Class PrepareMMcifIndexFile


  • public class PrepareMMcifIndexFile
    extends PrepareIndexFile
    A class to index all files in a PDB installation
    Since:
    1.7
    Author:
    Andreas Prlic
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.util.logging.Logger logger  
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void createMMcifInfoList​(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[] getAllMMcif​(java.io.File dir)  
      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
    • Field Detail

      • logger

        public static java.util.logging.Logger logger
    • Constructor Detail

      • PrepareMMcifIndexFile

        public PrepareMMcifIndexFile()
    • Method Detail

      • main

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

        public java.io.File[] getAllMMcif​(java.io.File dir)
      • prepareIndexFileForInstallation

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

        public void createMMcifInfoList​(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