Package org.biojava.nbio.structure.io.mmcif

Class DownloadChemCompProvider

  • All Implemented Interfaces:
    ChemCompProvider
    public class DownloadChemCompProvider
extends java.lang.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 Detail

      • CHEM_COMP_CACHE_DIRECTORY

        public static final java.lang.String CHEM_COMP_CACHE_DIRECTORY
        See Also:
        Constant Field Values

    • Constructor Detail

      • DownloadChemCompProvider

        public DownloadChemCompProvider()

      • DownloadChemCompProvider

        public DownloadChemCompProvider​(java.lang.String cacheFilePath)

    • Method Detail

      • getPath

        public static java.io.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​(java.lang.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 java.lang.String getLocalFileName​(java.lang.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:
        flag - if the all components should be downloaded and installed at startup. (default: false)