StructureImpl (biojava 5.3.0 API)

java.lang.Object
- org.biojava.nbio.structure.StructureImpl

All Implemented Interfaces:

Serializable, Cloneable, Structure
```
public class StructureImpl
extends Object
implements Structure
```
Implementation of a PDB Structure. This class provides the data contained in a PDB file. to get structure objects from different sources see io package.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic, Jules Jacobsen

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description
`StructureImpl()` Constructs a StructureImpl object.
`StructureImpl(Chain c)` construct a Structure object that contains a particular chain
`StructureImpl(Group g)` Construct a Structure object that only contains a single group

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`addChain(Chain chain)` Add a new chain to the first model
`void`	`addChain(Chain chain, int modelnr)` Add a new chain to the model specified by the given index
`void`	`addEntityInfo(EntityInfo entityInfo)` Add an EntityInfo to this Structure
`void`	`addModel(List<Chain> modelChains)` Add a new model.
`void`	`addSSBond(Bond ssbond)` Adds a single disulfide Bond to this structure
`Structure`	`clone()` returns an identical copy of this structure .
`Chain`	`findChain(String chainId)` Request a particular chain from a structure.
`Chain`	`findChain(String chainName, int modelnr)` Request a particular chain from a particular model
`Group`	`findGroup(String chainName, String pdbResnum)` Request a particular group from a structure.
`Group`	`findGroup(String chainName, String pdbResnum, int modelnr)` Request a particular group from a structure.
`Chain`	`getChain(String asymId)` Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model
`Chain`	`getChain(String asymId, int modelnr)` Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index
`Chain`	`getChainByIndex(int number)` Retrieve a chain by its index within the Structure .
`Chain`	`getChainByIndex(int modelnr, int number)` Retrieve a chain by its indices within the Structure and model.
`Chain`	`getChainByPDB(String chainId)` Request a chain by its public id (author id) for the first model.
`Chain`	`getChainByPDB(String authId, int modelnr)` Request a chain by its public id (author id) for the given model index.
`List<Chain>`	`getChains()` Retrieve all chains for the first model.
`List<Chain>`	`getChains(int modelIdx)` Retrieve all chains of a model.
`EntityInfo`	`getCompoundById(int molId)` Request a particular entity by its entity id (mol id in legacy PDB format)
`PDBCrystallographicInfo`	`getCrystallographicInfo()` Gets crystallographic information for this structure
`List<DBRef>`	`getDBRefs()` Get the list of database references
`EntityInfo`	`getEntityById(int entityId)` Request a particular entity by its entity id (mol id in legacy PDB format)
`List<EntityInfo>`	`getEntityInfos()` Get all the EntityInfo for this Structure.
`Long`	`getId()` get the ID used by Hibernate
`String`	`getIdentifier()` Get a string representing this structure's contents.
`JournalArticle`	`getJournalArticle()` get the associated publication as defined by the JRNL records in a PDB file.
`List<Chain>`	`getModel(int modelnr)` Retrieve all Chains belonging to a model .
`String`	`getName()` Get biological name of Structure.
`Chain`	`getNonPolyChain(String asymId)` Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first model
`Chain`	`getNonPolyChain(String asymId, int modelIdx)` Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model index
`List<Chain>`	`getNonPolyChains()` Return all non-polymeric chains for the first model
`List<Chain>`	`getNonPolyChains(int modelIdx)` Return all non-polymeric chains for the given model index.
`List<Chain>`	`getNonPolyChainsByPDB(String authId)` Retrieve all non-polymeric Chains corresponding to the given 'public' chain name (authId) for the first model.
`List<Chain>`	`getNonPolyChainsByPDB(String authId, int modelIdx)` Retrieve all non-polymeric Chains corresponding to the 'public' chain name (authId) and the given model index.
`String`	`getPDBCode()` Get PDB code of structure.
`PDBHeader`	`getPDBHeader()` Return the header information for this PDB file
`String`	`getPdbId()` Deprecated.
`Chain`	`getPolyChain(String asymId)` Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first model See `Structure.getPolyChainByPDB(String)` for a similar method using the chain name (authId).
