/*
** 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;
}