AdapterToStructureData (mmtf 1.0.0 API)

java.lang.Object
- org.rcsb.mmtf.encoder.AdapterToStructureData

All Implemented Interfaces:

StructureAdapterInterface, StructureDataInterface
```
public class AdapterToStructureData
extends Object
implements StructureDataInterface, StructureAdapterInterface
```
A class to move data from the StructureAdapterInterface to the StructureDataInterface.

Author:

Anthony Bradley

Constructor Summary

Constructors
Constructor and Description

AdapterToStructureData()

Constructors
Constructor and Description
`AdapterToStructureData()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`finalizeStructure()` A generic function to be used at the end of all data addition to do required cleanup on the structure
`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 `StructureDataInterface.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 `StructureDataInterface.getGroupTypeIndices()`.
`int[]`	`getGroupBondOrders(int groupInd)` Returns the bond orders for the group specified in `StructureDataInterface.getGroupTypeIndices()`.
`String`	`getGroupChemCompType(int groupInd)` Returns the chemical component type for the group specified in `StructureDataInterface.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 `StructureDataInterface.getGroupTypeIndices()`.
`int[]`	`getGroupSequenceIndices()` Returns an array containing the indices of groups (residues) in their corresponding sequences, obtainable through `StructureDataInterface.getEntitySequence(int)`.
`char`	`getGroupSingleLetterCode(int groupInd)` Returns the single letter amino acid code or nucleotide code for the group specified in `StructureDataInterface.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 `StructureDataInterface.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.
`void`	`initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups, int totalNumChains, int totalNumModels, String structureId)` Used before any additions to do any required pre-processing.
`void`	`setAtomInfo(String atomName, int serialNumber, char alternativeLocationId, float x, float y, float z, float occupancy, float temperatureFactor, String element, int charge)` Sets the atom level information for a given atom.
`void`	`setBioAssemblyTrans(int bioAssemblyIndex, int[] chainIndices, double[] transform, String name)` Sets a single Bioassembly transformation to a structure.
`void`	`setChainInfo(String chainId, String chainName, int groupCount)` Sets the information for a given chain.
`void`	`setEntityInfo(int[] chainIndices, String sequence, String description, String title)` Sets the entity level annotation for a chain(s).
`void`	`setGroupBond(int firstAtomIndex, int secondAtomIndex, int bondOrder)` Sets an intra-group bond.
`void`	`setGroupInfo(String groupName, int groupNumber, char insertionCode, String polymerType, int atomCount, int bondCount, char singleAtomCode, int sequenceIndex, int secStructType)` Sets the information for a given group / residue with atomic data.
`void`	`setHeaderInfo(float rFree, float rWork, float resolution, String title, String depositionDate, String releaseDate, String[] experimnetalMethods)` Sets the header information.
`void`	`setInterGroupBond(int firstAtomIndex, int secondAtomIndex, int bondOrder)` Sets an inter-group bond.
`void`	`setModelInfo(int modelId, int chainCount)` Sets the number of chains for a given model.
`void`	`setXtalInfo(String spaceGroup, float[] unitCell, double[][] ncsOperMatrixList)` Sets the space group and unit cell information.

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()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing the X coordinates of the atoms in Angstroms.
    
    Specified by:
    
    getxCoords in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with StructureDataInterface.getNumAtoms()
  - getyCoords
```
public float[] getyCoords()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing the Y coordinates of the atoms in Angstroms.
    
    Specified by:
    
    getyCoords in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with StructureDataInterface.getNumAtoms()
  - getzCoords
```
public float[] getzCoords()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing the Z coordinates of the atoms in Angstroms.
    
    Specified by:
    
    getzCoords in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with StructureDataInterface.getNumAtoms()
  - getbFactors
```
public float[] getbFactors()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing the B-factors (temperature factors) of the atoms in Angstroms^2.
    
    Specified by:
    
    getbFactors in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with StructureDataInterface.getNumAtoms()
  - getOccupancies
```
public float[] getOccupancies()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing the occupancy values of the atoms.
    
