How to use

MmtfStructure

in

org.rcsb.mmtf.dataholders

public MmtfStructure create(ObjectTree tree) {
  MmtfStructure s = new MmtfStructure();
  s.setxCoordList(tree.getByteArray("xCoordList"));
  s.setyCoordList(tree.getByteArray("yCoordList"));
  s.setzCoordList(tree.getByteArray("zCoordList"));
  s.setbFactorList(tree.getByteArray("bFactorList"));
  s.setOccupancyList(tree.getByteArray("occupancyList"));
  s.setNumAtoms(tree.getInt("numAtoms"));
  s.setAtomIdList(tree.getByteArray("atomIdList"));
  s.setAltLocList(tree.getByteArray("altLocList"));
  s.setInsCodeList(tree.getByteArray("insCodeList"));
  s.setGroupIdList(tree.getByteArray("groupIdList"));
  s.setGroupList(createGroupList(tree.getObjectArray("groupList")));
  s.setSequenceIndexList(tree.getByteArray("sequenceIndexList"));
  s.setGroupTypeList(tree.getByteArray("groupTypeList"));
  s.setChainNameList(tree.getByteArray("chainNameList"));
  s.setChainIdList(tree.getByteArray("chainIdList"));
  s.setNumBonds(tree.getInt("numBonds"));
  s.setBondAtomList(tree.getByteArray("bondAtomList"));
  s.setBondOrderList(tree.getByteArray("bondOrderList"));
  s.setSecStructList(tree.getByteArray("secStructList"));
  s.setChainsPerModel(tree.getIntArray("chainsPerModel"));
  s.setGroupsPerChain(tree.getIntArray("groupsPerChain"));
  s.setSpaceGroup(tree.getString("spaceGroup"));
  s.setUnitCell(tree.getFloatArray("unitCell"));
  s.setBioAssemblyList(createBioAssemblyList(tree.getObjectArray("bioAssemblyList")));
  s.setMmtfVersion(tree.getString("mmtfVersion"));
  s.setMmtfProducer(tree.getString("mmtfProducer"));
  s.setEntityList(createEntityList(tree.getObjectArray("entityList")));
  s.setStructureId(tree.getString("structureId"));

cartnX = FloatCodecs.decodeArr(inputData.getxCoordList());
cartnY = FloatCodecs.decodeArr(inputData.getyCoordList());
cartnZ = FloatCodecs.decodeArr(inputData.getzCoordList());
bFactor = FloatCodecs.decodeArr(inputData.getbFactorList());
occupancy = FloatCodecs.decodeArr(inputData.getOccupancyList());
atomId = IntCodecs.decodeArr(inputData.getAtomIdList());
altId = CharCodecs.decodeArr(inputData.getAltLocList());
insertionCodeList = CharCodecs.decodeArr(inputData.getInsCodeList());
groupNum = IntCodecs.decodeArr(inputData.getGroupIdList());
groupMap = inputData.getGroupList();
seqResGroupList = IntCodecs.decodeArr(inputData.getSequenceIndexList());
groupList = IntCodecs.decodeArr(inputData.getGroupTypeList());
publicChainIds = StringCodecs.decodeArr(inputData.getChainNameList());
chainList =  StringCodecs.decodeArr(inputData.getChainIdList());
interGroupBondIndices = IntCodecs.decodeArr(inputData.getBondAtomList());
interGroupBondOrders = IntCodecs.decodeArr(inputData.getBondOrderList());
secStructInfo = IntCodecs.decodeArr(inputData.getSecStructList());
chainsPerModel = inputData.getChainsPerModel();
groupsPerChain = inputData.getGroupsPerChain();
spaceGroup = inputData.getSpaceGroup();
unitCell = inputData.getUnitCell();

