/* ** Will run a user defined PDB through barrelEllipse, createing ** PDBs and CGOs helpful for determining if a successful betaBarrel ** was created by the program */ static public void testEllipseSinglePDB() { Stopwatch stopWatch = new Stopwatch(); string elapsedTime; TimeSpan ts; Console.WriteLine("Enter pdb:"); string pdb = Console.ReadLine(); string IN_FILE = Global.DB_DIR + pdb + ".pdb"; OUTPUT_PATH = Global.OUTPUT_DIR + "ellipse/"; SharedFunctions.create_dir(Global.OUTPUT_DIR + "ellipse"); stopWatch.Start(); if (File.Exists(IN_FILE)) { ts = stopWatch.Elapsed; elapsedTime = String.Format("{0:00}:{1:00}:{2:00}.{3:00}", ts.Hours, ts.Minutes, ts.Seconds, ts.Milliseconds / 10); Console.WriteLine("RunTime " + elapsedTime); BarrelEllipse newBarrel = new BarrelEllipse(pdb); } else { Console.WriteLine("I am in {0}", System.IO.Directory.GetCurrentDirectory()); Console.WriteLine("could not open {0}", IN_FILE); Console.ReadLine(); } ts = stopWatch.Elapsed; elapsedTime = String.Format("{0:00}:{1:00}:{2:00}.{3:00}", ts.Hours, ts.Minutes, ts.Seconds, ts.Milliseconds / 10); Console.WriteLine("RunTime " + elapsedTime); }
static void Main(string[] args) { DateTime startTime = DateTime.Now; string choice = ""; while (choice != "10") { menu(); choice = Console.ReadLine(); switch (choice) { case "1": BarrelEllipse.testEllipseSinglePDB(); break; case "2": BarrelEllipse.runEllipseData(); break; case "3": Data.getData(); break; case "4": AlignPDB testAlign = new AlignPDB(); break; case "5": run(); break; case "6": break; case "7": break; case "8": break; case "9": PDBInfo testInfo = new PDBInfo(); break; default: //10. Quit choice = "10"; break; } } Console.WriteLine("Program took from: \n start: {0} \n end: {1}", startTime, DateTime.Now); return; }
/* ** */ static public void runEllipseData() { Stopwatch stopWatch = new Stopwatch(); string elapsedTime; TimeSpan ts; string file; Console.WriteLine("Mono or Poly?(m/p)"); string input = Console.ReadLine(); if (input == "m") { DB_FILE = Global.MACMONODBDIR; OUTPUT_PATH = Global.MONO_OUTPUT_DIR + "ellipse\\"; } else { DB_FILE = Global.MACPOLYDBDIR; OUTPUT_PATH = Global.POLY_OUTPUT_DIR + "ellipse\\"; } stopWatch.Start(); file = OUTPUT_PATH + "ELLIPSE_RESULTS.txt"; using (System.IO.StreamWriter output = new System.IO.StreamWriter(file)) { output.Write("\tProtein:\tAngle Between Ellipsis\tTop Eccentricity:\tBottom Eccentricity:\tTop Deviation:\tBottom Deviation:"); } if (File.Exists(DB_FILE)) { using (StreamReader sr = new StreamReader(DB_FILE)) { String line; while ((line = sr.ReadLine()) != null) { string[] splitLine = line.Split(new char[] { ' ', '\t', ',' }); string pdb = splitLine[0]; ts = stopWatch.Elapsed; elapsedTime = String.Format("{0:00}:{1:00}:{2:00}.{3:00}", ts.Hours, ts.Minutes, ts.Seconds, ts.Milliseconds / 10); Console.WriteLine("RunTime " + elapsedTime); BarrelEllipse newBarrel = new BarrelEllipse(pdb); newBarrel.EllipseResults(pdb); } } } else { Console.WriteLine("I am in {0}", System.IO.Directory.GetCurrentDirectory()); Console.WriteLine("could not open {0}", DB_FILE); Console.ReadLine(); } ts = stopWatch.Elapsed; elapsedTime = String.Format("{0:00}:{1:00}:{2:00}.{3:00}", ts.Hours, ts.Minutes, ts.Seconds, ts.Milliseconds / 10); Console.WriteLine("RunTime " + elapsedTime); }
static void Main(string[] args) { DateTime startTime = DateTime.Now; string choice = ""; while (choice != "7") { menu(); choice = Console.ReadLine(); switch (choice) { case "1": RunPolarBearal(); break; case "2": CreateBetaBarrelProtein(); break; case "3": startSolubleBarrel(); break; case "4": startPolyBarrel(); break; case "5": BarrelEllipse.testEllipseSinglePDB(); break; } } Console.WriteLine("Program took from: \n start: {0} \n end: {1}", startTime, DateTime.Now); return; }
