org.biojava.bio.structure.io.mmcif

Class DownloadChemCompProvider

java.lang.Object

org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider

All Implemented Interfaces:

ChemCompProvider

public class DownloadChemCompProvider
extends Object
implements ChemCompProvider

This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site. It is the default way to access these definitions. If this provider is called he first time, it will download and install all chemical component definitions in a local directory. Once the definition files have been installed, it has quick startup time and low memory requirements. An alternative provider, that keeps all definitions in memory is the AllChemCompProvider. Another provider, that does not require any network access, but only can support a limited set of chemical component definitions, is the ReducedChemCompProvider.

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static String	CHEM_COMP_CACHE_DIRECTORY

Constructor Summary

Constructors

Constructor and Description
DownloadChemCompProvider()

Method Summary

Methods

Modifier and Type	Method and Description
void	checkDoFirstInstall() checks if the chemical components already have been installed into the PDB directory.
ChemComp	getChemComp(String recordName) Loads the definitions for this ChemComp from a local file and instantiates a new object.
static String	getLocalFileName(String recordName) Returns the file name that contains the definition for this ChemComp
boolean	isDownloadAll() By default this provider will download only some of the ChemComp files.
void	setDownloadAll(boolean downloadAll) By default this provider will download only some of the ChemComp files.
static void	setPath(String p) making sure we use the same path for the PDB installation as is used by the PdbFileReader

Methods inherited from class java.lang.Object

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

Field Detail

CHEM_COMP_CACHE_DIRECTORY

public static String CHEM_COMP_CACHE_DIRECTORY

Constructor Detail

DownloadChemCompProvider

public DownloadChemCompProvider()

Method Detail

checkDoFirstInstall

public void checkDoFirstInstall()

checks if the chemical components already have been installed into the PDB directory. If not, will download the chemical components definitions file and split it up into small subfiles.

getChemComp

public ChemComp getChemComp(String recordName)

Loads the definitions for this ChemComp from a local file and instantiates a new object.

Specified by:

getChemComp in interface ChemCompProvider

Parameters:

recordName - the ID of the ChemComp

Returns:

a new ChemComp definition.

getLocalFileName

public static String getLocalFileName(String recordName)

Returns the file name that contains the definition for this ChemComp

Parameters:

recordName - the ID of the ChemComp

Returns:

full path to the file

setPath

public static void setPath(String p)

making sure we use the same path for the PDB installation as is used by the PdbFileReader

Parameters:

p - path to PDB files.

isDownloadAll

public boolean isDownloadAll()

By default this provider will download only some of the ChemComp files. The user has to request that all files should be downloaded by setting this parameter to true.

Returns:

flag if the all components should be downloaded and installed at startup. (default: false)

setDownloadAll

public void setDownloadAll(boolean downloadAll)

By default this provider will download only some of the ChemComp files. The user has to request that all files should be downloaded by setting this parameter to true.

Parameters:

flag - if the all components should be downloaded and installed at startup. (default: false)