public List<ILoopTrimer> FindTrimerLoops(ILoopsCollection LoopsCollection, ILoopCriteria LoopCriteria)
{
List<ILoopTrimer> LoopTrimers = new List<ILoopTrimer>();
//Search for pairs if we specify
if (LoopCriteria.SearchForTrimer) {
foreach (ILoop LoopA in LoopsCollection.Loops) {
foreach (ILoop LoopB in LoopsCollection.Loops) {
double InterPairDistanceAB = EuclideanDistance(LoopA.ApexAtom, LoopB.ApexAtom);
if (InterPairDistanceAB > LoopCriteria.LoopTrimerDistanceLowerLimit &&
InterPairDistanceAB < LoopCriteria.LoopTrimerDistanceUpperLimit)
{
foreach (ILoop LoopC in LoopsCollection.Loops)
{
double InterPairDistanceAC = EuclideanDistance(LoopA.ApexAtom, LoopC.ApexAtom);
double InterPairDistanceBC = EuclideanDistance(LoopB.ApexAtom, LoopC.ApexAtom);
if (InterPairDistanceAC > LoopCriteria.LoopTrimerDistanceLowerLimit &&
InterPairDistanceAC < LoopCriteria.LoopTrimerDistanceUpperLimit &&
InterPairDistanceBC > LoopCriteria.LoopTrimerDistanceLowerLimit &&
InterPairDistanceBC < LoopCriteria.LoopTrimerDistanceUpperLimit)
{
ILoopTrimer LoopTrimer = new ILoopTrimer();
LoopTrimer.LoopA = LoopA;
LoopTrimer.LoopB = LoopB;
LoopTrimer.LoopC = LoopC;
LoopTrimers.Add(LoopTrimer);
Console.WriteLine("Added Trimer");
}
}
}
}
}
}
return (LoopTrimers);
//return CleanupLoopPairs(LoopPairs); //TODO -> Cleanup trimers
}
public List <ILoopTrimer> FindTrimerLoops(ILoopsCollection LoopsCollection, ILoopCriteria LoopCriteria)
{
List <ILoopTrimer> LoopTrimers = new List <ILoopTrimer>();
//Search for pairs if we specify
if (LoopCriteria.SearchForTrimer)
{
foreach (ILoop LoopA in LoopsCollection.Loops)
{
foreach (ILoop LoopB in LoopsCollection.Loops)
{
double InterPairDistanceAB = EuclideanDistance(LoopA.ApexAtom, LoopB.ApexAtom);
if (InterPairDistanceAB > LoopCriteria.LoopTrimerDistanceLowerLimit &&
InterPairDistanceAB < LoopCriteria.LoopTrimerDistanceUpperLimit)
{
foreach (ILoop LoopC in LoopsCollection.Loops)
{
double InterPairDistanceAC = EuclideanDistance(LoopA.ApexAtom, LoopC.ApexAtom);
double InterPairDistanceBC = EuclideanDistance(LoopB.ApexAtom, LoopC.ApexAtom);
if (InterPairDistanceAC > LoopCriteria.LoopTrimerDistanceLowerLimit &&
InterPairDistanceAC < LoopCriteria.LoopTrimerDistanceUpperLimit &&
InterPairDistanceBC > LoopCriteria.LoopTrimerDistanceLowerLimit &&
InterPairDistanceBC < LoopCriteria.LoopTrimerDistanceUpperLimit)
{
ILoopTrimer LoopTrimer = new ILoopTrimer();
LoopTrimer.LoopA = LoopA;
LoopTrimer.LoopB = LoopB;
LoopTrimer.LoopC = LoopC;
LoopTrimers.Add(LoopTrimer);
Console.WriteLine("Added Trimer");
}
}
}
}
}
}
return(LoopTrimers);
//return CleanupLoopPairs(LoopPairs); //TODO -> Cleanup trimers
}
public List <ILoopPair> FindMatchedLoops(ILoopsCollection LoopsCollection, ILoopCriteria LoopCriteria)
{
List <ILoopPair> LoopPairs = new List <ILoopPair>();
//Search for pairs if we specify
if (LoopCriteria.SearchForLoopPairs)
{
foreach (ILoop LoopA in LoopsCollection.Loops)
{
foreach (ILoop LoopB in LoopsCollection.Loops)
{
double InterPairDistance = EuclideanDistance(LoopA.ApexAtom, LoopB.ApexAtom);
if (InterPairDistance == 0)
{
//Same loop
continue;
}
double N0Distance = EuclideanDistance(LoopA.NTermAtom, LoopB.NTermAtom);
double N1Distance = EuclideanDistance(LoopA.NTermAtomP1, LoopB.NTermAtomP1);
double N2Distance = EuclideanDistance(LoopA.NTermAtomP2, LoopB.NTermAtomP2);
double C0Distance = EuclideanDistance(LoopA.CTermAtom, LoopB.CTermAtom);
double C1Distance = EuclideanDistance(LoopA.CTermAtomP1, LoopB.CTermAtomP1);
double C2Distance = EuclideanDistance(LoopA.CTermAtomP2, LoopB.CTermAtomP2);
