Class PrepareIndexFile

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void createPDBInfoList​(java.io.File[] pdbfiles, java.io.File outputFile, java.io.File chainInfoFile)
      parses a set of PDB files and writes info into a file the file is tab separated and has the following columns: name length resolution depositionDate modificationDate technique title classification filename binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup This method needs to be run, before a DBSearch can be performed, since the files created by this method are required for the DBSearch
      java.io.File[] getAllPDB​(java.io.File dir)
      get all PDBfiles from a directory
      protected void logPDBInfoFile​(java.io.PrintWriter pdbWriter, java.io.PrintWriter chainWriter, StructureIOFile pdbreader, java.io.File[] pdbfiles)  
      static void main​(java.lang.String[] args)  
      void prepareIndexFileForInstallation​(FlatFileInstallation installation)
      prepare the index file for this installation
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • PrepareIndexFile

        public PrepareIndexFile()
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
      • prepareIndexFileForInstallation

        public void prepareIndexFileForInstallation​(FlatFileInstallation installation)
                                             throws java.io.FileNotFoundException,
                                                    java.io.IOException
        prepare the index file for this installation
        Parameters:
        installation -
        Throws:
        java.io.FileNotFoundException
        java.io.IOException
      • createPDBInfoList

        public void createPDBInfoList​(java.io.File[] pdbfiles,
                                      java.io.File outputFile,
                                      java.io.File chainInfoFile)
                               throws java.io.FileNotFoundException,
                                      java.io.IOException
        parses a set of PDB files and writes info into a file the file is tab separated and has the following columns: name length resolution depositionDate modificationDate technique title classification filename binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup This method needs to be run, before a DBSearch can be performed, since the files created by this method are required for the DBSearch
        Parameters:
        pdbfiles -
        outputFile -
        Throws:
        java.io.FileNotFoundException
        java.io.IOException
      • logPDBInfoFile

        protected void logPDBInfoFile​(java.io.PrintWriter pdbWriter,
                                      java.io.PrintWriter chainWriter,
                                      StructureIOFile pdbreader,
                                      java.io.File[] pdbfiles)
                               throws java.io.IOException
        Throws:
        java.io.IOException
      • getAllPDB

        public java.io.File[] getAllPDB​(java.io.File dir)
        get all PDBfiles from a directory
        Parameters:
        dir - the directory that contains all PDB files
        Returns:
        an array of PDB Files