[] GetCoordinateSystems()
{
return(_symmetry.GetCoordinateSystems(_symmetry.EnabledUnits.First()));
}