MmtfStructure (mmtf 1.0.0 API)

java.lang.Object
- org.rcsb.mmtf.dataholders.MmtfStructure

All Implemented Interfaces:

Serializable
```
public class MmtfStructure
extends Object
implements Serializable
```
A class to store the data sent in an MMTF data source.

Author:

Anthony Bradley

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`CHAIN_LENGTH` The number of characters in a chain.
`static int`	`COORD_DIVIDER` The number to divide coordinate int values by.
`static int`	`OCCUPANCY_BFACTOR_DIVIDER` The number to divide occupancy and bfactor int values by.
`static char`	`UNAVAILABLE_CHAR_VALUE` The default value for a missing or null string field
`static float`	`UNAVAILABLE_R_VALUE` The default value for Rfree and Rwork
`static float`	`UNAVAILABLE_RESOLUTION_VALUE` The default value for resolution when not available or not applicable
`static String`	`VERSION` The version of MMTF

Constructor Summary

Constructors
Constructor and Description

MmtfStructure()
Constructor to set the default values for floats

Constructors
Constructor and Description
`MmtfStructure()` Constructor to set the default values for floats

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`byte[]`	`getAltLocList()` Gets the alternate location list.
`byte[]`	`getAtomIdList()` Gets the atom id list.
`byte[]`	`getbFactorList()`
`List<BioAssemblyData>`	`getBioAssemblyList()` Gets the bio assembly.
`byte[]`	`getBondAtomList()` Gets the bond atom list.
`byte[]`	`getBondOrderList()` Gets the bond order list.
`byte[]`	`getChainIdList()` Gets the internal chain list.
`byte[]`	`getChainNameList()` Gets the chain names.
`int[]`	`getChainsPerModel()` Gets the number of chains per model.
`String`	`getDepositionDate()`
`Entity[]`	`getEntityList()` Get the entity list.
`String[]`	`getExperimentalMethods()`
`byte[]`	`getGroupIdList()` Gets the group num list.
`Group[]`	`getGroupList()` Gets the group map.
`int[]`	`getGroupsPerChain()` Gets the number of groups per chain.
`byte[]`	`getGroupTypeList()` Gets the group type list.
`byte[]`	`getInsCodeList()` Gets the insertion code list.
`String`	`getMmtfProducer()` Gets the mmtf producer.
`String`	`getMmtfVersion()` Gets the mmtf version.
`double[][]`	`getNcsOperatorList()`
`int`	`getNumAtoms()` Gets the num atoms.
`int`	`getNumBonds()` Gets the num bonds.
`int`	`getNumChains()`
`int`	`getNumGroups()`
`int`	`getNumModels()`
`byte[]`	`getOccupancyList()` Gets the occupancy list - an encoded per atom list of occupancy values.
`String`	`getReleaseDate()`
`Float`	`getResolution()`
`Float`	`getrFree()`
`Float`	`getrWork()`
`byte[]`	`getSecStructList()` Gets the sec struct list.
`byte[]`	`getSequenceIndexList()`
`String`	`getSpaceGroup()` Gets the space group.
`String`	`getStructureId()` Gets the structure id.
`String`	`getTitle()` Gets the title.
`float[]`	`getUnitCell()` Gets the unit cell.
`byte[]`	`getxCoordList()`
`byte[]`	`getyCoordList()`
`byte[]`	`getzCoordList()`
`void`	`setAltLocList(byte[] inputAltLocList)` Sets the alt label list.
`void`	`setAtomIdList(byte[] inputAtomIdList)` Sets the atom id list.
`void`	`setbFactorList(byte[] bFactors)`
`void`	`setBioAssemblyList(List<BioAssemblyData> inputBioAssembly)` Sets the bioassembly information.
`void`	`setBondAtomList(byte[] inputBondAtomList)` Sets the bond atom list.
`void`	`setBondOrderList(byte[] inputBondOrderList)` Sets the bond order list.
`void`	`setChainIdList(byte[] inputInternalChainList)` Sets the internal chain list.
`void`	`setChainNameList(byte[] inputChainList)` Sets the chain names.
`void`	`setChainsPerModel(int[] inputInternalChainsPerModel)` Sets the number of chains per model.
`void`	`setDepositionDate(String depositionDate)`
`void`	`setEntityList(Entity[] entityList)` Set the entity list.
`void`	`setExperimentalMethods(String[] experimentalMethods)`
`void`	`setGroupIdList(byte[] inputGroupNumList)` Sets the group num list.
`void`	`setGroupList(Group[] inputGroupMap)` Sets the group map.
`void`	`setGroupsPerChain(int[] inputGroupsPerChain)` Sets the number of groups in a chain.
`void`	`setGroupTypeList(byte[] resOrder)` Sets the group type list.
`void`	`setInsCodeList(byte[] inputInsertionCodeList)` Sets the ins code list.
`void`	`setMmtfProducer(String inputMmtfProducer)` Sets the mmtf producer.
`void`	`setMmtfVersion(String inputMmtfVersion)` Sets the mmtf version.
`void`	`setNcsOperatorList(double[][] ncsOperatorList)`
`void`	`setNumAtoms(int inputNumAtoms)` Sets the num atoms.
`void`	`setNumBonds(int inputNumBonds)` Sets the number of bonds.
`void`	`setNumChains(int numChains)`
`void`	`setNumGroups(int numGroups)`
`void`	`setNumModels(int numModels)`
`void`	`setOccupancyList(byte[] inputOccupancyList)` Sets the occupancy list - an encoded per atom list of occupancy values.
`void`	`setReleaseDate(String releaseDate)`
`void`	`setResolution(float resolution)`
`void`	`setrFree(float rFree)`
`void`	`setrWork(float rWork)`
`void`	`setSecStructList(byte[] secStruct)` Sets the sec struct list.
`void`	`setSequenceIndexList(byte[] seqResGroupIds)`
`void`	`setSpaceGroup(String inputSpaceGroup)` Sets the space group.
`void`	`setStructureId(String inputId)` Sets the structure id.
`void`	`setTitle(String inputTitle)` Sets the title.
`void`	`setUnitCell(float[] inputUnitCell)` Sets the unit cell.
`void`	`setxCoordList(byte[] xCoords)`
`void`	`setyCoordList(byte[] yCoords)`
`void`	`setzCoordList(byte[] zCoords)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - COORD_DIVIDER
```
public static final int COORD_DIVIDER
```
    The number to divide coordinate int values by.
    
