public static void Run() { // get the primary structure Console.WriteLine("Parsing GRO File"); Stopwatch stopWatch = new Stopwatch(); stopWatch.Start(); PrimaryStructure primaryStructure = GROStructureParser.GetStructure(inputFilePath + inputFileName); stopWatch.Stop(); Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]"); // get the structure trajectory int atomCount = XTCTrajectoryParser.GetAtomCount(inputFilePath + trajectoryFileName); if (atomCount == primaryStructure.AtomCount()) { Console.WriteLine("Atom Count matches."); } else { Console.WriteLine("Atom count doesnt match between primary structure and trajectory"); } Stopwatch stopWatch2 = new Stopwatch(); stopWatch2.Start(); PrimaryStructureTrajectory trajectory = XTCTrajectoryParser.GetTrajectory(inputFilePath + trajectoryFileName, 0, 100, 1); stopWatch2.Stop(); Console.WriteLine("Trajectory Parsing Complete [" + stopWatch2.ElapsedMilliseconds + " ms]"); // get the secondary structure for the base primary structure Stopwatch stopWatch3 = new Stopwatch(); stopWatch3.Start(); SecondaryStructure secondaryStructure = SecondaryStructure.CreateFromPrimaryStructure(primaryStructure, strideExePath, tmpFilePath); Console.WriteLine("Main Secondary Structure Parsing Complete [" + stopWatch3.ElapsedMilliseconds + " ms]"); Console.WriteLine(secondaryStructure); // get the secondary structure for a frame of the trajectory Stopwatch stopWatch4 = new Stopwatch(); stopWatch4.Start(); SecondaryStructureTrajectory secondaryStructureTrajectory = new SecondaryStructureTrajectory(primaryStructure, trajectory, strideExePath, tmpFilePath); SecondaryStructure secondaryStructure2 = secondaryStructureTrajectory.GetStructure(50); Console.WriteLine("Secondary Structure Parsing for frame 50 Complete [" + stopWatch3.ElapsedMilliseconds + " ms]"); Console.WriteLine(secondaryStructure2); }
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"); //} } }
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); } } } }