Package 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

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

Field Summary

Fields

Modifier and Type	Field	Description
static final int	BONDS_INITIAL_CAPACITY	The inital capacity of the bonds list.

Constructor Summary

Constructors

Constructor	Description
AtomImpl()

Method Summary

Modifier and Type	Method	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.
short	getCharge()	Get the charge of this atom
double[]	getCoords()	Get the coordinates.
javax.vecmath.Point3d	getCoordsAsPoint3d()	Get the coordinates.
Element	getElement()	Get element of the atom, e.g.
Group	getGroup()	Return the parent Group of the Atom.
String	getName()	Get atom name, e.g.
float	getOccupancy()	Get occupancy.
int	getPDBserial()	Get PDB atom number.
float	getTempFactor()	Get temp factor.
double	getX()	Get coordinate X.
double	getY()	Get coordinate Y.
double	getZ()	Get coordinate Z.
boolean	hasBond(Atom other)	Test if another atom has a bond to this atom
void	setAltLoc(Character c)	Set alternate Location.
void	setBonds(List<Bond> bonds)	Sets the bonds
void	setCharge(short inputCharge)	Set the charge of this atom
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	setName(String s)	Set atom name, e.g.
void	setOccupancy(float occu)	Set occupancy.
void	setPDBserial(int i)	Set PDB atom number.
void	setTempFactor(float 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()

Methods inherited from class java.lang.Object

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

Field Details

BONDS_INITIAL_CAPACITY

public static final int BONDS_INITIAL_CAPACITY

The inital capacity of the bonds list. Most atoms have a maximum of 3 heavy atom neighbors.

See Also:

• Constant Field Values

Constructor Details

AtomImpl

public AtomImpl()

Method Details

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:

a new array of doubles representing the coords value

See Also:

• Atom.setCoords(double[])
• Atom.getCoordsAsPoint3d()

getCoordsAsPoint3d

public javax.vecmath.Point3d getCoordsAsPoint3d()

Get the coordinates.

Internally the coordinates are represented as Point3d so this is recommended over Atom.getCoords()

Specified by:

getCoordsAsPoint3d in interface Atom

Returns:

a reference to the Point3d coordinates

See Also:

• Atom.getCoords()

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)

Description copied from interface: Atom

Set alternate Location.

Specified by:

setAltLoc in interface Atom

Parameters:

c - a Character object specifying the alt loc value

See Also:

• Atom.getAltLoc()

getAltLoc

public Character getAltLoc()

Description copied from interface: Atom

Get alternate Location.

Specified by:

getAltLoc in interface Atom

Returns:

a Character object representing the alt loc value. Default altLoc ('.' in mmCIF files) is represented by ' ' (space character, ascii 32).

See Also:

• Atom.setAltLoc(java.lang.Character)

toString

public String toString()

Overrides:

toString in class Object

setOccupancy

public void setOccupancy(float occu)

Description copied from interface: Atom

Set occupancy.

Specified by:

setOccupancy in interface Atom

Parameters:

occu - a float specifying the occupancy value

See Also:

• Atom.getOccupancy()

getOccupancy

public float getOccupancy()

Description copied from interface: Atom

Get occupancy.

Specified by:

getOccupancy in interface Atom

Returns:

a float representing the occupancy value

See Also:

• Atom.setOccupancy(float)

setTempFactor

public void setTempFactor(float temp)

Description copied from interface: Atom

Set temp factor .

Specified by:

setTempFactor in interface Atom

Parameters:

temp - a float specifying the temp factor value

See Also:

• Atom.getTempFactor()

getTempFactor

public float getTempFactor()

Description copied from interface: Atom

Get temp factor.

Specified by:

getTempFactor in interface Atom

Returns:

a float representing the temp factor value

See Also:

• Atom.setTempFactor(float)

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()

Get all Bonds this atom is part of.

Specified by:

getBonds in interface Atom

Returns:

a list of Bonds or null if no bonds exist for this Atom

hasBond

public boolean hasBond(Atom other)

Test if another atom has a bond to this atom

Specified by:

hasBond in interface Atom

Parameters:

other -

Returns:

setBonds

public void setBonds(List<Bond> bonds)

Sets the bonds

Specified by:

setBonds in interface Atom

Parameters:

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()

getCharge

public short getCharge()

Description copied from interface: Atom

Get the charge of this atom

Specified by:

getCharge in interface Atom

Returns:

a the integer charge.

setCharge

public void setCharge(short inputCharge)

Description copied from interface: Atom

Set the charge of this atom

Specified by:

setCharge in interface Atom