public static void Run()
{
Console.WriteLine("Parsing PBD File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure model = PDBStructureParser.GetPrimaryStructure(inputFilePath + inputFileName);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
Console.WriteLine("Atom Count: " + model.Atoms().Count);
Console.WriteLine("Running Stride Analysis");
stopWatch = new Stopwatch();
stopWatch.Start();
StrideAnalysis stride = new StrideAnalysis(exePath);
SecondaryStructure structure = stride.GetSecondaryStructure(inputFilePath + inputFileName);
// Console.WriteLine("Secondary structure:\n\n" + structure);
stopWatch.Stop();
Console.WriteLine("Processing complete [" + stopWatch.ElapsedMilliseconds + " ms]");
Console.WriteLine("End Testing Stride");
foreach (Chain chain in model.Chains())
{
Console.WriteLine("Chain ID: " + chain.ID);
if (chain.ResidueType != StandardResidue.AminoAcid)
{
Console.WriteLine("Not a protein chain");
continue;
}
foreach (Residue residue in chain.MainChainResidues)
{
if (residue.CarbonylOxygen == null)
{
Console.WriteLine("Residue ID: " + residue.ID + " has no oxygen");
}
SecondaryStructureInfomation structureInfo = structure.GetStructureInformation(residue.Index);
if (structureInfo == null)
{
Console.WriteLine("Couldn't find structure info for residue index: " + residue.Index);
}
else
{
Console.WriteLine("Residue [" + residue.ID + "][" + residue.Name + "] has structure [" + structureInfo.ToString() + "] and Alpha Carbon: " + residue.AlphaCarbon);
}
}
}
}
public static void Run()
{
// get the primary structure
Console.WriteLine("Parsing GRO File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure primaryStructure = GROStructureParser.GetStructure(inputFilePath + inputFileName);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
// get the structure trajectory
int atomCount = XTCTrajectoryParser.GetAtomCount(inputFilePath + trajectoryFileName);
if (atomCount == primaryStructure.AtomCount())
{
Console.WriteLine("Atom Count matches.");
}
else
{
Console.WriteLine("Atom count doesnt match between primary structure and trajectory");
}
Stopwatch stopWatch2 = new Stopwatch();
stopWatch2.Start();
PrimaryStructureTrajectory trajectory = XTCTrajectoryParser.GetTrajectory(inputFilePath + trajectoryFileName, 0, 100, 1);
stopWatch2.Stop();
Console.WriteLine("Trajectory Parsing Complete [" + stopWatch2.ElapsedMilliseconds + " ms]");
// get the secondary structure for the base primary structure
Stopwatch stopWatch3 = new Stopwatch();
stopWatch3.Start();
SecondaryStructure secondaryStructure = SecondaryStructure.CreateFromPrimaryStructure(primaryStructure, strideExePath, tmpFilePath);
Console.WriteLine("Main Secondary Structure Parsing Complete [" + stopWatch3.ElapsedMilliseconds + " ms]");
Console.WriteLine(secondaryStructure);
// get the secondary structure for a frame of the trajectory
Stopwatch stopWatch4 = new Stopwatch();
stopWatch4.Start();
SecondaryStructureTrajectory secondaryStructureTrajectory = new SecondaryStructureTrajectory(primaryStructure, trajectory, strideExePath, tmpFilePath);
SecondaryStructure secondaryStructure2 = secondaryStructureTrajectory.GetStructure(50);
Console.WriteLine("Secondary Structure Parsing for frame 50 Complete [" + stopWatch3.ElapsedMilliseconds + " ms]");
Console.WriteLine(secondaryStructure2);
}
public static void Run()
{
Console.WriteLine("Parsing PDB File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure primaryStructure = PDBStructureParser.GetPrimaryStructure(filepath + structureFile);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
stopWatch.Reset();
stopWatch.Start();
SecondaryStructure.CreateFromPrimaryStructure(primaryStructure, strideExePath, tmpFilePath);
Console.WriteLine("Main Secondary Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
foreach (Chain chain in primaryStructure.Chains())
{
foreach (Atom atom in chain.MainChainAtoms)
{
// if no frame number use the base structure coordinates.