`Chain`	`getPolyChain(String asymId, int modelIdx)` Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model index See `Structure.getPolyChainByPDB(String, int)` for a similar method using the chain name (authId).
`Chain`	`getPolyChainByPDB(String authId)` Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first model See `Structure.getPolyChain(String)` for a similar method using the chain id (asymId).
`Chain`	`getPolyChainByPDB(String authId, int modelIdx)` Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.
`List<Chain>`	`getPolyChains()` Return all polymeric chains for the first model
`List<Chain>`	`getPolyChains(int modelIdx)` Return all polymeric chains for the given model index.
`List<String>`	`getRanges()` Deprecated.
`List<ResidueRange>`	`getResidueRanges()` Deprecated.
`List<Site>`	`getSites()`
`List<Bond>`	`getSSBonds()` Get the list of disulfide Bonds as they have been defined in the PDB files
`StructureIdentifier`	`getStructureIdentifier()` Get an identifier corresponding to this structure
`Chain`	`getWaterChain(String asymId)` Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model
`Chain`	`getWaterChain(String asymId, int modelIdx)` Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index
`Chain`	`getWaterChainByPDB(String authId)` Retrieve a water Chain based on the 'public' chain name (authId) for the first model
`Chain`	`getWaterChainByPDB(String authId, int modelIdx)` Retrieve a water Chain based on the 'public' chain name (authId) for the given model index
`List<Chain>`	`getWaterChains()` Return all water chains for the first model
`List<Chain>`	`getWaterChains(int modelIdx)` Return all water chains for the given model index
`boolean`	`hasChain(String authId)` Check if a chain with the chainId aymId is contained in this structure.
`boolean`	`hasJournalArticle()` Return whether or not the entry has an associated journal article or publication.
`boolean`	`hasNonPolyChain(String asymId)` Check if a non polymeric chain with chainId asymId is contained in the structure.
`boolean`	`hasPdbChain(String authId)` Check if a chain with chain name authId is contained in the structure
`boolean`	`isBiologicalAssembly()` Gets flag that indicates if this structure is a biological assembly
`boolean`	`isCrystallographic()` Whether this Structure is a crystallographic structure or not.
`boolean`	`isNmr()` Whether this Structure is a NMR structure or not.
`int`	`nrModels()` return number of models.
`void`	`resetModels()` Resets all models of this Structure
`void`	`setBiologicalAssembly(boolean biologicalAssembly)` Sets a flag to indicate if this structure is a biological assembly
`void`	`setChains(int modelnr, List<Chain> chains)` Set the chains for a model
`void`	`setChains(List<Chain> chains)` Set the chains of a structure, if this is a NMR structure, this will only set model 0.
`void`	`setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)` Sets crystallographic information for this structure
`void`	`setDBRefs(List<DBRef> dbrefs)` Set the list of database references for this structure
`void`	`setEntityInfos(List<EntityInfo> molList)` Set the EntityInfo
`void`	`setId(Long id)` set the ID used by Hibernate
`void`	`setJournalArticle(JournalArticle journalArticle)` set the associated publication as defined by the JRNL records in a PDB file.
`void`	`setModel(int position, List<Chain> modelChains)` A convenience function if one wants to edit and replace the models in a structure.
`void`	`setName(String nam)` Set biological name of Structure .
`void`	`setPDBCode(String pdb_id_)` Set PDB code of structure .
`void`	`setPDBHeader(PDBHeader pdbHeader)` Set the the header information for this PDB file
`void`	`setSites(List<Site> sites)`
`void`	`setSSBonds(List<Bond> ssbonds)` Set the list of SSBonds for this structure
`void`	`setStructureIdentifier(StructureIdentifier structureIdentifier)` Set the identifier corresponding to this structure
`int`	`size()` Return number of polymer Chains in this Structure for first model.
`int`	`size(int modelnr)` return number of chains of model.
`String`	`toMMCIF()` Create a String that contains this Structure's contents in MMCIF file format.
`String`	`toPDB()` Create a String that contains this Structure's contents in PDB file format.
`String`	`toString()` String representation.