    Specified by:
    
    getOccupancies in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with StructureDataInterface.getNumAtoms()
  - getAtomIds
```
public int[] getAtomIds()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array of atom serial ids (_atom_site.id in mmCIF dictionary).
    
    Specified by:
    
    getAtomIds in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with StructureDataInterface.getNumAtoms()
  - getAltLocIds
```
public char[] getAltLocIds()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array of location ids of the atoms. '\0' specifies a lack of alt id.
    
    Specified by:
    
    getAltLocIds in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of atoms in the structure, obtainable with StructureDataInterface.getNumAtoms()
  - getInsCodes
```
public char[] getInsCodes()
```
    Description copied from interface: StructureDataInterface
    
    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.
    
    Specified by:
    
    getInsCodes in interface StructureDataInterface
    
    Returns:
    
    an array with insertion codes, of size StructureDataInterface.getNumGroups()
    
    See Also:
    
    StructureDataInterface.getGroupIds()
  - getGroupIds
```
public int[] getGroupIds()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing residue numbers (auth_seq_id in mmCIF dictionary) for each residue (group).
    
    Specified by:
    
    getGroupIds in interface StructureDataInterface
    
    Returns:
    
    an array with with residue numbers, of size StructureDataInterface.getNumGroups()
    
    See Also:
    
    StructureDataInterface.getInsCodes()
  - getGroupName
```
public String getGroupName(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the group name for the group specified in StructureDataInterface.getGroupTypeIndices(). to link groups to the 3 letter group name, e.g. HIS.
    
    Specified by:
    
    getGroupName in interface StructureDataInterface
    
    Parameters:
    
    groupInd - The index of the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Returns:
    
    a 3 letter string specifiying the group name.
  - getNumAtomsInGroup
```
public int getNumAtomsInGroup(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the number of atoms in the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Specified by:
    
    getNumAtomsInGroup in interface StructureDataInterface
    
    Parameters:
    
    groupInd - The index of the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Returns:
    
    The number of atoms in the group
  - getGroupAtomNames
```
public String[] getGroupAtomNames(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the atom names (e.g. CB) for the group specified in StructureDataInterface.getGroupTypeIndices(). Atom names are unique for each unique atom in a group.
    
    Specified by:
    
    getGroupAtomNames in interface StructureDataInterface
    
    Parameters:
    
    groupInd - The index of the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Returns:
    
    A list of strings for the atom names.
  - getGroupElementNames
```
public String[] getGroupElementNames(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the IUPAC element names (e.g. Ca is calcium) for the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Specified by:
    
    getGroupElementNames in interface StructureDataInterface
    
    Parameters:
    
    groupInd - the index of the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Returns:
    
    an array of strings for the element information.
  - getGroupBondOrders
```
public int[] getGroupBondOrders(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the bond orders for the group specified in StructureDataInterface.getGroupTypeIndices(). A list of integers indicating the bond orders
    
    Specified by:
    
    getGroupBondOrders in interface StructureDataInterface
    
    Parameters:
    
    groupInd - the index of the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Returns:
    
    an array of integers (1,2 or 3) indicating the bond orders.
  - getGroupBondIndices
```
public int[] getGroupBondIndices(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the zero-based bond indices (in pairs) for the group specified in StructureDataInterface.getGroupTypeIndices(). (e.g. 0,1 means there is bond between atom 0 and 1).
    
    Specified by:
    
    getGroupBondIndices in interface StructureDataInterface
    
    Parameters:
    
    groupInd - the index of the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Returns:
    
    an array of integers specifying the bond indices (within the group). Indices are zero indexed.
  - getGroupAtomCharges
```
public int[] getGroupAtomCharges(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the atom charges for the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Specified by:
    
    getGroupAtomCharges in interface StructureDataInterface
    
    Parameters:
    
    groupInd - the index of the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Returns:
    
    an array of integers indicating the atomic charge for each atom in the group.
  - getGroupSingleLetterCode
```
public char getGroupSingleLetterCode(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the single letter amino acid code or nucleotide code for the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Specified by:
    
    getGroupSingleLetterCode in interface StructureDataInterface
    
    Parameters:
    
    groupInd - the index of the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Returns:
    
    the single letter amino acid or nucleotide, 'X' if non-standard amino acid or nucleotide
  - getGroupChemCompType
```
public String getGroupChemCompType(int groupInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the chemical component type for the group specified in StructureDataInterface.getGroupTypeIndices().
    
