Java AdapterToStructureData类代码示例

import org.rcsb.mmtf.encoder.AdapterToStructureData; //导入依赖的package包/类
/**
 * Adds bonds between groups to the reduced data structure.
 * @param full full representation of structure
 * @param reduced reduced representation of structure
 * @param atomMap maps original atom indices to atom indices in the reduced structures
 */
private static void addInterGroupBonds(StructureDataInterface full, AdapterToStructureData reduced, Map<Integer, Integer> atomMap) {

	for (int i = 0; i < full.getInterGroupBondOrders().length; i++) {
		int bondIndOne = full.getInterGroupBondIndices()[i*2];
		int bondIndTwo = full.getInterGroupBondIndices()[i*2+1];
		int bondOrder = full.getInterGroupBondOrders()[i];
		
		// some atoms may not exist in the reduced structure. 
		// check the atom map to see if both atoms of a bond still exist.
		Integer indexOne = atomMap.get(bondIndOne);
		
		if (indexOne != null) {
			Integer indexTwo = atomMap.get(bondIndTwo);
			if (indexTwo != null) {
				reduced.setInterGroupBond(indexOne, indexTwo, bondOrder);
			}
		}
	}
}
 

import org.rcsb.mmtf.encoder.AdapterToStructureData; //导入依赖的package包/类
/**
 * Test that we can round trip a simple structure.
 * @throws IOException an error reading the file
 * @throws StructureException an error parsing the structure
 */
@Test
public void testRoundTrip() throws IOException, StructureException {
	AtomCache cache = new AtomCache();
	cache.setUseMmCif(true);
	ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());
	
	
	StructureIO.setAtomCache(cache);
	Structure structure = StructureIO.getStructure("4CUP");
	AdapterToStructureData writerToEncoder = new AdapterToStructureData();
	new MmtfStructureWriter(structure, writerToEncoder);
	MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
	new StructureDataToAdapter(writerToEncoder, mmtfStructureReader);
	assertTrue(checkIfAtomsSame(structure,mmtfStructureReader.getStructure()));
}
 

import org.rcsb.mmtf.encoder.AdapterToStructureData; //导入依赖的package包/类
/**
 * Write a Structure object to a file.
 * @param structure the Structure to write
 * @param path the file to write
 * @throws IOException
 */
public static void writeToFile(Structure structure, Path path) throws IOException {
	// Set up this writer
	AdapterToStructureData writerToEncoder = new AdapterToStructureData();
	// Get the writer - this is what people implement
	new MmtfStructureWriter(structure, writerToEncoder);
	// Now write this data to file
	WriterUtils.writeDataToFile(writerToEncoder, path);
}
 

import org.rcsb.mmtf.encoder.AdapterToStructureData; //导入依赖的package包/类
/**
 * Write a Structure object to an {@link OutputStream}
 * @param structure the Structure to write
 * @param outputStream the {@link OutputStream} to write to
 * @throws IOException an error transferring the byte[]
 */
public static void writeToOutputStream(Structure structure, OutputStream outputStream) throws IOException{
	// Set up this writer
	AdapterToStructureData writerToEncoder = new AdapterToStructureData();
	// Get the writer - this is what people implement
	new MmtfStructureWriter(structure, writerToEncoder);
	// Now write this data to file
	byte[] outputBytes = WriterUtils.getDataAsByteArr(writerToEncoder);
	outputStream.write(outputBytes,0,outputBytes.length);
}
 

import org.rcsb.mmtf.encoder.AdapterToStructureData; //导入依赖的package包/类
/**
 * Get a {@link StructureDataInterface} from a Biojava {@link Structure}.
 * @param structure the input structure to covnert
 * @return the {@link StructureDataInterface} of the Biojava {@link Structure}
 */
public static StructureDataInterface convertToStructDataInt(Structure structure) {
	AdapterToStructureData writerToEncoder = new AdapterToStructureData();
	new MmtfStructureWriter(structure, writerToEncoder);
	return writerToEncoder;
}
 

import org.rcsb.mmtf.encoder.AdapterToStructureData; //导入依赖的package包/类
private static MmtfStructure encodeStructure(Structure structure) {
	AdapterToStructureData inflatorToGet = new AdapterToStructureData();
	new MmtfStructureWriter(structure, inflatorToGet);
	MmtfStructure mmtfStructure = new GenericEncoder(inflatorToGet).getMmtfEncodedStructure();
	return mmtfStructure;
}