StructureDataInterface (mmtf 1.0.0 API)

All Known Implementing Classes:

AdapterToStructureData, GenericDecoder
```
public interface StructureDataInterface
```
An interface describing the data API.
The structural data is accessible through this interface via a flat structure, instead of the usual hierarchical data encountered in PDB structures: structure to model to chain to group to atom. Going back to a hierarchical view of the structure can be achieved by using the getChainsPerModel(), getGroupsPerChain() and getGroupTypeIndices() methods so that the flat arrays can be reconstructed into a hierarchy.
Please refer to the full MMTF specification available at http://mmtf.rcsb.org. Further reference can be found in the mmCIF dictionary.

Author:

Anthony Bradley, Jose Duarte

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`char[]`	`getAltLocIds()` Returns an array of location ids of the atoms.
`int[]`	`getAtomIds()` Returns an array of atom serial ids (_atom_site.id in mmCIF dictionary).
`float[]`	`getbFactors()` Returns an array containing the B-factors (temperature factors) of the atoms in Angstroms^2.
`String`	`getBioassemblyName(int bioassemblyIndex)` Returns the name of the transformation for a bioassembly.
`String[]`	`getChainIds()` Returns an array of internal chain identifiers (asym_ids in mmCIF dictionary), of length the number of chains (polymeric, non-polymeric and water) in the structure.
`int[]`	`getChainIndexListForTransform(int bioassemblyIndex, int transformationIndex)` Returns the list of chain indices for the given transformation for the given bioassembly.
`String[]`	`getChainNames()` Returns an array of public chain identifiers (auth_ids in mmCIF dictionary), of length the number of chains (polymeric, non-polymeric and water) in the structure.
`int[]`	`getChainsPerModel()` Returns an array containing the number of chains (polymeric/non-polymeric/water) in each model.
`String`	`getDepositionDate()` Returns the deposition date of the structure as a string in ISO time standard format.
`int[]`	`getEntityChainIndexList(int entityInd)` Returns the chain indices for the entity specified by the index.
`String`	`getEntityDescription(int entityInd)` Returns the entity description (as defined in mmCIF dictionary) for the entity specified by the index.
`String`	`getEntitySequence(int entityInd)` Returns the sequence for the entity specified by the index.
`String`	`getEntityType(int entityInd)` Returns the entity type (polymer, non-polymer, water) for the entity specified by the index.
`String[]`	`getExperimentalMethods()` Returns the experimental methods as an array of strings.
`int[]`	`getGroupAtomCharges(int groupInd)` Returns the atom charges for the group specified in `getGroupTypeIndices()`.
`String[]`	`getGroupAtomNames(int groupInd)` Returns the atom names (e.g.
`int[]`	`getGroupBondIndices(int groupInd)` Returns the zero-based bond indices (in pairs) for the group specified in `getGroupTypeIndices()`.
`int[]`	`getGroupBondOrders(int groupInd)` Returns the bond orders for the group specified in `getGroupTypeIndices()`.
`String`	`getGroupChemCompType(int groupInd)` Returns the chemical component type for the group specified in `getGroupTypeIndices()`.
`String[]`	`getGroupElementNames(int groupInd)` Returns the IUPAC element names (e.g.
`int[]`	`getGroupIds()` Returns an array containing residue numbers (auth_seq_id in mmCIF dictionary) for each residue (group).
`String`	`getGroupName(int groupInd)` Returns the group name for the group specified in `getGroupTypeIndices()`.
`int[]`	`getGroupSequenceIndices()` Returns an array containing the indices of groups (residues) in their corresponding sequences, obtainable through `getEntitySequence(int)`.
`char`	`getGroupSingleLetterCode(int groupInd)` Returns the single letter amino acid code or nucleotide code for the group specified in `getGroupTypeIndices()`.
`int[]`	`getGroupsPerChain()` Returns an array containing the number of groups (residues) in each chain.
`int[]`	`getGroupTypeIndices()` Returns an array containing indices to be used to obtain group level information, e.g.
`char[]`	`getInsCodes()` Returns an array containing the insertion codes (pdbx_PDB_ins_code in mmCIF dictionary) for each residue (group).
`int[]`	`getInterGroupBondIndices()` Returns the zero-based bond indices (in pairs) for the structure.
`int[]`	`getInterGroupBondOrders()` Returns an array of bond orders (1,2,3) of inter-group bonds with length number of inter-group bonds
`double[]`	`getMatrixForTransform(int bioassemblyIndex, int transformationIndex)` Returns a 4x4 transformation matrix for the given transformation for the given bioassembly.
`String`	`getMmtfProducer()` Returns a string describing the producer of the MMTF file.
`String`	`getMmtfVersion()` Returns the MMTF version number (from the specification).
`double[][]`	`getNcsOperatorList()` Returns the NCS operation matrix list.
`int`	`getNumAtoms()` Returns the number of atoms in the structure.
`int`	`getNumAtomsInGroup(int groupInd)` Returns the number of atoms in the group specified in `getGroupTypeIndices()`.
`int`	`getNumBioassemblies()` Returns the number of bioassemblies in this structure.
`int`	`getNumBonds()` Returns the total number of bonds in the structure
`int`	`getNumChains()` Returns the number of chains (for all models) in the structure.
`int`	`getNumEntities()` Returns the number of entities (as defined in mmCIF dictionary) in the structure
`int`	`getNumGroups()` Returns the number of groups (residues) in the structure that have experimentally determined 3D coordinates.
`int`	`getNumModels()` Returns the number of models in the structure.
`int`	`getNumTransInBioassembly(int bioassemblyIndex)` Returns the number of transformations in a given bioassembly.
`float[]`	`getOccupancies()` Returns an array containing the occupancy values of the atoms.
`String`	`getReleaseDate()` Returns the release date of the structure as a string in ISO time standard format.
`float`	`getResolution()` Returns the resolution of the dataset.
`float`	`getRfree()` Returns the Rfree of the dataset.
`float`	`getRwork()` Returns the Rwork of the dataset.
`int[]`	`getSecStructList()` Returns the secondary structure information for the structure as a list of integers
`String`	`getSpaceGroup()` Returns the space group of the structure.
`String`	`getStructureId()` Returns the identifier of the structure.
`String`	`getTitle()` Returns the title of the structure.
`float[]`	`getUnitCell()` Returns the 6 floats that describe the unit cell.
`float[]`	`getxCoords()` Returns an array containing the X coordinates of the atoms in Angstroms.
`float[]`	`getyCoords()` Returns an array containing the Y coordinates of the atoms in Angstroms.
`float[]`	`getzCoords()` Returns an array containing the Z coordinates of the atoms in Angstroms.