    Specified by:
    
    getGroupChemCompType in interface StructureDataInterface
    
    Parameters:
    
    groupInd - The index of the group specified in StructureDataInterface.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
```
public int[] getGroupTypeIndices()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing indices to be used to obtain group level information, e.g. through StructureDataInterface.getGroupAtomCharges(int).
    
    Specified by:
    
    getGroupTypeIndices in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of groups (residues) in the structure, obtainable with StructureDataInterface.getNumGroups()
  - getGroupSequenceIndices
```
public int[] getGroupSequenceIndices()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing the indices of groups (residues) in their corresponding sequences, obtainable through StructureDataInterface.getEntitySequence(int). The indices are 0-based and specified per entity, -1 indicates the group is not present in the sequence.
    
    Specified by:
    
    getGroupSequenceIndices in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of groups (residues) in the structure, obtainable with StructureDataInterface.getNumGroups()
  - getChainIds
```
public String[] getChainIds()
```
    Description copied from interface: StructureDataInterface
    
    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.
    
    Specified by:
    
    getChainIds in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of chains in the structure, obtainable with StructureDataInterface.getNumChains()
    
    See Also:
    
    StructureDataInterface.getChainNames()
  - getChainNames
```
public String[] getChainNames()
```
    Description copied from interface: StructureDataInterface
    
    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.
    
    Specified by:
    
    getChainNames in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of chains in the structure, obtainable with StructureDataInterface.getNumChains()
    
    See Also:
    
    StructureDataInterface.getChainIds()
  - getChainsPerModel
```
public int[] getChainsPerModel()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing the number of chains (polymeric/non-polymeric/water) in each model.
    
    Specified by:
    
    getChainsPerModel in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of models in the structure, obtainable with StructureDataInterface.getNumModels()
  - getGroupsPerChain
```
public int[] getGroupsPerChain()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array containing the number of groups (residues) in each chain.
    
    Specified by:
    
    getGroupsPerChain in interface StructureDataInterface
    
    Returns:
    
    an array of length the number of chains in the structure, obtainable with StructureDataInterface.getNumChains()
  - getSpaceGroup
```
public String getSpaceGroup()
```
    Description copied from interface: StructureDataInterface
    
    Returns the space group of the structure.
    
    Specified by:
    
    getSpaceGroup in interface StructureDataInterface
    
    Returns:
    
    the space group name (e.g. "P 21 21 21") or null if the structure is not crystallographic
  - getUnitCell
```
public float[] getUnitCell()
```
    Description copied from interface: StructureDataInterface
    
    Returns the 6 floats that describe the unit cell.
    
    Specified by:
    
    getUnitCell in interface StructureDataInterface
    
    Returns:
    
    an array of size 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma
  - getNumBioassemblies
```
public int getNumBioassemblies()
```
    Description copied from interface: StructureDataInterface
    
    Returns the number of bioassemblies in this structure.
    
    Specified by:
    
    getNumBioassemblies in interface StructureDataInterface
    
    Returns:
    
    the number of bioassemblies.
  - getNumTransInBioassembly
```
public int getNumTransInBioassembly(int bioassemblyIndex)
```
    Description copied from interface: StructureDataInterface
    
    Returns the number of transformations in a given bioassembly.
    
    Specified by:
    
    getNumTransInBioassembly in interface StructureDataInterface
    
    Parameters:
    
    bioassemblyIndex - an integer specifying the bioassembly index (zero indexed).
    
    Returns:
    
    an integer specifying the number of transformations in a given bioassembly.
  - getChainIndexListForTransform
```
public int[] getChainIndexListForTransform(int bioassemblyIndex,
                                           int transformationIndex)
```
    Description copied from interface: StructureDataInterface
    
    Returns the list of chain indices for the given transformation for the given bioassembly.
    
