A B C D E F G H I M N O P R S T U V W

A

AdapterToStructureData - Class in org.rcsb.mmtf.encoder

A class to move data from the StructureAdapterInterface to the StructureDataInterface.

AdapterToStructureData() - Constructor for class org.rcsb.mmtf.encoder.AdapterToStructureData

addEntityInfo(StructureDataInterface, StructureAdapterInterface) - Static method in class org.rcsb.mmtf.decoder.DecoderUtils

Add the entity info to the structure.

addHeaderInfo(StructureDataInterface, StructureAdapterInterface) - Static method in class org.rcsb.mmtf.decoder.DecoderUtils

Add ancilliary header information to the structure.

addInterGroupBonds(StructureDataInterface, StructureAdapterInterface) - Static method in class org.rcsb.mmtf.decoder.DecoderUtils

Generate inter group bonds.

addXtalographicInfo(StructureDataInterface, StructureAdapterInterface) - Static method in class org.rcsb.mmtf.decoder.DecoderUtils

Add the crystallographic data to the structure.

ArrayConverters - Class in org.rcsb.mmtf.codec

Class of functions to convert arrays to readable types.

ArrayConverters() - Constructor for class org.rcsb.mmtf.codec.ArrayConverters

ArrayDecoders - Class in org.rcsb.mmtf.decoder

A class of array decoders.

ArrayDecoders() - Constructor for class org.rcsb.mmtf.decoder.ArrayDecoders

ArrayEncoders - Class in org.rcsb.mmtf.encoder

A class of methods to encode arrays.

ArrayEncoders() - Constructor for class org.rcsb.mmtf.encoder.ArrayEncoders

B

BASE_URL - Static variable in class org.rcsb.mmtf.utils.CodecUtils

The base url for this version of MMTF.

BioAssemblyData - Class in org.rcsb.mmtf.dataholders

Data store for the biological assembly annotation as provided by the PDB.

BioAssemblyData(String) - Constructor for class org.rcsb.mmtf.dataholders.BioAssemblyData

Constructor setting the name and initialising an empty transform list.

BioAssemblyData() - Constructor for class org.rcsb.mmtf.dataholders.BioAssemblyData

Constructor without setting the name.

BioAssemblyTransformation - Class in org.rcsb.mmtf.dataholders

The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.

BioAssemblyTransformation() - Constructor for class org.rcsb.mmtf.dataholders.BioAssemblyTransformation

C

CHAIN_LENGTH - Static variable in class org.rcsb.mmtf.dataholders.MmtfStructure

The number of characters in a chain.

CharCodecInterface - Interface in org.rcsb.mmtf.codec

An interface all char codecs must implement

CharCodecs - Enum in org.rcsb.mmtf.codec

An enum of char codecs.

CodecInterface - Interface in org.rcsb.mmtf.codec

Generic interface for an untyped codec strategy

CodecUtils - Class in org.rcsb.mmtf.utils

A utility class of static methods and constants for the codec project.

CodecUtils() - Constructor for class org.rcsb.mmtf.utils.CodecUtils

combineIntegers(int[], int[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Combine integer arrays.

convertByteToIntegers(byte[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert a byte array containing two bytes to integers in an integer array.

convertCharToIntegers(char[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert a char array to an integer array using the ASCII code for characters

convertFloatsToInts(float[], float) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert an integer array to a float array by multiplying by a float.

convertFourByteToIntegers(byte[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert a byte array containing four bytes to integers in an integer array.

convertIntegersToBytes(int[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert an integer array to byte array, where each integer is encoded by a single byte.

convertIntegersToFourByte(int[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert an integer array to byte array, where each integer is encoded by a four bytes.

convertIntegersToTwoBytes(int[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert an integer array to byte array, where each integer is encoded by a two bytes.

convertIntegerToChar(int[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert an integer array to a char array.

convertIntsToFloats(int[], float) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert an integer array to a float array by dividing by a float.

convertShortsToTwoBytes(short[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert a short array to byte array, where each short is encoded by a two bytes.

convertToIntArray(List<Integer>) - Static method in class org.rcsb.mmtf.utils.CodecUtils

Convert an integer list to an integer array

convertTwoBytesToShorts(byte[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert to byte integers to a short array.

convertTwoByteToIntegers(byte[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert a byte array containing two bytes to integers in an integer array.

COORD_DIVIDER - Static variable in class org.rcsb.mmtf.dataholders.MmtfStructure

The number to divide coordinate int values by.