- Method Detail
  - getxCoords
```
float[] getxCoords()
```
    Returns an array containing the X coordinates of the atoms in Angstroms.
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with getNumAtoms()
  - getyCoords
```
float[] getyCoords()
```
    Returns an array containing the Y coordinates of the atoms in Angstroms.
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with getNumAtoms()
  - getzCoords
```
float[] getzCoords()
```
    Returns an array containing the Z coordinates of the atoms in Angstroms.
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with getNumAtoms()
  - getbFactors
```
float[] getbFactors()
```
    Returns an array containing the B-factors (temperature factors) of the atoms in Angstroms^2.
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with getNumAtoms()
  - getOccupancies
```
float[] getOccupancies()
```
    Returns an array containing the occupancy values of the atoms.
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with getNumAtoms()
  - getAtomIds
```
int[] getAtomIds()
```
    Returns an array of atom serial ids (_atom_site.id in mmCIF dictionary).
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with getNumAtoms()
  - getAltLocIds
```
char[] getAltLocIds()
```
    Returns an array of location ids of the atoms. '\0' specifies a lack of alt id.
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with getNumAtoms()
  - getInsCodes
```
char[] getInsCodes()
```
    Returns an array containing the insertion codes (pdbx_PDB_ins_code in mmCIF dictionary) for each residue (group). '\0' specifies a lack of insertion code.
    
    Returns:
    
    an array with insertion codes, of size getNumGroups()
    
    See Also:
    
    getGroupIds()
  - getGroupIds
```
int[] getGroupIds()
```
    Returns an array containing residue numbers (auth_seq_id in mmCIF dictionary) for each residue (group).
    
    Returns:
    
    an array with with residue numbers, of size getNumGroups()
    
    See Also:
    
    getInsCodes()
  - getGroupName
```
String getGroupName(int groupInd)
```
    Returns the group name for the group specified in getGroupTypeIndices(). to link groups to the 3 letter group name, e.g. HIS.
    
