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 |
static java.util.logging.Logger |
logger
|
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
logger
public static java.util.logging.Logger logger
PrepareMMcifIndexFile
public PrepareMMcifIndexFile()
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