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()
{
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);
}
}
}
}
