Package org.biojava.nbio.structure.chem

Class ZipChemCompProvider

java.lang.Object

org.biojava.nbio.structure.chem.ZipChemCompProvider

All Implemented Interfaces:

ChemCompProvider

public class ZipChemCompProvider
extends Object
implements ChemCompProvider

This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction. If the archive does not contain the record, an attempt is made to download it using DownloadChemCompProvider. The downloaded file is then added to the archive. The class is thread-safe and the same ZipChemCompProvider should be used by all threads to prevent simultaneous read or write to the zip archive. A zip archive will be created if missing.

Since:

12/05/12 updated 3/5/2016 for Java 7 ZipFileSystem

Author:

edlunde, larsonm

Constructor Summary

Constructors

Constructor	Description
ZipChemCompProvider(String chemicalComponentDictionaryFile, String tempDir)	ZipChemCompProvider is a Chemical Component provider that stores chemical components in a zip archive.

Method Summary

Modifier and Type	Method	Description
ChemComp	getChemComp(String recordName)	(non-Javadoc)
static void	purgeTempFiles(String tempdir)	Cleanup chemical component (.cif.gz) files downloaded to tmpdir.
void	setRemoveCif(boolean doRemove)	Remove downloaded .cif.gz after adding to zip archive?

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ZipChemCompProvider

public ZipChemCompProvider(String chemicalComponentDictionaryFile,
                           String tempDir)
                    throws IOException

ZipChemCompProvider is a Chemical Component provider that stores chemical components in a zip archive. Missing chemical components are downloaded and appended to the archive. If non-existent a new zip archive will be created.

Parameters:

chemicalComponentDictionaryFile - : path to zip archive for chemical components.

tempDir - : path for temporary directory, (null) defaults to path in property "java.io.tmpdir".

Throws:

IOException

Method Detail

setRemoveCif

public void setRemoveCif(boolean doRemove)

Remove downloaded .cif.gz after adding to zip archive? Default is true.

Parameters:

doRemove -

getChemComp

public ChemComp getChemComp(String recordName)

(non-Javadoc)

Specified by:

getChemComp in interface ChemCompProvider

Parameters:

recordName - : three letter PDB name for a residue

Returns:

ChemComp from .zip or ChemComp from repository. Will return empty ChemComp when unable to find a residue and will return null if not provided a valid recordName.

See Also:

ChemCompProvider.getChemComp(java.lang.String)

purgeTempFiles

public static void purgeTempFiles(String tempdir)

Cleanup chemical component (.cif.gz) files downloaded to tmpdir.

Parameters:

tempdir - : path to temporary directory for chemical components