D

data - Variable in class org.rcsb.mmtf.codec.OptionParser

The byte array of the data without the header.

decode(byte[], int) - Method in interface org.rcsb.mmtf.codec.CharCodecInterface

Decode a byte array to a char array.

decode(byte[], int) - Method in interface org.rcsb.mmtf.codec.FloatCodecInterface

Decode a byte array to a float array.

decode(byte[], int) - Method in interface org.rcsb.mmtf.codec.IntCodecInterface

Decode a byte array to a int array.

decode(byte[], int) - Method in interface org.rcsb.mmtf.codec.StringCodecsInterface

Decode a byte array to a String array.

decodeArr(byte[]) - Static method in enum org.rcsb.mmtf.codec.CharCodecs

Decode a byte array from an input array.

decodeArr(byte[]) - Static method in enum org.rcsb.mmtf.codec.FloatCodecs

Decode a byte array from an input array.

decodeArr(byte[]) - Static method in enum org.rcsb.mmtf.codec.IntCodecs

Decode a byte array from an input array.

decodeArr(byte[]) - Static method in enum org.rcsb.mmtf.codec.StringCodecs

Decode a byte array from an input array.

decodeChainList(byte[], int) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Find all the chain ids from a single byte array.

DecoderUtils - Class in org.rcsb.mmtf.decoder

A class of static functions to be used to aid decoding from StructureDataInterface to StructureAdapterInterface.

DecoderUtils() - Constructor for class org.rcsb.mmtf.decoder.DecoderUtils

deflateGzip(byte[]) - Static method in class org.rcsb.mmtf.decoder.ReaderUtils

Deflate a gzip byte array.

deltaDecode(int[]) - Static method in class org.rcsb.mmtf.decoder.ArrayDecoders

Delta decode an array of integers.

deltaEncode(int[]) - Static method in class org.rcsb.mmtf.encoder.ArrayEncoders

Delta encode an array of integers.

deserialize(InputStream) - Method in class org.rcsb.mmtf.serialization.MessagePackSerialization

deserialize(InputStream) - Method in interface org.rcsb.mmtf.serialization.MmtfStructureSerializationInterface

Deserialize an MmtfStructure from an input stream.

DsspType - Enum in org.rcsb.mmtf.dataholders

The encoding of secondary structure types.

dsspTypeFromInt(int) - Static method in enum org.rcsb.mmtf.dataholders.DsspType

Creates a new DsspType from an int val Returns DsspType.NULL_ENTRY if dsspType is -1 or not one of the supported standard types.

dsspTypeFromString(String) - Static method in enum org.rcsb.mmtf.dataholders.DsspType

Creates a new DsspType from a String value.

E

encode(char[], int) - Method in interface org.rcsb.mmtf.codec.CharCodecInterface

Encode a char array to a byte array.

encode(float[], int) - Method in interface org.rcsb.mmtf.codec.FloatCodecInterface

Encode a float array to a byte array.

encode(int[], int) - Method in interface org.rcsb.mmtf.codec.IntCodecInterface

Encode a int array to a byte array.

encode(String[], int) - Method in interface org.rcsb.mmtf.codec.StringCodecsInterface

Encode a String array to a byte array.

encodeByteArr(FloatCodecs, float[], int) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Method to prepend a byte array with a byte.

encodeByteArr(IntCodecs, int[], int) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Method to prepend a byte array with a byte.

encodeByteArr(CharCodecs, char[], int) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Method to prepend a byte array with a byte.

encodeByteArr(StringCodecs, String[], int) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Method to prepend a byte array with a byte.

encodeChainList(String[], int) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert the chain names to a byte array.

EncoderInterface - Interface in org.rcsb.mmtf.encoder

The interface all encoders must implement.

EncoderUtils - Class in org.rcsb.mmtf.encoder

A class of static utility functions to aid encoding of data.

EncoderUtils() - Constructor for class org.rcsb.mmtf.encoder.EncoderUtils

Entity - Class in org.rcsb.mmtf.dataholders

Entity level data store.

Entity() - Constructor for class org.rcsb.mmtf.dataholders.Entity

equals(Object) - Method in class org.rcsb.mmtf.dataholders.Group

F

finalizeStructure() - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

A generic function to be used at the end of all data addition to do required cleanup on the structure

finalizeStructure() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

FloatCodecInterface - Interface in org.rcsb.mmtf.codec

An interface all float codecs must implement

FloatCodecs - Enum in org.rcsb.mmtf.codec

An enum defining the encoding and decoding strategies.

