StructureImpl (biojava 3.0.3 API)

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

All Implemented Interfaces:

Serializable, Cloneable, Structure
```
public class StructureImpl
extends Object
implements Structure, Serializable
```
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

Methods
Modifier and Type	Method and Description
`void`	`addChain(Chain chain)` add a new chain.
`void`	`addChain(Chain chain, int modelnr)` add a new chain, if several models are available.
`void`	`addModel(List<Chain> model)` add a new model.
`void`	`addSSBond(SSBond ssbond)` add a single SSBond 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 chainId, 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 chainId, String pdbResnum, int modelnr)` request a particular group from a structure.
`Chain`	`getChain(int number)` retrieve a chain by it's position within the Structure.
`Chain`	`getChain(int modelnr, int number)` retrieve a chain by it's position within the Structure and model number.
`Chain`	`getChainByPDB(String chainId)` request a chain by it's PDB code by default takes only the first model
`Chain`	`getChainByPDB(String chainId, int modelnr)` request a chain by it's PDB code by default takes only the first model
`List<Chain>`	`getChains()` retrieve all chains - if it is a NMR structure will return the chains of the first model.
`List<Chain>`	`getChains(int modelnr)` retrieve all chains of a model.
`Compound`	`getCompoundById(String molId)` request a particular compound by its id
`List<Compound>`	`getCompounds()` get all the Compounds that are defined in the PDB Header
`List<Map<String,Integer>>`	`getConnections()` Returns the connections value.
`List<DBRef>`	`getDBRefs()` get the list of database references
`Map<String,Object>`	`getHeader()` get Header data.
`List<Group>`	`getHetGroups()`
`Long`	`getId()` get the ID used by Hibernate
`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.
`String`	`getPDBCode()` get PDB code of structure .
`PDBHeader`	`getPDBHeader()` return the header information for this PDB file
`List<Site>`	`getSites()`
`List<SSBond>`	`getSSBonds()` get the list of SSBonds as they have been defined in the PDB files
`boolean`	`hasChain(String chainId)` check if a chain with the id chainId is contained in this structure.
`boolean`	`hasJournalArticle()` Return whether or not the entry has an associated journal article or publication.
`boolean`	`isBiologicalAssembly()` Gets flag that indicates if this structure is a biological assembly
`boolean`	`isNmr()` is this structure an nmr structure ?
`int`	`nrModels()` return number of models.
`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`	`setCompounds(List<Compound> molList)` set the compounts
`void`	`setConnections(List<Map<String,Integer>> conns)` sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file: COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "CONECT" 7 - 11 Integer serial Atom serial number 12 - 16 Integer serial Serial number of bonded atom 17 - 21 Integer serial Serial number of bonded atom 22 - 26 Integer serial Serial number of bonded atom 27 - 31 Integer serial Serial number of bonded atom 32 - 36 Integer serial Serial number of hydrogen bonded atom 37 - 41 Integer serial Serial number of hydrogen bonded atom 42 - 46 Integer serial Serial number of salt bridged atom 47 - 51 Integer serial Serial number of hydrogen bonded atom 52 - 56 Integer serial Serial number of hydrogen bonded atom 57 - 61 Integer serial Serial number of salt bridged atom the HashMap for a single CONECT line contains the following fields: atomserial (mandatory) : Atom serial number bond1 .. bond4 (optional): Serial number of bonded atom hydrogen1 .. hydrogen4 (optional):Serial number of hydrogen bonded atom salt1 .. salt2 (optional): Serial number of salt bridged atom
`void`	`setDBRefs(List<DBRef> dbrefs)` set the list of database references for this structure
`void`	`setHeader(Map<String,Object> h)` set the Header data.
`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> model)` 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.
`void`	`setName(String nam)` set biological name of Structure.
`void`	`setNmr(boolean nmr)` set NMR flag.
`void`	`setPDBCode(String pdb_id_)` set PDB code of structure .
`void`	`setPDBHeader(PDBHeader pdbHeader)` the the header information for this PDB file
`void`	`setSites(List<Site> sites)`
`void`	`setSSBonds(List<SSBond> ssbonds)` set the list of SSBonds for this structure
`int`	`size()` return number of chains , if NMR return number of chains of first model .
`int`	`size(int modelnr)` return number of chains of model.
`String`	`toPDB()` create a String that contains the contents of a PDB file.
`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 -
  - StructureImpl
```
public StructureImpl(Chain c)
```
    construct a Structure object that contains a particular chain
    
    Parameters:
    c -
- 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 -
  - 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 chainId,
              String pdbResnum,
              int modelnr)
                throws StructureException
```
    Description copied from interface: Structure
    
    request a particular group from a structure. considers only model nr X. count starts with 0.
    
    Specified by:
    
    findGroup in interface Structure
    
    Parameters:
    chainId - the ID 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
```
    Description copied from interface: Structure
    
    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 ID 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 chainId,
              int modelnr)
                throws StructureException
```
    Description copied from interface: Structure
    
    request a particular chain from a particular model
    
    Specified by:
    
    findChain in interface Structure
    
    Parameters:
    chainId - the ID 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
```
    Description copied from interface: Structure
    
    request a particular chain from a structure. by default considers only the first model.
    
