B C D E G H L M O R S U V

B

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.

CodecUtils - Class in org.rcsb.mmtf.utils

A utility class of static methods and constants

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

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

Converts an integer list to an integer array

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

The number to divide coordinate int values by.

create(ObjectTree) - Method in class org.rcsb.mmtf.dataholders.MmtfStructureFactory

D

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

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

G

get(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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.

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

Gets the atom info.

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

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

Gets the bio assembly.

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.

getByteArray(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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

Gets the internal chain list.

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.

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

Gets the chain names.

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

Gets the number of chains per model.

getChar(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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

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

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

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

Get the description of the entity.

getDoubleArray(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

getDoubleArray2d(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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

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

Get the entity list.

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

getFloat(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

getFloatArray(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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

Gets the atom charges.

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

Gets the group num list.

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

Gets the group map.

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

Gets the group name.

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

Gets the number of groups per chain.

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

Gets the group type list.

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

Gets the insertion code list.

getInt(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

getIntArray(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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

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

getMmtfBaseUrl(boolean, boolean) - Static method in class org.rcsb.mmtf.utils.CodecUtils

Returns the base URL to retrieve MMTF files.

getMmtfEntryUrl(String, boolean, boolean) - Static method in class org.rcsb.mmtf.utils.CodecUtils

Returns the RESTful URL to an MMTF encoded PDB entry.

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

Gets the mmtf producer.

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

Gets the mmtf version.

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

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

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

Gets the num atoms.

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

Gets the num bonds.

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

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

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

getObjectArray(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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

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

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

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

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

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

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

Gets the sec struct list.

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 class org.rcsb.mmtf.dataholders.MmtfStructure

Gets the space group.

getString(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

getStringArray(String) - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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

Gets the structure id.

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

Gets the title.

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.

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

Gets the unit cell.

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

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

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

Group - Class in org.rcsb.mmtf.dataholders

Group (residue) level data store.

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

H

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

L

Lines - Class in org.rcsb.mmtf.utils

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

M

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

The maximum number of chars in a chain entry.

MessagePackReader - Class in org.rcsb.mmtf.serialization.quickmessagepackdeserialization

A simple MessagePack reader.

MessagePackReader(DataInputStream, boolean) - Constructor for class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.MessagePackReader

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.

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

MmtfStructureFactory - Class in org.rcsb.mmtf.dataholders

This class constructs MmtfStructure objects from tree-like structure containing the data.

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

MmtfStructureSerializationInterface - Interface in org.rcsb.mmtf.serialization

An interface to carry out serializing / deserializing to MmtfStructure.

O

ObjectTree - Class in org.rcsb.mmtf.serialization.quickmessagepackdeserialization

Utility class represeting an object whose attributes does not have types yet.

ObjectTree(Map<String, Object>) - Constructor for class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

ObjectTree(Hashtable<String, Object>) - Constructor for class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.ObjectTree

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

The number to divide occupancy and bfactor int values by.

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

Beans and classes to store data for data transfer.

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

Serialization and deserialization of data.

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

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

Utility functions and variables for coding and decoding.

R

readFile(File) - Static method in class org.rcsb.mmtf.utils.Lines

Read lines from a file.

readMap() - Method in class org.rcsb.mmtf.serialization.quickmessagepackdeserialization.MessagePackReader

readResource(String) - Static method in class org.rcsb.mmtf.utils.Lines

Read lines from a resource specified by absolute path, e.g.

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.

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.

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.

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

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.

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

Sets the group num list.

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.

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

Sets the ins code list.

setJackson(boolean) - Static method in class org.rcsb.mmtf.serialization.MessagePackSerialization

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.

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

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

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

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.dataholders.DsspType

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

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

B C D E G H L M O R S U V