G

generateBioassemblies(StructureDataInterface) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Find the bioassembly information as a list from the StructureDataInterface.

generateBioAssembly(StructureDataInterface, StructureAdapterInterface) - Static method in class org.rcsb.mmtf.decoder.DecoderUtils

Parses the bioassembly data and inputs it to the structure inflator

generateEntityList(StructureDataInterface) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Generate the entity level information from the StructureDataInterface.

generateGroupList(StructureDataInterface) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Regenerate a group map from the StructureDataInterface.

GenericDecoder - Class in org.rcsb.mmtf.decoder

A genric decoder of MMTF data - that does not hard code the encoding strategy.

GenericDecoder(MmtfStructure) - Constructor for class org.rcsb.mmtf.decoder.GenericDecoder

Constructor for the default decoder.

GenericEncoder - Class in org.rcsb.mmtf.encoder

An encoder for encoding with the generic strategy.

GenericEncoder(StructureDataInterface) - Constructor for class org.rcsb.mmtf.encoder.GenericEncoder

The constructor for the encoder.

GenericEncoder(StructureDataInterface, int) - Constructor for class org.rcsb.mmtf.encoder.GenericEncoder

The constructor for the encoder.

getAltLocIds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of location ids of the atoms.

getAltLocIds() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getAltLocIds() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getAltLocList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the alternate location list.

getAtomIdList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the atom id list.

getAtomIds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of atom serial ids (_atom_site.id in mmCIF dictionary).

getAtomIds() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getAtomIds() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getAtomNameList() - Method in class org.rcsb.mmtf.dataholders.Group

Gets the atom info.

getbFactorList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getbFactors() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the B-factors (temperature factors) of the atoms in Angstroms^2.

getbFactors() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getbFactors() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getBioAssemblyList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the bio assembly.

getBioassemblyName(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the name of the transformation for a bioassembly.

getBioassemblyName(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getBioassemblyName(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getBondAtomList() - Method in class org.rcsb.mmtf.dataholders.Group

Gets the bond indices.

getBondAtomList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the bond atom list.

getBondOrderList() - Method in class org.rcsb.mmtf.dataholders.Group

Gets the bond orders.

getBondOrderList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the bond order list.

getByteArrayFromUrl(String) - Static method in class org.rcsb.mmtf.decoder.ReaderUtils

Get the GZIP compressed and messagepack serialized data from the MMTF servers

getChainIdList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the internal chain list.

getChainIds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of internal chain identifiers (asym_ids in mmCIF dictionary), of length the number of chains (polymeric, non-polymeric and water) in the structure.

getChainIds() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getChainIds() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getChainIndexList() - Method in class org.rcsb.mmtf.dataholders.BioAssemblyTransformation

Gets the indices of the chains this bioassembly refers to.

getChainIndexList() - Method in class org.rcsb.mmtf.dataholders.Entity

Get a list of integers specifying the indices of the chains related to this entity.

getChainIndexListForTransform(int, int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the list of chain indices for the given transformation for the given bioassembly.

getChainIndexListForTransform(int, int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getChainIndexListForTransform(int, int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getChainNameList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the chain names.

getChainNames() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of public chain identifiers (auth_ids in mmCIF dictionary), of length the number of chains (polymeric, non-polymeric and water) in the structure.

getChainNames() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getChainNames() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getChainsPerModel() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the number of chains (polymeric/non-polymeric/water) in each model.

getChainsPerModel() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the number of chains per model.

getChainsPerModel() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getChainsPerModel() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getChemCompType() - Method in class org.rcsb.mmtf.dataholders.Group

Get the chemical component type (in mmCIF as _chem_comp.type).

getCodec(int) - Static method in enum org.rcsb.mmtf.codec.CharCodecs

Get the codec from an input integer.

getCodec(int) - Static method in enum org.rcsb.mmtf.codec.FloatCodecs

Get the codec from an input byte.

getCodec(int) - Static method in enum org.rcsb.mmtf.codec.IntCodecs

Get the codec from an input byte.

getCodec(int) - Static method in enum org.rcsb.mmtf.codec.StringCodecs

Decode a byte array from an input array.

