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 Summary

Constructors

Constructor	Description
DemoChangeChemCompProvider()

Method Summary

Modifier and Type	Method	Description
void	basicLoad(PDBFileReader reader, boolean loadChemComp, String pdbId)
static void	main(String[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DemoChangeChemCompProvider

public DemoChangeChemCompProvider()

Method Detail

main

public static void main(String[] args)

basicLoad

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