    Parameters:
    
    groupInd - The index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    a 3 letter string specifiying the group name.
  - getNumAtomsInGroup
```
int getNumAtomsInGroup(int groupInd)
```
    Returns the number of atoms in the group specified in getGroupTypeIndices().
    
    Parameters:
    
    groupInd - The index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    The number of atoms in the group
  - getGroupAtomNames
```
String[] getGroupAtomNames(int groupInd)
```
    Returns the atom names (e.g. CB) for the group specified in getGroupTypeIndices(). Atom names are unique for each unique atom in a group.
    
    Parameters:
    
    groupInd - The index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    A list of strings for the atom names.
  - getGroupElementNames
```
String[] getGroupElementNames(int groupInd)
```
    Returns the IUPAC element names (e.g. Ca is calcium) for the group specified in getGroupTypeIndices().
    
    Parameters:
    
    groupInd - the index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    an array of strings for the element information.
  - getGroupBondOrders
```
int[] getGroupBondOrders(int groupInd)
```
    Returns the bond orders for the group specified in getGroupTypeIndices(). A list of integers indicating the bond orders
    
    Parameters:
    
    groupInd - the index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    an array of integers (1,2 or 3) indicating the bond orders.
  - getGroupBondIndices
```
int[] getGroupBondIndices(int groupInd)
```
    Returns the zero-based bond indices (in pairs) for the group specified in getGroupTypeIndices(). (e.g. 0,1 means there is bond between atom 0 and 1).
    
    Parameters:
    
    groupInd - the index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    an array of integers specifying the bond indices (within the group). Indices are zero indexed.
  - getGroupAtomCharges
```
int[] getGroupAtomCharges(int groupInd)
```
    Returns the atom charges for the group specified in getGroupTypeIndices().
    
    Parameters:
    
    groupInd - the index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    an array of integers indicating the atomic charge for each atom in the group.
  - getGroupSingleLetterCode
```
char getGroupSingleLetterCode(int groupInd)
```
    Returns the single letter amino acid code or nucleotide code for the group specified in getGroupTypeIndices().
    
    Parameters:
    
    groupInd - the index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    the single letter amino acid or nucleotide, 'X' if non-standard amino acid or nucleotide
  - getGroupChemCompType
```
String getGroupChemCompType(int groupInd)
```
    Returns the chemical component type for the group specified in getGroupTypeIndices().
    
    Parameters:
    
    groupInd - The index of the group specified in getGroupTypeIndices().
    
    Returns:
    
    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
  - getGroupTypeIndices
```
int[] getGroupTypeIndices()
```
    Returns an array containing indices to be used to obtain group level information, e.g. through getGroupAtomCharges(int).
    
    Returns:
    
    an array of length the number of groups (residues) in the structure, obtainable with getNumGroups()
  - getGroupSequenceIndices
```
int[] getGroupSequenceIndices()
```
    Returns an array containing the indices of groups (residues) in their corresponding sequences, obtainable through getEntitySequence(int). The indices are 0-based and specified per entity, -1 indicates the group is not present in the sequence.
    
    Returns:
    
    an array of length the number of groups (residues) in the structure, obtainable with getNumGroups()
  - getChainIds
```
String[] getChainIds()
```
    Returns an array of internal chain identifiers (asym_ids in mmCIF dictionary), of length the number of chains (polymeric, non-polymeric and water) in the structure.
    
    Returns:
    
    an array of length the number of chains in the structure, obtainable with getNumChains()
    
    See Also:
    
    getChainNames()
  - getChainNames
```
String[] getChainNames()
```
    Returns an array of public chain identifiers (auth_ids in mmCIF dictionary), of length the number of chains (polymeric, non-polymeric and water) in the structure.
    
    Returns:
    
    an array of length the number of chains in the structure, obtainable with getNumChains()
    
    See Also:
    
    getChainIds()
  - getChainsPerModel
```
int[] getChainsPerModel()
```
    Returns an array containing the number of chains (polymeric/non-polymeric/water) in each model.
    
    Returns:
    
    an array of length the number of models in the structure, obtainable with getNumModels()
  - getGroupsPerChain
```
int[] getGroupsPerChain()
```
    Returns an array containing the number of groups (residues) in each chain.
    