getCodecId() - Method in enum org.rcsb.mmtf.codec.CharCodecs

getCodecId() - Method in interface org.rcsb.mmtf.codec.CodecInterface

getCodecId() - Method in enum org.rcsb.mmtf.codec.FloatCodecs

getCodecId() - Method in enum org.rcsb.mmtf.codec.IntCodecs

getCodecId() - Method in enum org.rcsb.mmtf.codec.StringCodecs

getCodecName() - Method in enum org.rcsb.mmtf.codec.CharCodecs

getCodecName() - Method in interface org.rcsb.mmtf.codec.CodecInterface

getCodecName() - Method in enum org.rcsb.mmtf.codec.FloatCodecs

getCodecName() - Method in enum org.rcsb.mmtf.codec.IntCodecs

getCodecName() - Method in enum org.rcsb.mmtf.codec.StringCodecs

getDataAsByteArr(AdapterToStructureData) - Static method in class org.rcsb.mmtf.encoder.WriterUtils

Function to take data from a writer and return as a byte array (MessagePacked serialized).

getDataFromFile(Path) - Static method in class org.rcsb.mmtf.decoder.ReaderUtils

A function to get MMTF data from a file path.

getDataFromUrl(String) - Static method in class org.rcsb.mmtf.decoder.ReaderUtils

Find the message pack byte array from the web using the input code and a base url.

getDepositionDate() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the deposition date of the structure as a string in ISO time standard format.

getDepositionDate() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getDepositionDate() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getDepositionDate() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getDescription() - Method in class org.rcsb.mmtf.dataholders.Entity

Get the description of the entity.

getDsspIndex() - Method in enum org.rcsb.mmtf.dataholders.DsspType

Returns the index of the Dssp as an integer

getDsspType() - Method in enum org.rcsb.mmtf.dataholders.DsspType

Returns the type of the DSSP as a String

getElementList() - Method in class org.rcsb.mmtf.dataholders.Group

getEntityChainIndexList(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the chain indices for the entity specified by the index.

getEntityChainIndexList(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getEntityChainIndexList(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getEntityDescription(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the entity description (as defined in mmCIF dictionary) for the entity specified by the index.

getEntityDescription(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getEntityDescription(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getEntityList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Get the entity list.

getEntitySequence(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the sequence for the entity specified by the index.

getEntitySequence(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getEntitySequence(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getEntityType(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the entity type (polymer, non-polymer, water) for the entity specified by the index.

getEntityType(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getEntityType(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getExperimentalMethods() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the experimental methods as an array of strings.

getExperimentalMethods() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getExperimentalMethods() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getExperimentalMethods() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getFormalChargeList() - Method in class org.rcsb.mmtf.dataholders.Group

Gets the atom charges.

getGroupAtomCharges(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the atom charges for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupAtomCharges(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupAtomCharges(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupAtomNames(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the atom names (e.g.

getGroupAtomNames(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupAtomNames(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupBondIndices(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the zero-based bond indices (in pairs) for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupBondIndices(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupBondIndices(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupBondOrders(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the bond orders for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupBondOrders(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupBondOrders(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupChemCompType(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the chemical component type for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupChemCompType(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupChemCompType(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupElementNames(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the IUPAC element names (e.g.

getGroupElementNames(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupElementNames(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupIdList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the group num list.

getGroupIds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing residue numbers (auth_seq_id in mmCIF dictionary) for each residue (group).

getGroupIds() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupIds() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the group map.

getGroupName(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the group name for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupName() - Method in class org.rcsb.mmtf.dataholders.Group

Gets the group name.

getGroupName(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupName(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupSequenceIndices() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the indices of groups (residues) in their corresponding sequences, obtainable through StructureDataInterface.getEntitySequence(int).

getGroupSequenceIndices() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupSequenceIndices() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupSingleLetterCode(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the single letter amino acid code or nucleotide code for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupSingleLetterCode(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupSingleLetterCode(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupsPerChain() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the number of groups (residues) in each chain.

getGroupsPerChain() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the number of groups per chain.

getGroupsPerChain() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupsPerChain() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupTypeIndices() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing indices to be used to obtain group level information, e.g.

getGroupTypeIndices() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getGroupTypeIndices() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getGroupTypeList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the group type list.

getHeader() - Method in class org.rcsb.mmtf.codec.OptionParser

Get the header for this option as a byte array.

getInsCodeList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the insertion code list.

getInsCodes() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the insertion codes (pdbx_PDB_ins_code in mmCIF dictionary) for each residue (group).

getInsCodes() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getInsCodes() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getInterGroupBondIndices() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the zero-based bond indices (in pairs) for the structure.

