org.biojava.bio.structure.server

Class PrepareMMcifIndexFile

java.lang.Object

org.biojava.bio.structure.server.PrepareIndexFile

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

Fields

Modifier and Type	Field and Description
static Logger	logger

Constructor Summary

Constructors

Constructor and Description
PrepareMMcifIndexFile()

Method Summary

Methods

Modifier and Type	Method and Description
void	createMMcifInfoList(File[] pdbfiles, File outputFile, 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
File[]	getAllMMcif(File dir)
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 Logger logger

Constructor Detail

PrepareMMcifIndexFile

public PrepareMMcifIndexFile()

Method Detail

getAllMMcif

public File[] getAllMMcif(File dir)

prepareIndexFileForInstallation

public void prepareIndexFileForInstallation(FlatFileInstallation installation)
                                     throws FileNotFoundException,
                                            IOException

prepare the index file for this installation

Overrides:

prepareIndexFileForInstallation in class PrepareIndexFile

Parameters:

installation -

Throws:

FileNotFoundException

IOException

createMMcifInfoList

public void createMMcifInfoList(File[] pdbfiles,
                       File outputFile,
                       File chainInfoFile)
                         throws FileNotFoundException,
                                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:

FileNotFoundException

IOException