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); } }