    See Also:
    
    Constant Field Values
  - OCCUPANCY_BFACTOR_DIVIDER
```
public static final int OCCUPANCY_BFACTOR_DIVIDER
```
    The number to divide occupancy and bfactor int values by.
    
    See Also:
    
    Constant Field Values
  - UNAVAILABLE_R_VALUE
```
public static final float UNAVAILABLE_R_VALUE
```
    The default value for Rfree and Rwork
    
    See Also:
    
    Constant Field Values
  - UNAVAILABLE_RESOLUTION_VALUE
```
public static final float UNAVAILABLE_RESOLUTION_VALUE
```
    The default value for resolution when not available or not applicable
    
    See Also:
    
    Constant Field Values
  - UNAVAILABLE_CHAR_VALUE
```
public static final char UNAVAILABLE_CHAR_VALUE
```
    The default value for a missing or null string field
    
    See Also:
    
    Constant Field Values
  - CHAIN_LENGTH
```
public static final int CHAIN_LENGTH
```
    The number of characters in a chain.
    
    See Also:
    
    Constant Field Values
  - VERSION
```
public static final String VERSION
```
    The version of MMTF
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MmtfStructure
```
public MmtfStructure()
```
    Constructor to set the default values for floats
- Method Detail
  - getResolution
```
public Float getResolution()
```
    Returns:
    
    the resolution
  - setResolution
```
public void setResolution(float resolution)
```
    Parameters:
    
    resolution - the resolution to set
  - getrFree
```
public Float getrFree()
```
    Returns:
    
    the rFree
  - setrFree
```
public void setrFree(float rFree)
```
    Parameters:
    
    rFree - the rFree to set
  - getrWork
```
public Float getrWork()
```
    Returns:
    
    the rWork
  - setrWork
```
public void setrWork(float rWork)
```
    Parameters:
    
    rWork - the rWork to set
  - getSpaceGroup
```
public String getSpaceGroup()
```
    Gets the space group.
    
    Returns:
    
    the space group
  - setSpaceGroup
```
public void setSpaceGroup(String inputSpaceGroup)
```
    Sets the space group.
    
