Package org.biojava.bio.structure.server
Class PrepareIndexFile
- java.lang.Object
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- org.biojava.bio.structure.server.PrepareIndexFile
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- Direct Known Subclasses:
PrepareMMcifIndexFile
public class PrepareIndexFile extends java.lang.Object
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Constructor Summary
Constructors Constructor Description PrepareIndexFile()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 DBSearchjava.io.File[]
getAllPDB(java.io.File dir)
get all PDBfiles from a directoryprotected 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
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Method Detail
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main
public static void main(java.lang.String[] args)
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prepareIndexFileForInstallation
public void prepareIndexFileForInstallation(FlatFileInstallation installation) throws java.io.FileNotFoundException, java.io.IOException
prepare the index file for this installation- Parameters:
installation
-- Throws:
java.io.FileNotFoundException
java.io.IOException
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createPDBInfoList
public void createPDBInfoList(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
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logPDBInfoFile
protected void logPDBInfoFile(java.io.PrintWriter pdbWriter, java.io.PrintWriter chainWriter, StructureIOFile pdbreader, java.io.File[] pdbfiles) throws java.io.IOException
- Throws:
java.io.IOException
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getAllPDB
public java.io.File[] getAllPDB(java.io.File dir)
get all PDBfiles from a directory- Parameters:
dir
- the directory that contains all PDB files- Returns:
- an array of PDB Files
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