private void runDbSearch(AtomCache cache, String searchFile,
			String outputFile,int useNrCPUs, StartupParameters params) throws ConfigurationException {


		System.out.println("will use " + useNrCPUs + " CPUs.");

		PDBFileReader reader = new PDBFileReader();
		Structure structure1 = null ;
		try {
			structure1 = reader.getStructure(searchFile);
		} catch (IOException e) {
			throw new ConfigurationException("could not parse as PDB file: " + searchFile);
		}

		File searchF = new File(searchFile);
		String name1 = "CUSTOM";



		StructureAlignment algorithm =  getAlgorithm();

		MultiThreadedDBSearch dbSearch = new MultiThreadedDBSearch(name1,
				structure1,
				outputFile,
				algorithm,
				useNrCPUs,
				params.isDomainSplit());

		dbSearch.setCustomFile1(searchF.getAbsolutePath());

		dbSearch.run();


	}
private void runDbSearch ( AtomCache cache , String searchFile , String outputFile , int useNrCPUs , StartupParameters params ) throws ConfigurationException { System . out . println ( "will use " + useNrCPUs + " CPUs." ) ; PDBFileReader reader = new PDBFileReader ( ) ; Structure structure1 = null ; try { structure1 = reader . getStructure ( searchFile ) ; } catch ( IOException e ) { throw new ConfigurationException ( "could not parse as PDB file: " + searchFile ) ; } File searchF = new File ( searchFile ) ; String name1 = "CUSTOM" ; StructureAlignment algorithm = getAlgorithm ( ) ; MultiThreadedDBSearch dbSearch = new MultiThreadedDBSearch ( name1 , structure1 , outputFile , algorithm , useNrCPUs , params . isDomainSplit ( ) ) ; dbSearch . setCustomFile1 ( searchF . getAbsolutePath ( ) ) ; dbSearch . run ( ) ; }
Do a DB search with the input file against representative PDB domains

@param cache
@param searchFile
@param outputFile
@throws ConfigurationException