//Old
//if (InterPairDistance > LoopCriteria.LoopPairDistanceLowerLimit &&
// InterPairDistance < LoopCriteria.LoopPairDistanceUpperLimit) {
//New
if (N0Distance < LoopCriteria.NNP0DistanceUpper && N0Distance > LoopCriteria.NNP0DistanceLower &&
N1Distance < LoopCriteria.NNP1DistanceUpper && N1Distance > LoopCriteria.NNP1DistanceLower &&
N2Distance < LoopCriteria.NNP2DistanceUpper && N2Distance > LoopCriteria.NNP2DistanceLower &&
C0Distance < LoopCriteria.CCP0DistanceUpper && C0Distance > LoopCriteria.CCP0DistanceLower &&
C1Distance < LoopCriteria.CCP1DistanceUpper && C1Distance > LoopCriteria.CCP1DistanceLower &&
C2Distance < LoopCriteria.CCP2DistanceUpper && C2Distance > LoopCriteria.CCP2DistanceLower)
{
Vector3D vector1 = new Vector3D(1, 0, 0);
Vector3D vector2 = new Vector3D(0, 0, 1);
double crossProduct3D;
// crossProduct is equal to 50
crossProduct3D = Vector3D.AngleBetween(LoopA.UnitVector, LoopB.UnitVector);
if (LoopCriteria.RequireLoopsOnSameChain)
{
if (crossProduct3D > LoopCriteria.LoopOrientationAngleLower &&
crossProduct3D < LoopCriteria.LoopOrientationAngleUpper)
{
if (LoopA.Chain == LoopB.Chain)
{
ILoopPair LoopPair = new ILoopPair();
LoopPair.LoopA = LoopA;
LoopPair.LoopB = LoopB;
LoopPairs.Add(LoopPair);
}
}
}
}
}
}
}
//return (LoopPairs);
return(CleanupLoopPairs(LoopPairs));
}
private IResidue IsLoopSolventAccessible(List <IResidue> PdbResidues, List <IResidue> LoopResidues, ILoopCriteria LoopCriteria)
{
var PdbGuids = from p in PdbResidues
select p;
var LoopGuids = from c in LoopResidues
select c;
var PdbWithoutLoop = PdbGuids.Except(LoopGuids);
//Grad the Apex atom from the loop segment
double MaxApexDistance = 0.0;
double ApexDistance = 0.0;
IResidue ApexResidue = new IResidue();
IResidue NTermResidue = LoopResidues.First();
IResidue CTermResidue = LoopResidues.Last();
double TerminalDistance = EuclideanDistance(NTermResidue, CTermResidue);
IResidue PseudoTermResidue = new IResidue(0, "", "Virtual", "V", 0,
((NTermResidue.X + CTermResidue.X) / 2),
((NTermResidue.Y + CTermResidue.Y) / 2),
((NTermResidue.Z + CTermResidue.Z) / 2));
//Determine the Apex Residue
foreach (IResidue Residue in LoopResidues)
{
ApexDistance = EuclideanDistance(PseudoTermResidue, Residue);
if (ApexDistance > MaxApexDistance)
{
MaxApexDistance = ApexDistance;
ApexResidue = Residue;
}
}
//Now calculate the distances between the Apex residue and all the other atoms in the PDB (minus the loop residues)
foreach (IResidue Residue in PdbWithoutLoop)
{
if (EuclideanDistance(ApexResidue, Residue) < LoopCriteria.SolventExposedThreshold)
{
//Not solvent accessible
return(null);
}
}
return(ApexResidue);
}
private IResidue IsLoopVectorSolventAccessible(List <IResidue> PdbResidues, List <IResidue> LoopResidues, int VectorScale, ILoopCriteria LoopCriteria)
{
var PdbGuids = from p in PdbResidues
select p;
var LoopGuids = from c in LoopResidues
select c;
var PdbWithoutLoop = PdbGuids.Except(LoopGuids);
IResidue[] LoopArray = LoopResidues.ToArray();
IResidue NTerm = LoopArray[0];
IResidue NTermP1 = LoopArray[1]; //Might not use this...
IResidue NTermP2 = LoopArray[2];
IResidue CTerm = LoopArray[LoopArray.Count() - 1]; //Zero base
IResidue CTermP1 = LoopArray[LoopArray.Count() - 2]; //Might not use this...
IResidue CTermP2 = LoopArray[LoopArray.Count() - 3];
//Average the positions of the N aand C sides of the loops
IResidue P0Term = new IResidue(0, "Virtual", "VP0", "N", 0,
(NTerm.X + CTerm.X) / 2,
(NTerm.Y + CTerm.Y) / 2,
(NTerm.Z + CTerm.Z) / 2);
//Might not use this...