    Specified by:
    
    getChainIndexListForTransform in interface StructureDataInterface
    
    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
```
public double[] getMatrixForTransform(int bioassemblyIndex,
                                      int transformationIndex)
```
    Description copied from interface: StructureDataInterface
    
    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).
    
    Specified by:
    
    getMatrixForTransform in interface StructureDataInterface
    
    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
```
public int[] getInterGroupBondIndices()
```
    Description copied from interface: StructureDataInterface
    
    Returns the zero-based bond indices (in pairs) for the structure. (e.g. 0,1 means there is bond between atom 0 and 1).
    
    Specified by:
    
    getInterGroupBondIndices in interface StructureDataInterface
    
    Returns:
    
    an array of integers specifying the bond indices (within the structure). Indices are zero-based.
  - getInterGroupBondOrders
```
public int[] getInterGroupBondOrders()
```
    Description copied from interface: StructureDataInterface
    
    Returns an array of bond orders (1,2,3) of inter-group bonds with length number of inter-group bonds
    
    Specified by:
    
    getInterGroupBondOrders in interface StructureDataInterface
    
    Returns:
    
    the bond orders for bonds within a group
  - getMmtfVersion
```
public String getMmtfVersion()
```
    Description copied from interface: StructureDataInterface
    
    Returns the MMTF version number (from the specification).
    
    Specified by:
    
    getMmtfVersion in interface StructureDataInterface
    
    Returns:
    
    the version
  - getMmtfProducer
```
public String getMmtfProducer()
```
    Description copied from interface: StructureDataInterface
    
    Returns a string describing the producer of the MMTF file. e.g. "RCSB-PDB Generator---version: 6b8635f8d319beea9cd7cc7f5dd2649578ac01a0"
    
    Specified by:
    
    getMmtfProducer in interface StructureDataInterface
    
    Returns:
    
    a string describing the producer
  - getNumEntities
```
public int getNumEntities()
```
    Description copied from interface: StructureDataInterface
    
    Returns the number of entities (as defined in mmCIF dictionary) in the structure
    
    Specified by:
    
    getNumEntities in interface StructureDataInterface
    
    Returns:
    
    the number of entities in the structure
  - getEntityDescription
```
public String getEntityDescription(int entityInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the entity description (as defined in mmCIF dictionary) for the entity specified by the index.
    
    Specified by:
    
    getEntityDescription in interface StructureDataInterface
    
    Parameters:
    
    entityInd - the index of the specified entity.
    
    Returns:
    
    the description of the entity
  - getEntityType
```
public String getEntityType(int entityInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the entity type (polymer, non-polymer, water) for the entity specified by the index.
    
    Specified by:
    
    getEntityType in interface StructureDataInterface
    
    Parameters:
    
    entityInd - the index of the specified entity.
    
    Returns:
    
