public static SBarrel runSolBarrel(string pdb, ref Dictionary <string, AminoAcid> _aaDict, ref Dictionary <Tuple <string, string>, double> partialChargesDict)
{
Directory.SetCurrentDirectory(Global.SOL_DB_DIR);
string fileName2 = pdb + ".pdb";
Console.WriteLine("opened {0}", fileName2);
AtomParser.AtomCategory myAtomCat = new AtomParser.AtomCategory();
myAtomCat = readPdbFile(fileName2, ref partialChargesDict);
string pdbName = pdb.Substring(0, 4).ToUpper();
int chainNum = 0;
//if (pdbName == "3RFZ" || pdbName == "3KVN") chainNum = 1;
int stop = myAtomCat.ChainAtomList.Count();
Console.Write("Protein Class {0}", chainNum);
Protein newProt = new MonoProtein(ref myAtomCat, chainNum, pdbName);
//Console.WriteLine("ChainNum {0}", chainNum);
Console.Write("creating barrel class..");
SBarrel myBarrel = new SBarrel(newProt.Chains[0], newProt);
return(myBarrel);
}
static public void startSolubleBarrel()
{
//for making barrel
Dictionary <string, int> pdbBeta = new Dictionary <string, int>();
//PDBIDs that will be run
string fileOfPDBs = Global.SOL_DB_DIR + "Thornton1989.txt"; //input file with list of pdb files
if (File.Exists(fileOfPDBs))
{
using (StreamReader sr = new StreamReader(fileOfPDBs))
{
String line;
string fileLocation2 = Global.SOL_OUTPUT_DIR + "AllSolubleChar.txt";
using (System.IO.StreamWriter file = new System.IO.StreamWriter(fileLocation2))
{
string newLine = "PDB" + "\t\t" + "Total Chains" + "\t" + "Total Strands" + "\t" + "Length" + "\t" + "AvgLength" + "\t" + "MinLength" + "\t" + "MaxLength";
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")
{
SBarrel myBarrel = runSolBarrel(pdb, ref Global.AADict, ref Global.partialChargesDict);
/*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 char4 = myBarrel.protoBarrel.Count().ToString();
* string char5 = myBarrel.Strands.Count().ToString();
* newLine = char1 + "\t" + char4 + "\t" + char5 + "\t" + char2 + "\t" + char7 + "\t" + char8 + "\t" + char9 + "\t" + char3 + "\t" + char6;
* file.WriteLine(newLine);*/
}
}
}
}
}
else
{
Console.WriteLine("could not open {0}", fileOfPDBs);
Console.ReadLine();
}
}
