public class PrepareIndexFile extends Object
Constructor and Description |
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PrepareIndexFile() |
Modifier and Type | Method and Description |
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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
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File[] |
getAllPDB(File dir)
get all PDBfiles from a directory
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protected void |
logPDBInfoFile(PrintWriter pdbWriter,
PrintWriter chainWriter,
StructureIOFile pdbreader,
File[] pdbfiles) |
static void |
main(String[] args) |
void |
prepareIndexFileForInstallation(FlatFileInstallation installation)
prepare the index file for this installation
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public static void main(String[] args)
public void prepareIndexFileForInstallation(FlatFileInstallation installation) throws FileNotFoundException, IOException
installation
- FileNotFoundException
IOException
public void createPDBInfoList(File[] pdbfiles, File outputFile, File chainInfoFile) throws FileNotFoundException, IOException
pdbfiles
- outputFile
- FileNotFoundException
IOException
protected void logPDBInfoFile(PrintWriter pdbWriter, PrintWriter chainWriter, StructureIOFile pdbreader, File[] pdbfiles) throws IOException
IOException