IResidue P1Term = new IResidue(0, "Virtual", "VP1", "N", 0,
(NTermP1.X + CTermP1.X) / 2,
(NTermP1.Y + CTermP1.Y) / 2,
(NTermP1.Z + CTermP1.Z) / 2);
IResidue P2Term = new IResidue(0, "Virtual", "VP2", "N", 0,
(NTermP2.X + CTermP2.X) / 2,
(NTermP2.Y + CTermP2.Y) / 2,
(NTermP2.Z + CTermP2.Z) / 2);
//Calculate the unit vector (not using P1 for now)
double unitX = P2Term.X - P0Term.X;
double unitY = P2Term.Y - P0Term.Y;
double unitZ = P2Term.Z - P0Term.Z;
//Scaled PsuedoResidue out in the solvent
IResidue SolventResidue = new IResidue(0, "Virtual", "Solvent", "N", 0,
(unitX * VectorScale) + P0Term.X,
(unitY * VectorScale) + P0Term.Y,
(unitZ * VectorScale) + P0Term.Z);
//Now calculate the distances between the Apex residue and all the other atoms in the PDB (minus the loop residues)
foreach (IResidue Residue in PdbWithoutLoop)
{
if (EuclideanDistance(SolventResidue, Residue) < LoopCriteria.SolventExposedThreshold)
{
//Not solvent accessible
return(null);
}
}
//Determine the Apex Residue
IResidue ApexResidue = new IResidue();
double MaxApexDistance = 0.0;
double ApexDistance = 0.0;
foreach (IResidue Residue in LoopResidues)
{
ApexDistance = EuclideanDistance(P0Term, Residue);
if (ApexDistance > MaxApexDistance)
{
MaxApexDistance = ApexDistance;
ApexResidue = Residue;
}
}
return(ApexResidue);
}
public ILoopsCollection Search(IPdb Pdb)
{
ILoopsCollection LoopsCollection = new ILoopsCollection();
ILoopCriteria LoopCriteria = new ILoopCriteria(true);
//Try some LINQ on this beast
var Chains = (from p in Pdb.Atoms select p.Chain).Distinct();
foreach (string ChainName in Chains)
{
//Get all the atoms in the chain
var Chain = (from p in Pdb.Atoms where p.Chain == ChainName select p);
IResidue[] AtomsInChain = Chain.ToArray();
//Set the chain length if it is not explicitly set (full length here)
if (LoopCriteria.Start == -1)
{
LoopCriteria.Start = 0;
}
if (LoopCriteria.End == -1)
{
LoopCriteria.End = AtomsInChain.Count();
}
//Search for the loops
if (LoopCriteria.Length > AtomsInChain.Count())
{
continue;
}
for (int i = LoopCriteria.Start; i < LoopCriteria.End - LoopCriteria.Length - 1; i++)
{
//Check for the terminal distances
double eDistance = EuclideanDistance(AtomsInChain[i], AtomsInChain[i + LoopCriteria.Length]);
if (eDistance < LoopCriteria.TerminiDistanceThreshold)
{
//Passes the Distance Test
//Check for the solvent accessible regions
if (LoopCriteria.SolventAccessible)
{
List <IResidue> LoopResidues = new List <IResidue>();
for (int j = i; j < i + LoopCriteria.Length; j++)
{
LoopResidues.Add(AtomsInChain[j]);
}
IResidue ApexResidue = IsLoopVectorSolventAccessible(Pdb.Atoms, LoopResidues, 4, LoopCriteria);
//IResidue ApexResidue = IsLoopSolventAccessible(Pdb.Atoms, LoopResidues, LoopCriteria);
if (ApexResidue != null)
{
//Passes the solvent test, add it to the loop collection
ILoop Loop = new ILoop();
Loop.NTermAtom = AtomsInChain[i];
Loop.NTermAtomP1 = AtomsInChain[i + 1];
Loop.NTermAtomP2 = AtomsInChain[i + 2];
Loop.CTermAtom = AtomsInChain[i + LoopCriteria.Length];
Loop.CTermAtomP1 = AtomsInChain[i + LoopCriteria.Length - 1];
Loop.CTermAtomP2 = AtomsInChain[i + LoopCriteria.Length - 2];
Loop.LoopLength = LoopCriteria.Length;
Loop.PdbCode = Pdb.PdbCode;
Loop.Chain = ChainName;
Loop.ApexAtom = ApexResidue;
Loop.UnitVector = new Vector3D(((Loop.NTermAtomP2.X + Loop.CTermAtomP2.X) / 2) - ((Loop.NTermAtom.X + Loop.CTermAtom.X) / 2),
((Loop.NTermAtomP2.Y + Loop.CTermAtomP2.Y) / 2) - ((Loop.NTermAtom.Y + Loop.CTermAtom.Y) / 2),
((Loop.NTermAtomP2.X + Loop.CTermAtomP2.X) / 2) - ((Loop.NTermAtom.X + Loop.CTermAtom.X) / 2));
//Ensure Beta-Loop-Beta
if (EuclideanDistance(Loop.NTermAtom, Loop.CTermAtom) < LoopCriteria.TerminiDistanceThreshold &&
EuclideanDistance(Loop.NTermAtomP1, Loop.CTermAtomP1) < LoopCriteria.TerminiDistanceThreshold &&
