Package org.biojava.nbio.structure.chem

Class DownloadChemCompProvider

java.lang.Object

org.biojava.nbio.structure.chem.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	Description
static String	CHEM_COMP_CACHE_DIRECTORY
static String	DEFAULT_CHEMCOMP_PATHURL_TEMPLATE
static String	DEFAULT_SERVER_URL
static String	serverBaseUrl	The base URL to which the full path specified via setChemCompPathUrlTemplate(String) is appended.

Constructor Summary

Constructors

Constructor	Description
DownloadChemCompProvider()
DownloadChemCompProvider(String cacheFilePath)

Method Summary

Modifier and Type	Method	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
static File	getPath()	Get this provider's cache path
boolean	isDownloadAll()	By default this provider will download only some of the ChemComp files.
static void	setChemCompPathUrlTemplate(String chemCompPathUrlTemplate)	Set the path to append to the serverBaseUrl (settable in setServerBaseUrl(String)).
void	setDownloadAll(boolean downloadAll)	By default this provider will download only some of the ChemComp files.
static void	setServerBaseUrl(String serverBaseUrl)	Set the base URL for the location of all chemical component CIF files, to which the chemCompPathUrlTemplate is appended, settable in setChemCompPathUrlTemplate(String).

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 final String CHEM_COMP_CACHE_DIRECTORY

See Also:

Constant Field Values

DEFAULT_SERVER_URL

public static final String DEFAULT_SERVER_URL

See Also:

Constant Field Values

DEFAULT_CHEMCOMP_PATHURL_TEMPLATE

public static final String DEFAULT_CHEMCOMP_PATHURL_TEMPLATE

See Also:

Constant Field Values

serverBaseUrl

public static String serverBaseUrl

The base URL to which the full path specified via setChemCompPathUrlTemplate(String) is appended. It is assumed that it has a trailing slash.

Constructor Detail

DownloadChemCompProvider

public DownloadChemCompProvider()

DownloadChemCompProvider

public DownloadChemCompProvider(String cacheFilePath)

Method Detail

setServerBaseUrl

public static void setServerBaseUrl(String serverBaseUrl)

Set the base URL for the location of all chemical component CIF files, to which the chemCompPathUrlTemplate is appended, settable in setChemCompPathUrlTemplate(String). A trailing slash is appended if not present.

setChemCompPathUrlTemplate

public static void setChemCompPathUrlTemplate(String chemCompPathUrlTemplate)

Set the path to append to the serverBaseUrl (settable in setServerBaseUrl(String)). The string can contain placeholders that will be expanded at runtime:

"{ccd_id}" to be replaced by the chemical component identifier, in capitals "{ccd_id:beginIndex-endIndex}" to be replaced by a substring of the chemical component identifier in capitals, with indices following the same convention as String.substring(int, int) "{ccd_id:index}" to be replaced by a substring of the chemical component identifier in capitals, with index either a positive or negative integer to substring from left or right of the string respectively. If any of the indices are off-bounds, then the full chemical component identifier is replaced

getPath

public static File getPath()

Get this provider's cache path

Returns:

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

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:

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