public static TwoAxisRealignment Create(string symmetry, string axisId1, string axisId2)
{
SymmetryBuilder builder = SymmetryBuilderFactory.CreateFromSymmetryName(symmetry);
TwoAxisRealignment result = Create(builder, axisId1, axisId2);
return(result);
}
new public static IEnumerable <string> GetUsageOptions()
{
IEnumerable <string> options = FusionFlags.GetUsageOptions();
List <string> additionalOptions = new List <string>();
List <string> symmetries = SymmetryBuilderFactory.GetKnownSymmetryNames().Where(sym => !sym.StartsWith("C")).ToList();
// architecture options
additionalOptions.Add(GetFormattedOptionString("-arch <architecture>", "desired symmetry architecture, options are:"));
additionalOptions.Add(GetFormattedOptionString("", symmetries.Aggregate((a, b) => a + ", " + b)));
// axis1 options
additionalOptions.Add(GetFormattedOptionString("-axis1 <axis>", "first axis name corresponding to selected architecture"));
foreach (string symmetry in symmetries)
{
additionalOptions.Add(GetFormattedOptionString("", String.Format("\t{0} available in architecture {1}", GetAxesOptionsString(symmetry), symmetry)));
}
// axis2 options
additionalOptions.Add(GetFormattedOptionString("-axis2 <axis>", "first axis name corresponding to selected architecture"));
foreach (string symmetry in symmetries)
{
additionalOptions.Add(GetFormattedOptionString("", String.Format("\t{0} available in architecture {1}", GetAxesOptionsString(symmetry), symmetry)));
}
// oligomer selection
additionalOptions.Add(GetFormattedOptionString("-regex_oligomer1 <regex>", "oligomer1 pdb search pattern"));
additionalOptions.Add(GetFormattedOptionString("-regex_oligomer2 <regex>", "oligomer2 pdb search pattern"));
return(options.Concat(additionalOptions));
}
static string GetAxesOptionsString(string symmetry)
{
string[] units = SymmetryBuilderFactory.GetSymmetryUnitIds(symmetry);
if (units.Length == 1)
{
return(units[0]);
}
return(units.Aggregate((a, b) => a + ", " + b));
}
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);
}
}
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);
}
}
}
}
public override bool ParseArgs(string[] args)
{
if (args.FirstOrDefault() != InstanceBaseFlag)
{
return(false);
}
if (!base.ParseArgs(args))
{
return(false);
}
for (int i = 0; i < args.Length; i++)
{
if (args[i] == "-arch")
{
Architecture = args[i + 1];
if (!SymmetryBuilderFactory.GetKnownSymmetryNames().Contains(Architecture))
{
Console.WriteLine("Unknown '-arch' value - allowed values are:");
Console.Write(SymmetryBuilderFactory.GetKnownSymmetryNames().Aggregate("", (a, b) => a + "\n\t" + b));
Console.WriteLine();
return(false);
}
i++;
continue;
}
if (args[i] == "-regex_oligomer1")
{
OligomerRegex1 = args[i + 1];
i++;
continue;
}
if (args[i] == "-regex_oligomer2")
{
OligomerRegex2 = args[i + 1];
i++;
continue;
}
if (args[i] == "-axis1")
{
UnitId1 = args[i + 1];
i++;
continue;
}
if (args[i] == "-axis2")
{
UnitId2 = args[i + 1];
i++;
continue;
}
}
if (Architecture == null || !SymmetryBuilderFactory.GetKnownSymmetryNames().Contains(Architecture))
{
Console.WriteLine("Mandatory '-arch' flag missing or invalid - allowed values are:");
Console.Write(SymmetryBuilderFactory.GetKnownSymmetryNames().Aggregate("", (a, b) => a + "\n\t" + b));
Console.WriteLine();
return(false);
}
if (UnitId1 == null || !SymmetryBuilderFactory.GetSymmetryUnitIds(Architecture).Contains(UnitId1))
{
Console.WriteLine("Mandatory '-axis1' flag is missing or invalid - allowed values are:");
Console.Write(SymmetryBuilderFactory.GetSymmetryUnitIds(Architecture).Aggregate("", (a, b) => a + "\n\t" + b));
return(false);
}
if (UnitId2 == null || !SymmetryBuilderFactory.GetSymmetryUnitIds(Architecture).Contains(UnitId2))
{
Console.WriteLine("Mandatory '-axis1' flag is missing or invalid - allowed values are:");
Console.Write(SymmetryBuilderFactory.GetSymmetryUnitIds(Architecture).Aggregate("", (a, b) => a + "\n\t" + b));
return(false);
}
return(true);
}
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);
}
}
}
}
}
}
}
}
}
