org.biojava.bio.structure
Class StructureImpl

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

All Implemented Interfaces:

Structure

public class StructureImpl

extends Object

implements Structure

Implementation of a PDBStructure. This class provides the data contained in a PDB file.

Constructor Summary

StructureImpl()

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(ArrayList model) add a new model
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
ArrayList	getChains(int modelnr) retrieve all chains of a model
ArrayList	getConnections()
HashMap	getHeader() get Header data
ArrayList	getModel(int modelnr) retrieve all Chains belonging to a model
String	getName() get biological name of Structure
String	getPDBCode() get PDB code of structure
boolean	isNmr() is this structure an nmr strucutre ?
int	nrModels() return number of models
void	setConnections(ArrayList conns) CONECT data sets/gets an ArrayList of HashMaps which corresponds to the CONECT lines in the PDB file:
void	setHeader(HashMap h) set the Header data
void	setName(String nam) set biological name of Structure
void	setNmr(boolean nmr)
void	setPDBCode(String pdb_id_) set PDB code of structure
int	size() return number of chains in this container
int	size(int modelnr) return number of chains of 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

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

StructureImpl

public StructureImpl()

Method Detail

setPDBCode

public void setPDBCode(String pdb_id_)

set PDB code of structure

Specified by:

setPDBCode in interface Structure

getPDBCode

public String getPDBCode()

get PDB code of structure

Specified by:

getPDBCode in interface Structure

setName

public void setName(String nam)

set biological name of Structure

Specified by:

setName in interface Structure

getName

public String getName()

get biological name of Structure

Specified by:

getName in interface Structure

setHeader

public void setHeader(HashMap h)

set the Header data

Specified by:

setHeader in interface Structure

getHeader

public HashMap getHeader()

get Header data

Specified by:

getHeader in interface Structure

setConnections

public void setConnections(ArrayList conns)

Description copied from interface: Structure

CONECT data sets/gets an ArrayList of HashMaps 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

See Also:

interface

getConnections

public ArrayList getConnections()

Specified by:

getConnections in interface Structure

See Also:

interface

addChain

public void addChain(Chain chain)

add a new chain

Specified by:

addChain in interface Structure

addChain

public void addChain(Chain chain,
                     int modelnr)

add a new chain, if several models are available

Specified by:

addChain in interface Structure

getChain

public Chain getChain(int number)

retrieve a chain by it's position within the Structure

Specified by:

getChain in interface Structure

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

addModel

public void addModel(ArrayList model)

add a new model

Specified by:

addModel in interface Structure

toString

public String toString()

string representation

Specified by:

toString in interface Structure

size

public int size()

return number of chains in this container

Specified by:

size in interface Structure

size

public int size(int modelnr)

return number of chains of of model

Specified by:

size in interface Structure

nrModels

public int nrModels()

return number of models

Specified by:

nrModels in interface Structure

isNmr

public boolean isNmr()

is this structure an nmr strucutre ?

Specified by:

isNmr in interface Structure

setNmr

public void setNmr(boolean nmr)

Specified by:

setNmr in interface Structure

getChains

public ArrayList getChains(int modelnr)

retrieve all chains of a model

Specified by:

getChains in interface Structure

See Also:

getModel

getModel

public ArrayList getModel(int modelnr)

retrieve all Chains belonging to a model

Specified by:

getModel in interface Structure

See Also:

getChains

toPDB

public String toPDB()

create a String that contains the contents of a PDB file

Specified by:

toPDB in interface Structure