Package demo

Class DemoChangeChemCompProvider

java.lang.Object
demo.DemoChangeChemCompProvider
public class DemoChangeChemCompProvider extends Object
This demo shows how to use an alternative ChemCompProvider. The default mechanism in BioJava is to access chemical components by using the DownloadChemCompProvider. It fetches and locally caches chemical component definitions as they are encountered during file parsing. It can be enabled by using the FileParsingParameters#setLoadChemCompInfo(boolean) method. The AllChemCompProvider downloads and unpacks all chemcomps. It is slower and requires more memory than the default DownloadChemCompProvider, but it avoids network access to the FTP site, if a new chemcomp is detected, that has not been downloaded yet. Since all chemcomps will be kept in memory, the standard memory that is available to a JVM will not be sufficient in order to run this demo. Please start with -Xmx200M
Author:
Andreas Prlic

  • Constructor Details

    • DemoChangeChemCompProvider

      public DemoChangeChemCompProvider()

  • Method Details

    • main

      public static void main(String[] args)

    • basicLoad

      public void basicLoad(PDBFileReader reader, boolean loadChemComp, String pdbId)