astex
Class Chain

java.lang.Object
  astex.Chain

All Implemented Interfaces:

Selectable

public class Chain
extends java.lang.Object
implements Selectable

A class for storing a group of atoms that form part of a protein chain.

Field Summary

static java.lang.String	undefinedChainName Undefined resiude name.
static int	undefinedChainNumber Undefined residue number.

Method Summary

Residue	addResidue() Add a residue to the chain.
static Chain	create() Public interface for creating chains.
Residue	getCurrentResidue() Return the current residue.
char	getInsertionCode() Get the insertion code.
int	getMaximumResidueId() Get maximum residue id.
java.lang.String	getName() Get the chain name.
int	getNumber() Get the chain number.
Molecule	getParent() Get the parent.
Residue	getResidue(int index) Return the specified atom.
int	getResidueCount() Return the number of atoms in the molecule.
void	removeResidue(Residue res) Remove a residue from the chain.
int	select(int state) Apply a selection recursively.
java.lang.String	selectStatement()
void	setInsertionCode(char code) Set the insertion code.
void	setName(java.lang.String newName) Set the chain name.
void	setNumber(int newNumber) Set the chain number.
void	setParent(Molecule molecule) Set the parent molecule.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

undefinedChainNumber

public static int undefinedChainNumber

Undefined residue number.

undefinedChainName

public static java.lang.String undefinedChainName

Undefined resiude name.

Method Detail

create

public static Chain create()

Public interface for creating chains.

setParent

public void setParent(Molecule molecule)

Set the parent molecule.

getParent

public Molecule getParent()

Get the parent.

setInsertionCode

public void setInsertionCode(char code)

Set the insertion code.

getInsertionCode

public char getInsertionCode()

Get the insertion code.

setName

public void setName(java.lang.String newName)

Set the chain name.

getName

public java.lang.String getName()

Get the chain name.

setNumber

public void setNumber(int newNumber)

Set the chain number.

getNumber

public int getNumber()

Get the chain number.

getResidueCount

public int getResidueCount()

Return the number of atoms in the molecule.

getResidue

public Residue getResidue(int index)

Return the specified atom.

addResidue

public Residue addResidue()

Add a residue to the chain.

removeResidue

public void removeResidue(Residue res)

Remove a residue from the chain.

getCurrentResidue

public Residue getCurrentResidue()

Return the current residue.

getMaximumResidueId

public int getMaximumResidueId()

Get maximum residue id.

selectStatement

public java.lang.String selectStatement()

Specified by:

selectStatement in interface Selectable

select

public int select(int state)

Apply a selection recursively.

Specified by:

select in interface Selectable