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

Class AllChemCompProvider

java.lang.Object
org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
All Implemented Interfaces:
Runnable, ChemCompProvider
public class AllChemCompProvider extends Object implements ChemCompProvider, Runnable
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site. It then loads all chemical components at startup and keeps them in memory. This provider is not used as a default since it is slower at startup and requires more memory than the DownloadChemCompProvider that is used by default.
Author:
Andreas Prlic

  • Field Details

  • Constructor Details

    • AllChemCompProvider

      public AllChemCompProvider()

  • Method Details

    • downloadFile

      public static void downloadFile() throws IOException
      Downloads the components.cif.gz file from the wwPDB site.
      Throws:
      IOException

    • getChemComp

      public ChemComp getChemComp(String recordName)
      Returns a new instance of a chemical component definition.
      Specified by:
      getChemComp in interface ChemCompProvider
      Parameters:
      recordName - the ID of the ChemComp
      Returns:
      a new ChemComp definition.

    • run

      public void run()
      Do the actual loading of the dictionary in a thread.
      Specified by:
      run in interface Runnable