static public void startPolyBarrel()
{
//for making barrel
Dictionary <string, int> pdbBeta = new Dictionary <string, int>();
//PDBIDs that will be run
string fileOfPDBs = Global.POLY_DB_DIR + "PolyDBList.txt"; //input file with list of polymeric xml files
if (File.Exists(fileOfPDBs))
{
using (StreamReader sr = new StreamReader(fileOfPDBs))
{
String line;
string fileLocation2 = Global.POLY_OUTPUT_DIR + "AllBarrelChar.txt";
using (System.IO.StreamWriter file = new System.IO.StreamWriter(fileLocation2))
{
string newLine = "PDB" + "\t\t" + "Length" + "\t" + "AvgLength" + "\t" + "MinLength" + "\t" + "MaxLength" + "\t" + "Radius" + "\t\t" + "Total Chains" + "\t" + "Total Strands" + "\t" + "Barrel Tilt";
file.WriteLine(newLine);
// Read and display lines from the file until the end of the file is reached.
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")
{
PolyBarrel myBarrel = runPBetaBarrel(pdb, ref Global.AADict);
string char1 = myBarrel.PdbName;
string char2 = myBarrel.Axis.Length.ToString();
string char7 = myBarrel.StrandLength.Average().ToString();
string char8 = myBarrel.StrandLength.Min().ToString();
string char9 = myBarrel.StrandLength.Max().ToString();
string char3 = myBarrel.AvgRadius.ToString();
string char4 = myBarrel.protoBarrel.Count().ToString();
string char5 = myBarrel.Strands.Count().ToString();
string char6 = myBarrel.AvgTilt.ToString();
newLine = char1 + "\t" + char2 + "\t" + char7 + "\t" + char8 + "\t" + char9 + "\t" + char3 + "\t" + char4 + "\t" + char5 + "\t" + char6;
file.WriteLine(newLine);
}
}
}
}
}
else
{
Console.WriteLine("could not open {0}", fileOfPDBs);
Console.ReadLine();
}
}
public static PolyBarrel runPBetaBarrel(string pdb, ref Dictionary <string, AminoAcid> _aaDict)
{
Directory.SetCurrentDirectory(Global.POLY_DB_DIR);
string pdbFileName = pdb + ".pdb";
AtomParser.AtomCategory myAtomCat = new AtomParser.AtomCategory();
if (File.Exists(pdbFileName))
{
Console.WriteLine("opened {0}", pdbFileName);
myAtomCat = readPdbFile(pdbFileName, ref Global.partialChargesDict);
}
PolyProtein newProt = new PolyProtein(ref myAtomCat, pdb); //For considering all chains
Console.WriteLine("creating barrel class..");
PolyBarrel myBarrel = new PolyBarrel(newProt, Global.POLY_OUTPUT_DIR, Global.POLY_DB_DIR);
return(myBarrel);
}