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

- Constructor Detail
  - StructureImpl
```
public StructureImpl()
```
    Constructs a StructureImpl object.
  - StructureImpl
```
public StructureImpl(Group g)
```
    Construct a Structure object that only contains a single group
    
    Parameters:
    
    g - group object
  - StructureImpl
```
public StructureImpl(Chain c)
```
    construct a Structure object that contains a particular chain
    
    Parameters:
    
    c - chain
- Method Detail
  - getId
```
public Long getId()
```
    get the ID used by Hibernate
    
    Specified by:
    
    getId in interface Structure
    
    Returns:
    
    the ID used by Hibernate
  - setId
```
public void setId(Long id)
```
    set the ID used by Hibernate
    
    Specified by:
    
    setId in interface Structure
    
    Parameters:
    
    id - the hibernate ID
  - clone
```
public Structure clone()
```
    returns an identical copy of this structure .
    
    Specified by:
    
    clone in interface Structure
    
    Overrides:
    
    clone in class Object
    
    Returns:
    
    an identical Structure object
  - findGroup
```
public Group findGroup(String chainName,
                       String pdbResnum,
                       int modelnr)
                throws StructureException
```
    Request a particular group from a structure. considers only model nr X. count starts with 0.
    
    Specified by:
    
    findGroup in interface Structure
    
    Parameters:
    
    chainName - the chain name of the chain to use
    
    pdbResnum - the PDB residue number of the requested group
    
    modelnr - the number of the model to use
    
    Returns:
    
    Group the requested Group
    
    Throws:
    
    StructureException
  - findGroup
```
public Group findGroup(String chainName,
                       String pdbResnum)
                throws StructureException
```
    Request a particular group from a structure. by default considers only the first model in the structure.
    
    Specified by:
    
    findGroup in interface Structure
    
    Parameters:
    
    chainName - the name of the chain to use
    
    pdbResnum - the PDB residue number of the requested group
    
    Returns:
    
    Group the requested Group
    
    Throws:
    
    StructureException
  - findChain
```
public Chain findChain(String chainName,
                       int modelnr)
                throws StructureException
```
    Request a particular chain from a particular model
    
    Specified by:
    
    findChain in interface Structure
    
    Parameters:
    
    chainName - the name of a chain that should be returned
    
    modelnr - the number of the model to use
    
    Returns:
    
    Chain the requested chain
    
    Throws:
    
    StructureException
  - findChain
```
public Chain findChain(String chainId)
                throws StructureException
```
    Request a particular chain from a structure. by default considers only the first model.
    
    Specified by:
    
    findChain in interface Structure
    
    Parameters:
    
    chainId - name of a chain that should be returned
    
    Returns:
    
    Chain the requested chain
    
    Throws:
    
    StructureException
  - setPDBCode
```
public void setPDBCode(String pdb_id_)
```
    Set PDB code of structure .
    
    Specified by:
    
    setPDBCode in interface Structure
    
    Parameters:
    
    pdb_id_ - a String specifying the PDBCode
    
    See Also:
    
    Structure.getPDBCode()
  - getPDBCode
```
public String getPDBCode()
```
    Get PDB code of structure.
    
    Specified by:
    
    getPDBCode in interface Structure
    
    Returns:
    
    a String representing the PDBCode value
    
    See Also:
    
    Structure.setPDBCode(java.lang.String)
  - setName
```
public void setName(String nam)
```
    Set biological name of Structure .
    
    Specified by:
    
    setName in interface Structure
    
    Parameters:
    
    nam - a String specifying the biological name of the Structure
    
    See Also:
    
    Structure.getName()
  - getName
```
public String getName()
```
    Get biological name of Structure.
    
    Specified by:
    
    getName in interface Structure
    
    Returns:
    
    a String representing the biological name of the Structure
    
    See Also:
    
    Structure.setName(java.lang.String)
  - getStructureIdentifier
```
public StructureIdentifier getStructureIdentifier()
```
    Description copied from interface: Structure
    
    Get an identifier corresponding to this structure
    
    Specified by:
    
    getStructureIdentifier in interface Structure
    
    Returns:
    
    The StructureIdentifier used to create this structure
  - setStructureIdentifier
```
public void setStructureIdentifier(StructureIdentifier structureIdentifier)
```
    Description copied from interface: Structure
    
    Set the identifier corresponding to this structure
    
    Specified by:
    
    setStructureIdentifier in interface Structure
    
    Parameters:
    
    structureIdentifier - the structureIdentifier corresponding to this structure
  - addChain
```
public void addChain(Chain chain)
```
    Add a new chain to the first model
    
    Specified by:
    
    addChain in interface Structure
    
    Parameters:
    
    chain - a Chain object
  - addChain
```
public void addChain(Chain chain,
                     int modelnr)
```
    Add a new chain to the model specified by the given index
    
    Specified by:
    
    addChain in interface Structure
    
    Parameters:
    
    chain - a Chain object
    
    modelnr - an int specifying to which model the Chain should be added
  - getChainByIndex
```
public Chain getChainByIndex(int number)
```
    Retrieve a chain by its index within the Structure .
    