    Specified by:
    
    findChain in interface Structure
    
    Parameters:
    chainId - the ID 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:
    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:
    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:
    getName()
  - getName
```
public String getName()
```
    get biological name of Structure.
    
    Specified by:
    
    getName in interface Structure
    
    Returns:
    a String representing the name
    See Also:
    setName(java.lang.String)
  - setHeader
```
public void setHeader(Map<String,Object> h)
```
    set the Header data.
    
    Specified by:
    
    setHeader in interface Structure
    
    Parameters:
    h - a Map object specifying the header
    See Also:
    getHeader()
  - getHeader
```
public Map<String,Object> getHeader()
```
    get Header data.
    
    Specified by:
    
    getHeader in interface Structure
    
    Returns:
    a Map object representing the header of the Structure
    See Also:
    setHeader(java.util.Map<java.lang.String, java.lang.Object>)
  - setConnections
```
public void setConnections(List<Map<String,Integer>> conns)
```
    Description copied from interface: Structure
    sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
```
       COLUMNS         DATA TYPE        FIELD           DEFINITION
       ---------------------------------------------------------------------------------
        1 -  6         Record name      "CONECT"
        7 - 11         Integer          serial          Atom serial number
       12 - 16         Integer          serial          Serial number of bonded atom
       17 - 21         Integer          serial          Serial number of bonded atom
       22 - 26         Integer          serial          Serial number of bonded atom
       27 - 31         Integer          serial          Serial number of bonded atom
       32 - 36         Integer          serial          Serial number of hydrogen bonded
       atom
       37 - 41         Integer          serial          Serial number of hydrogen bonded
       atom
       42 - 46         Integer          serial          Serial number of salt bridged
       atom
       47 - 51         Integer          serial          Serial number of hydrogen bonded
       atom
       52 - 56         Integer          serial          Serial number of hydrogen bonded
       atom
       57 - 61         Integer          serial          Serial number of salt bridged
       atom
       
```
    the HashMap for a single CONECT line contains the following fields:
  - atomserial (mandatory) : Atom serial number
  - bond1 .. bond4 (optional): Serial number of bonded atom
  - hydrogen1 .. hydrogen4 (optional):Serial number of hydrogen bonded atom
  - salt1 .. salt2 (optional): Serial number of salt bridged atom

Specified by:: setConnections in interface Structure
Parameters:: conns - a List object specifying the connections
See Also:: interface.

getConnections
```
public List<Map<String,Integer>> getConnections()
```
Returns the connections value.

Specified by:

getConnections in interface Structure

Returns:
a List object representing the connections value
See Also:
interface, setConnections(java.util.List<java.util.Map<java.lang.String, java.lang.Integer>>)

addChain
```
public void addChain(Chain chain)
```
add a new chain.

Specified by:

addChain in interface Structure

Parameters:
chain - a Chain object

addChain
```
public void addChain(Chain chain,
            int modelnr)
```
add a new chain, if several models are available.

Specified by:

addChain in interface Structure

Parameters:
chain - a Chain object
modelnr - an int specifying to which model the Chain should be added

getChain
```
public Chain getChain(int number)
```
retrieve a chain by it's position within the Structure.

Specified by:

getChain in interface Structure

Parameters:
number - an int

Returns:
a Chain object

getChain
```
public Chain getChain(int modelnr,
             int number)
```
retrieve a chain by it's position within the Structure and model number.

Specified by:

getChain in interface Structure

Parameters:
modelnr - an int
number - an int

Returns:
a Chain object

addModel
```
public void addModel(List<Chain> model)
```
add a new model.

