Serialized Form (mmtf 1.0.0 API)

Package org.rcsb.mmtf.dataholders
- Class org.rcsb.mmtf.dataholders.BioAssemblyData extends Object implements Serializable
  
  serialVersionUID:
  
  -8448351152898393978L
  - Serialized Fields
    - transformList
```
List<E> transformList
```
      The transformations of this bioassembly.
    - name
```
String name
```
      The name of the Bioassembly. Can be user defined.
- Class org.rcsb.mmtf.dataholders.BioAssemblyTransformation extends Object implements Serializable
  
  serialVersionUID:
  
  -3874846890822791985L
  - Serialized Fields
    - chainIndexList
```
int[] chainIndexList
```
      The indices of the chains this bioassembly references.
    - matrix
```
double[] matrix
```
      The 4x4 matrix transformation specifying a rotation and a translation. Stored linearly in row major order.
- Class org.rcsb.mmtf.dataholders.Entity extends Object implements Serializable
  
  serialVersionUID:
  
  9090730105071948103L
  - Serialized Fields
    - description
```
String description
```
      The description based on the PDBx model
    - type
```
String type
```
      The type (polymer, non-polymer, water)
    - chainIndexList
```
int[] chainIndexList
```
      The chain index list - referencing the entity of the asym id
    - sequence
```
String sequence
```
      The sequence for this entity
- Class org.rcsb.mmtf.dataholders.Group extends Object implements Serializable
  
  serialVersionUID:
  
  2880633780569899800L
  - Serialized Fields
    - groupName
```
String groupName
```
      The group name. (e.g. HIS)
    - atomNameList
```
String[] atomNameList
```
      The atom names. A list of strings indicating the atom names (e.g. CA for C-alpha).
    - elementList
```
String[] elementList
```
      The element names. A list of strings indicating the element names (e.g. Ca for Calcium).
    - bondOrderList
```
int[] bondOrderList
```
      The bond orders. A list of integers indicating the bond orders
    - bondAtomList
```
int[] bondAtomList
```
      The bond indices (in pairs). (e.g. 0,1 means there is bond between atom 0 and 1).
    - formalChargeList
```
int[] formalChargeList
```
      The formal charges on the atoms.
    - singleLetterCode
```
char singleLetterCode
```
      The single letter code.
    - chemCompType
```
String chemCompType
```
      A string (taken from the chemical component dictionary) indicating the type of the group. Corresponds to: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx.dic/Items/_chem_comp.type.html
- Class org.rcsb.mmtf.dataholders.MmtfStructure extends Object implements Serializable
  
  serialVersionUID:
  
  384559979573830324L
  - Serialized Fields
    - mmtfVersion
```
String mmtfVersion
```
      The mmtf version.
    - mmtfProducer
```
String mmtfProducer
```
      The mmtf producer.
    - numBonds
```
int numBonds
```
      The number of bonds.
    - numAtoms
```
int numAtoms
```
      The number of atoms.
    - numGroups
```
int numGroups
```
      The number of groups.
    - numChains
```
int numChains
```
      The number of chains.
    - numModels
```
int numModels
```
      The number of models.
    - structureId
```
String structureId
```
      The structure Id. Most commonly this will be the four character PDB id.
    - title
```
String title
```
      The title.
    - chainsPerModel
```
int[] chainsPerModel
```
      The number of chains per model.
    - groupsPerChain
```
int[] groupsPerChain
```
      The internal groups per chain.
    - chainNameList
```
byte[] chainNameList
```
      The names of the chains. Each chain is allocated four bytes. Chain names can be up to four characters long. 0 bytes indicate the end of the chain name. These are taken from the auth id.
    - chainIdList
```
byte[] chainIdList
```
      The names of the chains. Each chain is allocated four bytes. Chain names can be up to four characters long. 0 bytes indicate the end of the chain name. These are taken from the asym id.
    - spaceGroup
```
String spaceGroup
```
      The space group.
    - unitCell
```
float[] unitCell
```
      The unit cell.
    - bioAssemblyList
```
List<E> bioAssemblyList
```
      The bio assembly.
    - bondAtomList
```
byte[] bondAtomList
```
      The bond atom (indices) list.
    - bondOrderList
```
byte[] bondOrderList
```
      The bond order list.
    - groupList
```
Group[] groupList
```
      The list of different PDBGroups in the structure.
    - xCoordList
```
byte[] xCoordList
```
      The encoded X coordinates.
    - yCoordList
```
byte[] yCoordList
```
      The encoded Y coordinates.
    - zCoordList
```
byte[] zCoordList
```
      The encoded Z coordinates.
    - bFactorList
```
byte[] bFactorList
```
      The encoded B-factors.
    - secStructList
```
byte[] secStructList
```
      The secondary structure list. Stored as 1 byte ints.
    - occupancyList
```
byte[] occupancyList
```
      The occupancy list.
    - altLocList
```
byte[] altLocList
```
      The list of alternate location ids.
    - insCodeList
```
byte[] insCodeList
```
      The insertion code list.
    - groupTypeList
```
byte[] groupTypeList
```
      The group type list.
    - groupIdList
```
byte[] groupIdList
```
      The group id list. Identifies each group along the chain.
    - atomIdList
```
byte[] atomIdList
```
      The atom id list.
    - sequenceIndexList
```
byte[] sequenceIndexList
```
      The SeqRes group ids.
    - experimentalMethods
```
String[] experimentalMethods
```
      The experimental method(s).
    - resolution
```
float resolution
```
      The resolution in Angstrom. Null if not applicable
    - rFree
```
float rFree
```
      The rfree. Null if not applicable
    - rWork
```
float rWork
```
      The r-work. Null if not applicable
    - entityList
```
Entity[] entityList
```
      The list of entities in this structure.
    - depositionDate
```
String depositionDate
```
      The deposition date of the structure in ISO time standard format. https://www.cl.cam.ac.uk/~mgk25/iso-time.html
    - releaseDate
```
String releaseDate
```
      The release data of the structure in ISO time standard format. https://www.cl.cam.ac.uk/~mgk25/iso-time.html
    - ncsOperatorList
```
double[][] ncsOperatorList
```
      A float array for the NCS operator expression matrices, derived from the mmCIF file.

Serialized Form

Package org.rcsb.mmtf.dataholders

Class org.rcsb.mmtf.dataholders.BioAssemblyData extends Object implements Serializable

Serialized Fields

transformList

name

Class org.rcsb.mmtf.dataholders.BioAssemblyTransformation extends Object implements Serializable

Serialized Fields

chainIndexList

matrix

Class org.rcsb.mmtf.dataholders.Entity extends Object implements Serializable

Serialized Fields

description

type

chainIndexList

sequence

Class org.rcsb.mmtf.dataholders.Group extends Object implements Serializable

Serialized Fields

groupName

atomNameList

elementList

bondOrderList

bondAtomList

formalChargeList

singleLetterCode

chemCompType

Class org.rcsb.mmtf.dataholders.MmtfStructure extends Object implements Serializable

Serialized Fields

mmtfVersion

mmtfProducer

numBonds

numAtoms

numGroups

numChains

numModels

structureId

title

chainsPerModel

groupsPerChain

chainNameList

chainIdList

spaceGroup

unitCell

bioAssemblyList

bondAtomList

bondOrderList

groupList

xCoordList

yCoordList

zCoordList

bFactorList

secStructList

occupancyList

altLocList

insCodeList

groupTypeList

groupIdList

atomIdList

sequenceIndexList

experimentalMethods

resolution

rFree

rWork

entityList

depositionDate

releaseDate

ncsOperatorList