if (atom == null)
{
Console.WriteLine("Main chain atom is null");
}
else
{
Console.WriteLine("Atom found: " + atom.ToString());
}
}
//Console.WriteLine("\n---------------------\n");
//Console.WriteLine("Chain ID: " + chain.ID);
//Console.WriteLine("Chain Residue Count: " + chain.Residues.Count);
//if (chain.ResidueType == MolecularDynamics.Definitions.StandardResidue.AminoAcid) {
// foreach (Residue residue in chain.Residues) {
// Console.WriteLine("Residue index: " + residue.Index + ", ResidueID: " + residue.ID + ", Residue Name: " + residue.Name);
// SecondaryStructureInfomation information = secondaryStructure.GetStructureInformation(residue.Index);
// if (information == null) {
// Console.WriteLine("information null: " + residue.Index);
// }
// }
//}
//else {
// Console.WriteLine("Not an amino acid residue");
//}
}
}
public static SecondaryStructure CreateFromPrimaryStructure(PrimaryStructure primaryStructure, string strideExePath, string tmpFilePath)
{
string tmpFileName = tmpFilePath + @"tempStructure.pdb";
PDBStructureCreator pdbCreator = new PDBStructureCreator(primaryStructure, null);
//pdbCreator.CreatePDBFile(tmpFileName, true, true, true);
pdbCreator.CreatePDBFile(tmpFileName);
SecondaryStructure secondaryStructure = null;
try {
StrideAnalysis stride = new StrideAnalysis(strideExePath);
secondaryStructure = stride.GetSecondaryStructure(tmpFileName);
}
finally {
FileUtil.DeleteFile(tmpFileName);
}
return(secondaryStructure);
}
private SecondaryStructure CalculateSecondaryStructure(int frameNumber)
{
string tmpFileName = tmpFilePath + @"tempStructure_" + frameNumber + ".pdb";
PDBStructureCreator pdbCreator = new PDBStructureCreator(primaryStructure, primaryTrajectory.GetFrame(frameNumber));
pdbCreator.CreatePDBFile(tmpFileName, true, true, true);
SecondaryStructure frame = null;
try {
StrideAnalysis stride = new StrideAnalysis(strideExePath);
frame = stride.GetSecondaryStructure(tmpFileName);
}
catch (StrideException ex) {
throw new StrideException(ex.Message);
}
finally {
FileUtil.DeleteFile(tmpFileName);
}
return(frame);
}
public static void Run()
{
Console.WriteLine("Parsing GRO File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure primaryStructure = GROStructureParser.GetStructure(filepath + structureFile);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
stopWatch.Reset();
stopWatch.Start();
SecondaryStructure secondaryStructure = SecondaryStructure.CreateFromPrimaryStructure(primaryStructure, strideExePath, tmpFilePath);
Console.WriteLine("Main Secondary Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
foreach (Chain chain in primaryStructure.Chains())
{
Console.WriteLine("\n---------------------\n");
Console.WriteLine("Chain ID: " + chain.ID);
Console.WriteLine("Chain Residue Count: " + chain.Residues.Count);
foreach (Residue residue in chain.Residues)
{
Console.WriteLine("Residue index: " + residue.Index + ", ResidueID: " + residue.ID + ", Residue Name: " + residue.Name);
SecondaryStructureInfomation information = secondaryStructure.GetStructureInformation(residue.Index);
if (information == null)
{
Console.WriteLine("information null: " + residue.Index);
}
}
}
}
private SecondaryStructure parseStrideOutput(string strideOutput)
{
SecondaryStructure ss = new SecondaryStructure();
using (StringReader reader = new StringReader(strideOutput)) {
string line;
int residueIndex = 0;
while ((line = reader.ReadLine()) != null)
{
// Console.WriteLine("Processing line: [" + line + "]");
if (!line.StartsWith("ASG "))
{
continue;
}
if (int.TryParse(line.Substring(10, 5), out residueIndex))
{
string structureCode = line.Substring(24, 1);
SecondaryStructureType structure;
switch (structureCode)
{
case "G":
structure = SecondaryStructureType.ThreeHelix;
break;
case "H":
structure = SecondaryStructureType.AlphaHelix;
break;
case "I":
structure = SecondaryStructureType.FiveHelix;
break;
case "T":
structure = SecondaryStructureType.Turn;
break;
case "E":
structure = SecondaryStructureType.BetaSheet;
break;
case "B":
structure = SecondaryStructureType.BetaBridge;
break;
case "S":
structure = SecondaryStructureType.Bend;
break;
default:
structure = SecondaryStructureType.Coil;
break;
}
string phi = line.Substring(42, 7);
string psi = line.Substring(52, 7);
SecondaryStructureInfomation information = new SecondaryStructureInfomation();
information.type = structure;
information.phi = float.Parse(phi);
information.psi = float.Parse(psi);
ss.AddStructureInformation(residueIndex, information);
Console.WriteLine("Added structure information for residue index: " + residueIndex);
}
}
}
return(ss);
}