EuclideanDistance(Loop.NTermAtomP2, Loop.CTermAtomP2) < LoopCriteria.TerminiDistanceThreshold)
{
LoopsCollection.Add(Loop);
}
}
}
}
}
LoopCriteria.End = -1;
LoopCriteria.Start = -1;
}
//Cleanup
LoopCriteria = null;
//Return
return(CleanupLoops(LoopsCollection));
}
static void Main(string[] args)
{
#region Argument Parameters
string OutputFilename;
string PdbDirectory = @"C:\PDB\Monomer";
string PdbMultimerDirectory = @"C:\Archives\Biounits";
string PdbFile = @"C:\PDB\Monomer\pdb1rcv.ent.gz";
bool useMultimeric = false;
#endregion
ILoopCriteria LoopCriteria = new ILoopCriteria();
Arguments CommandLine = new Arguments(args);
if (CommandLine["directory"] != null) {
PdbDirectory = CommandLine["directory"];
}
if (CommandLine["multimeric"] != null) {
useMultimeric = true;
}
if (CommandLine["searchfortrimer"] != null)
{
LoopCriteria.SearchForTrimer = true;
LoopCriteria.SearchForLoopPairs = false;
}
if (CommandLine["file"] != null) {
PdbFile = CommandLine["file"];
}
if (CommandLine["match"] != null) {
LoopCriteria.SearchForLoopPairs = true;
if (CommandLine["lower"] != null) {
LoopCriteria.LoopPairDistanceLowerLimit = Convert.ToDouble(CommandLine["lower"]);
}
if (CommandLine["upper"] != null) {
LoopCriteria.LoopPairDistanceUpperLimit = Convert.ToDouble(CommandLine["upper"]);
}
}
else {
LoopCriteria.SearchForLoopPairs = false;
}
if (CommandLine["out"] != null) {
OutputFilename = CommandLine["out"];
}
else {
OutputFilename = "ScaffoldFinderLog_" + DateTime.Now.ToString("yyyyMMddHHmmss") + ".txt";
}
string LogFilename = @"c:\Archives\Output\" + OutputFilename;
FileStream LogStream = File.Open(LogFilename,
FileMode.CreateNew,
FileAccess.Write);
StreamWriter LogFile = new StreamWriter(LogStream, Encoding.UTF8);
//Write the lof file header
if (LoopCriteria.SearchForLoopPairs) {
LogFile.WriteLine("PDB,ChainA,NTermLoopA,CTermLoopA,Length,ChainB,NTermLoopB,CTermLoopB,LengthB,Size");
}
else if (LoopCriteria.SearchForTrimer)
{
LogFile.WriteLine("PDB,ChainA,NTermLoopA,CTermLoopA,Length,ChainB,NTermLoopB,CTermLoopB,LengthB,ChainC,NTermLoopC,CTermLoopC,LengthC");
}
else
{
LogFile.WriteLine("PDB,Chain,NTerm,CTerm,Length");
}
//Loop through the directory to get the PDBs
DirectoryInfo Directory;
if (useMultimeric) {
Directory = new DirectoryInfo(PdbMultimerDirectory);
}
else {
Directory = new DirectoryInfo(PdbDirectory);
}
int FileCounter = 0;
int FileTotals = Directory.GetFiles().Count();
foreach (FileInfo file in Directory.GetFiles())
{
FileCounter++;
if (FileCounter % 500 == 0) {
Console.WriteLine("[" + FileCounter + "/" + FileTotals + "]: " + file.FullName);
}
//Console.SetCursorPosition(0, Console.CursorTop);
//Console.WriteLine("Filename: " + file.Name + " Size: " + file.Length);
if (file.Length > 500000)
{
continue;
}
IPdb Pdb = new IPdb(file.FullName, useMultimeric);
ILoopsCollection LoopsCollection = new ILoopsCollection();
if (Pdb.Atoms.Count() != 0) { // Implies Nucleic Acid
FindLoops findLoops = new FindLoops();
LoopsCollection = findLoops.Search(Pdb);
//LoopsCollection = FindLoops.Search(Pdb);
findLoops = null;
}
else {
continue;
}
//Search for three loops that match the trimer constraints
if(LoopCriteria.SearchForTrimer) {
FindLoops findLoops = new FindLoops();
List<ILoopTrimer> LoopTrimer = findLoops.FindTrimerLoops(LoopsCollection, LoopCriteria);
foreach (ILoopTrimer Loops in LoopTrimer)
{
LogFile.WriteLine(Loops.LoopA.PdbCode + "," +
Loops.LoopA.Chain + "," +
Loops.LoopA.NTermAtom.ResidueNumber + Loops.LoopA.NTermAtom.ResidueExtension + "," +
Loops.LoopA.CTermAtom.ResidueNumber + Loops.LoopA.CTermAtom.ResidueExtension + "," +
Loops.LoopA.LoopLength + "," +
Loops.LoopB.Chain + "," +
Loops.LoopB.NTermAtom.ResidueNumber + Loops.LoopB.NTermAtom.ResidueExtension + "," +
