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"); //} } }