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 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 SecondaryStructure GetSecondaryStructure(string inputFilePath, string strideExePath)
{
StrideAnalysis stride = new StrideAnalysis(strideExePath);
return(stride.GetSecondaryStructure(inputFilePath));
}