    the entity type (polymer, non-polymer, water)
  - getEntityChainIndexList
```
public int[] getEntityChainIndexList(int entityInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the chain indices for the entity specified by the index.
    
    Specified by:
    
    getEntityChainIndexList in interface StructureDataInterface
    
    Parameters:
    
    entityInd - the index of the specified entity.
    
    Returns:
    
    the chain index list - referencing the entity to the chains.
  - getEntitySequence
```
public String getEntitySequence(int entityInd)
```
    Description copied from interface: StructureDataInterface
    
    Returns the sequence for the entity specified by the index.
    
    Specified by:
    
    getEntitySequence in interface StructureDataInterface
    
    Parameters:
    
    entityInd - the index of the specified entity.
    
    Returns:
    
    the one letter sequence for this entity. Empty string if no sequence is applicable.
  - getStructureId
```
public String getStructureId()
```
    Description copied from interface: StructureDataInterface
    
    Returns the identifier of the structure. For instance the 4-letter PDB id
    
    Specified by:
    
    getStructureId in interface StructureDataInterface
    
    Returns:
    
    the identifier
  - getNumModels
```
public int getNumModels()
```
    Description copied from interface: StructureDataInterface
    
    Returns the number of models in the structure.
    
    Specified by:
    
    getNumModels in interface StructureDataInterface
    
    Returns:
    
    the number of models
  - getNumChains
```
public int getNumChains()
```
    Description copied from interface: StructureDataInterface
    
    Returns the number of chains (for all models) in the structure.
    
    Specified by:
    
    getNumChains in interface StructureDataInterface
    
    Returns:
    
    the number of chains for all models
    
    See Also:
    
    StructureDataInterface.getChainsPerModel()
  - getNumGroups
```
public int getNumGroups()
```
    Description copied from interface: StructureDataInterface
    
    Returns the number of groups (residues) in the structure that have experimentally determined 3D coordinates.
    
    Specified by:
    
    getNumGroups in interface StructureDataInterface
    
    Returns:
    
    the number of residues in the structure, for all models and chains
  - getNumAtoms
```
public int getNumAtoms()
```
    Description copied from interface: StructureDataInterface
    
    Returns the number of atoms in the structure.
    
    Specified by:
    
    getNumAtoms in interface StructureDataInterface
    
    Returns:
    
    the number of atoms in the structure, for all models and chains
  - getRfree
```
public float getRfree()
```
    Description copied from interface: StructureDataInterface
    
    Returns the Rfree of the dataset.
    
    Specified by:
    
    getRfree in interface StructureDataInterface
    
    Returns:
    
    the Rfree value
  - getRwork
```
public float getRwork()
```
    Description copied from interface: StructureDataInterface
    
    Returns the Rwork of the dataset.
    
    Specified by:
    
    getRwork in interface StructureDataInterface
    
    Returns:
    
    the Rwork value
  - getResolution
```
public float getResolution()
```
    Description copied from interface: StructureDataInterface
    
    Returns the resolution of the dataset.
    
    Specified by:
    
    getResolution in interface StructureDataInterface
    
    Returns:
    
    the resolution value in Angstroms
  - getTitle
```
public String getTitle()
```
    Description copied from interface: StructureDataInterface
    
    Returns the title of the structure.
    
    Specified by:
    
    getTitle in interface StructureDataInterface
    
    Returns:
    
    the title of the structure.
  - getExperimentalMethods
```
public String[] getExperimentalMethods()
```
    Description copied from interface: StructureDataInterface
    
    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
    
    Specified by:
    
    getExperimentalMethods in interface StructureDataInterface
    
    Returns:
    
    the list of experimental methods
  - getDepositionDate
```
public String getDepositionDate()
```
    Description copied from interface: StructureDataInterface
    
    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
    
    Specified by:
    
    getDepositionDate in interface StructureDataInterface
    
    Returns:
    
    the deposition date of the structure.
  - initStructure
```
public void initStructure(int totalNumBonds,
                          int totalNumAtoms,
                          int totalNumGroups,
                          int totalNumChains,
                          int totalNumModels,
                          String structureId)
```
    Description copied from interface: StructureAdapterInterface
    
    Used before any additions to do any required pre-processing. For example the user could use this to specify the amount of memory to be allocated.
    
    Specified by:
    
    initStructure in interface StructureAdapterInterface
    
    Parameters:
    
    totalNumBonds - the total number of bonds in the structure
    
    totalNumAtoms - the total number of atoms found in the data.
    
    totalNumGroups - the total number of groups found in the data.
    
    totalNumChains - the total number of chains found in the data.
    
    totalNumModels - the total number of models found in the data.
    
    structureId - an identifier for the structure (e.g. PDB id).
  - finalizeStructure
```
public void finalizeStructure()
```
    Description copied from interface: StructureAdapterInterface
    
    A generic function to be used at the end of all data addition to do required cleanup on the structure
    
    Specified by:
    
    finalizeStructure in interface StructureAdapterInterface
  - setModelInfo
```
public void setModelInfo(int modelId,
                         int chainCount)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets the number of chains for a given model.
    
