public class PrepareIndexFile
extends java.lang.Object
Constructor and Description |
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PrepareIndexFile() |
Modifier and Type | Method and Description |
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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
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java.io.File[] |
getAllPDB(java.io.File dir)
get all PDBfiles from a directory
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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
|
public static void main(java.lang.String[] args)
public void prepareIndexFileForInstallation(FlatFileInstallation installation) throws java.io.FileNotFoundException, java.io.IOException
installation
- java.io.FileNotFoundException
java.io.IOException
public void createPDBInfoList(java.io.File[] pdbfiles, java.io.File outputFile, java.io.File chainInfoFile) throws java.io.FileNotFoundException, java.io.IOException
pdbfiles
- outputFile
- java.io.FileNotFoundException
java.io.IOException
protected void logPDBInfoFile(java.io.PrintWriter pdbWriter, java.io.PrintWriter chainWriter, StructureIOFile pdbreader, java.io.File[] pdbfiles) throws java.io.IOException
java.io.IOException
public java.io.File[] getAllPDB(java.io.File dir)
dir
- the directory that contains all PDB files