org.biojava.bio.structure.server
Class PrepareMMcifIndexFile

java.lang.Object
  extended by org.biojava.bio.structure.server.PrepareIndexFile
      extended by org.biojava.bio.structure.server.PrepareMMcifIndexFile

public class PrepareMMcifIndexFile
extends PrepareIndexFile

A class to index all files in a PDB installation

Since:
1.7
Author:
Andreas Prlic

Field Summary
static java.util.logging.Logger logger
           
 
Constructor Summary
PrepareMMcifIndexFile()
           
 
Method Summary
 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 org.biojava.bio.structure.server.PrepareIndexFile
createPDBInfoList, getAllPDB, logPDBInfoFile
 
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