Loops.LoopB.CTermAtom.ResidueNumber + Loops.LoopB.CTermAtom.ResidueExtension + "," +
Loops.LoopB.LoopLength + "," +
Loops.LoopC.Chain + "," +
Loops.LoopC.NTermAtom.ResidueNumber + Loops.LoopC.NTermAtom.ResidueExtension + "," +
Loops.LoopC.CTermAtom.ResidueNumber + Loops.LoopC.CTermAtom.ResidueExtension + "," +
Loops.LoopC.LoopLength);
}
LoopTrimer = null;
findLoops = null;
}
else if (LoopCriteria.SearchForLoopPairs) {
FindLoops findLoops = new FindLoops();
List<ILoopPair> LoopPairs = findLoops.FindMatchedLoops(LoopsCollection, LoopCriteria);
foreach (ILoopPair LoopPair in LoopPairs)
{
Console.WriteLine("Found: " + LoopPair.LoopA.PdbCode);
LogFile.WriteLine(LoopPair.LoopA.PdbCode + "," +
LoopPair.LoopA.Chain + "," +
LoopPair.LoopA.NTermAtom.ResidueNumber + LoopPair.LoopA.NTermAtom.ResidueExtension + "," +
LoopPair.LoopA.CTermAtom.ResidueNumber + LoopPair.LoopA.CTermAtom.ResidueExtension + "," +
LoopPair.LoopA.LoopLength + "," +
LoopPair.LoopB.Chain + "," +
LoopPair.LoopB.NTermAtom.ResidueNumber + LoopPair.LoopB.NTermAtom.ResidueExtension + "," +
LoopPair.LoopB.CTermAtom.ResidueNumber + LoopPair.LoopB.CTermAtom.ResidueExtension + "," +
LoopPair.LoopB.LoopLength + "," +
Pdb.Atoms.Count()) ;
}
LoopPairs = null;
findLoops = null;
}
else
{
foreach (ILoop Loop in LoopsCollection.Loops)
{
LogFile.WriteLine(Loop.PdbCode + "," +
Loop.Chain + "," +
Loop.NTermAtom.ResidueNumber + Loop.NTermAtom.ResidueExtension + "," +
Loop.CTermAtom.ResidueNumber + Loop.CTermAtom.ResidueExtension + "," +
Loop.LoopLength);
}
//Cleanup
}
}
LogFile.Close();
LogStream.Close();
// Console.ReadLine();
}
static void Main(string[] args)
{
#region Argument Parameters
string OutputFilename;
string PdbDirectory = @"C:\PDB\Monomer";
string PdbMultimerDirectory = @"C:\Archives\Biounits";
string PdbFile = @"C:\PDB\Monomer\pdb1rcv.ent.gz";
bool useMultimeric = false;
#endregion
ILoopCriteria LoopCriteria = new ILoopCriteria();
Arguments CommandLine = new Arguments(args);
if (CommandLine["directory"] != null)
{
PdbDirectory = CommandLine["directory"];
}
if (CommandLine["multimeric"] != null)
{
useMultimeric = true;
}
if (CommandLine["searchfortrimer"] != null)
{
LoopCriteria.SearchForTrimer = true;
LoopCriteria.SearchForLoopPairs = false;
}
if (CommandLine["file"] != null)
{
PdbFile = CommandLine["file"];
}
if (CommandLine["match"] != null)
{
LoopCriteria.SearchForLoopPairs = true;
if (CommandLine["lower"] != null)
{
LoopCriteria.LoopPairDistanceLowerLimit = Convert.ToDouble(CommandLine["lower"]);
}
if (CommandLine["upper"] != null)
{
LoopCriteria.LoopPairDistanceUpperLimit = Convert.ToDouble(CommandLine["upper"]);
}
}
else
{
LoopCriteria.SearchForLoopPairs = false;
}
if (CommandLine["out"] != null)
{
OutputFilename = CommandLine["out"];
}
else
{
OutputFilename = "ScaffoldFinderLog_" + DateTime.Now.ToString("yyyyMMddHHmmss") + ".txt";
}
string LogFilename = @"c:\Archives\Output\" + OutputFilename;
FileStream LogStream = File.Open(LogFilename,
FileMode.CreateNew,
FileAccess.Write);
StreamWriter LogFile = new StreamWriter(LogStream, Encoding.UTF8);
//Write the lof file header
if (LoopCriteria.SearchForLoopPairs)
{
LogFile.WriteLine("PDB,ChainA,NTermLoopA,CTermLoopA,Length,ChainB,NTermLoopB,CTermLoopB,LengthB,Size");
}
else if (LoopCriteria.SearchForTrimer)
{
LogFile.WriteLine("PDB,ChainA,NTermLoopA,CTermLoopA,Length,ChainB,NTermLoopB,CTermLoopB,LengthB,ChainC,NTermLoopC,CTermLoopC,LengthC");
}
else
{
LogFile.WriteLine("PDB,Chain,NTerm,CTerm,Length");
}
//Loop through the directory to get the PDBs
DirectoryInfo Directory;
if (useMultimeric)
{
Directory = new DirectoryInfo(PdbMultimerDirectory);
}
else
{
Directory = new DirectoryInfo(PdbDirectory);
}
int FileCounter = 0;
int FileTotals = Directory.GetFiles().Count();
foreach (FileInfo file in Directory.GetFiles())