    Specified by:
    
    getChainByIndex in interface Structure
    
    Parameters:
    
    number - the index of the desired chain in the structure
    
    Returns:
    
    a Chain object
  - getChainByIndex
```
public Chain getChainByIndex(int modelnr,
                             int number)
```
    Retrieve a chain by its indices within the Structure and model.
    
    Specified by:
    
    getChainByIndex in interface Structure
    
    Parameters:
    
    modelnr - the model the desired chain is in
    
    number - the index of the desired chain in the structure
    
    Returns:
    
    a Chain object
  - addModel
```
public void addModel(List<Chain> modelChains)
```
    Add a new model.
    
    Specified by:
    
    addModel in interface Structure
    
    Parameters:
    
    modelChains - a List object containing the Chains of the new Model
  - setChains
```
public void setChains(List<Chain> chains)
```
    Set the chains of a structure, if this is a NMR structure, this will only set model 0.
    
    Specified by:
    
    setChains in interface Structure
    
    Parameters:
    
    chains - the list of chains for this structure.
    
    See Also:
    
    Structure.setChains(int, List)
  - setModel
```
public void setModel(int position,
                     List<Chain> modelChains)
```
    A convenience function if one wants to edit and replace the models in a structure. Allows to set (replace) the model at position with the new List of Chains.
    
    Specified by:
    
    setModel in interface Structure
    
    Parameters:
    
    position - starting at 0
    
    modelChains - list of chains representing a model
  - toString
```
public String toString()
```
    String representation.
    
    Specified by:
    
    toString in interface Structure
    
    Overrides:
    
    toString in class Object
  - size
```
public int size()
```
    Description copied from interface: Structure
    
    Return number of polymer Chains in this Structure for first model.
    
    Specified by:
    
    size in interface Structure
    
    Returns:
    
    the number of polymer Chains in this Structure
  - size
```
public int size(int modelnr)
```
    return number of chains of model.
    
    Specified by:
    
    size in interface Structure
    
    Parameters:
    
    modelnr - an int specifying the number of the Model that should be used
    
    Returns:
    
    an int representing the number of Chains in this Model
  - nrModels
```
public int nrModels()
```
    return number of models.
    
    Specified by:
    
    nrModels in interface Structure
    
    Returns:
    
    an int representing the number of models in this Structure
    
    See Also:
    
    Structure.isNmr()
  - isCrystallographic
```
public boolean isCrystallographic()
```
    Whether this Structure is a crystallographic structure or not. It will first check the experimental technique and if not present it will try to guess from the presence of a space group and sensible cell parameters
    
    Specified by:
    
    isCrystallographic in interface Structure
    
    Returns:
    
    true if crystallographic, false otherwise
  - isNmr
```
public boolean isNmr()
```
    Whether this Structure is a NMR structure or not. It will first check the experimental technique and if not present it will try to guess from the presence of more than 1 model and from b-factors being 0 in first chain of first model
    
    Specified by:
    
    isNmr in interface Structure
    
    Returns:
    
    true if NMR, false otherwise
    
    See Also:
    
    Structure.nrModels()
  - getChains
```
public List<Chain> getChains(int modelIdx)
```
    Retrieve all chains of a model.
    
    Specified by:
    
    getChains in interface Structure
    
    Parameters:
    
    modelIdx - an int
    
    Returns:
    
    a List object containing the Chains of Model nr. modelnr
    
    See Also:
    
    Structure.getModel(int)
  - getChains
```
public List<Chain> getChains()
```
    Retrieve all chains for the first model. This is the same as getChains(0);
    
    Specified by:
    
    getChains in interface Structure
    
    Returns:
    
    a List object containing the Chains of Model nr. modelnr
    
    See Also:
    
    Structure.getModel(int modelnr), Structure.getChains(int modelnr)
  - getPolyChains
```
public List<Chain> getPolyChains()
```
    Description copied from interface: Structure
    
    Return all polymeric chains for the first model
    
    Specified by:
    
    getPolyChains in interface Structure
    
    Returns:
    
    all polymeric chains.
  - getPolyChains
```
public List<Chain> getPolyChains(int modelIdx)
```
    Description copied from interface: Structure
    
    Return all polymeric chains for the given model index.
    
    Specified by:
    
    getPolyChains in interface Structure
    
    Parameters:
    
    modelIdx - the model index
    
    Returns:
    
    all polymeric chains.
  - getNonPolyChains
```
public List<Chain> getNonPolyChains()
```
    Description copied from interface: Structure
    
    Return all non-polymeric chains for the first model
    
    Specified by:
    
    getNonPolyChains in interface Structure
    
    Returns:
    
    all non-polymeric chains.
  - getNonPolyChains
```
public List<Chain> getNonPolyChains(int modelIdx)
```
    Description copied from interface: Structure
    
    Return all non-polymeric chains for the given model index.
    
