org.rcsb.mmtf.decoder

Class GenericDecoder

java.lang.Object

org.rcsb.mmtf.decoder.GenericDecoder

All Implemented Interfaces:

java.io.Serializable, StructureDataInterface

public class GenericDecoder
extends java.lang.Object
implements StructureDataInterface, java.io.Serializable

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

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
GenericDecoder(MmtfStructure inputData) Constructor for the default decoder.

Method Summary

Modifier and Type	Method and Description
char[]	getAltLocIds()
int[]	getAtomIds()
float[]	getbFactors()
java.lang.String	getBioassemblyName(int bioassemblyIndex)
java.lang.String[]	getChainIds()
int[]	getChainIndexListForTransform(int bioassemblyIndex, int transformationIndex)
java.lang.String[]	getChainNames()
int[]	getChainsPerModel()
java.lang.String	getDepositionDate()
int[]	getEntityChainIndexList(int entityInd)
java.lang.String	getEntityDescription(int entityInd)
java.lang.String	getEntitySequence(int entityInd)
java.lang.String	getEntityType(int entityInd)
java.lang.String[]	getExperimentalMethods()
int[]	getGroupAtomCharges(int groupInd)
java.lang.String[]	getGroupAtomNames(int groupInd)
int[]	getGroupBondIndices(int groupInd)
int[]	getGroupBondOrders(int groupInd)
java.lang.String	getGroupChemCompType(int groupInd)
java.lang.String[]	getGroupElementNames(int groupInd)
int[]	getGroupIds()
java.lang.String	getGroupName(int groupInd)
int[]	getGroupSequenceIndices()
char	getGroupSingleLetterCode(int groupInd)
int[]	getGroupsPerChain()
int[]	getGroupTypeIndices()
char[]	getInsCodes()
int[]	getInterGroupBondIndices()
int[]	getInterGroupBondOrders()
double[]	getMatrixForTransform(int bioassemblyIndex, int transformationIndex)
java.lang.String	getMmtfProducer()
java.lang.String	getMmtfVersion()
double[][]	getNcsOperatorList()
int	getNumAtoms()
int	getNumAtomsInGroup(int groupInd)
int	getNumBioassemblies()
int	getNumBonds()
int	getNumChains()
int	getNumEntities()
int	getNumGroups()
int	getNumModels()
int	getNumTransInBioassembly(int bioassemblyIndex)
float[]	getOccupancies()
java.lang.String	getReleaseDate()
float	getResolution()
float	getRfree()
float	getRwork()
int[]	getSecStructList()
java.lang.String	getSpaceGroup()
java.lang.String	getStructureId()
java.lang.String	getTitle()
float[]	getUnitCell()
float[]	getxCoords()
float[]	getyCoords()
float[]	getzCoords()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenericDecoder

public GenericDecoder(MmtfStructure inputData)

Constructor for the default decoder.

Parameters:

inputData - The input mmtfBean data to be decompressed.

Method Detail

getxCoords

public float[] getxCoords()

Specified by:

getxCoords in interface StructureDataInterface

getyCoords

public float[] getyCoords()

Specified by:

getyCoords in interface StructureDataInterface

getzCoords

public float[] getzCoords()

Specified by:

getzCoords in interface StructureDataInterface

getbFactors

public float[] getbFactors()

Specified by:

getbFactors in interface StructureDataInterface

getOccupancies

public float[] getOccupancies()

Specified by:

getOccupancies in interface StructureDataInterface

getAtomIds

public int[] getAtomIds()

Specified by:

getAtomIds in interface StructureDataInterface

getAltLocIds

public char[] getAltLocIds()

Specified by:

getAltLocIds in interface StructureDataInterface

getInsCodes

public char[] getInsCodes()

Specified by:

getInsCodes in interface StructureDataInterface

getGroupIds

public int[] getGroupIds()

Specified by:

getGroupIds in interface StructureDataInterface

getGroupTypeIndices

public int[] getGroupTypeIndices()

Specified by:

getGroupTypeIndices in interface StructureDataInterface

getGroupSequenceIndices

public int[] getGroupSequenceIndices()

Specified by:

getGroupSequenceIndices in interface StructureDataInterface

getChainNames

public java.lang.String[] getChainNames()

Specified by:

getChainNames in interface StructureDataInterface

getChainsPerModel

public int[] getChainsPerModel()

Specified by:

getChainsPerModel in interface StructureDataInterface

getGroupsPerChain

public int[] getGroupsPerChain()

Specified by:

getGroupsPerChain in interface StructureDataInterface

getSpaceGroup

public java.lang.String getSpaceGroup()

Specified by:

getSpaceGroup in interface StructureDataInterface

getUnitCell

public float[] getUnitCell()

Specified by:

getUnitCell in interface StructureDataInterface

getInterGroupBondIndices

public int[] getInterGroupBondIndices()

Specified by:

getInterGroupBondIndices in interface StructureDataInterface

getInterGroupBondOrders

public int[] getInterGroupBondOrders()

