Exemple #1
0
        public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
            : base(dcd, alignFile, flag, refJuryProfile)
        {
            DCDReader readDCD = new DCDReader(dcd);

            dirSettings.Load();

            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);
            if (pdbs is ErrorBase)
            {
                AddErrors(pdbs.errors);
            }
            opt = new Optimization();

            structNames = CheckAvailableStructures();
            order       = true;
        }
Exemple #2
0
        public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
            : base(dcd, alignFile, flag, refJuryProfile)
        {
            DCDReader readDCD = new DCDReader(dcd);
                dirSettings.Load();
            
            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);
            if(pdbs is ErrorBase)
                AddErrors(pdbs.errors);
            opt = new Optimization();

            structNames = CheckAvailableStructures();
            order = true;
        }
Exemple #3
0
        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();
        }
Exemple #4
0
        public Rmsd(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
            : base(fileNames, alignFile, flag, refJuryProfile)
        {
            dirSettings.Load();
            pdbs = new PDBFiles();

            pdbs.AddPDB(fileNames, allAtoms);
            pdbs.FindReferenceSeq();
            pdbs.MakeAlignment(null);
            opt         = new Optimization();
            structNames = CheckAvailableStructures();
            order       = true;
        }
Exemple #5
0
        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();
        }
Exemple #6
0
        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();
        }
Exemple #7
0
        public Rmsd(string dirName, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null) : base(dirName, alignFile, flag, refJuryProfile)
        {
            dirSettings.Load();
            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);
            }

            string refSeqFile = dirName + ".ref";

            pdbs.ReadRefSeq(refSeqFile);


            pdbs.AddPDB(files, allAtoms);

            if (pdbs.molDic.Keys.Count == 0)
            {
                throw new Exception("Non pdb files correctly read");
            }
            pdbs.FindReferenceSeq();
            pdbs.MakeAlignment(alignFile);
            opt         = new Optimization();
            structNames = CheckAvailableStructures();
            order       = true;
        }
Exemple #8
0
        public Rmsd(string dirName,string alignFile,bool flag,PDBMODE allAtoms,string refJuryProfile=null):base(dirName,alignFile,flag,refJuryProfile)
        {

            dirSettings.Load();
            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);

            string refSeqFile = dirName + ".ref";
            pdbs.ReadRefSeq(refSeqFile);


            pdbs.AddPDB(files, allAtoms);

            if (pdbs.molDic.Keys.Count == 0)
                throw new Exception("Non pdb files correctly read");
            pdbs.FindReferenceSeq();
            pdbs.MakeAlignment(alignFile);
			opt=new Optimization();
            structNames = CheckAvailableStructures();
            order = true;
         }
Exemple #9
0
        public Rmsd(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms,string refJuryProfile=null)
            : base(fileNames, alignFile, flag,refJuryProfile)
        {

            dirSettings.Load();
            pdbs = new PDBFiles();

            pdbs.AddPDB(fileNames, allAtoms);
            pdbs.FindReferenceSeq();
            pdbs.MakeAlignment(null);
            opt = new Optimization();
            structNames = CheckAvailableStructures();
            order = true;
        }
Exemple #10
0
        public override void RunThreads(string fileName)
        {
            List <string> files = CheckFile(fileName);

            if (files.Count == 0)
            {
                return;
            }

            //Task[] runnigTask = new Task[threadNumbers];
            //Task startProg;
            maxV = files.Count * 2;
            ReadPdbs(files);
            if (pdbs.molDic.Count == 0)
            {
                return;
            }
            string aux = Path.GetDirectoryName(files[0]).TrimEnd(Path.DirectorySeparatorChar);

            string refSeqFile = aux + ".ref";

            if (File.Exists(refSeqFile))
            {
                pdbs.ReadRefSeq(refSeqFile);
            }
            else
            {
                pdbs.FindReferenceSeq();
            }
            pdbs.MakeAlignment(null);

            if (contOne == null)
            {
                string molDicKey = "";
                foreach (var item in pdbs.molDic.Keys)
                {
                    molDicKey = item;
                    break;
                }
                int len = pdbs.molDic[molDicKey].indexMol.Length;
                contOne         = new int[len * (len + 1) / 2];
                contact         = new byte[threadNumbers][];
                contactToString = new char [threadNumbers][];

                for (int i = 0; i < threadNumbers; i++)
                {
                    contact[i]         = new byte [len * (len + 1) / 2];
                    contactToString[i] = new char [len * (len + 1)];
                }

                for (int i = 0; i < contOne.Length; i++)
                {
                    contOne[i] = 0;
                }
                for (int i = 0; i < threadNumbers; i++)
                {
                    for (int j = 0; j < contOne.Length; j++)
                    {
                        contact[i][j] = 0;
                    }
                }
            }

            auxFiles = new List <string> [threadNumbers];
            List <string> allFiles = new List <string>(pdbs.molDic.Keys);



            for (int i = 0; i < threadNumbers; i++)
            {
                auxFiles[i] = new List <string>((i + 1) * pdbs.molDic.Count / threadNumbers - i * pdbs.molDic.Count / threadNumbers);
                for (int j = i * allFiles.Count / threadNumbers; j < (i + 1) * allFiles.Count / threadNumbers; j++)
                {
                    auxFiles[i].Add(files[j]);
                }
            }
            for (int i = 0; i < threadNumbers; i++)
            {
                Params p = new Params();
                p.fileName = fileName;
                p.k        = i;

                resetEvents[p.k] = new ManualResetEvent(false);
                ThreadPool.QueueUserWorkItem(new WaitCallback(RunMakeProfiles), (object)p);
            }
            for (int i = 0; i < threadNumbers; i++)
            {
                resetEvents[i].WaitOne();
            }

            //JoinFiles(fileName);

            CuttProfiles(fileName);
            currentProgress = maxV;
        }