getInterGroupBondIndices() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getInterGroupBondIndices() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getInterGroupBondOrders() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of bond orders (1,2,3) of inter-group bonds with length number of inter-group bonds

getInterGroupBondOrders() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getInterGroupBondOrders() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getMatrix() - Method in class org.rcsb.mmtf.dataholders.BioAssemblyTransformation

Gets the 4x4 matrix transformation specifying a rotation and a translation.

getMatrixForTransform(int, int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns a 4x4 transformation matrix for the given transformation for the given bioassembly.

getMatrixForTransform(int, int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getMatrixForTransform(int, int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getMmtfEncodedStructure() - Method in interface org.rcsb.mmtf.encoder.EncoderInterface

Get the MmtfStructure of encoded data.

getMmtfEncodedStructure() - Method in class org.rcsb.mmtf.encoder.GenericEncoder

getMmtfProducer() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns a string describing the producer of the MMTF file.

getMmtfProducer() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the mmtf producer.

getMmtfProducer() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getMmtfProducer() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getMmtfVersion() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the MMTF version number (from the specification).

getMmtfVersion() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the mmtf version.

getMmtfVersion() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getMmtfVersion() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getName() - Method in class org.rcsb.mmtf.dataholders.BioAssemblyData

getNcsOperatorList() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the NCS operation matrix list.

getNcsOperatorList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getNcsOperatorList() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNcsOperatorList() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumAtoms() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of atoms in the structure.

getNumAtoms() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the num atoms.

getNumAtoms() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumAtoms() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumAtomsInGroup(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of atoms in the group specified in StructureDataInterface.getGroupTypeIndices().

getNumAtomsInGroup(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumAtomsInGroup(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumBioassemblies() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of bioassemblies in this structure.

getNumBioassemblies() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumBioassemblies() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumBonds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the total number of bonds in the structure

getNumBonds() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the num bonds.

getNumBonds() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumBonds() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumChains() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of chains (for all models) in the structure.

getNumChains() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getNumChains() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumChains() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumEntities() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of entities (as defined in mmCIF dictionary) in the structure

getNumEntities() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumEntities() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumGroups() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of groups (residues) in the structure that have experimentally determined 3D coordinates.

getNumGroups() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getNumGroups() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumGroups() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumModels() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of models in the structure.

getNumModels() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getNumModels() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumModels() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getNumTransInBioassembly(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of transformations in a given bioassembly.

getNumTransInBioassembly(int) - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getNumTransInBioassembly(int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getOccupancies() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the occupancy values of the atoms.

getOccupancies() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getOccupancies() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getOccupancyList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the occupancy list - an encoded per atom list of occupancy values.

getReduced(StructureDataInterface) - Static method in class org.rcsb.mmtf.encoder.ReducedEncoder

Get the reduced form of the input StructureDataInterface.

getReleaseDate() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the release date of the structure as a string in ISO time standard format.

getReleaseDate() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getReleaseDate() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getReleaseDate() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getResolution() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the resolution of the dataset.

getResolution() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getResolution() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getResolution() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getRfree() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the Rfree of the dataset.

getrFree() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getRfree() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getRfree() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getRwork() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the Rwork of the dataset.

getrWork() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getRwork() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getRwork() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getSecStructList() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the secondary structure information for the structure as a list of integers

getSecStructList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the sec struct list.

getSecStructList() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getSecStructList() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getSequence() - Method in class org.rcsb.mmtf.dataholders.Entity

Get the sequence of the entity.

getSequenceIndexList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getSingleLetterCode() - Method in class org.rcsb.mmtf.dataholders.Group

Gets the single letter code.

getSpaceGroup() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the space group of the structure.

getSpaceGroup() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the space group.

getSpaceGroup() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getSpaceGroup() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getStructureId() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the identifier of the structure.

getStructureId() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the structure id.

getStructureId() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getStructureId() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getTitle() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the title of the structure.

getTitle() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the title.

getTitle() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getTitle() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getTransformList() - Method in class org.rcsb.mmtf.dataholders.BioAssemblyData

Gets the list of transforms.

getType() - Method in class org.rcsb.mmtf.dataholders.Entity

The type of this Entity, one of: polymer, non-polymer, macrolide or water.

getTypeFromChainId(StructureDataInterface, int) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Get the type of a given chain index.

getUnitCell() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the 6 floats that describe the unit cell.

getUnitCell() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the unit cell.

getUnitCell() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getUnitCell() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getxCoordList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getxCoords() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the X coordinates of the atoms in Angstroms.

getxCoords() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getxCoords() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getyCoordList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getyCoords() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the Y coordinates of the atoms in Angstroms.

getyCoords() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getyCoords() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

getzCoordList() - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

getzCoords() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the Z coordinates of the atoms in Angstroms.

getzCoords() - Method in class org.rcsb.mmtf.decoder.GenericDecoder

getzCoords() - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

Group - Class in org.rcsb.mmtf.dataholders

Group (residue) level data store.