    Returns:
    
    an array of length the number of chains in the structure, obtainable with getNumChains()
  - getSpaceGroup
```
String getSpaceGroup()
```
    Returns the space group of the structure.
    
    Returns:
    
    the space group name (e.g. "P 21 21 21") or null if the structure is not crystallographic
  - getUnitCell
```
float[] getUnitCell()
```
    Returns the 6 floats that describe the unit cell.
    
    Returns:
    
    an array of size 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma
  - getNumBioassemblies
```
int getNumBioassemblies()
```
    Returns the number of bioassemblies in this structure.
    
    Returns:
    
    the number of bioassemblies.
  - getNumTransInBioassembly
```
int getNumTransInBioassembly(int bioassemblyIndex)
```
    Returns the number of transformations in a given bioassembly.
    
    Parameters:
    
    bioassemblyIndex - an integer specifying the bioassembly index (zero indexed).
    
    Returns:
    
    an integer specifying the number of transformations in a given bioassembly.
  - getBioassemblyName
```
String getBioassemblyName(int bioassemblyIndex)
```
    Returns the name of the transformation for a bioassembly.
    
    Parameters:
    
    bioassemblyIndex - an integer specifying the bioassembly index (zero indexed).
    
    Returns:
    
    a string specifying the name of a given bioassembly.
  - getChainIndexListForTransform
```
int[] getChainIndexListForTransform(int bioassemblyIndex,
                                    int transformationIndex)
```
    Returns the list of chain indices for the given transformation for the given bioassembly.
    
    Parameters:
    
    bioassemblyIndex - an integer specifying the bioassembly index (zero indexed).
    
    transformationIndex - an integer specifying the index (zero indexed) for the desired transformation.
    
    Returns:
    
    a list of indices showing the chains involved in this transformation.
  - getMatrixForTransform
```
double[] getMatrixForTransform(int bioassemblyIndex,
                               int transformationIndex)
```
    Returns a 4x4 transformation matrix for the given transformation for the given bioassembly. It is row-packed as per the convention of vecmath. (The first four elements are in the first row of the overall matrix).
    
    Parameters:
    
    bioassemblyIndex - an integer specifying the bioassembly index (zero indexed).
    
    transformationIndex - an integer specifying the index for the desired transformation (zero indexed).
    
    Returns:
    
    the transformation matrix for this transformation.
  - getInterGroupBondIndices
```
int[] getInterGroupBondIndices()
```
    Returns the zero-based bond indices (in pairs) for the structure. (e.g. 0,1 means there is bond between atom 0 and 1).
    
    Returns:
    
    an array of integers specifying the bond indices (within the structure). Indices are zero-based.
  - getInterGroupBondOrders
```
int[] getInterGroupBondOrders()
```
    Returns an array of bond orders (1,2,3) of inter-group bonds with length number of inter-group bonds
    
    Returns:
    
    the bond orders for bonds within a group
  - getMmtfVersion
```
String getMmtfVersion()
```
    Returns the MMTF version number (from the specification).
    
    Returns:
    
    the version
  - getMmtfProducer
```
String getMmtfProducer()
```
    Returns a string describing the producer of the MMTF file. e.g. "RCSB-PDB Generator---version: 6b8635f8d319beea9cd7cc7f5dd2649578ac01a0"
    
    Returns:
    
    a string describing the producer
  - getNumEntities
```
int getNumEntities()
```
    Returns the number of entities (as defined in mmCIF dictionary) in the structure
    
    Returns:
    
    the number of entities in the structure
  - getEntityDescription
```
String getEntityDescription(int entityInd)
```
    Returns the entity description (as defined in mmCIF dictionary) for the entity specified by the index.
    
    Parameters:
    
    entityInd - the index of the specified entity.
    
    Returns:
    
    the description of the entity
  - getEntityType
```
String getEntityType(int entityInd)
```
    Returns the entity type (polymer, non-polymer, water) for the entity specified by the index.
    
    Parameters:
    
    entityInd - the index of the specified entity.
    
    Returns:
    
    the entity type (polymer, non-polymer, water)
  - getEntityChainIndexList
```
int[] getEntityChainIndexList(int entityInd)
```
    Returns the chain indices for the entity specified by the index.
    
    Parameters:
    
    entityInd - the index of the specified entity.
    
