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); }