Class DownloadChemCompProvider
java.lang.Object
org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
- All Implemented Interfaces:
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
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionvoid
Checks if the chemical components already have been installed into the PDB directory.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
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 Details
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CHEM_COMP_CACHE_DIRECTORY
- See Also:
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SERVER_LOCATION
- See Also:
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Constructor Details
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DownloadChemCompProvider
public DownloadChemCompProvider() -
DownloadChemCompProvider
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Method Details
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getPath
Get this provider's cache path- Returns:
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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. -
getChemComp
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
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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