code: private void makeCompounds(List<String> compoundList,
  			List<String> sourceList) {
  		//		System.out.println("[makeCompounds] making compounds from compoundLines");
  
  		for (String line : compoundList) {
  			if (compoundList.indexOf(line) + 1 == compoundList.size()) {
  				//				System.out.println("[makeCompounds] Final line in compoundLines.");
  				isLastCompndLine = true;
  			}
  			pdb_COMPND_Handler(line);
  
  		}
  		//		System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
  		// since we're starting again from the first compound, reset it here
  		if ( entities.size() == 0){
  			current_compound = new EntityInfo();
  		} else {
  			current_compound = entities.get(0);
  		}
  		for (String line : sourceList) {
  			if (sourceList.indexOf(line) + 1 == sourceList.size()) {
  				//				System.out.println("[makeCompounds] Final line in sourceLines.");
  				isLastSourceLine = true;
  			}
  			pdb_SOURCE_Handler(line);
  		}
  
  	}
docs: This is the new method for building the COMPND and SOURCE records. Now each method is self-contained.
  @author Jules Jacobsen
  @param  compoundList
  @param  sourceList