Group() - Constructor for class org.rcsb.mmtf.dataholders.Group

gzipCompress(byte[]) - Static method in class org.rcsb.mmtf.encoder.WriterUtils

Compress a byte array using Gzip.

H

hashCode() - Method in class org.rcsb.mmtf.dataholders.Group

I

initStructure(int, int, int, int, int, String) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Used before any additions to do any required pre-processing.

initStructure(int, int, int, int, int, String) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

IntCodecInterface - Interface in org.rcsb.mmtf.codec

Interface all integer codecs must implement.

IntCodecs - Enum in org.rcsb.mmtf.codec

Codecs for Integer encoding and decoding.

M

MAX_CHARS_PER_CHAIN_ENTRY - Static variable in class org.rcsb.mmtf.utils.CodecUtils

The maximum number of chars in a chain entry.

MessagePackSerialization - Class in org.rcsb.mmtf.serialization

A message pack implementation of the MmtfStructure serializer / deserializer.

MessagePackSerialization() - Constructor for class org.rcsb.mmtf.serialization.MessagePackSerialization

Constructor for the MessagePackSerialization class.

methodNumber - Variable in class org.rcsb.mmtf.codec.OptionParser

The number of the method.

MmtfStructure - Class in org.rcsb.mmtf.dataholders

A class to store the data sent in an MMTF data source.

MmtfStructure() - Constructor for class org.rcsb.mmtf.dataholders.MmtfStructure

Constructor to set the default values for floats

MmtfStructureSerializationInterface - Interface in org.rcsb.mmtf.serialization

An interface to carry out serializing / deserializing to MmtfStructure.

N

NULL_PARAM - Static variable in class org.rcsb.mmtf.encoder.EncoderUtils

The Null parameter for encoding (i.e.

numAtoms - Variable in class org.rcsb.mmtf.encoder.SummaryData

The number of atoms in the structure.

numBonds - Variable in class org.rcsb.mmtf.encoder.SummaryData

The number of bonds in the structure.

numChains - Variable in class org.rcsb.mmtf.encoder.SummaryData

The number of chains in the structure.

numGroups - Variable in class org.rcsb.mmtf.encoder.SummaryData

The number of groups in the structure.

numModels - Variable in class org.rcsb.mmtf.encoder.SummaryData

The number of models in the structure.

O

OCCUPANCY_BFACTOR_DIVIDER - Static variable in class org.rcsb.mmtf.dataholders.MmtfStructure

The number to divide occupancy and bfactor int values by.

OptionParser - Class in org.rcsb.mmtf.codec

Class to parse the options for a given byte[]

OptionParser(byte[]) - Constructor for class org.rcsb.mmtf.codec.OptionParser

Constructor to take the options from the byte array and allow access to the options and the raw data.

OptionParser(Integer, Integer, Integer) - Constructor for class org.rcsb.mmtf.codec.OptionParser

Construct the option header from the input variables.

org.rcsb.mmtf.api - package org.rcsb.mmtf.api

APIs to accessing and passing on the data.

org.rcsb.mmtf.codec - package org.rcsb.mmtf.codec

General encoding and decoding structures.

org.rcsb.mmtf.dataholders - package org.rcsb.mmtf.dataholders

Beans and classes to store data for data transfer.

org.rcsb.mmtf.decoder - package org.rcsb.mmtf.decoder

Decoding structure data from a compressed form.

org.rcsb.mmtf.encoder - package org.rcsb.mmtf.encoder

Encoding structure data to a compressed form.

org.rcsb.mmtf.serialization - package org.rcsb.mmtf.serialization

Serialization and deserialization of data.

org.rcsb.mmtf.utils - package org.rcsb.mmtf.utils

Utility functions and variables for coding and decoding.

outputLength - Variable in class org.rcsb.mmtf.codec.OptionParser

The length of the output array.

P

param - Variable in class org.rcsb.mmtf.codec.OptionParser

The integer encoding the parameter.

R

ReaderUtils - Class in org.rcsb.mmtf.decoder

A class of static utility methods for reading data.

