protected void InitMeasure(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null) { base.InitMeasure(dcd, alignFile, flag, refJuryProfile); DCDReader readDCD = new DCDReader(dcd); pdbs = new PDBFiles(); readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile); int counter = 0; bool cont = true; do { MemoryStream mStream = new MemoryStream(); StreamWriter wStream = new StreamWriter(mStream); cont = readDCD.ReadAndSavePDB(wStream); string name = "Model" + counter++; mStream.Position = 0; pdbs.AddPDB(mStream, allAtoms, name); }while(cont); readDCD.FinishDCDReading(); pdbs.FindReferenceSeq(); pdbs.MakeAlignment(alignFile); structNames = CheckAvailableStructures(); atomDic = pdbs.MakeAllAtomsDic(); }
protected void InitMeasure(string dirName, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null) { base.InitMeasure(dirName, alignFile, flag, refJuryProfile); pdbs = new PDBFiles(); string[] files; if (dirSettings.extension == null) { files = Directory.GetFiles(dirName); } else { files = Directory.GetFiles(dirName, dirSettings.extension); } if (files.Length == 0) { throw new Exception("In selected directory " + dirName + " there are no files with extesion " + dirSettings.extension); } maxV = files.Length; string refSeqFile = dirName + ".ref"; pdbs.ReadRefSeq(refSeqFile); currentV = 0; pdbs.AddPDB(files, allAtoms, ref currentV); if (pdbs.molDic.Keys.Count == 0) { throw new Exception("Non pdb files correctly read"); } pdbs.FindReferenceSeq(); pdbs.MakeAlignment(alignFile); structNames = CheckAvailableStructures(); order = true; atomDic = pdbs.MakeAllAtomsDic(); }
protected void InitMeasure(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null) { base.InitMeasure(fileNames, alignFile, flag, refJuryProfile); dirSettings.Load(); pdbs = new PDBFiles(); maxV = fileNames.Count; currentV = 0; pdbs.AddPDB(fileNames, allAtoms, ref currentV); if (pdbs.molDic.Keys.Count == 0) { throw new Exception("Unable to read pdb data!!"); } pdbs.FindReferenceSeq(); if (pdbs.molDic.Count == 0) { throw new Exception("All pdb structures have been removed. No Data!"); } pdbs.MakeAlignment(null); structNames = CheckAvailableStructures(); order = true; atomDic = pdbs.MakeAllAtomsDic(); }