Class DownloadChemCompProvider
- java.lang.Object
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- org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
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- 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 theAllChemCompProvider
. Another provider, that does not require any network access, but only can support a limited set of chemical component definitions, is theReducedChemCompProvider
.- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static String
CHEM_COMP_CACHE_DIRECTORY
static String
DEFAULT_SERVER_URL
static String
serverBaseUrl
static boolean
useDefaultUrlLayout
Use default RCSB server layout (true) or internal RCSB server layout (false)
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Constructor Summary
Constructors Constructor Description DownloadChemCompProvider()
DownloadChemCompProvider(String cacheFilePath)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 thisChemComp
from a local file and instantiates a new object.static String
getLocalFileName(String recordName)
Returns the file name that contains the definition for thisChemComp
static File
getPath()
Get this provider's cache pathboolean
isDownloadAll()
By default this provider will download only some of theChemComp
files.void
setDownloadAll(boolean downloadAll)
By default this provider will download only some of theChemComp
files.
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Field Detail
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CHEM_COMP_CACHE_DIRECTORY
public static final String CHEM_COMP_CACHE_DIRECTORY
- See Also:
- Constant Field Values
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DEFAULT_SERVER_URL
public static final String DEFAULT_SERVER_URL
- See Also:
- Constant Field Values
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serverBaseUrl
public static String serverBaseUrl
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useDefaultUrlLayout
public static boolean useDefaultUrlLayout
Use default RCSB server layout (true) or internal RCSB server layout (false)
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Constructor Detail
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DownloadChemCompProvider
public DownloadChemCompProvider()
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DownloadChemCompProvider
public DownloadChemCompProvider(String cacheFilePath)
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Method Detail
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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.
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getChemComp
public ChemComp getChemComp(String recordName)
Loads the definitions for thisChemComp
from a local file and instantiates a new object.- Specified by:
getChemComp
in interfaceChemCompProvider
- Parameters:
recordName
- the ID of theChemComp
- Returns:
- a new
ChemComp
definition.
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getLocalFileName
public static String getLocalFileName(String recordName)
Returns the file name that contains the definition for thisChemComp
- Parameters:
recordName
- the ID of theChemComp
- Returns:
- full path to the file
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isDownloadAll
public boolean isDownloadAll()
By default this provider will download only some of theChemComp
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)
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setDownloadAll
public void setDownloadAll(boolean downloadAll)
By default this provider will download only some of theChemComp
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)
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