ReaderUtils() - Constructor for class org.rcsb.mmtf.decoder.ReaderUtils

recursiveIndexDecode(int[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Decodes an input array of integers following a Recursive Indexing strategy.

recursiveIndexEncode(int[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Encodes an input array of integers following a Recursive Indexing strategy (uses a reduced alphabet with fixed limits).

ReducedEncoder - Class in org.rcsb.mmtf.encoder

Convert a full format of the file to a reduced format.

ReducedEncoder() - Constructor for class org.rcsb.mmtf.encoder.ReducedEncoder

runlengthDecode(int[]) - Static method in class org.rcsb.mmtf.decoder.ArrayDecoders

Run length decode an array of integers.

runlengthEncode(int[]) - Static method in class org.rcsb.mmtf.encoder.ArrayEncoders

Run length encode an array of integers.

S

serialize(MmtfStructure, OutputStream) - Method in class org.rcsb.mmtf.serialization.MessagePackSerialization

serialize(MmtfStructure, OutputStream) - Method in interface org.rcsb.mmtf.serialization.MmtfStructureSerializationInterface

Serialize an MmtfStructure to a generic output stream.

setAltLocList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the alt label list.

setAtomIdList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the atom id list.

setAtomInfo(String, int, char, float, float, float, float, float, String, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the atom level information for a given atom.

setAtomInfo(String, int, char, float, float, float, float, float, String, int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setAtomNameList(String[]) - Method in class org.rcsb.mmtf.dataholders.Group

Sets the atom info.

setbFactorList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setBioAssemblyList(List<BioAssemblyData>) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the bioassembly information.

setBioAssemblyTrans(int, int[], double[], String) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets a single Bioassembly transformation to a structure.

setBioAssemblyTrans(int, int[], double[], String) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setBondAtomList(int[]) - Method in class org.rcsb.mmtf.dataholders.Group

Sets the bond indices.

setBondAtomList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the bond atom list.

setBondOrderList(int[]) - Method in class org.rcsb.mmtf.dataholders.Group

Sets the bond orders.

setBondOrderList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the bond order list.

setChainIdList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the internal chain list.

setChainIndexList(int[]) - Method in class org.rcsb.mmtf.dataholders.BioAssemblyTransformation

Sets the chain id.

setChainIndexList(int[]) - Method in class org.rcsb.mmtf.dataholders.Entity

Set a list of integers specifying the indices of the chains related to this entity.

setChainInfo(String, String, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the information for a given chain.

setChainInfo(String, String, int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setChainNameList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the chain names.

setChainsPerModel(int[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the number of chains per model.

setChemCompType(String) - Method in class org.rcsb.mmtf.dataholders.Group

setDepositionDate(String) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setDescription(String) - Method in class org.rcsb.mmtf.dataholders.Entity

Set the description of this entity.

setElementList(String[]) - Method in class org.rcsb.mmtf.dataholders.Group

setEntityInfo(int[], String, String, String) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the entity level annotation for a chain(s).

setEntityInfo(int[], String, String, String) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setEntityList(Entity[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Set the entity list.

setExperimentalMethods(String[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setFormalChargeList(int[]) - Method in class org.rcsb.mmtf.dataholders.Group

Sets the atom charges.

setGroupBond(int, int, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets an intra-group bond.

setGroupBond(int, int, int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setGroupIdList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the group num list.

setGroupInfo(String, int, char, String, int, int, char, int, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the information for a given group / residue with atomic data.

setGroupInfo(String, int, char, String, int, int, char, int, int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setGroupList(Group[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the group map.

setGroupName(String) - Method in class org.rcsb.mmtf.dataholders.Group

Sets the group name.

setGroupsPerChain(int[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the number of groups in a chain.

setGroupTypeList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the group type list.

setHeaderInfo(float, float, float, String, String, String, String[]) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the header information.

setHeaderInfo(float, float, float, String, String, String, String[]) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setInsCodeList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the ins code list.

setInterGroupBond(int, int, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets an inter-group bond.

setInterGroupBond(int, int, int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setMatrix(double[]) - Method in class org.rcsb.mmtf.dataholders.BioAssemblyTransformation

Sets the 4x4 matrix transformation specifying a rotation and a translation.

setMmtfProducer(String) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the mmtf producer.

setMmtfVersion(String) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the mmtf version.

setModelInfo(int, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the number of chains for a given model.

setModelInfo(int, int) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setName(String) - Method in class org.rcsb.mmtf.dataholders.BioAssemblyData

setNcsOperatorList(double[][]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setNumAtoms(int) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the num atoms.

