Package org.biojava.nbio.structure

Interface Atom

All Superinterfaces:

Cloneable, PDBRecord, Serializable

All Known Implementing Classes:

AtomImpl

public interface Atom
extends Cloneable, PDBRecord

A simple interface for an Atom. The coordinates can be accessed via the getCoords(), or the getX(), getY(), getZ() methods. There are a few additional methods here to provide some PDB specific information.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic, Horvath Tamas

Method Summary

Modifier and Type	Method	Description
void	addBond(Bond bond)	Add a bond
Object	clone()	Return an 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 charge)	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 occupancy)	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.

Methods inherited from interface org.biojava.nbio.structure.PDBRecord

toPDB, toPDB

Method Detail

setName

void setName(String s)

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

Parameters:

s - a trimmed String specifying the name value

See Also:

getName()

getName

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 getElement()

Returns:

a trimmed String representing the name value

See Also:

setName(java.lang.String)

setElement

void setElement(Element e)

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

Parameters:

e - an Element enumeration

See Also:

getElement()

getElement

Element getElement()

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

Returns:

an Element enumeration

See Also:

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

setPDBserial

void setPDBserial(int i)

Set PDB atom number.

Parameters:

i - an int specifying the PDBserial value

See Also:

getPDBserial()

getPDBserial

int getPDBserial()

Get PDB atom number.

Returns:

an int representing the PDBserial value

See Also:

setPDBserial(int)

setCoords

void setCoords(double[] c)

Set the coordinates.

Parameters:

c - an array of doubles specifying the coords value

See Also:

getCoords()

getCoords

double[] getCoords()

Get the coordinates.

Returns:

a new array of doubles representing the coords value

See Also:

setCoords(double[]), getCoordsAsPoint3d()

getCoordsAsPoint3d

javax.vecmath.Point3d getCoordsAsPoint3d()

Get the coordinates.

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

Returns:

a reference to the Point3d coordinates

See Also:

getCoords()

setX

void setX(double x)

Set the X coordinate.

Parameters:

x - a double

See Also:

getX()

setY

void setY(double y)

Set the Y coordinate.

Parameters:

y - a double

See Also:

getY()

setZ

void setZ(double z)

Set the Z coordinate.

Parameters:

z - a double

See Also:

getZ()

getX

double getX()

Get coordinate X.

Returns:

a double

See Also:

setX(double)

getY

double getY()

Get coordinate Y.

Returns:

a double

See Also:

setY(double)

getZ

double getZ()

Get coordinate Z.

Returns:

a double

See Also:

setZ(double)

setAltLoc

void setAltLoc(Character c)

Set alternate Location.

Parameters:

c - a Character object specifying the alt loc value

See Also:

getAltLoc()

getAltLoc

Character getAltLoc()

Get alternate Location.

Returns:

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

See Also:

setAltLoc(java.lang.Character)

setOccupancy

void setOccupancy(float occupancy)

Set occupancy.

Parameters:

occupancy - a float specifying the occupancy value

See Also:

getOccupancy()

getOccupancy

float getOccupancy()

Get occupancy.

Returns:

a float representing the occupancy value

See Also:

setOccupancy(float)

setTempFactor

void setTempFactor(float temp)

Set temp factor .

Parameters:

temp - a float specifying the temp factor value

See Also:

getTempFactor()

getTempFactor

float getTempFactor()

Get temp factor.

Returns:

a float representing the temp factor value

See Also:

setTempFactor(float)

clone

Object clone()

Return an identical copy of this object .

Returns:

an identical copy of this object

setGroup

void setGroup(Group parent)

Set the back-reference to its parent Group.

Parameters:

parent - the parent Group

See Also:

getGroup()

getGroup

Group getGroup()

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

Returns:

Group the parent Group of the Atom, or null

See Also:

setGroup(Group)

addBond

void addBond(Bond bond)

Add a bond

Parameters:

bond - to be added

See Also:

getBonds()

getBonds

List<Bond> getBonds()

Get all Bonds this atom is part of.

Returns:

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

setBonds

void setBonds(List<Bond> bonds)

Sets the bonds

Parameters:

bonds -

hasBond

boolean hasBond(Atom other)

Test if another atom has a bond to this atom

Parameters:

other -

Returns:

getCharge

short getCharge()

Get the charge of this atom

Returns:

a the integer charge.

setCharge

void setCharge(short charge)

Set the charge of this atom