org.biojava.bio.structure.server

Class PrepareIndexFile

java.lang.Object

org.biojava.bio.structure.server.PrepareIndexFile

Direct Known Subclasses:

PrepareMMcifIndexFile

public class PrepareIndexFile
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
PrepareIndexFile()

Method Summary

Methods

Modifier and Type	Method and 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