Specified by:

getInterGroupBondOrders in interface StructureDataInterface

getChainIds

public java.lang.String[] getChainIds()

Specified by:

getChainIds in interface StructureDataInterface

getMmtfVersion

public java.lang.String getMmtfVersion()

Specified by:

getMmtfVersion in interface StructureDataInterface

getMmtfProducer

public java.lang.String getMmtfProducer()

Specified by:

getMmtfProducer in interface StructureDataInterface

getStructureId

public java.lang.String getStructureId()

Specified by:

getStructureId in interface StructureDataInterface

getNumGroups

public int getNumGroups()

Specified by:

getNumGroups in interface StructureDataInterface

getNumChains

public int getNumChains()

Specified by:

getNumChains in interface StructureDataInterface

getNumModels

public int getNumModels()

Specified by:

getNumModels in interface StructureDataInterface

getNumAtoms

public int getNumAtoms()

Specified by:

getNumAtoms in interface StructureDataInterface

getRfree

public float getRfree()

Specified by:

getRfree in interface StructureDataInterface

getResolution

public float getResolution()

Specified by:

getResolution in interface StructureDataInterface

getRwork

public float getRwork()

Specified by:

getRwork in interface StructureDataInterface

getTitle

public java.lang.String getTitle()

Specified by:

getTitle in interface StructureDataInterface

getExperimentalMethods

public java.lang.String[] getExperimentalMethods()

Specified by:

getExperimentalMethods in interface StructureDataInterface

getGroupName

public java.lang.String getGroupName(int groupInd)

Specified by:

getGroupName in interface StructureDataInterface

getNumAtomsInGroup

public int getNumAtomsInGroup(int groupInd)

Specified by:

getNumAtomsInGroup in interface StructureDataInterface

getGroupAtomNames

public java.lang.String[] getGroupAtomNames(int groupInd)

Specified by:

getGroupAtomNames in interface StructureDataInterface

getGroupElementNames

public java.lang.String[] getGroupElementNames(int groupInd)

Specified by:

getGroupElementNames in interface StructureDataInterface

getGroupBondOrders

public int[] getGroupBondOrders(int groupInd)

Specified by:

getGroupBondOrders in interface StructureDataInterface

getGroupBondIndices

public int[] getGroupBondIndices(int groupInd)

Specified by:

getGroupBondIndices in interface StructureDataInterface

getGroupAtomCharges

public int[] getGroupAtomCharges(int groupInd)

Specified by:

getGroupAtomCharges in interface StructureDataInterface

getGroupSingleLetterCode

public char getGroupSingleLetterCode(int groupInd)

Specified by:

getGroupSingleLetterCode in interface StructureDataInterface

getGroupChemCompType

public java.lang.String getGroupChemCompType(int groupInd)

Specified by:

getGroupChemCompType in interface StructureDataInterface

getEntityDescription

public java.lang.String getEntityDescription(int entityInd)

Specified by:

getEntityDescription in interface StructureDataInterface

getEntityType

public java.lang.String getEntityType(int entityInd)

Specified by:

getEntityType in interface StructureDataInterface

getEntityChainIndexList

public int[] getEntityChainIndexList(int entityInd)

Specified by:

getEntityChainIndexList in interface StructureDataInterface

getEntitySequence

public java.lang.String getEntitySequence(int entityInd)

Specified by:

getEntitySequence in interface StructureDataInterface

getNumEntities

public int getNumEntities()

Specified by:

getNumEntities in interface StructureDataInterface

getNumBioassemblies

public int getNumBioassemblies()

Specified by:

getNumBioassemblies in interface StructureDataInterface

getNumTransInBioassembly

public int getNumTransInBioassembly(int bioassemblyIndex)

Specified by:

getNumTransInBioassembly in interface StructureDataInterface

getChainIndexListForTransform

public int[] getChainIndexListForTransform(int bioassemblyIndex,
                                           int transformationIndex)

Specified by:

getChainIndexListForTransform in interface StructureDataInterface

getMatrixForTransform

public double[] getMatrixForTransform(int bioassemblyIndex,
                                      int transformationIndex)

Specified by:

getMatrixForTransform in interface StructureDataInterface

getDepositionDate

public java.lang.String getDepositionDate()

Specified by:

getDepositionDate in interface StructureDataInterface

getNumBonds

public int getNumBonds()

Specified by:

getNumBonds in interface StructureDataInterface

getSecStructList

public int[] getSecStructList()

Specified by:

getSecStructList in interface StructureDataInterface

getReleaseDate

public java.lang.String getReleaseDate()

Specified by:

getReleaseDate in interface StructureDataInterface

getNcsOperatorList

public double[][] getNcsOperatorList()

Specified by:

getNcsOperatorList in interface StructureDataInterface

getBioassemblyName

public java.lang.String getBioassemblyName(int bioassemblyIndex)

Specified by:

getBioassemblyName in interface StructureDataInterface