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 void AddStructureInformation(int residueIndex, SecondaryStructureInfomation structure) { if (secondaryStructure.ContainsKey(residueIndex)) { secondaryStructure[residueIndex] = structure; } else { secondaryStructure.Add(residueIndex, structure); } }
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); }