static public void run_HighLowData() { Console.WriteLine("Starting highLowRes"); string file = @"highLowRes.txt"; using (System.IO.StreamWriter output = new System.IO.StreamWriter(Global.OUTPUT_DIR + file)) { output.Write("\n{0}\t{1}\t{2}\t{3}\t{4}\t{5}", "pdb", "StrandNum", "ThreeLetCode", "ResNum", "Z", "high/low"); } string fileOfPDBs = Global.DB_file; //input file with list of monomeric xml files if (File.Exists(fileOfPDBs)) { using (StreamReader sr = new StreamReader(fileOfPDBs)) { String line; while ((line = sr.ReadLine()) != null) { string[] splitLine = Array.FindAll <string>(((string)line).Split( new char[] { ' ', '\t', ',' }), delegate(string s) { return(!String.IsNullOrEmpty(s)); }); string pdb = splitLine[0]; if (pdb != "IDs") { Console.WriteLine("running {0}", pdb); //string fileName = pdb.Substring(0, 4).ToUpper(); BarrelEllipse newBarrel = new BarrelEllipse(pdb); } } } } else { Console.WriteLine("could not open {0}", fileOfPDBs); Console.ReadLine(); } }
static void Main(string[] args) { DateTime startTime = DateTime.Now; //using (StreamWriter log = File.AppendText(Global.OUTPUT_DIR + "log.txt")) //{ // log.WriteLine("working with db ({0})", DateTime.Now); // //log.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", "PdbName", "Success", "barrelType", "chainID", "numberOfStrands"); //} string choice = ""; string method_input = "3"; string use_method = "all"; while (choice != "10") { Display_menu(); choice = Console.ReadLine(); switch (choice) { case "1": // Test B-Barrel: check if a specific PDB can have its barrel read in and works BarrelStructures.Protein _protein = null; BarrelStructures.Barrel _barrel = null; Console.WriteLine("Enter pdb:"); string PDBid = Console.ReadLine(); Console.WriteLine("Enter method (1=mono, 2=poly, default=all):"); method_input = Console.ReadLine(); use_method = "all"; if (method_input == "1") { use_method = "mono"; } if (method_input == "2") { use_method = "poly"; } Console.WriteLine("Attempting to run {0} with {1} code. Output will be in \n{2}", PDBid, use_method, Global.OUTPUT_DIR); // change method from mono depending on wht method you want to use runThisBetaBarrel(PDBid, use_method, ref _barrel, ref _protein); break; case "2": BarrelEllipse.testEllipseSinglePDB(); //BarrelEllipse.runEllipseData(); break; case "3": Global.change_dataset(); Console.WriteLine("Using dataset in the file: {0}", Global.DB_file); Console.WriteLine("Reading input files from: {0}", Global.DB_DIR); Console.WriteLine("Writing output files to: {0}", Global.OUTPUT_DIR); using (StreamWriter log = File.AppendText(Global.OUTPUT_DIR + "log.txt")) log.WriteLine("working with db ({0})", DateTime.Now); break; case "4": //AlignPDB testAlign = new AlignPDB(); break; case "5": PolarBearal.RunPolarBearal(); break; case "6": Console.WriteLine("This has not been checked in a bit. Proceed with caution"); Console.WriteLine("Enter method (1=mono, 2=poly, default=all):"); method_input = Console.ReadLine(); use_method = "all"; if (method_input == "1") { use_method = "mono"; } if (method_input == "2") { use_method = "poly"; } Console.WriteLine("Using {1} code. Output will be in \n{2}", use_method, Global.OUTPUT_DIR); SharedFunctions.RunCbeta2Axis(use_method); break; case "7": Console.WriteLine("This has not been checked in a bit. Proceed with caution"); Console.WriteLine("Enter method (1=mono, 2=poly, default=all):"); method_input = Console.ReadLine(); use_method = "all"; if (method_input == "1") { use_method = "mono"; } if (method_input == "2") { use_method = "poly"; } Console.WriteLine("Using {1} code. Output will be in \n{2}", use_method, Global.OUTPUT_DIR); SharedFunctions.run_Centroids(use_method); break; case "8": Console.WriteLine("This has not been checked in a bit. Proceed with caution"); BarrelEllipse.run_HighLowData(); break; case "9": PDBInfo testInfo = new PDBInfo(); break; default: using (StreamWriter log = File.AppendText(Global.OUTPUT_DIR + "log.txt")) { log.WriteLine("ended program at {0} \n\n", DateTime.Now); } //10. Quit choice = "10"; break; } } Console.WriteLine("Program took from: \n start: {0} \n end: {1}", startTime, DateTime.Now); return; }