    Returns:
    
    the chain index list - referencing the entity to the chains.
  - getEntitySequence
```
String getEntitySequence(int entityInd)
```
    Returns the sequence for the entity specified by the index.
    
    Parameters:
    
    entityInd - the index of the specified entity.
    
    Returns:
    
    the one letter sequence for this entity. Empty string if no sequence is applicable.
  - getStructureId
```
String getStructureId()
```
    Returns the identifier of the structure. For instance the 4-letter PDB id
    
    Returns:
    
    the identifier
  - getNumModels
```
int getNumModels()
```
    Returns the number of models in the structure.
    
    Returns:
    
    the number of models
  - getNumBonds
```
int getNumBonds()
```
    Returns the total number of bonds in the structure
    
    Returns:
    
    the number of bonds
  - getNumChains
```
int getNumChains()
```
    Returns the number of chains (for all models) in the structure.
    
    Returns:
    
    the number of chains for all models
    
    See Also:
    
    getChainsPerModel()
  - getNumGroups
```
int getNumGroups()
```
    Returns the number of groups (residues) in the structure that have experimentally determined 3D coordinates.
    
    Returns:
    
    the number of residues in the structure, for all models and chains
  - getNumAtoms
```
int getNumAtoms()
```
    Returns the number of atoms in the structure.
    
    Returns:
    
    the number of atoms in the structure, for all models and chains
  - getRfree
```
float getRfree()
```
    Returns the Rfree of the dataset.
    
    Returns:
    
    the Rfree value
  - getRwork
```
float getRwork()
```
    Returns the Rwork of the dataset.
    
    Returns:
    
    the Rwork value
  - getResolution
```
float getResolution()
```
    Returns the resolution of the dataset.
    
    Returns:
    
    the resolution value in Angstroms
  - getTitle
```
String getTitle()
```
    Returns the title of the structure.
    
    Returns:
    
    the title of the structure.
  - getExperimentalMethods
```
String[] getExperimentalMethods()
```
    Returns the experimental methods as an array of strings. Normally only one experimental method is available, but structures solved with hybrid methods will have more than one method. The possible experimental method values are described in data item _exptl.method of the mmCIF dictionary
    
    Returns:
    
    the list of experimental methods
  - getDepositionDate
```
String getDepositionDate()
```
    Returns the deposition date of the structure as a string in ISO time standard format. https://www.cl.cam.ac.uk/~mgk25/iso-time.html
    
    Returns:
    
    the deposition date of the structure.
  - getReleaseDate
```
String getReleaseDate()
```
    Returns the release date of the structure as a string in ISO time standard format. https://www.cl.cam.ac.uk/~mgk25/iso-time.html
    
    Returns:
    
    the release date of the structure.
  - getSecStructList
```
int[] getSecStructList()
```
    Returns the secondary structure information for the structure as a list of integers
    
    Returns:
    
    the array of secondary structure informations
  - getNcsOperatorList
```
double[][] getNcsOperatorList()
```
    Returns the NCS operation matrix list.
    
    Returns:
    
    the NCS operation matrix list for this structure

Interface StructureDataInterface

Method Summary

Method Detail

getxCoords

getyCoords

getzCoords

getbFactors

getOccupancies

getAtomIds

getAltLocIds

getInsCodes

getGroupIds

getGroupName

getNumAtomsInGroup

getGroupAtomNames

getGroupElementNames

getGroupBondOrders

getGroupBondIndices

getGroupAtomCharges

getGroupSingleLetterCode

getGroupChemCompType

getGroupTypeIndices

getGroupSequenceIndices

getChainIds

getChainNames

getChainsPerModel

getGroupsPerChain

getSpaceGroup

getUnitCell

getNumBioassemblies

getNumTransInBioassembly

getBioassemblyName

getChainIndexListForTransform

getMatrixForTransform

getInterGroupBondIndices

getInterGroupBondOrders

getMmtfVersion

getMmtfProducer

getNumEntities

getEntityDescription

getEntityType

getEntityChainIndexList

getEntitySequence

getStructureId

getNumModels

getNumBonds

getNumChains

getNumGroups

getNumAtoms

getRfree

getRwork

getResolution

getTitle

getExperimentalMethods

getDepositionDate

getReleaseDate

getSecStructList

getNcsOperatorList