groupList = ArrayConverters.convertFourByteToIntegers(inputData.getGroupTypeList());
            ArrayConverters.convertTwoByteToIntegers(inputData.getxCoordSmall()),
            ArrayConverters.convertFourByteToIntegers(inputData.getxCoordBig()))),
    MmtfStructure.COORD_DIVIDER);
cartnY = ArrayConverters.convertIntsToFloats(
    ArrayDecoders.deltaDecode(
        ArrayConverters.combineIntegers(
            ArrayConverters.convertTwoByteToIntegers(inputData.getyCoordSmall()),
            ArrayConverters.convertFourByteToIntegers(inputData.getyCoordBig()))),
    MmtfStructure.COORD_DIVIDER);
cartnZ = ArrayConverters.convertIntsToFloats(
    ArrayDecoders.deltaDecode(
        ArrayConverters.combineIntegers(
            ArrayConverters.convertTwoByteToIntegers(inputData.getzCoordSmall()),
            ArrayConverters.convertFourByteToIntegers(inputData.getzCoordBig()))),
    MmtfStructure.COORD_DIVIDER);
bFactor = ArrayConverters.convertIntsToFloats(
    ArrayDecoders.deltaDecode(
        ArrayConverters.combineIntegers(
            ArrayConverters.convertTwoByteToIntegers(inputData.getbFactorSmall()),
            ArrayConverters.convertFourByteToIntegers(inputData.getbFactorBig()))),
    MmtfStructure.OCCUPANCY_BFACTOR_DIVIDER);
        ArrayConverters.convertFourByteToIntegers(inputData.getOccupancyList())), 
    MmtfStructure.OCCUPANCY_BFACTOR_DIVIDER);
        ArrayConverters.convertFourByteToIntegers(inputData.getAtomIdList())));

private void encode(StructureDataInterface structureDataInterface) {
  mmtfBean = new MmtfStructure();
  mmtfBean.setxCoordList(EncoderUtils.encodeByteArr(FloatCodecs.INT_DELTA_RECURSIVE,structureDataInterface.getxCoords(),coordDivider));
  mmtfBean.setyCoordList(EncoderUtils.encodeByteArr(FloatCodecs.INT_DELTA_RECURSIVE,structureDataInterface.getyCoords(),coordDivider));
  mmtfBean.setzCoordList(EncoderUtils.encodeByteArr(FloatCodecs.INT_DELTA_RECURSIVE,structureDataInterface.getzCoords(),coordDivider));
  mmtfBean.setbFactorList(EncoderUtils.encodeByteArr(FloatCodecs.INT_DELTA_RECURSIVE,structureDataInterface.getbFactors(),bfactorOccDivider));
  mmtfBean.setOccupancyList(EncoderUtils.encodeByteArr(FloatCodecs.INT_RUNLENGTH,structureDataInterface.getOccupancies(),bfactorOccDivider));
  mmtfBean.setAtomIdList(EncoderUtils.encodeByteArr(IntCodecs.RUN_LENGTH_DELTA,structureDataInterface.getAtomIds(),EncoderUtils.NULL_PARAM));
  mmtfBean.setAltLocList(EncoderUtils.encodeByteArr(CharCodecs.RUN_LENGTH,structureDataInterface.getAltLocIds(),EncoderUtils.NULL_PARAM));
  mmtfBean.setInsCodeList(EncoderUtils.encodeByteArr(CharCodecs.RUN_LENGTH,structureDataInterface.getInsCodes(),EncoderUtils.NULL_PARAM));
  mmtfBean.setGroupIdList(EncoderUtils.encodeByteArr(IntCodecs.RUN_LENGTH_DELTA,structureDataInterface.getGroupIds(),EncoderUtils.NULL_PARAM));
  mmtfBean.setSequenceIndexList(EncoderUtils.encodeByteArr(IntCodecs.RUN_LENGTH_DELTA,structureDataInterface.getGroupSequenceIndices(),EncoderUtils.NULL_PARAM));
  mmtfBean.setChainNameList(EncoderUtils.encodeByteArr(StringCodecs.ENCOODE_CHAINS,structureDataInterface.getChainNames(),MmtfStructure.CHAIN_LENGTH));
  mmtfBean.setChainIdList(EncoderUtils.encodeByteArr(StringCodecs.ENCOODE_CHAINS,structureDataInterface.getChainIds(),MmtfStructure.CHAIN_LENGTH));
  mmtfBean.setBondAtomList(EncoderUtils.encodeByteArr(IntCodecs.CONVERT_4_BYTE,structureDataInterface.getInterGroupBondIndices(),EncoderUtils.NULL_PARAM));
  mmtfBean.setGroupTypeList(EncoderUtils.encodeByteArr(IntCodecs.CONVERT_4_BYTE,structureDataInterface.getGroupTypeIndices(),EncoderUtils.NULL_PARAM));
  mmtfBean.setSecStructList(EncoderUtils.encodeByteArr(IntCodecs.CONVERT_BYTE,structureDataInterface.getSecStructList(),EncoderUtils.NULL_PARAM));
  mmtfBean.setBondOrderList(EncoderUtils.encodeByteArr(IntCodecs.CONVERT_BYTE,structureDataInterface.getInterGroupBondOrders(),EncoderUtils.NULL_PARAM));
  mmtfBean.setGroupList(EncoderUtils.generateGroupList(structureDataInterface));