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
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	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	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 -