{
FileCounter++;
if (FileCounter % 500 == 0)
{
Console.WriteLine("[" + FileCounter + "/" + FileTotals + "]: " + file.FullName);
}
//Console.SetCursorPosition(0, Console.CursorTop);
//Console.WriteLine("Filename: " + file.Name + " Size: " + file.Length);
if (file.Length > 500000)
{
continue;
}
IPdb Pdb = new IPdb(file.FullName, useMultimeric);
ILoopsCollection LoopsCollection = new ILoopsCollection();
if (Pdb.Atoms.Count() != 0) // Implies Nucleic Acid
{
FindLoops findLoops = new FindLoops();
LoopsCollection = findLoops.Search(Pdb);
//LoopsCollection = FindLoops.Search(Pdb);
findLoops = null;
}
else
{
continue;
}
//Search for three loops that match the trimer constraints
if (LoopCriteria.SearchForTrimer)
{
FindLoops findLoops = new FindLoops();
List <ILoopTrimer> LoopTrimer = findLoops.FindTrimerLoops(LoopsCollection, LoopCriteria);
foreach (ILoopTrimer Loops in LoopTrimer)
{
LogFile.WriteLine(Loops.LoopA.PdbCode + "," +
Loops.LoopA.Chain + "," +
Loops.LoopA.NTermAtom.ResidueNumber + Loops.LoopA.NTermAtom.ResidueExtension + "," +
Loops.LoopA.CTermAtom.ResidueNumber + Loops.LoopA.CTermAtom.ResidueExtension + "," +
Loops.LoopA.LoopLength + "," +
Loops.LoopB.Chain + "," +
Loops.LoopB.NTermAtom.ResidueNumber + Loops.LoopB.NTermAtom.ResidueExtension + "," +
Loops.LoopB.CTermAtom.ResidueNumber + Loops.LoopB.CTermAtom.ResidueExtension + "," +
Loops.LoopB.LoopLength + "," +
Loops.LoopC.Chain + "," +
Loops.LoopC.NTermAtom.ResidueNumber + Loops.LoopC.NTermAtom.ResidueExtension + "," +
Loops.LoopC.CTermAtom.ResidueNumber + Loops.LoopC.CTermAtom.ResidueExtension + "," +
Loops.LoopC.LoopLength);
}
LoopTrimer = null;
findLoops = null;
}
else if (LoopCriteria.SearchForLoopPairs)
{
FindLoops findLoops = new FindLoops();
List <ILoopPair> LoopPairs = findLoops.FindMatchedLoops(LoopsCollection, LoopCriteria);
foreach (ILoopPair LoopPair in LoopPairs)
{
Console.WriteLine("Found: " + LoopPair.LoopA.PdbCode);
LogFile.WriteLine(LoopPair.LoopA.PdbCode + "," +
LoopPair.LoopA.Chain + "," +
LoopPair.LoopA.NTermAtom.ResidueNumber + LoopPair.LoopA.NTermAtom.ResidueExtension + "," +
LoopPair.LoopA.CTermAtom.ResidueNumber + LoopPair.LoopA.CTermAtom.ResidueExtension + "," +
LoopPair.LoopA.LoopLength + "," +
LoopPair.LoopB.Chain + "," +
LoopPair.LoopB.NTermAtom.ResidueNumber + LoopPair.LoopB.NTermAtom.ResidueExtension + "," +
LoopPair.LoopB.CTermAtom.ResidueNumber + LoopPair.LoopB.CTermAtom.ResidueExtension + "," +
LoopPair.LoopB.LoopLength + "," +
Pdb.Atoms.Count());
}
LoopPairs = null;
findLoops = null;
}
else
{
foreach (ILoop Loop in LoopsCollection.Loops)
{
LogFile.WriteLine(Loop.PdbCode + "," +
Loop.Chain + "," +
Loop.NTermAtom.ResidueNumber + Loop.NTermAtom.ResidueExtension + "," +
Loop.CTermAtom.ResidueNumber + Loop.CTermAtom.ResidueExtension + "," +
Loop.LoopLength);
}
//Cleanup
}
}
LogFile.Close();
LogStream.Close();
// Console.ReadLine();
}
private IResidue IsLoopVectorSolventAccessible(List<IResidue> PdbResidues, List<IResidue> LoopResidues, int VectorScale, ILoopCriteria LoopCriteria)
{
var PdbGuids = from p in PdbResidues
select p;
var LoopGuids = from c in LoopResidues
select c;
var PdbWithoutLoop = PdbGuids.Except(LoopGuids);
IResidue[] LoopArray = LoopResidues.ToArray();
IResidue NTerm = LoopArray[0];
IResidue NTermP1 = LoopArray[1]; //Might not use this...
IResidue NTermP2 = LoopArray[2];
IResidue CTerm = LoopArray[LoopArray.Count()- 1]; //Zero base
IResidue CTermP1 = LoopArray[LoopArray.Count() - 2]; //Might not use this...
IResidue CTermP2 = LoopArray[LoopArray.Count() - 3];
//Average the positions of the N aand C sides of the loops
IResidue P0Term = new IResidue(0, "Virtual", "VP0", "N", 0,
(NTerm.X + CTerm.X) / 2,
(NTerm.Y + CTerm.Y) / 2,
(NTerm.Z + CTerm.Z) / 2);
//Might not use this...
