Exemplo n.º 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;
        }
Exemplo n.º 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;
        }
Exemplo n.º 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();
        }
Exemplo n.º 4
0
        public override void Run(DCDFile dcd)
        {
            DCDReader                dcdReader = new DCDReader(null);
            string                   modelName = null;
            int                      counter   = 0;
            string                   fileName;
            StreamWriter             wr;
            PDBFiles                 pdbs      = new PDBFiles();
            Dictionary <string, int> modelList = null;

            fileName = GetProfileFileName(dcd);

            if (File.Exists(fileName))
            {
                modelList = CheckFile(dcd);

                wr = File.AppendText(fileName);
            }
            else
            {
                wr = new StreamWriter(fileName);
            }

            if (wr == null)
            {
                throw new Exception("Cannot open file: " + fileName);
            }

            dcdReader.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
            bool cont = true;

            do
            {
                MemoryStream mStream = new MemoryStream();
                StreamWriter write   = new StreamWriter(mStream);
                cont = dcdReader.ReadAndSavePDB(write);

                modelName = "Model" + counter++;
                if (modelList == null || modelList.ContainsKey(modelName))
                {
                    continue;
                }

                mStream.Position = 0;
                if (this.GetType() == typeof(ContactProfile))
                {
                    pdbs.AddPDB(mStream, PDBMODE.ALL_ATOMS, modelName);
                }
                else
                {
                    pdbs.AddPDB(mStream, PDBMODE.ONLY_CA, modelName);
                }
                if (pdbs.molDic.ContainsKey(modelName))
                {
                    MakeProfiles(modelName, pdbs.molDic[modelName], wr);
                }
            }while (cont);

            dcdReader.FinishDCDReading();

            wr.Close();
        }