org.rcsb.mmtf.encoder

Class AdapterToStructureData

java.lang.Object

org.rcsb.mmtf.encoder.AdapterToStructureData

All Implemented Interfaces:

java.io.Serializable, StructureAdapterInterface, StructureDataInterface

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

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

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
AdapterToStructureData()

Method Summary

Modifier and Type	Method and Description
void	finalizeStructure()
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()
void	initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups, int totalNumChains, int totalNumModels, java.lang.String structureId)
void	setAtomInfo(java.lang.String atomName, int serialNumber, char alternativeLocationId, float x, float y, float z, float occupancy, float temperatureFactor, java.lang.String element, int charge)
void	setBioAssemblyTrans(int bioAssemblyIndex, int[] chainIndices, double[] transform, java.lang.String name)
void	setChainInfo(java.lang.String chainId, java.lang.String chainName, int groupCount)
void	setEntityInfo(int[] chainIndices, java.lang.String sequence, java.lang.String description, java.lang.String title)
void	setGroupBond(int firstAtomIndex, int secondAtomIndex, int bondOrder)
void	setGroupInfo(java.lang.String groupName, int groupNumber, char insertionCode, java.lang.String polymerType, int atomCount, int bondCount, char singleAtomCode, int sequenceIndex, int secStructType)
void	setHeaderInfo(float rFree, float rWork, float resolution, java.lang.String title, java.lang.String depositionDate, java.lang.String releaseDate, java.lang.String[] experimnetalMethods)
void	setInterGroupBond(int firstAtomIndex, int secondAtomIndex, int bondOrder)
void	setMmtfProducer(java.lang.String mmtfProducer)
void	setModelInfo(int modelId, int chainCount)
void	setXtalInfo(java.lang.String spaceGroup, float[] unitCell, double[][] ncsOperMatrixList)

Methods inherited from class java.lang.Object

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

Constructor Detail

AdapterToStructureData

public AdapterToStructureData()

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

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

getGroupTypeIndices

public int[] getGroupTypeIndices()

Specified by:

getGroupTypeIndices in interface StructureDataInterface

getGroupSequenceIndices

public int[] getGroupSequenceIndices()

Specified by:

getGroupSequenceIndices in interface StructureDataInterface

getChainIds

public java.lang.String[] getChainIds()

Specified by:

getChainIds 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

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

getInterGroupBondIndices

public int[] getInterGroupBondIndices()

Specified by:

getInterGroupBondIndices in interface StructureDataInterface

getInterGroupBondOrders

public int[] getInterGroupBondOrders()

Specified by:

getInterGroupBondOrders 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

getNumEntities

public int getNumEntities()

Specified by:

getNumEntities 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

getStructureId

public java.lang.String getStructureId()

Specified by:

getStructureId in interface StructureDataInterface

getNumModels

public int getNumModels()

Specified by:

getNumModels in interface StructureDataInterface

getNumChains

public int getNumChains()

Specified by:

getNumChains in interface StructureDataInterface

getNumGroups

public int getNumGroups()

Specified by:

getNumGroups in interface StructureDataInterface

getNumAtoms

public int getNumAtoms()

Specified by:

getNumAtoms in interface StructureDataInterface

getRfree

public float getRfree()

Specified by:

getRfree in interface StructureDataInterface

getRwork

public float getRwork()

Specified by:

getRwork in interface StructureDataInterface

getResolution

public float getResolution()

Specified by:

getResolution 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

getDepositionDate

public java.lang.String getDepositionDate()

Specified by:

getDepositionDate in interface StructureDataInterface

initStructure

public void initStructure(int totalNumBonds,
                          int totalNumAtoms,
                          int totalNumGroups,
                          int totalNumChains,
                          int totalNumModels,
                          java.lang.String structureId)

Specified by:

initStructure in interface StructureAdapterInterface

finalizeStructure

public void finalizeStructure()

Specified by:

finalizeStructure in interface StructureAdapterInterface

setModelInfo

public void setModelInfo(int modelId,
                         int chainCount)

Specified by:

setModelInfo in interface StructureAdapterInterface

setChainInfo

public void setChainInfo(java.lang.String chainId,
                         java.lang.String chainName,
                         int groupCount)

Specified by:

setChainInfo in interface StructureAdapterInterface

setEntityInfo

public void setEntityInfo(int[] chainIndices,
                          java.lang.String sequence,
                          java.lang.String description,
                          java.lang.String title)

Specified by:

setEntityInfo in interface StructureAdapterInterface

setGroupInfo

public void setGroupInfo(java.lang.String groupName,
                         int groupNumber,
                         char insertionCode,
                         java.lang.String polymerType,
                         int atomCount,
                         int bondCount,
                         char singleAtomCode,
                         int sequenceIndex,
                         int secStructType)

Specified by:

setGroupInfo in interface StructureAdapterInterface

setAtomInfo

public void setAtomInfo(java.lang.String atomName,
                        int serialNumber,
                        char alternativeLocationId,
                        float x,
                        float y,
                        float z,
                        float occupancy,
                        float temperatureFactor,
                        java.lang.String element,
                        int charge)

Specified by:

setAtomInfo in interface StructureAdapterInterface

setBioAssemblyTrans

public void setBioAssemblyTrans(int bioAssemblyIndex,
                                int[] chainIndices,
                                double[] transform,
                                java.lang.String name)

Specified by:

setBioAssemblyTrans in interface StructureAdapterInterface

setXtalInfo

public void setXtalInfo(java.lang.String spaceGroup,
                        float[] unitCell,
                        double[][] ncsOperMatrixList)

Specified by:

setXtalInfo in interface StructureAdapterInterface

setGroupBond

public void setGroupBond(int firstAtomIndex,
                         int secondAtomIndex,
                         int bondOrder)

Specified by:

setGroupBond in interface StructureAdapterInterface

setInterGroupBond

public void setInterGroupBond(int firstAtomIndex,
                              int secondAtomIndex,
                              int bondOrder)

Specified by:

setInterGroupBond in interface StructureAdapterInterface

setHeaderInfo

public void setHeaderInfo(float rFree,
                          float rWork,
                          float resolution,
                          java.lang.String title,
                          java.lang.String depositionDate,
                          java.lang.String releaseDate,
                          java.lang.String[] experimnetalMethods)

Specified by:

setHeaderInfo in interface StructureAdapterInterface

setMmtfProducer

public void setMmtfProducer(java.lang.String mmtfProducer)

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