    Parameters:
    
    inputSpaceGroup - the new space group
  - getUnitCell
```
public float[] getUnitCell()
```
    Gets the unit cell.
    
    Returns:
    
    the unit cell
  - setUnitCell
```
public void setUnitCell(float[] inputUnitCell)
```
    Sets the unit cell.
    
    Parameters:
    
    inputUnitCell - the new unit cell
  - getGroupIdList
```
public byte[] getGroupIdList()
```
    Gets the group num list.
    
    Returns:
    
    the group num list
  - setGroupIdList
```
public void setGroupIdList(byte[] inputGroupNumList)
```
    Sets the group num list.
    
    Parameters:
    
    inputGroupNumList - the new group num list
  - getAltLocList
```
public byte[] getAltLocList()
```
    Gets the alternate location list.
    
    Returns:
    
    the alternate location list
  - setAltLocList
```
public void setAltLocList(byte[] inputAltLocList)
```
    Sets the alt label list.
    
    Parameters:
    
    inputAltLocList - the new alternation location label list
  - getBioAssemblyList
```
public List<BioAssemblyData> getBioAssemblyList()
```
    Gets the bio assembly.
    
    Returns:
    
    the bio assembly
  - getChainNameList
```
public byte[] getChainNameList()
```
    Gets the chain names. The byte array indicating the (up to four characters) name of the chain. This is taken from the auth id.
    
    Returns:
    
    the chain list
  - setChainNameList
```
public void setChainNameList(byte[] inputChainList)
```
    Sets the chain names. The byte array indicating the (up to four characters) name of the chain. This is taken from the auth id.
    
    Parameters:
    
    inputChainList - the new chain list
  - setBioAssemblyList
```
public void setBioAssemblyList(List<BioAssemblyData> inputBioAssembly)
```
    Sets the bioassembly information.
    
    Parameters:
    
    inputBioAssembly - the bio assembly
  - getNumAtoms
```
public int getNumAtoms()
```
    Gets the num atoms.
    
    Returns:
    
    the num atoms
  - setNumAtoms
```
public void setNumAtoms(int inputNumAtoms)
```
    Sets the num atoms.
    
    Parameters:
    
    inputNumAtoms - the new num atoms
  - getOccupancyList
```
public byte[] getOccupancyList()
```
    Gets the occupancy list - an encoded per atom list of occupancy values.
    
    Returns:
    
    the occupancy list - an encoded per atom list of occupancy values.
  - setOccupancyList
```
public void setOccupancyList(byte[] inputOccupancyList)
```
    Sets the occupancy list - an encoded per atom list of occupancy values.
    
    Parameters:
    
    inputOccupancyList - the occupancy list - an encoded per atom list of occupancy values.
  - getInsCodeList
```
public byte[] getInsCodeList()
```
    Gets the insertion code list.
    
    Returns:
    
    the insertion code list
  - setInsCodeList
```
public void setInsCodeList(byte[] inputInsertionCodeList)
```
    Sets the ins code list.
    
    Parameters:
    
    inputInsertionCodeList - the new insertion code list
  - getGroupList
```
public Group[] getGroupList()
```
    Gets the group map.
    
    Returns:
    
    the group map
  - setGroupList
```
public void setGroupList(Group[] inputGroupMap)
```
    Sets the group map.
    
    Parameters:
    
    inputGroupMap - the group map
  - getSecStructList
```
public byte[] getSecStructList()
```
    Gets the sec struct list.
    
    Returns:
    
    the sec struct list
  - setSecStructList
```
public void setSecStructList(byte[] secStruct)
```
    Sets the sec struct list.
    
    Parameters:
    
    secStruct - the new sec struct list
  - getGroupTypeList
```
public byte[] getGroupTypeList()
```
    Gets the group type list.
    
    Returns:
    
    the group type list
  - setGroupTypeList
```
public void setGroupTypeList(byte[] resOrder)
```
    Sets the group type list.
    
    Parameters:
    
    resOrder - the new group type list
  - getAtomIdList
```
public byte[] getAtomIdList()
```
    Gets the atom id list.
    
    Returns:
    
    the atom id list
  - setAtomIdList
```
public void setAtomIdList(byte[] inputAtomIdList)
```
    Sets the atom id list.
    
    Parameters:
    
    inputAtomIdList - the new atom id list
  - getTitle
```
public String getTitle()
```
    Gets the title.
    