    Specified by:
    
    getNonPolyChains in interface Structure
    
    Parameters:
    
    modelIdx - the model index
    
    Returns:
    
    all non-polymeric chains.
  - getWaterChains
```
public List<Chain> getWaterChains()
```
    Description copied from interface: Structure
    
    Return all water chains for the first model
    
    Specified by:
    
    getWaterChains in interface Structure
    
    Returns:
  - getWaterChains
```
public List<Chain> getWaterChains(int modelIdx)
```
    Description copied from interface: Structure
    
    Return all water chains for the given model index
    
    Specified by:
    
    getWaterChains in interface Structure
    
    Returns:
  - setChains
```
public void setChains(int modelnr,
                      List<Chain> chains)
```
    Set the chains for a model
    
    Specified by:
    
    setChains in interface Structure
    
    Parameters:
    
    modelnr - the number of the model
    
    chains - the chains for a model
  - getModel
```
public List<Chain> getModel(int modelnr)
```
    Retrieve all Chains belonging to a model .
    
    Specified by:
    
    getModel in interface Structure
    
    Parameters:
    
    modelnr - an int
    
    Returns:
    
    a List object
    
    See Also:
    
    Structure.getChains(int modelnr)
  - getChainByPDB
```
public Chain getChainByPDB(String authId,
                           int modelnr)
                    throws StructureException
```
    Request a chain by its public id (author id) for the given model index. Before 5.0 it returned a Chain that had both polymeric and non-polymeric groups following the PDB-file data model. Since 5.0 it only returns the polymeric part of the chain.
    
    Specified by:
    
    getChainByPDB in interface Structure
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    modelnr - the index of the required model (0-based)
    
    Returns:
    
    the Chain that matches the authId in the model
    
    Throws:
    
    StructureException - if chain can't be found
  - getChain
```
public Chain getChain(String asymId,
                      int modelnr)
```
    Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index
    
    Specified by:
    
    getChain in interface Structure
    
    Parameters:
    
    asymId - the asymId (chainId)
    
    modelnr - the index of the required model (0-based)
    
    Returns:
    
    See Also:
    
    Structure.getPolyChain(String, int), Structure.getNonPolyChain(String, int), Structure.getWaterChain(String, int)
  - getChain
```
public Chain getChain(String asymId)
```
    Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model
    
    Specified by:
    
    getChain in interface Structure
    
    Parameters:
    
    asymId - the asymId (chainId)
    
    Returns:
    
    See Also:
    
    Structure.getPolyChain(String), Structure.getNonPolyChain(String), Structure.getWaterChain(String)
  - getChainByPDB
```
public Chain getChainByPDB(String chainId)
                    throws StructureException
```
    Request a chain by its public id (author id) for the first model. Before 5.0 it returned a Chain that had both polymeric and non-polymeric groups following the PDB-file data model. Since 5.0 it only returns the polymeric part of the chain.
    
    Specified by:
    
    getChainByPDB in interface Structure
    
    Parameters:
    
    chainId - the author id (chainName, public chain id)
    
    Returns:
    
    the Chain that matches the authId
    
    Throws:
    
    StructureException - if chain can't be found
  - getPolyChain
```
public Chain getPolyChain(String asymId)
```
    Description copied from interface: Structure
    
    Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first model
    See Structure.getPolyChainByPDB(String) for a similar method using the chain name (authId).
    
    Specified by:
    
    getPolyChain in interface Structure
    
    Parameters:
    
    asymId - the asymId (chainId)
    
    Returns:
    
    a polymeric Chain or null if it can't be found
  - getPolyChain
```
public Chain getPolyChain(String asymId,
                          int modelIdx)
```
    Description copied from interface: Structure
    
    Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model index
    See Structure.getPolyChainByPDB(String, int) for a similar method using the chain name (authId).
    
