org.biojava.nbio.structure

Class AtomImpl

java.lang.Object

org.biojava.nbio.structure.AtomImpl

All Implemented Interfaces:

Serializable, Cloneable, Atom, PDBRecord

public class AtomImpl
extends Object
implements Atom, Serializable, PDBRecord

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

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
AtomImpl()

Method Summary

Methods

Modifier and Type	Method and Description
void	addBond(Bond bond) Add a bond
Object	clone() returns and identical copy of this object .
Character	getAltLoc() get alternate Location.
List<Bond>	getBonds() Get all Bonds this atom is part of.
double[]	getCoords() Get the coordinates.
Element	getElement() Get element of the atom, e.g.
Group	getGroup() Return the parent Group of the Atom.
long	getId() Get the Hibernate database ID.
String	getName() Get atom name, e.g.
double	getOccupancy() Get occupancy.
int	getPDBserial() Get PDB atom number.
double	getTempFactor() Get temp factor.
double	getX() Get coordinate X.
double	getY() Get coordinate Y.
double	getZ() Get coordinate Z.
void	setAltLoc(Character c) set alternate Location.
void	setCoords(double[] c) Set the coordinates.
void	setElement(Element e) Set element of the atom name, e.g.
void	setGroup(Group parent) Set the back-reference to its parent Group.
void	setId(long id) Set the Hibernate database ID.
void	setName(String s) Set atom name, e.g.
void	setOccupancy(double occu) Set occupancy.
void	setPDBserial(int i) Set PDB atom number.
void	setTempFactor(double temp) 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	toPDB() Returns a PDB file like representation of this record.
void	toPDB(StringBuffer buf) Appends a PDB file like representation of this record to the provided StringBuffer.
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

getId

public long getId()

Get the Hibernate database ID.

Returns:

the id

See Also:

setId(long)

setId

public void setId(long id)

Set the Hibernate database ID.

Parameters:

id - the hibernate id

See Also:

getId()

setName

public void setName(String s)

Set atom name, e.g. "CA".

Specified by:

setName in interface Atom

Parameters:

s - a trimmed String specifying the name value

See Also:

Atom.getName()

getName

public String getName()

Get atom name, e.g. "CA". Beware that some PDB atom names are ambiguous (e.g. CA, which means C-alpha or Calcium), the ambiguity can simply be resolved by also checking the element with Atom.getElement()

Specified by:

getName in interface Atom

Returns:

a trimmed String representing the name value

See Also:

Atom.setName(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:

Atom.getPDBserial()

getPDBserial

public int getPDBserial()

Get PDB atom number.

Specified by:

getPDBserial in interface Atom

Returns:

an int representing the PDBserial value

See Also:

Atom.setPDBserial(int)

setCoords

public void setCoords(double[] c)

Set the coordinates.

Specified by:

setCoords in interface Atom

Parameters:

c - an array of doubles specifying the coords value

See Also:

Atom.getCoords()

getCoords

public double[] getCoords()

Get the coordinates.

Specified by:

getCoords in interface Atom

Returns:

an array of doubles representing the coords value

See Also:

Atom.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

See Also:

Atom.getX()

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

See Also:

Atom.getY()

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

See Also:

Atom.getZ()

getX

public double getX()

Get coordinate X.

Specified by:

getX in interface Atom

Returns:

a double

See Also:

Atom.setX(double)

getY

public double getY()

Get coordinate Y.

Specified by:

getY in interface Atom

Returns:

a double

See Also:

Atom.setY(double)

getZ

public double getZ()

Get coordinate Z.

Specified by:

getZ in interface Atom

Returns:

a double

See Also:

Atom.setZ(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)

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

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 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

setGroup

public void setGroup(Group parent)

Set the back-reference to its parent Group.

Specified by:

setGroup in interface Atom

Parameters:

parent - the parent Group

See Also:

Atom.getGroup()

getGroup

public Group getGroup()

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

Specified by:

getGroup in interface Atom

Returns:

Group the parent Group of the Atom, or null

See Also:

Atom.setGroup(Group)

getElement

public Element getElement()

Get element of the atom, e.g. Element.Ca

Specified by:

getElement in interface Atom

Returns:

an Element enumeration

See Also:

Atom.setElement(org.biojava.nbio.structure.Element)

setElement

public void setElement(Element e)

Set element of the atom name, e.g. Element.Fe

Specified by:

setElement in interface Atom

Parameters:

e - an Element enumeration

See Also:

Atom.getElement()

toPDB

public String toPDB()

Description copied from interface: PDBRecord

Returns a PDB file like representation of this record.

Specified by:

toPDB in interface PDBRecord

Returns:

a String providing a PDB file like representation of the record.

toPDB

public void toPDB(StringBuffer buf)

Description copied from interface: PDBRecord

Appends a PDB file like representation of this record to the provided StringBuffer.

Specified by:

toPDB in interface PDBRecord

getBonds

public List<Bond> getBonds()

Description copied from interface: Atom

Get all Bonds this atom is part of.

Specified by:

getBonds in interface Atom

Returns:

a list of Bonds.

addBond

public void addBond(Bond bond)

Description copied from interface: Atom

Add a bond

Specified by:

addBond in interface Atom

Parameters:

bond - to be added

See Also:

Atom.getBonds()