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 PDB File");
PrimaryStructure primaryStructure = PDBStructureParser.GetPrimaryStructure(inputFilePath + inputFileName);
// dump structure to PDB file. Can check this file against the original input file for equivalence
string tmpFileName = tmpFilePath + @"tempStructure.pdb";
PDBStructureCreator pdbCreator = new PDBStructureCreator(primaryStructure, null);
pdbCreator.CreatePDBFile(tmpFileName, true, true);
// FileUtil.DeleteFile(tmpFileName);
}
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");
//}
}
}