    Specified by:
    
    getPolyChain in interface Structure
    
    Parameters:
    
    asymId - the asymId (chainId)
    
    modelIdx - the index of the required model (0-based)
    
    Returns:
    
    a polymeric Chain or null if it can't be found
  - getNonPolyChain
```
public Chain getNonPolyChain(String asymId)
```
    Description copied from interface: Structure
    
    Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first model
    
    Specified by:
    
    getNonPolyChain in interface Structure
    
    Parameters:
    
    asymId - the asymId (chainId)
    
    Returns:
    
    a non-polymeric chain or null if it can't be found
  - getNonPolyChain
```
public Chain getNonPolyChain(String asymId,
                             int modelIdx)
```
    Description copied from interface: Structure
    
    Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model index
    
    Specified by:
    
    getNonPolyChain in interface Structure
    
    Parameters:
    
    asymId - the asymId (chainId)
    
    modelIdx - the index of the required model (0-based)
    
    Returns:
    
    a non-polymeric Chain or null if it can't be found
  - getPolyChainByPDB
```
public Chain getPolyChainByPDB(String authId)
```
    Description copied from interface: Structure
    
    Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first model
    See Structure.getPolyChain(String) for a similar method using the chain id (asymId).
    
    Specified by:
    
    getPolyChainByPDB in interface Structure
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    Returns:
    
    a polymeric Chain or null if it can't be found
  - getPolyChainByPDB
```
public Chain getPolyChainByPDB(String authId,
                               int modelIdx)
```
    Description copied from interface: Structure
    
    Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.
    See Structure.getPolyChain(String, int) for a similar method using the chain id (asymId).
    
    Specified by:
    
    getPolyChainByPDB in interface Structure
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    modelIdx - the index of the required model (0-based)
    
    Returns:
    
    a polymeric Chain or null if it can't be found
  - getNonPolyChainsByPDB
```
public List<Chain> getNonPolyChainsByPDB(String authId)
```
    Description copied from interface: Structure
    
    Retrieve all non-polymeric Chains corresponding to the given 'public' chain name (authId) for the first model.
    
    Specified by:
    
    getNonPolyChainsByPDB in interface Structure
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    Returns:
    
    a list of non-polymeric Chains, if none found the list will be empty
  - getNonPolyChainsByPDB
```
public List<Chain> getNonPolyChainsByPDB(String authId,
                                         int modelIdx)
```
    Description copied from interface: Structure
    
    Retrieve all non-polymeric Chains corresponding to the 'public' chain name (authId) and the given model index.
    
    Specified by:
    
    getNonPolyChainsByPDB in interface Structure
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    modelIdx - the index of the required model (0-based)
    
    Returns:
    
    a list of non-polymeric Chains, if none found the list will be empty
  - getWaterChain
```
public Chain getWaterChain(String asymId)
```
    Description copied from interface: Structure
    
    Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model
    
    Specified by:
    
    getWaterChain in interface Structure
    
    Parameters:
    
    asymId - the asymId (chainId)
    
    Returns:
    
    a water Chain or null if it can't be found
  - getWaterChain
```
public Chain getWaterChain(String asymId,
                           int modelIdx)
```
    Description copied from interface: Structure
    
    Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index
    
    Specified by:
    
    getWaterChain in interface Structure
    
    Parameters:
    
    asymId - the asymId (chainId)
    
    modelIdx - the index of the required model (0-based)
    
    Returns:
  - getWaterChainByPDB
```
public Chain getWaterChainByPDB(String authId)
```
    Description copied from interface: Structure
    
    Retrieve a water Chain based on the 'public' chain name (authId) for the first model
    
    Specified by:
    
    getWaterChainByPDB in interface Structure
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    Returns:
  - getWaterChainByPDB
```
public Chain getWaterChainByPDB(String authId,
                                int modelIdx)
```
    Description copied from interface: Structure
    
    Retrieve a water Chain based on the 'public' chain name (authId) for the given model index
    
    Specified by:
    
    getWaterChainByPDB in interface Structure
    
    Parameters:
    
    authId - the author id (chainName, public chain id)
    
    modelIdx - the index of the required model (0-based)
    
    Returns:
  - toPDB
```
public String toPDB()
```
    Create a String that contains this Structure's contents in PDB file format.
    
    Specified by:
    
    toPDB in interface Structure
    
    Returns:
    
    a String that looks like a PDB file
    
    See Also:
    
    FileConvert
  - toMMCIF
```
public String toMMCIF()
```
    Create a String that contains this Structure's contents in MMCIF file format.
    
    Specified by:
    
    toMMCIF in interface Structure
    
    Returns:
    
    a String representation of the Structure object in mmCIF.
  - hasChain
```
public boolean hasChain(String authId)
```
    Check if a chain with the chainId aymId is contained in this structure.
    