    Returns:
    
    the title
  - setTitle
```
public void setTitle(String inputTitle)
```
    Sets the title.
    
    Parameters:
    
    inputTitle - the new title
  - getStructureId
```
public String getStructureId()
```
    Gets the structure id. Should be used as a unique identifier of this structure.
    
    Returns:
    
    the the structure id a unique String id of this structure.
  - setStructureId
```
public void setStructureId(String inputId)
```
    Sets the structure id. Should be used as a unique identifier of this structure.
    
    Parameters:
    
    inputId - a unique String id of this structure.
  - getMmtfProducer
```
public String getMmtfProducer()
```
    Gets the mmtf producer.
    
    Returns:
    
    the mmtf producer
  - setMmtfProducer
```
public void setMmtfProducer(String inputMmtfProducer)
```
    Sets the mmtf producer.
    
    Parameters:
    
    inputMmtfProducer - the new mmtf producer
  - getMmtfVersion
```
public String getMmtfVersion()
```
    Gets the mmtf version.
    
    Returns:
    
    the mmtf version
  - setMmtfVersion
```
public void setMmtfVersion(String inputMmtfVersion)
```
    Sets the mmtf version.
    
    Parameters:
    
    inputMmtfVersion - the new mmtf version
  - getNumBonds
```
public int getNumBonds()
```
    Gets the num bonds.
    
    Returns:
    
    the num bonds
  - setNumBonds
```
public void setNumBonds(int inputNumBonds)
```
    Sets the number of bonds.
    
    Parameters:
    
    inputNumBonds - the new num bonds
  - getBondAtomList
```
public byte[] getBondAtomList()
```
    Gets the bond atom list.
    
    Returns:
    
    the bond atom list
  - setBondAtomList
```
public void setBondAtomList(byte[] inputBondAtomList)
```
    Sets the bond atom list.
    
    Parameters:
    
    inputBondAtomList - the new bond atom list
  - getBondOrderList
```
public byte[] getBondOrderList()
```
    Gets the bond order list.
    
    Returns:
    
    the bond order list
  - setBondOrderList
```
public void setBondOrderList(byte[] inputBondOrderList)
```
    Sets the bond order list.
    
    Parameters:
    
    inputBondOrderList - the new bond order list
  - getChainsPerModel
```
public int[] getChainsPerModel()
```
    Gets the number of chains per model. Chains are currently specified by asym (internal) chain ids.
    
    Returns:
    
    the list of chains per model.
  - setChainsPerModel
```
public void setChainsPerModel(int[] inputInternalChainsPerModel)
```
    Sets the number of chains per model. Currently specified by asy (internal) chain ids.
    
    Parameters:
    
    inputInternalChainsPerModel - the new list of chains per model.
  - getGroupsPerChain
```
public int[] getGroupsPerChain()
```
    Gets the number of groups per chain.
    
    Returns:
    
    the internal groups per chain
  - setGroupsPerChain
```
public void setGroupsPerChain(int[] inputGroupsPerChain)
```
    Sets the number of groups in a chain.
    
    Parameters:
    
    inputGroupsPerChain - the new internal groups per chain
  - getChainIdList
```
public byte[] getChainIdList()
```
    Gets the internal chain list.
    
    Returns:
    
    the internal chain list
  - setChainIdList
```
public void setChainIdList(byte[] inputInternalChainList)
```
    Sets the internal chain list.
    
    Parameters:
    
    inputInternalChainList - the new internal chain list
  - getExperimentalMethods
```
public String[] getExperimentalMethods()
```
    Returns:
    
    the experimental methods
  - setExperimentalMethods
```
public void setExperimentalMethods(String[] experimentalMethods)
```
    Parameters:
    
    experimentalMethods - the experimental methods to set
  - getSequenceIndexList
```
public byte[] getSequenceIndexList()
```
    Returns:
    
    the seqResGroupIds
  - setSequenceIndexList
```
public void setSequenceIndexList(byte[] seqResGroupIds)
```
    Parameters:
    
    seqResGroupIds - the seqResGroupIds to set
  - getEntityList
```
public Entity[] getEntityList()
```
    Get the entity list.
    
    Returns:
    
    the list of entities for this structure.
  - setEntityList
```
public void setEntityList(Entity[] entityList)
```
    Set the entity list.
    
