Package org.biojava.bio.structure.server
Class PrepareMMcifIndexFile
- java.lang.Object
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- org.biojava.bio.structure.server.PrepareIndexFile
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- org.biojava.bio.structure.server.PrepareMMcifIndexFile
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public class PrepareMMcifIndexFile extends PrepareIndexFile
A class to index all files in a PDB installation- Since:
- 1.7
- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static java.util.logging.Logger
logger
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Constructor Summary
Constructors Constructor Description PrepareMMcifIndexFile()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 DBSearchjava.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 org.biojava.bio.structure.server.PrepareIndexFile
createPDBInfoList, getAllPDB, logPDBInfoFile
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Method Detail
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main
public static void main(java.lang.String[] args)
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getAllMMcif
public java.io.File[] getAllMMcif(java.io.File dir)
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prepareIndexFileForInstallation
public void prepareIndexFileForInstallation(FlatFileInstallation installation) throws java.io.FileNotFoundException, java.io.IOException
prepare the index file for this installation- Overrides:
prepareIndexFileForInstallation
in classPrepareIndexFile
- Parameters:
installation
-- Throws:
java.io.FileNotFoundException
java.io.IOException
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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
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