float maxResolution = 3.0f;
float maxRfree = 0.3f;
StructureDataRDD structureData = new StructureDataRDD("/path/to/file")
			.filterResolution(maxResolution)
			.filterRfree(maxRfree);

Map<String, Long> elementCountMap = BiojavaSparkUtils.findAtoms(structureData).countByElement();

Double mean = BiojavaSparkUtils.findContacts(structureData,
		new AtomSelectObject()
				.groupNameList(new String[] {"PRO","LYS"})
				.elementNameList(new String[] {"C"})
				.atomNameList(new String[] {"CA"}),
				cutoff)
		.getDistanceDistOfAtomInts("CA", "CA")
		.mean();
System.out.println("\nMean PRO-LYS CA-CA distance: " + mean);