    Specified by:
    
    setModelInfo in interface StructureAdapterInterface
    
    Parameters:
    
    modelId - identifier of the model within the structure
    
    chainCount - total number of chains within this model
  - setChainInfo
```
public void setChainInfo(String chainId,
                         String chainName,
                         int groupCount)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets the information for a given chain.
    
    Specified by:
    
    setChainInfo in interface StructureAdapterInterface
    
    Parameters:
    
    chainId - chain identifier - length of one to four
    
    chainName - chain name - public chain id
    
    groupCount - number of groups/residues in chain
  - setEntityInfo
```
public void setEntityInfo(int[] chainIndices,
                          String sequence,
                          String description,
                          String title)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets the entity level annotation for a chain(s). ChainIds is a list of integers that indicate the chains this information refers to. Sequence is the one letter amino acid sequence. Description and title are both free forms strings describing the entity and acting as a title for the entity.
    
    Specified by:
    
    setEntityInfo in interface StructureAdapterInterface
    
    Parameters:
    
    chainIndices - the indices of the chain this refers to.
    
    sequence - the full sequence of the entity
    
    description - the text description of the entity
    
    title - as a string (POLYMER/NON-POLYMER and WATER)
  - setGroupInfo
```
public void setGroupInfo(String groupName,
                         int groupNumber,
                         char insertionCode,
                         String polymerType,
                         int atomCount,
                         int bondCount,
                         char singleAtomCode,
                         int sequenceIndex,
                         int secStructType)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets the information for a given group / residue with atomic data.
    
    Specified by:
    
    setGroupInfo in interface StructureAdapterInterface
    
    Parameters:
    
    groupName - 3 letter code name of this group/residue
    
    groupNumber - sequence position of this group
    
    insertionCode - the one letter insertion code
    
    polymerType - a string indicating the type of group (as found in the chemcomp dictionary. Empty string if none available.
    
    atomCount - the number of atoms in the group
    
    bondCount - the number of unique bonds in the group
    
    singleAtomCode - the single letter code of the group
    
    sequenceIndex - the index of this group in the sequence
    
    secStructType - the type of secondary structure used (types are according to DSSP and number to type mappings are defined in the specification)
  - setAtomInfo
```
public void setAtomInfo(String atomName,
                        int serialNumber,
                        char alternativeLocationId,
                        float x,
                        float y,
                        float z,
                        float occupancy,
                        float temperatureFactor,
                        String element,
                        int charge)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets the atom level information for a given atom.
    
    Specified by:
    
    setAtomInfo in interface StructureAdapterInterface
    
    Parameters:
    
    atomName - 1-3 long string of the unique name of the atom
    
    serialNumber - a number counting atoms in a structure
    
    alternativeLocationId - a character indicating the alternate location of the atom
    
    x - the x cartesian coordinate
    
    y - the y cartesian coordinate
    
    z - the z cartesian coordinate
    
    occupancy - the atomic occupancy
    
    temperatureFactor - the B factor (temperature factor)
    
    element - a 1-3 long string indicating the chemical element of the atom
    
    charge - the atomic charge
  - setBioAssemblyTrans
```
public void setBioAssemblyTrans(int bioAssemblyIndex,
                                int[] chainIndices,
                                double[] transform,
                                String name)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets a single Bioassembly transformation to a structure. bioAssemblyId indicates the index of the bioassembly.
    
    Specified by:
    
    setBioAssemblyTrans in interface StructureAdapterInterface
    
    Parameters:
    
    bioAssemblyIndex - an integer index of this bioassembly.
    
    chainIndices - the integer indices of the chains involved in this bioassembly.
    
    transform - a list of doubles indicating the transform for this bioassembly.
    
    name - the name of the bioassembly
  - setXtalInfo
```
public void setXtalInfo(String spaceGroup,
                        float[] unitCell,
                        double[][] ncsOperMatrixList)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets the space group and unit cell information.
    