Specified by:

addModel in interface Structure

Parameters:
model - a List object containing the Chains of the new Model

setChains
```
public void setChains(List<Chain> chains)
```
Description copied from interface: Structure

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> model)
```
Description copied from interface: Structure

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

toString
```
public String toString()
```
string representation.

Specified by:

toString in interface Structure

Overrides:

toString in class Object

size
```
public int size()
```
return number of chains , if NMR return number of chains of first model .

Specified by:

size in interface Structure

Returns:
an int representing the number of 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

isNmr
```
public boolean isNmr()
```
is this structure an nmr structure ?

Specified by:

isNmr in interface Structure

Returns:
true if this Structure has been resolved by NMR

setNmr
```
public void setNmr(boolean nmr)
```
Description copied from interface: Structure

set NMR flag.

Specified by:

setNmr in interface Structure

Parameters:
nmr - true to declare that this Structure has been solved by NMR.

getChains
```
public List<Chain> getChains(int modelnr)
```
retrieve all chains of a model.

Specified by:

getChains in interface Structure

Parameters:
modelnr - an int

Returns:
a List object
See Also:
Structure.getModel(int)

getChains
```
public List<Chain> getChains()
```
Description copied from interface: Structure

retrieve all chains - if it is a NMR structure will return the chains of 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)

setChains
```
public void setChains(int modelnr,
             List<Chain> chains)
```
Description copied from interface: Structure

set the chains for a model

Specified by:

setChains in interface Structure

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 chainId,
                  int modelnr)
                    throws StructureException
```
Description copied from interface: Structure

request a chain by it's PDB code by default takes only the first model

Specified by:

getChainByPDB in interface Structure

Parameters:
chainId - the chain identifier
modelnr - request a particular model;

Returns:
the Chain that matches the chainID in the model

Throws:

StructureException

getChainByPDB
```
public Chain getChainByPDB(String chainId)
                    throws StructureException
```
Description copied from interface: Structure

request a chain by it's PDB code by default takes only the first model

Specified by:

getChainByPDB in interface Structure

Parameters:
chainId - the chain identifier

Returns:
the Chain that matches the chainID

Throws:

StructureException

toPDB
```
public String toPDB()
```
create a String that contains the contents of a PDB file.

Specified by:

toPDB in interface Structure

Returns:
a String that represents the structure as a PDB file.
See Also:
FileConvert

hasChain
```
public boolean hasChain(String chainId)
```
Description copied from interface: Structure

check if a chain with the id chainId is contained in this structure.

Specified by:

hasChain in interface Structure

Parameters:
chainId - the name of the chain

Returns:
true if a chain with the id (name) chainId is found

setCompounds
```
public void setCompounds(List<Compound> molList)
```
Description copied from interface: Structure

set the compounts

Specified by:

setCompounds in interface Structure

getCompounds
```
public List<Compound> getCompounds()
```
Description copied from interface: Structure

get all the Compounds that are defined in the PDB Header

Specified by:

getCompounds in interface Structure

Returns:
a list of compound

getCompoundById
```
public Compound getCompoundById(String molId)
```
Description copied from interface: Structure

request a particular compound by its id

Specified by:

getCompoundById in interface Structure

Returns:
a compound

getDBRefs
```
public List<DBRef> getDBRefs()
```
Description copied from interface: Structure

get the list of database references

Specified by:

getDBRefs in interface Structure

Returns:
list of DBRef objects

setDBRefs
```
public void setDBRefs(List<DBRef> dbrefs)
```
Description copied from interface: Structure

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()
```
Description copied from interface: Structure

return the header information for this PDB file

Specified by:

getPDBHeader in interface Structure

Returns:
the PDBHeader object

setPDBHeader
```
public void setPDBHeader(PDBHeader pdbHeader)
```
Description copied from interface: Structure

the the header information for this PDB file

Specified by:

setPDBHeader in interface Structure

Parameters:
pdbHeader - the PDBHeader object

getSSBonds
```
public List<SSBond> getSSBonds()
```
get the list of SSBonds as they have been defined in the PDB files

Specified by:

getSSBonds in interface Structure

Returns:
a list of SSBonds

setSSBonds
```
public void setSSBonds(List<SSBond> ssbonds)
```
set the list of SSBonds for this structure

Specified by:

setSSBonds in interface Structure

Parameters:
ssbonds -

addSSBond
```
public void addSSBond(SSBond ssbond)
```
add a single SSBond 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

getHetGroups
```
public List<Group> getHetGroups()
```
Specified by:

getHetGroups in interface Structure

Returns:
a list of Groups listed in the HET records - this will not include any waters.

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

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

setHeader

getHeader

setConnections

getConnections

addChain

addChain

getChain

getChain

addModel

setChains

setModel

toString

size

size

nrModels

isNmr

setNmr

getChains

getChains

setChains

getModel

getChainByPDB

getChainByPDB

toPDB

hasChain

setCompounds

getCompounds

getCompoundById

getDBRefs

setDBRefs

getPDBHeader

setPDBHeader

getSSBonds

setSSBonds

addSSBond

hasJournalArticle

getJournalArticle

setJournalArticle

getSites

setSites

getHetGroups

setBiologicalAssembly

isBiologicalAssembly