    Parameters:
    
    entityList - the input list of entities.
  - getDepositionDate
```
public String getDepositionDate()
```
    Returns:
    
    the deposition date of the structure in ISO time standard.
  - setDepositionDate
```
public void setDepositionDate(String depositionDate)
```
    Parameters:
    
    depositionDate - a string indicating the deposition date to set.
  - getReleaseDate
```
public String getReleaseDate()
```
    Returns:
    
    the release date of the structure in ISO time standard.
  - setReleaseDate
```
public void setReleaseDate(String releaseDate)
```
    Parameters:
    
    releaseDate - a string indicating the deposition date to set.
  - getxCoordList
```
public byte[] getxCoordList()
```
    Returns:
    
    the X coords as an encoded byte array.
  - setxCoordList
```
public void setxCoordList(byte[] xCoords)
```
    Parameters:
    
    xCoords - the X coords as an encoded byte array.
  - getyCoordList
```
public byte[] getyCoordList()
```
    Returns:
    
    the the Y coords as an encoded byte array.
  - setyCoordList
```
public void setyCoordList(byte[] yCoords)
```
    Parameters:
    
    yCoords - the Y coords as an encoded byte array.
  - getzCoordList
```
public byte[] getzCoordList()
```
    Returns:
    
    the Z coords as an encoded byte array.
  - setzCoordList
```
public void setzCoordList(byte[] zCoords)
```
    Parameters:
    
    zCoords - the Z coords as an encoded byte array.
  - getbFactorList
```
public byte[] getbFactorList()
```
    Returns:
    
    the atomic B-factors as an encoded byte array.
  - setbFactorList
```
public void setbFactorList(byte[] bFactors)
```
    Parameters:
    
    bFactors - the atomic B-factors as an encoded byte array.
  - getNumGroups
```
public int getNumGroups()
```
    Returns:
    
    the number of groups in the structure
  - setNumGroups
```
public void setNumGroups(int numGroups)
```
    Parameters:
    
    numGroups - the number of groups in the structure
  - getNumChains
```
public int getNumChains()
```
    Returns:
    
    the number of chains in the structure
  - setNumChains
```
public void setNumChains(int numChains)
```
    Parameters:
    
    numChains - the number of chains in the structure
  - getNumModels
```
public int getNumModels()
```
    Returns:
    
    the number of models in the structure
  - setNumModels
```
public void setNumModels(int numModels)
```
    Parameters:
    
    numModels - the number of models in the structure
  - getNcsOperatorList
```
public double[][] getNcsOperatorList()
```
    Returns:
    
    the ncsOperMatrixList
  - setNcsOperatorList
```
public void setNcsOperatorList(double[][] ncsOperatorList)
```
    Parameters:
    
    ncsOperatorList - the ncsOperMatrixList to set

Class MmtfStructure

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

COORD_DIVIDER

OCCUPANCY_BFACTOR_DIVIDER

UNAVAILABLE_R_VALUE

UNAVAILABLE_RESOLUTION_VALUE

UNAVAILABLE_CHAR_VALUE

CHAIN_LENGTH

VERSION

Constructor Detail

MmtfStructure

Method Detail

getResolution

setResolution

getrFree

setrFree

getrWork

setrWork

getSpaceGroup

setSpaceGroup

getUnitCell

setUnitCell

getGroupIdList

setGroupIdList

getAltLocList

setAltLocList

getBioAssemblyList

getChainNameList

setChainNameList

setBioAssemblyList

getNumAtoms

setNumAtoms

getOccupancyList

setOccupancyList

getInsCodeList

setInsCodeList

getGroupList

setGroupList

getSecStructList

setSecStructList

getGroupTypeList

setGroupTypeList

getAtomIdList

setAtomIdList

getTitle

setTitle

getStructureId

setStructureId

getMmtfProducer

setMmtfProducer

getMmtfVersion

setMmtfVersion

getNumBonds

setNumBonds

getBondAtomList

setBondAtomList

getBondOrderList

setBondOrderList

getChainsPerModel

setChainsPerModel

getGroupsPerChain

setGroupsPerChain

getChainIdList

setChainIdList

getExperimentalMethods

setExperimentalMethods

getSequenceIndexList

setSequenceIndexList

getEntityList

setEntityList

getDepositionDate

setDepositionDate

getReleaseDate

setReleaseDate

getxCoordList

setxCoordList