static public void RunBetaBarrelProteinDatabase()
{
string fileOfPDBs = Global.MacmonoDBDir; //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")
{
string fileName = pdb;
PolarBearal polarRetest = new PolarBearal(fileName);
}
}
}
}
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;
}