IResidue P1Term = new IResidue(0, "Virtual", "VP1", "N", 0,
(NTermP1.X + CTermP1.X) / 2,
(NTermP1.Y + CTermP1.Y) / 2,
(NTermP1.Z + CTermP1.Z) / 2);
IResidue P2Term = new IResidue(0, "Virtual", "VP2", "N", 0,
(NTermP2.X + CTermP2.X) / 2,
(NTermP2.Y + CTermP2.Y) / 2,
(NTermP2.Z + CTermP2.Z) / 2);
//Calculate the unit vector (not using P1 for now)
double unitX = P2Term.X - P0Term.X;
double unitY = P2Term.Y - P0Term.Y;
double unitZ = P2Term.Z - P0Term.Z;
//Scaled PsuedoResidue out in the solvent
IResidue SolventResidue = new IResidue(0, "Virtual", "Solvent", "N", 0,
(unitX * VectorScale) + P0Term.X,
(unitY * VectorScale) + P0Term.Y,
(unitZ * VectorScale) + P0Term.Z);
//Now calculate the distances between the Apex residue and all the other atoms in the PDB (minus the loop residues)
foreach (IResidue Residue in PdbWithoutLoop)
{
if (EuclideanDistance(SolventResidue, Residue) < LoopCriteria.SolventExposedThreshold)
{
//Not solvent accessible
return null;
}
}
//Determine the Apex Residue
IResidue ApexResidue = new IResidue();
double MaxApexDistance = 0.0;
double ApexDistance = 0.0;
foreach (IResidue Residue in LoopResidues)
{
ApexDistance = EuclideanDistance(P0Term, Residue);
if (ApexDistance > MaxApexDistance)
{
MaxApexDistance = ApexDistance;
ApexResidue = Residue;
}
}
return ApexResidue;
}
private IResidue IsLoopSolventAccessible(List<IResidue> PdbResidues, List<IResidue> LoopResidues, ILoopCriteria LoopCriteria)
{
var PdbGuids = from p in PdbResidues
select p;
var LoopGuids = from c in LoopResidues
select c;
var PdbWithoutLoop = PdbGuids.Except(LoopGuids);
//Grad the Apex atom from the loop segment
double MaxApexDistance = 0.0;
double ApexDistance = 0.0;
IResidue ApexResidue = new IResidue();
IResidue NTermResidue = LoopResidues.First();
IResidue CTermResidue = LoopResidues.Last();
double TerminalDistance = EuclideanDistance(NTermResidue, CTermResidue);
IResidue PseudoTermResidue = new IResidue(0, "", "Virtual", "V", 0,
((NTermResidue.X + CTermResidue.X) / 2),
((NTermResidue.Y+CTermResidue.Y) / 2),
((NTermResidue.Z+CTermResidue.Z) / 2));
//Determine the Apex Residue
foreach (IResidue Residue in LoopResidues) {
ApexDistance = EuclideanDistance(PseudoTermResidue, Residue);
if (ApexDistance > MaxApexDistance) {
MaxApexDistance = ApexDistance;
ApexResidue = Residue;
}
}
//Now calculate the distances between the Apex residue and all the other atoms in the PDB (minus the loop residues)
foreach (IResidue Residue in PdbWithoutLoop) {
if (EuclideanDistance(ApexResidue, Residue) < LoopCriteria.SolventExposedThreshold) {
//Not solvent accessible
return null;
}
}
return ApexResidue;
}
public ILoopsCollection Search(IPdb Pdb)
{
ILoopsCollection LoopsCollection = new ILoopsCollection();
ILoopCriteria LoopCriteria = new ILoopCriteria(true);
//Try some LINQ on this beast
var Chains = (from p in Pdb.Atoms select p.Chain).Distinct();
foreach (string ChainName in Chains)
{
//Get all the atoms in the chain
var Chain = (from p in Pdb.Atoms where p.Chain == ChainName select p);
IResidue[] AtomsInChain = Chain.ToArray();
//Set the chain length if it is not explicitly set (full length here)
if(LoopCriteria.Start == -1) { LoopCriteria.Start = 0; }
if(LoopCriteria.End == -1) { LoopCriteria.End = AtomsInChain.Count(); }
//Search for the loops
if (LoopCriteria.Length > AtomsInChain.Count()) { continue; }
for (int i = LoopCriteria.Start; i < LoopCriteria.End - LoopCriteria.Length-1; i++)
{
//Check for the terminal distances
double eDistance = EuclideanDistance(AtomsInChain[i], AtomsInChain[i + LoopCriteria.Length]);
if (eDistance < LoopCriteria.TerminiDistanceThreshold) {
//Passes the Distance Test
//Check for the solvent accessible regions
if (LoopCriteria.SolventAccessible) {
List<IResidue> LoopResidues = new List<IResidue>();
