org.biojava.bio.structure.server
Class PrepareIndexFile
java.lang.Object
org.biojava.bio.structure.server.PrepareIndexFile
- Direct Known Subclasses:
- PrepareMMcifIndexFile
public class PrepareIndexFile
- extends Object
Method Summary |
void |
createPDBInfoList(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[] |
getAllPDB(File dir)
get all PDBfiles from a directory |
protected void |
logPDBInfoFile(PrintWriter pdbWriter,
PrintWriter chainWriter,
StructureIOFile pdbreader,
File[] pdbfiles)
|
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 |
PrepareIndexFile
public PrepareIndexFile()
prepareIndexFileForInstallation
public void prepareIndexFileForInstallation(FlatFileInstallation installation)
throws FileNotFoundException,
IOException
- prepare the index file for this installation
- Parameters:
installation
-
- Throws:
FileNotFoundException
IOException
createPDBInfoList
public void createPDBInfoList(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
logPDBInfoFile
protected void logPDBInfoFile(PrintWriter pdbWriter,
PrintWriter chainWriter,
StructureIOFile pdbreader,
File[] pdbfiles)
throws IOException
- Throws:
IOException
getAllPDB
public File[] getAllPDB(File dir)
- get all PDBfiles from a directory
- Parameters:
dir
- the directory that contains all PDB files
- Returns:
- an array of PDB Files