public static TwoAxisRealignment Create(string symmetry, string axisId1, string axisId2)
{
SymmetryBuilder builder = SymmetryBuilderFactory.CreateFromSymmetryName(symmetry);
TwoAxisRealignment result = Create(builder, axisId1, axisId2);
return(result);
}
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();
}
public static TwoAxisRealignment Create(SymmetryBuilder builder, int multiplicity1, int multiplicity2)
{
string axis1 = builder.GetUnits().First(axis => builder.GetMultiplicity(axis) == multiplicity1);
string axis2 = builder.GetUnits().First(axis => builder.GetMultiplicity(axis) == multiplicity2 && axis != axis1);
TwoAxisRealignment result = Create(builder, axis1, axis2);
return(result);
}
public static TwoAxisRealignment Create(string symmetry, int multiplicity1, int multiplicity2)
{
SymmetryBuilder builder = SymmetryBuilderFactory.CreateFromSymmetryName(symmetry);
string axis1 = builder.GetUnits().First(axis => builder.GetMultiplicity(axis) == multiplicity1);
string axis2 = builder.GetUnits().First(axis => builder.GetMultiplicity(axis) == multiplicity2 && axis != axis1);
TwoAxisRealignment result = Create(symmetry, axis1, axis2);
return(result);
}
public SymdefPattern(SymmetryBuilder builder, string pattern, T item = null)
{
_symmetry = SymmetryBuilderFactory.Clone(builder);
_symmetry.EnabledUnits = new string[] { pattern };
OnCoordinateSystemsInitialized();
if (item != null)
{
base.Add(item);
}
}
public SymdefPattern(string symmetry, string pattern, T item = null)
{
_symmetry = SymmetryBuilderFactory.CreateFromSymmetryName(symmetry);
_symmetry.EnabledUnits = new string[] { pattern };
OnCoordinateSystemsInitialized();
if (item != null)
{
base.Add(item);
}
}
public static TwoAxisRealignment Create(SymmetryBuilder builder, string axis1, string axis2)
{
CoordinateSystem coordinateSystem1 = builder.GetPrincipalCoordinateSystem(axis1);
CoordinateSystem coordinateSystem2 = builder.GetPrincipalCoordinateSystem(axis2);
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);
float angleDegrees = (float)VectorMath.GetAngleDegrees(principalAxis1.Direction, principalAxis2.Direction);
TwoAxisRealignment result = TwoAxisRealignment.Create(angleDegrees, principalAxis1, principalAxis2);
return(result);
}
public PatternStructure(SymmetryBuilder symmetry)
{
SetSymmetry(symmetry);
}
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 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 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();
}
static void Main(string[] args)
{
string[] skip = new string[]
{
// questionable C2 scaffolds, IMO - don't use them
"ZC",
"4pwwfrxC2",
"bex2C2G2",
"Di13",
// questionable C3 scaffolds IMO or lacking free termini - don't use them
"2L6HC3",
"C3-1BH",
"EXTN8",
"1na0C3int2-xtal",
"C3V"
};
foreach (string symmetry in new string[] { "T" })
{
string basedir = Directory.GetCurrentDirectory();
foreach (string fileNameOligomer1 in Directory.EnumerateFiles(Path.Combine(basedir, @"Database\Scaffolds\Denovo\C3")))
{
if (skip.Any(str => fileNameOligomer1.Contains(str)))
{
continue;
}
IStructure oligomer1 = PdbQuick.AssemblyFromFileOrCode(fileNameOligomer1);
foreach (string fileNameOligomer2 in Directory.EnumerateFiles(Path.Combine(basedir, @"Database\Scaffolds\Denovo\C2")))
{
if (skip.Any(str => fileNameOligomer2.Contains(str)))
{
continue;
}
IStructure oligomer2 = PdbQuick.AssemblyFromFileOrCode(fileNameOligomer2);
foreach (string fileNameStrut in Directory.EnumerateFiles(Path.Combine(basedir, @"Database\Scaffolds\Denovo\repeats\saxs_and_crystal")))
{
IStructure strut = PdbQuick.AssemblyFromFileOrCode(fileNameStrut);
string basenameC3 = (new FileInfo(fileNameOligomer1)).Name;
string basenameC2 = (new FileInfo(fileNameOligomer2)).Name;
string basenameStrut = (new FileInfo(fileNameStrut)).Name;
string outputBase = String.Format("{0}32_{1}_{2}_{3}", symmetry, basenameC3, basenameStrut, basenameC2).Replace(".pdb", "");
Console.WriteLine("Trying {0} + {1} + {2}", basenameC3, basenameC2, basenameStrut);
SymmetryBuilder builder = SymmetryBuilderFactory.CreateFromSymmetryName(symmetry);
List <Model> models = SymmetricFusionGenerator.CnSnCn(oligomer1, oligomer2, new IStructure[] { strut },
new int[] { 0 }, new int[] { 0 }, new int[][] { new int[] { 0 } }, builder, "C3X", "C2", 5, 5, 5, 20);
for (int i = 0; i < models.Count; i++)
{
Model model = models[i];
string outputName = outputBase + "_" + i;
PdbQuick.Save(outputName + ".pdb", model.Structure);
foreach (KeyValuePair <string, Selection> kvp in model.Selections)
{
string selectionName = kvp.Key;
Selection selection = kvp.Value;
if (model.AsymmetricUnit != null)
{
Resfile resfile = new Resfile();
resfile.SetDesignOperation(model.AsymmetricUnit, selection, ResfileDesignOperation.NOTAA, new char[] { 'W', 'M', 'P', 'C' });
if (resfile.DesignOperationsCount > 0)
{
string[] lines = resfile.GetFileText();
string resfileName = String.Format("{0}_{1}_asu.resfile", outputName, selectionName);
File.WriteAllLines(resfileName, lines);
}
}
}
}
}
}
}
}
}
public Pattern(SymmetryBuilder symmetry)
{
SetSymmetry(symmetry);
}