for (int j = i; j < i + LoopCriteria.Length; j++) { LoopResidues.Add(AtomsInChain[j]); }
IResidue ApexResidue = IsLoopVectorSolventAccessible(Pdb.Atoms, LoopResidues, 4, LoopCriteria);
//IResidue ApexResidue = IsLoopSolventAccessible(Pdb.Atoms, LoopResidues, LoopCriteria);
if (ApexResidue!=null) {
//Passes the solvent test, add it to the loop collection
ILoop Loop = new ILoop();
Loop.NTermAtom = AtomsInChain[i];
Loop.NTermAtomP1 = AtomsInChain[i + 1];
Loop.NTermAtomP2 = AtomsInChain[i + 2];
Loop.CTermAtom = AtomsInChain[i + LoopCriteria.Length];
Loop.CTermAtomP1 = AtomsInChain[i + LoopCriteria.Length - 1];
Loop.CTermAtomP2 = AtomsInChain[i + LoopCriteria.Length - 2];
Loop.LoopLength = LoopCriteria.Length;
Loop.PdbCode = Pdb.PdbCode;
Loop.Chain = ChainName;
Loop.ApexAtom = ApexResidue;
Loop.UnitVector = new Vector3D(((Loop.NTermAtomP2.X + Loop.CTermAtomP2.X) / 2) - ((Loop.NTermAtom.X + Loop.CTermAtom.X) / 2),
((Loop.NTermAtomP2.Y + Loop.CTermAtomP2.Y) / 2) - ((Loop.NTermAtom.Y + Loop.CTermAtom.Y) / 2),
((Loop.NTermAtomP2.X + Loop.CTermAtomP2.X) / 2) - ((Loop.NTermAtom.X + Loop.CTermAtom.X) / 2));
//Ensure Beta-Loop-Beta
if (EuclideanDistance(Loop.NTermAtom, Loop.CTermAtom) < LoopCriteria.TerminiDistanceThreshold &&
EuclideanDistance(Loop.NTermAtomP1, Loop.CTermAtomP1) < LoopCriteria.TerminiDistanceThreshold &&
EuclideanDistance(Loop.NTermAtomP2, Loop.CTermAtomP2) < LoopCriteria.TerminiDistanceThreshold)
{
LoopsCollection.Add(Loop);
}
}
}
}
}
LoopCriteria.End = -1;
LoopCriteria.Start = -1;
}
//Cleanup
LoopCriteria = null;
//Return
return CleanupLoops(LoopsCollection);
}
public List<ILoopPair> FindMatchedLoops(ILoopsCollection LoopsCollection, ILoopCriteria LoopCriteria)
{
List<ILoopPair> LoopPairs = new List<ILoopPair>();
//Search for pairs if we specify
if (LoopCriteria.SearchForLoopPairs)
{
foreach (ILoop LoopA in LoopsCollection.Loops)
{
foreach (ILoop LoopB in LoopsCollection.Loops)
{
double InterPairDistance = EuclideanDistance(LoopA.ApexAtom, LoopB.ApexAtom);
if(InterPairDistance==0) {
//Same loop
continue;
}
double N0Distance = EuclideanDistance(LoopA.NTermAtom, LoopB.NTermAtom);
double N1Distance = EuclideanDistance(LoopA.NTermAtomP1, LoopB.NTermAtomP1);
double N2Distance = EuclideanDistance(LoopA.NTermAtomP2, LoopB.NTermAtomP2);
double C0Distance = EuclideanDistance(LoopA.CTermAtom, LoopB.CTermAtom);
double C1Distance = EuclideanDistance(LoopA.CTermAtomP1, LoopB.CTermAtomP1);
double C2Distance = EuclideanDistance(LoopA.CTermAtomP2, LoopB.CTermAtomP2);
//Old
//if (InterPairDistance > LoopCriteria.LoopPairDistanceLowerLimit &&
// InterPairDistance < LoopCriteria.LoopPairDistanceUpperLimit) {
//New
if( N0Distance < LoopCriteria.NNP0DistanceUpper && N0Distance > LoopCriteria.NNP0DistanceLower &&
N1Distance < LoopCriteria.NNP1DistanceUpper && N1Distance > LoopCriteria.NNP1DistanceLower &&
N2Distance < LoopCriteria.NNP2DistanceUpper && N2Distance > LoopCriteria.NNP2DistanceLower &&
C0Distance < LoopCriteria.CCP0DistanceUpper && C0Distance > LoopCriteria.CCP0DistanceLower &&
C1Distance < LoopCriteria.CCP1DistanceUpper && C1Distance > LoopCriteria.CCP1DistanceLower &&
C2Distance < LoopCriteria.CCP2DistanceUpper && C2Distance > LoopCriteria.CCP2DistanceLower) {
Vector3D vector1 = new Vector3D(1, 0, 0);
Vector3D vector2 = new Vector3D(0, 0, 1);
double crossProduct3D;
// crossProduct is equal to 50
crossProduct3D = Vector3D.AngleBetween(LoopA.UnitVector, LoopB.UnitVector);
if (LoopCriteria.RequireLoopsOnSameChain)
{
if (crossProduct3D > LoopCriteria.LoopOrientationAngleLower &&
crossProduct3D < LoopCriteria.LoopOrientationAngleUpper)
{
if (LoopA.Chain == LoopB.Chain)
{
ILoopPair LoopPair = new ILoopPair();
LoopPair.LoopA = LoopA;
LoopPair.LoopB = LoopB;
LoopPairs.Add(LoopPair);
}
}
}
}
}
}
}
//return (LoopPairs);
return CleanupLoopPairs(LoopPairs);
}