A C D E F G I M N O P R S T 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

C

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

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.

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.

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.

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

F

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 class org.rcsb.mmtf.decoder.GenericDecoder

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

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

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

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

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

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

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

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

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

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

Gets the GZIP compressed and messagepack serialized data from the MMTF servers.

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

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

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

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

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

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

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

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

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

Reads and deserializes an uncompressed MMTF file.

getDataFromInputStream(InputStream) - Static method in class org.rcsb.mmtf.decoder.ReaderUtils

Read an input stream to an MmtfStructure object.

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

Returns a full (atom atom) MmmtfStructure given a PDB Id from the MMTF web server using HTTP.

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

Returns an MmmtfStructure given a PDB Id from the MMTF web server.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Get the header for this option as a byte array.

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

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

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

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

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

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

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 class org.rcsb.mmtf.decoder.GenericDecoder

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Gets the reduced form of the input StructureDataInterface.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Get the type of a given chain index.

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

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

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

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

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

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

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

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

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

Compress a byte array using Gzip.

I

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

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

The number of the method.

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

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.codec - package org.rcsb.mmtf.codec

General encoding and decoding structures.

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.

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

This class provides methods to retrieve and decode MMTF data from the MMTF server and MMTF files.

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

Converts a full (all-atom) MMTF structure data representation to a reduced version.

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

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

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

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

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

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

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

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

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

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

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

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

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.

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.

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.

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.

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 C D E F G I M N O P R S T V W