StructureImpl (biojava 4.2.0 API)

java.lang.Object
- org.biojava.nbio.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`	`addCompound(Compound compound)` Add a Compound to this Structure
`void`	`addModel(List<Chain> model)` 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 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 its position within the Structure .
`Chain`	`getChain(int modelnr, int number)` Retrieve a chain by its position within the Structure and model number.
`Chain`	`getChainByPDB(String chainId)` Request a chain by its PDB code by default takes only the first model
`Chain`	`getChainByPDB(String chainId, int modelnr)` Request a chain by its 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(int molId)` Request a particular compound by its molId (entity_id in mmCIF dictionary)
`List<Compound>`	`getCompounds()` Get all the Compounds for this Structure.
`List<Map<String,Integer>>`	`getConnections()` Return the connections value.
`PDBCrystallographicInfo`	`getCrystallographicInfo()` Gets crystallographic information for this structure
`List<DBRef>`	`getDBRefs()` Get the list of database references
`List<Group>`	`getHetGroups()` Caution: we should probably remove this to avoid confusion.
`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.
`String`	`getPDBCode()` Get PDB code of structure.
`PDBHeader`	`getPDBHeader()` Return the header information for this PDB file
`String`	`getPdbId()` Deprecated.
`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
`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`	`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`	`setCompounds(List<Compound> molList)` Set the Compounds
`void`	`setConnections(List<Map<String,Integer>> conns)` sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
`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`	`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.
`void`	`setName(String nam)` Set biological name of Structure .
`void`	`setNmr(boolean nmr)` Deprecated.
`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 chains , if NMR return number of chains of 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 -
  - 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
```
    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
```
    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
```
    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
```
    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:
    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
  - setConnections
```
public 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

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

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

Specified by:

getConnections in interface Structure

Returns:
a List object representing the connections value
See Also:
Structure.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 its position within the Structure .

Specified by:

getChain in interface Structure

Parameters:
number - an int for the position in the List of Chains.

Returns:
a Chain object

getChain
```
public Chain getChain(int modelnr,
             int number)
```
Retrieve a chain by its 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)
```
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)
```
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
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()

setNmr
```
@Deprecated
public void setNmr(boolean nmr)
```
Deprecated.

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()
```
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)

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
```
Request a chain by its 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
```
Request a chain by its 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 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:

hasChain
```
public boolean hasChain(String chainId)
```
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)
```
Set the Compounds

Specified by:

setCompounds in interface Structure

addCompound
```
public void addCompound(Compound compound)
```
Add a Compound to this Structure

Specified by:

addCompound in interface Structure

getCompounds
```
public List<Compound> getCompounds()
```
Get all the Compounds for this Structure. Compounds are called Entities in mmCIF dictionary.

Specified by:

getCompounds in interface Structure

Returns:
a list of Compounds

getCompoundById
```
public Compound getCompoundById(int molId)
```
Request a particular compound by its molId (entity_id in mmCIF dictionary)

Specified by:

getCompoundById in interface Structure

Returns:
a compound

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

getHetGroups
```
public List<Group> getHetGroups()
```
Caution: we should probably remove this to avoid confusion. Currently this is always an empty list!

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

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

setConnections

getConnections

addChain

addChain

getChain

getChain

addModel

setChains

setModel

toString

size

size

nrModels

isCrystallographic

isNmr

setNmr

getChains

getChains

setChains

getModel

getChainByPDB

getChainByPDB

toPDB

toMMCIF

hasChain

setCompounds

addCompound

getCompounds

getCompoundById

getDBRefs

setDBRefs

getPDBHeader

setPDBHeader

getSSBonds

setSSBonds

addSSBond

hasJournalArticle

getJournalArticle

setJournalArticle

getSites

setSites

getHetGroups

setBiologicalAssembly

isBiologicalAssembly

setCrystallographicInfo

getCrystallographicInfo

getIdentifier

getPdbId

resetModels

getResidueRanges

getRanges