org.biojava.bio.structure
Class AtomImpl

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

All Implemented Interfaces:

Atom

public class AtomImpl
extends Object
implements Atom

Implementation of an Atom of a PDB file. currently the coordinates of an atom are represented by a doubl[3] array.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic

Constructor Summary

AtomImpl()

Method Summary

Object	clone() returns and identical copy of this object .
Character	getAltLoc() get alternate Location.
double[]	getCoords() get the coordinates as a double[3] array .
String	getFullName() get full name of atom e.g.
String	getName() Gets this object's name.
double	getOccupancy() get occupancy.
Group	getParent() Returns the parent Group of the Atom returns null if the referenced object is not Group
String	getPDBline() get the whole line .
int	getPDBserial() get PDB atom number.
double	getTempFactor() get set temp factor.
double	getX() get the X coordinate.
double	getY() get the Y coordinate.
double	getZ() get the Z coordinate.
void	setAltLoc(Character c) set alternate Location.
void	setCoords(double[] c) the coordinates.
void	setFullName(String s) set full name of atom e.g.
void	setName(String s) trimmed version of atom name, e.g.
void	setOccupancy(double occu) set occupancy.
void	setParent(Group parent) Sets the back-reference to its parent Group
void	setPDBline(String s) store the whole line.
void	setPDBserial(int i) set PDB atom number.
void	setTempFactor(double temp) get set temp factor .
void	setX(double x) set the X coordinate
void	setY(double y) set the Y coordinate
void	setZ(double z) set the Z coordinate
String	toString() string representation.

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomImpl

public AtomImpl()

Method Detail

setName

public void setName(String s)

trimmed version of atom name, e.g. "CA"

Specified by:

setName in interface Atom

Parameters:

s - a String specifying the name value

See Also:

getName()

getName

public String getName()

Gets this object's name.

Specified by:

getName in interface Atom

Returns:

a String representing the name value

See Also:

setName(java.lang.String)

setFullName

public void setFullName(String s)

set full name of atom e.g. " CA " .

Specified by:

setFullName in interface Atom

Parameters:

s - a String specifying the full name value

See Also:

getFullName()

getFullName

public String getFullName()

get full name of atom e.g. " CA ".

Specified by:

getFullName in interface Atom

Returns:

a String representing the full name value

See Also:

setFullName(java.lang.String)

setPDBserial

public void setPDBserial(int i)

set PDB atom number.

Specified by:

setPDBserial in interface Atom

Parameters:

i - an int specifying the PDBserial value

See Also:

getPDBserial()

getPDBserial

public int getPDBserial()

get PDB atom number.

Specified by:

getPDBserial in interface Atom

Returns:

an int representing the PDBserial value

See Also:

setPDBserial(int)

setCoords

public void setCoords(double[] c)

the coordinates.

Specified by:

setCoords in interface Atom

Parameters:

c - an array of doubles specifying the coords value

See Also:

getCoords()

getCoords

public double[] getCoords()

get the coordinates as a double[3] array .

Specified by:

getCoords in interface Atom

Returns:

an array of doubles representing the coords value

See Also:

setCoords(double[])

setX

public void setX(double x)

Description copied from interface: Atom

set the X coordinate

Specified by:

setX in interface Atom

Parameters:

x - a double

setY

public void setY(double y)

Description copied from interface: Atom

set the Y coordinate

Specified by:

setY in interface Atom

Parameters:

y - a double

setZ

public void setZ(double z)

Description copied from interface: Atom

set the Z coordinate

Specified by:

setZ in interface Atom

Parameters:

z - a double

getX

public double getX()

get the X coordinate.

Specified by:

getX in interface Atom

Returns:

a double

getY

public double getY()

get the Y coordinate.

Specified by:

getY in interface Atom

Returns:

a double

getZ

public double getZ()

get the Z coordinate.

Specified by:

getZ in interface Atom

Returns:

a double

setAltLoc

public void setAltLoc(Character c)

set alternate Location.

Specified by:

setAltLoc in interface Atom

Parameters:

c - a Character object specifying the alt loc value

See Also:

getAltLoc()

getAltLoc

public Character getAltLoc()

get alternate Location.

Specified by:

getAltLoc in interface Atom

Returns:

a Character object representing the alt loc value

See Also:

setAltLoc(java.lang.Character)

setPDBline

public void setPDBline(String s)

store the whole line.

Specified by:

setPDBline in interface Atom

Parameters:

s - a String specifying the PDBline value

See Also:

getPDBline()

getPDBline

public String getPDBline()

get the whole line .

Specified by:

getPDBline in interface Atom

Returns:

a String representing the PDBline value

See Also:

setPDBline(java.lang.String)

toString

public String toString()

string representation.

Overrides:

toString in class Object

setOccupancy

public void setOccupancy(double occu)

Description copied from interface: Atom

set occupancy.

Specified by:

setOccupancy in interface Atom

Parameters:

occu - a double specifying the occupancy value

See Also:

Atom.getOccupancy()

getOccupancy

public double getOccupancy()

Description copied from interface: Atom

get occupancy.

Specified by:

getOccupancy in interface Atom

Returns:

a double representing the occupancy value

See Also:

Atom.setOccupancy(double)

setTempFactor

public void setTempFactor(double temp)

Description copied from interface: Atom

get set temp factor .

Specified by:

setTempFactor in interface Atom

Parameters:

temp - a double specifying the temp factor value

See Also:

Atom.getTempFactor()

getTempFactor

public double getTempFactor()

Description copied from interface: Atom

get set temp factor.

Specified by:

getTempFactor in interface Atom

Returns:

a double representing the temp factor value

See Also:

Atom.setTempFactor(double)

clone

public Object clone()

returns and identical copy of this object .

Specified by:

clone in interface Atom

Overrides:

clone in class Object

Returns:

and identical copy of this object

setParent

public void setParent(Group parent)

Description copied from interface: Atom

Sets the back-reference to its parent Group

Specified by:

setParent in interface Atom

Parameters:

parent - the parent Group

getParent

public Group getParent()

Description copied from interface: Atom

Returns the parent Group of the Atom returns null if the referenced object is not Group

Specified by:

getParent in interface Atom

Returns:

Group the parent Group of the Atom, or null