    Specified by:
    
    hasChain in interface Structure
    
    Parameters:
    
    authId - the Id of the chain
    
    Returns:
    
    true if a chain with the id asymId is found
  - hasNonPolyChain
```
public boolean hasNonPolyChain(String asymId)
```
    Check if a non polymeric chain with chainId asymId is contained in the structure.
    
    Specified by:
    
    hasNonPolyChain in interface Structure
    
    Parameters:
    
    asymId - the id of the chain
    
    Returns:
    
    true if a nonpolymeric chain with the asymId is found
  - hasPdbChain
```
public boolean hasPdbChain(String authId)
```
    Check if a chain with chain name authId is contained in the structure
    
    Specified by:
    
    hasPdbChain in interface Structure
    
    Parameters:
    
    authId - the chain name
    
    Returns:
    
    true if a chain with the name authId is found
  - setEntityInfos
```
public void setEntityInfos(List<EntityInfo> molList)
```
    Set the EntityInfo
    
    Specified by:
    
    setEntityInfos in interface Structure
    
    Parameters:
    
    molList - list of entityinfo objects
  - addEntityInfo
```
public void addEntityInfo(EntityInfo entityInfo)
```
    Add an EntityInfo to this Structure
    
    Specified by:
    
    addEntityInfo in interface Structure
  - getEntityInfos
```
public List<EntityInfo> getEntityInfos()
```
    Get all the EntityInfo for this Structure.
    
    Specified by:
    
    getEntityInfos in interface Structure
    
    Returns:
    
    a list of EntityInfos
  - getCompoundById
```
public EntityInfo getCompoundById(int molId)
```
    Request a particular entity by its entity id (mol id in legacy PDB format)
    
    Specified by:
    
    getCompoundById in interface Structure
    
    Parameters:
    
    molId - the number of the entity
    
    Returns:
    
    a entityInfo
  - getEntityById
```
public EntityInfo getEntityById(int entityId)
```
    Request a particular entity by its entity id (mol id in legacy PDB format)
    
    Specified by:
    
    getEntityById in interface Structure
    
    Parameters:
    
    entityId - the number of the entity
    
    Returns:
    
    an entity, or null if the molId was not found
  - getDBRefs
```
public List<DBRef> getDBRefs()
```
    Get the list of database references
    
    Specified by:
    
    getDBRefs in interface Structure
    
    Returns:
    
    list of DBRef objects
  - setDBRefs
```
public void setDBRefs(List<DBRef> dbrefs)
```
    Set the list of database references for this structure
    
    Specified by:
    
    setDBRefs in interface Structure
    
    Parameters:
    
    dbrefs - list of DBRef objects
  - getPDBHeader
```
public PDBHeader getPDBHeader()
```
    Return the header information for this PDB file
    
    Specified by:
    
    getPDBHeader in interface Structure
    
    Returns:
    
    the PDBHeader object
  - setPDBHeader
```
public void setPDBHeader(PDBHeader pdbHeader)
```
    Set the the header information for this PDB file
    
    Specified by:
    
    setPDBHeader in interface Structure
    
    Parameters:
    
    pdbHeader - the PDBHeader object
  - getSSBonds
```
public List<Bond> getSSBonds()
```
    Get the list of disulfide Bonds as they have been defined in the PDB files
    
    Specified by:
    
    getSSBonds in interface Structure
    
    Returns:
    
    a list of Bonds
  - setSSBonds
```
public void setSSBonds(List<Bond> ssbonds)
```
    Set the list of SSBonds for this structure
    
    Specified by:
    
    setSSBonds in interface Structure
  - addSSBond
```
public void addSSBond(Bond ssbond)
```
    Adds a single disulfide Bond to this structure
    
    Specified by:
    
    addSSBond in interface Structure
    
    Parameters:
    
    ssbond - the SSBond.
  - hasJournalArticle
```
public boolean hasJournalArticle()
```
    Return whether or not the entry has an associated journal article or publication. The JRNL section is not mandatory and thus may not be present.
    
    Specified by:
    
    hasJournalArticle in interface Structure
    
    Returns:
    
    flag if a JournalArticle could be found.
  - getJournalArticle
```
public JournalArticle getJournalArticle()
```
    get the associated publication as defined by the JRNL records in a PDB file.
    
    Specified by:
    
    getJournalArticle in interface Structure
    
    Returns:
    
    a JournalArticle
  - setJournalArticle
```
public void setJournalArticle(JournalArticle journalArticle)
```
    set the associated publication as defined by the JRNL records in a PDB file.
    