    Specified by:
    
    setXtalInfo in interface StructureAdapterInterface
    
    Parameters:
    
    spaceGroup - the space group name, e.g. "P 21 21 21"
    
    unitCell - an array of length 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma
    
    ncsOperMatrixList - the list of NCS operation matrices
  - setGroupBond
```
public void setGroupBond(int firstAtomIndex,
                         int secondAtomIndex,
                         int bondOrder)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets an intra-group bond.
    
    Specified by:
    
    setGroupBond in interface StructureAdapterInterface
    
    Parameters:
    
    firstAtomIndex - the atom index of the first partner in the bond
    
    secondAtomIndex - the atom index of the second partner in the bond
    
    bondOrder - the bond order
  - setInterGroupBond
```
public void setInterGroupBond(int firstAtomIndex,
                              int secondAtomIndex,
                              int bondOrder)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets an inter-group bond.
    
    Specified by:
    
    setInterGroupBond in interface StructureAdapterInterface
    
    Parameters:
    
    firstAtomIndex - the atom index of the first partner in the bond
    
    secondAtomIndex - the atom index of the second partner in the bond
    
    bondOrder - the bond order
  - setHeaderInfo
```
public void setHeaderInfo(float rFree,
                          float rWork,
                          float resolution,
                          String title,
                          String depositionDate,
                          String releaseDate,
                          String[] experimnetalMethods)
```
    Description copied from interface: StructureAdapterInterface
    
    Sets the header information.
    
    Specified by:
    
    setHeaderInfo in interface StructureAdapterInterface
    
    Parameters:
    
    rFree - the measured R-Free for the structure
    
    rWork - the measure R-Work for the structure
    
    resolution - the resolution of the structure
    
    title - the title of the structure
    
    depositionDate - the deposition date of the structure
    
    releaseDate - the release date of the structure
    
    experimnetalMethods - the list of experimental methods in the structure
  - getNumBonds
```
public int getNumBonds()
```
    Description copied from interface: StructureDataInterface
    
    Returns the total number of bonds in the structure
    
    Specified by:
    
    getNumBonds in interface StructureDataInterface
    
    Returns:
    
    the number of bonds
  - getSecStructList
```
public int[] getSecStructList()
```
    Description copied from interface: StructureDataInterface
    
    Returns the secondary structure information for the structure as a list of integers
    
    Specified by:
    
    getSecStructList in interface StructureDataInterface
    
    Returns:
    
    the array of secondary structure informations
  - getReleaseDate
```
public String getReleaseDate()
```
    Description copied from interface: StructureDataInterface
    
    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
    
    Specified by:
    
    getReleaseDate in interface StructureDataInterface
    
    Returns:
    
    the release date of the structure.
  - getNcsOperatorList
```
public double[][] getNcsOperatorList()
```
    Description copied from interface: StructureDataInterface
    
    Returns the NCS operation matrix list.
    
    Specified by:
    
    getNcsOperatorList in interface StructureDataInterface
    
    Returns:
    
    the NCS operation matrix list for this structure
  - getBioassemblyName
```
public String getBioassemblyName(int bioassemblyIndex)
```
    Description copied from interface: StructureDataInterface
    
    Returns the name of the transformation for a bioassembly.
    
    Specified by:
    
    getBioassemblyName in interface StructureDataInterface
    
    Parameters:
    
    bioassemblyIndex - an integer specifying the bioassembly index (zero indexed).
    
    Returns:
    
    a string specifying the name of a given bioassembly.

Class AdapterToStructureData

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AdapterToStructureData

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

getChainIndexListForTransform

getMatrixForTransform

getInterGroupBondIndices

getInterGroupBondOrders

getMmtfVersion

getMmtfProducer

getNumEntities

getEntityDescription

getEntityType

getEntityChainIndexList

getEntitySequence

getStructureId

getNumModels

getNumChains

getNumGroups

getNumAtoms

getRfree

getRwork

getResolution

getTitle

getExperimentalMethods

getDepositionDate

initStructure

finalizeStructure

setModelInfo

setChainInfo

setEntityInfo

setGroupInfo

setAtomInfo

setBioAssemblyTrans

setXtalInfo

setGroupBond

setInterGroupBond

setHeaderInfo

getNumBonds

getSecStructList

getReleaseDate

getNcsOperatorList

getBioassemblyName