org.biojava.bio.structure
Interface Structure

All Known Implementing Classes:

StructureImpl

public interface Structure

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 pos) retrieve a chain by it's position within the Structure
Chain	getChain(int pos, int modelnr) 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() test if this structure is an nmr structure
int	nrModels() return number of models in this implementation also XRAY structures have "1 model", since model is the container for the chains.
void	setConnections(ArrayList connections) 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 name) 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 file
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 of object

Method Detail

toString

public String toString()

String representation of object

setPDBCode

public void setPDBCode(String pdb_id)

set PDB code of structure

getPDBCode

public String getPDBCode()

get PDB code of structure

setName

public void setName(String name)

set biological name of Structure

getName

public String getName()

get biological name of Structure

setHeader

public void setHeader(HashMap h)

set the Header data

getHeader

public HashMap getHeader()

get Header data

setConnections

public void setConnections(ArrayList connections)

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

getConnections

public ArrayList getConnections()

size

public int size()

return number of Chains in file

size

public int size(int modelnr)

return number of chains of model

nrModels

public int nrModels()

return number of models in this implementation also XRAY structures have "1 model", since model is the container for the chains. to test if a Structure is an NMR structure use @see isNMR , since this is based on the info in the PDB file header.

isNmr

public boolean isNmr()

test if this structure is an nmr structure

setNmr

public void setNmr(boolean nmr)

addModel

public void addModel(ArrayList model)

add a new model

getModel

public ArrayList getModel(int modelnr)

retrieve all Chains belonging to a model

See Also:

getChains

getChains

public ArrayList getChains(int modelnr)

retrieve all chains of a model

See Also:

getModel

addChain

public void addChain(Chain chain)

add a new chain

addChain

public void addChain(Chain chain,
                     int modelnr)

add a new chain, if several models are available

getChain

public Chain getChain(int pos)

retrieve a chain by it's position within the Structure

getChain

public Chain getChain(int pos,
                      int modelnr)

retrieve a chain by it's position within the Structure and model number

toPDB

public String toPDB()

create a String that contains the contents of a PDB file