Package org.biojava.nbio.structure.chem

Class AllChemCompProvider

java.lang.Object

org.biojava.nbio.structure.chem.AllChemCompProvider

All Implemented Interfaces:

Runnable, ChemCompProvider

public class AllChemCompProvider
extends Object
implements ChemCompProvider, Runnable

A ChemComp provider that downloads and caches the components.cif file from the wwPDB site. It then loads all chemical components at startup and keeps them in memory. This provider is not used as a default since it is slower at startup and requires more memory than the DownloadChemCompProvider that is used by default.

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field	Description
static final String	COMPONENTS_FILE_LOCATION

Constructor Summary

Constructors

Constructor	Description
AllChemCompProvider()

Method Summary

Modifier and Type	Method	Description
static void	downloadFile()	Downloads the components.cif.gz file from the wwPDB site.
ChemComp	getChemComp(String recordName)	Returns a new instance of a chemical component definition.
void	run()	Do the actual loading of the dictionary in a thread.

Methods inherited from class java.lang.Object

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

Field Details

COMPONENTS_FILE_LOCATION

public static final String COMPONENTS_FILE_LOCATION

See Also:

• Constant Field Values

Constructor Details

AllChemCompProvider

public AllChemCompProvider()

Method Details

downloadFile

public static void downloadFile()
                         throws IOException

Downloads the components.cif.gz file from the wwPDB site.

Throws:

IOException

getChemComp

public ChemComp getChemComp(String recordName)

Returns a new instance of a chemical component definition.

Specified by:

getChemComp in interface ChemCompProvider

Parameters:

recordName - the ID of the ChemComp

Returns:

a new ChemComp definition.

run

public void run()

Do the actual loading of the dictionary in a thread.

Specified by:

run in interface Runnable