public static Barrel runBetaBarrel(string pdb, ref Dictionary <string, AminoAcid> _aaDict, ref Dictionary <Tuple <string, string>, double> partialChargesDict)
{
Directory.SetCurrentDirectory(Global.MONO_DB_DIR);
string PDB = pdb.Substring(0, 4).ToUpper();
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);
}
int chainNum = 0;
int stop = myAtomCat.ChainAtomList.Count();
Console.Write("Protein Class {0}", chainNum);
Protein newProt = new MonoProtein(ref myAtomCat, chainNum, PDB);
Console.Write("creating barrel class..");
Barrel myBarrel = new MonoBarrel(newProt.Chains[0], newProt);
return(myBarrel);
}
public static void run()
{
/*string head = Global.DB_DIR;
* head = "U:\\v5\\pdb_files";
* string tail = ".pdb";
* Console.WriteLine("head: " + head);
* Console.WriteLine("tail: " + tail);
* String[] files = Directory.GetFiles(head);
*/
string fileOfPDBs = "U:/v4/MonoDBList_v4_85.txt";
string[] pdb_files;
List <String> files = new List <String>();
if (File.Exists(fileOfPDBs))
{
using (StreamReader sr = new StreamReader(fileOfPDBs))
{
String line;
while ((line = sr.ReadLine()) != null)
{
files.Add(line);
}
}
}
foreach (String f in files)
{
//Console.Write(f);
Protein m_Protein = null;
Barrel m_Barrel = null;
AtomParser.AtomCategory myAtomCat = new AtomParser.AtomCategory();
////Console.WriteLine("opened {0}", pdbFileName);
try
{
string head = Global.DB_DIR;
string pattern = f + "*";
pdb_files = Directory.GetFiles(head, pattern);
//Console.WriteLine(pdb_files);
string pdb_file = pdb_files[0];
string pdb = f;
myAtomCat = Program.readPdbFile(pdb_file, ref Global.partialChargesDict);
int chainNum = 0;
int stop = myAtomCat.ChainAtomList.Count();
////Console.Write("Protein Class {0}", chainNum);
Console.WriteLine(pdb_file);
m_Protein = new MonoProtein(ref myAtomCat, chainNum, pdb);
////Console.Write("creating barrel class..");
m_Barrel = new MonoBarrel(m_Protein.Chains[0], m_Protein);
SharedFunctions.writePymolScriptForStrands(m_Barrel.Strands, Global.OUTPUT_DIR, Global.DB_DIR, pdb);
}
catch (Exception e)
{
}
}
}
public static void runThisBetaBarrel(string pdb, string method, ref Barrel ThisBarrel, ref Protein newProt)
{
string PDB = pdb.Substring(0, 4).ToUpper();
string pdbFileName = Global.DB_DIR + pdb + ".pdb";
if (File.Exists(pdbFileName))
{
AtomParser.AtomCategory myAtomCat = new AtomParser.AtomCategory();
//Console.WriteLine("opened {0}", pdbFileName);
myAtomCat = Program.ReadPdbFile(pdbFileName, ref Global.partialChargesDict);
Console.WriteLine("\nAttempting {0}", pdb);
// use poly method
if ("poly" == method)
{
try
{
Console.WriteLine("Generating poly protein");
Poly.PolyProtein newPolyProt = new Poly.PolyProtein(ref myAtomCat, pdb);
Console.WriteLine("Generating poly barrel");
ThisBarrel = new Poly.PolyBarrel(ref newPolyProt);
newProt = newPolyProt;
}
catch
{
Console.WriteLine("Failed to run {0} using the poly methods\n", pdb);
}
}
// use all method
else if ("all" == method)
{
try //if (File.Exists(pdbFileName))
{
Console.WriteLine("all method for protein...");
newProt = new AllProtein(ref myAtomCat, PDB);
Console.WriteLine("all method for barrel...");
ThisBarrel = new AllBarrel(ref newProt);
}
catch
{
Console.WriteLine("Failed to run {0} using the all methods\n", pdb);
}
}
// default to mono method
else //if ("mono" == method)
{
try
{
Console.WriteLine("Generating mono protein");
newProt = new MonoProtein(ref myAtomCat, 0, PDB);
Console.WriteLine("Generating mono barrel");
ThisBarrel = new MonoBarrel(newProt.Chains[0], newProt);
}
catch
{
Console.WriteLine("Failed to run {0} using the mono methods\n", pdb);
}
}
}
else
{
Console.WriteLine("could not find {0}", pdbFileName);
}
}
