org.biojava.bio.structure
Class StructureImpl

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

All Implemented Interfaces:

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

Constructor Summary

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

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.
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<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	isNmr() is this structure an nmr structure ?
int	nrModels() return number of models.
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:
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.
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	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)

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>)

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