setNumBonds(int) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the number of bonds.

setNumChains(int) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setNumGroups(int) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setNumModels(int) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setOccupancyList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the occupancy list - an encoded per atom list of occupancy values.

setReleaseDate(String) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setResolution(float) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setrFree(float) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setrWork(float) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setSecStructList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the sec struct list.

setSequence(String) - Method in class org.rcsb.mmtf.dataholders.Entity

Set the sequence of the entity.

setSequenceIndexList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setSingleLetterCode(char) - Method in class org.rcsb.mmtf.dataholders.Group

Sets the single letter code.

setSpaceGroup(String) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the space group.

setStructureId(String) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the structure id.

setTitle(String) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the title.

setTransformList(List<BioAssemblyTransformation>) - Method in class org.rcsb.mmtf.dataholders.BioAssemblyData

Sets the transforms.

setType(String) - Method in class org.rcsb.mmtf.dataholders.Entity

Set the type of the entity, one of: polymer, non-polymer, macrolide or water.

setUnitCell(float[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

Sets the unit cell.

setxCoordList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setXtalInfo(String, float[], double[][]) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the space group and unit cell information.

setXtalInfo(String, float[], double[][]) - Method in class org.rcsb.mmtf.encoder.AdapterToStructureData

setyCoordList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

setzCoordList(byte[]) - Method in class org.rcsb.mmtf.dataholders.MmtfStructure

splitIntegers(int[]) - Static method in class org.rcsb.mmtf.codec.ArrayConverters

Convert an input array of integers to two arrays.

StringCodecs - Enum in org.rcsb.mmtf.codec

An enum defining the string encoding and decoding strategies.

StringCodecsInterface - Interface in org.rcsb.mmtf.codec

Interface all String codecs must implement.

StructureAdapterInterface - Interface in org.rcsb.mmtf.api

Interface to inflate a given MMTF data source.

StructureDataInterface - Interface in org.rcsb.mmtf.api

An interface describing the data API.

StructureDataToAdapter - Class in org.rcsb.mmtf.decoder

Pass data from a StructureDataInterface into a StructureAdapterInterface.

StructureDataToAdapter(StructureDataInterface, StructureAdapterInterface) - Constructor for class org.rcsb.mmtf.decoder.StructureDataToAdapter

Passes data from the data interface to the inflator interface.

SummaryData - Class in org.rcsb.mmtf.encoder

Class to store summary data about a structure.

SummaryData() - Constructor for class org.rcsb.mmtf.encoder.SummaryData

T

transferBioassembly(StructureDataInterface, AdapterToStructureData) - Static method in class org.rcsb.mmtf.encoder.EncoderUtils

Transfer bioassembly data from a StructureDataInterface to an AdapterToStructureData.

U

UNAVAILABLE_CHAR_VALUE - Static variable in class org.rcsb.mmtf.dataholders.MmtfStructure

The default value for a missing or null string field

UNAVAILABLE_R_VALUE - Static variable in class org.rcsb.mmtf.dataholders.MmtfStructure

The default value for Rfree and Rwork

UNAVAILABLE_RESOLUTION_VALUE - Static variable in class org.rcsb.mmtf.dataholders.MmtfStructure

The default value for resolution when not available or not applicable

V

valueOf(String) - Static method in enum org.rcsb.mmtf.codec.CharCodecs

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.rcsb.mmtf.codec.FloatCodecs

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.rcsb.mmtf.codec.IntCodecs

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.rcsb.mmtf.codec.StringCodecs

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.rcsb.mmtf.dataholders.DsspType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.rcsb.mmtf.codec.CharCodecs

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.rcsb.mmtf.codec.FloatCodecs

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.rcsb.mmtf.codec.IntCodecs

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.rcsb.mmtf.codec.StringCodecs

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.rcsb.mmtf.dataholders.DsspType

Returns an array containing the constants of this enum type, in the order they are declared.

VERSION - Static variable in class org.rcsb.mmtf.dataholders.MmtfStructure

The version of MMTF

W

writeDataToFile(AdapterToStructureData, Path) - Static method in class org.rcsb.mmtf.encoder.WriterUtils

Function to write data to a file.

WriterUtils - Class in org.rcsb.mmtf.encoder

A class of static utility methods to aid writing of data.

WriterUtils() - Constructor for class org.rcsb.mmtf.encoder.WriterUtils

A B C D E F G H I M N O P R S T U V W