    Specified by:
    
    setJournalArticle in interface Structure
    
    Parameters:
    
    journalArticle - the article
  - getSites
```
public List<Site> getSites()
```
    Specified by:
    
    getSites in interface Structure
    
    Returns:
    
    the sites contained in this structure
  - setSites
```
public void setSites(List<Site> sites)
```
    Specified by:
    
    setSites in interface Structure
    
    Parameters:
    
    sites - the sites to set in the structure
  - setBiologicalAssembly
```
public void setBiologicalAssembly(boolean biologicalAssembly)
```
    Sets a flag to indicate if this structure is a biological assembly
    
    Specified by:
    
    setBiologicalAssembly in interface Structure
    
    Parameters:
    
    biologicalAssembly - true if biological assembly, otherwise false
    
    Since:
    
    3.2
  - isBiologicalAssembly
```
public boolean isBiologicalAssembly()
```
    Gets flag that indicates if this structure is a biological assembly
    
    Specified by:
    
    isBiologicalAssembly in interface Structure
    
    Returns:
    
    the sites contained in this structure
    
    Since:
    
    3.2
  - setCrystallographicInfo
```
public void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)
```
    Sets crystallographic information for this structure
    
    Specified by:
    
    setCrystallographicInfo in interface Structure
    
    Parameters:
    
    crystallographicInfo - crystallographic information
    
    Since:
    
    3.2
  - getCrystallographicInfo
```
public PDBCrystallographicInfo getCrystallographicInfo()
```
    Gets crystallographic information for this structure
    
    Specified by:
    
    getCrystallographicInfo in interface Structure
    
    Returns:
    
    PDBCrystallographicInfo crystallographic information
    
    Since:
    
    3.2
  - getIdentifier
```
public String getIdentifier()
```
    Get a string representing this structure's contents. The following places are searched for a non-null value, with the first being returned:
    1. Structure.getStructureIdentifier().getIdentifier(), which should give the string originally used to create the structure
    2. Structure.getName()
    3. A combination of Structure.getPDBCode() with a heuristic description of the residue ranges, in SubstructureIdentifier format.
    Specified by:
    
    getIdentifier in interface Structure
    
    Returns:
    
    A SubstructureIdentifier-format string describing the residue ranges in this structure
  - getPdbId
```
@Deprecated
public String getPdbId()
```
    Deprecated.
    
    Returns the PDB identifier associated with this StructureIdentifier.
    
    Specified by:
    
    getPdbId in interface Structure
  - resetModels
```
public void resetModels()
```
    Resets all models of this Structure
    
    Specified by:
    
    resetModels in interface Structure
  - getResidueRanges
```
@Deprecated
public List<ResidueRange> getResidueRanges()
```
    Deprecated.
    
    Returns the list of ResidueRanges that this StructureIdentifier defines. This is a unique representation.
    
    Specified by:
    
    getResidueRanges in interface Structure
  - getRanges
```
@Deprecated
public List<String> getRanges()
```
    Deprecated.
    Returns a list of residue ranges. For example:
```
 getRanges().get(0): 'A'
 getRanges().get(1): 'B_5-100'
 
```
    This is a unique representation.
    Specified by:
    
    getRanges in interface Structure

Class StructureImpl

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

StructureImpl

StructureImpl

StructureImpl

Method Detail

getId

setId

clone

findGroup

findGroup

findChain

findChain

setPDBCode

getPDBCode

setName

getName

getStructureIdentifier

setStructureIdentifier

addChain

addChain

getChainByIndex

getChainByIndex

addModel

setChains

setModel

toString

size

size

nrModels

isCrystallographic

isNmr

getChains

getChains

getPolyChains

getPolyChains

getNonPolyChains

getNonPolyChains

getWaterChains

getWaterChains

setChains

getModel

getChainByPDB

getChain

getChain

getChainByPDB

getPolyChain

getPolyChain

getNonPolyChain

getNonPolyChain

getPolyChainByPDB

getPolyChainByPDB

getNonPolyChainsByPDB

getNonPolyChainsByPDB

getWaterChain

getWaterChain

getWaterChainByPDB

getWaterChainByPDB

toPDB

toMMCIF

hasChain

hasNonPolyChain

hasPdbChain

setEntityInfos

addEntityInfo

getEntityInfos

getCompoundById

getEntityById

getDBRefs

setDBRefs

getPDBHeader

setPDBHeader

getSSBonds

setSSBonds

addSSBond

hasJournalArticle

getJournalArticle