org.biojava.bio.structure

Interface Atom

All Superinterfaces:

java.lang.Cloneable, PDBRecord

All Known Implementing Classes:

AtomImpl

public interface Atom
extends java.lang.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

Methods

Modifier and Type	Method and Description
void	addBond(Bond bond) Adds a bond
java.lang.Object	clone() returns and identical copy of this object .
java.lang.Character	getAltLoc() get set alternate Location.
java.util.List<Bond>	getBonds() Gets all Bonds this atom is part of.
double[]	getCoords() get the coordinates.
Element	getElement() get element of the atom, e.g.
java.lang.String	getFullName() get full name of atom e.g.
Group	getGroup() Returns the parent Group of the Atom.
java.lang.String	getName() get trimmed version of atom name, e.g.
double	getOccupancy() get occupancy.
Group	getParent() Deprecated. replaced by getGroup()
java.lang.String	getPDBline() Deprecated. @deprecated replaced by PDBRecord.toPDB()
int	getPDBserial() get PDB atom number.
double	getTempFactor() get set temp factor.
double	getX() Get coordinate X.
double	getY() Get coordinate Y.
double	getZ() Get coordinate Z.
void	setAltLoc(java.lang.Character c) get set alternate Location.
void	setCoords(double[] c) set the coordinates.
void	setElement(Element e) set element of the atom name, e.g.
void	setFullName(java.lang.String s) set full name of atom e.g.
void	setGroup(Group parent) Sets the back-reference to its parent Group.
void	setName(java.lang.String s) set trimmed version of atom name, e.g.
void	setOccupancy(double occupancy) set occupancy.
void	setParent(Group parent) Deprecated. replaced by setGroup(Group)
void	setPDBline(java.lang.String s) Deprecated. replaced by PDBRecord.toPDB()
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.

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

toPDB, toPDB

Method Detail

setName

void setName(java.lang.String s)

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

Parameters:

s - a String specifying the name value

See Also:

getName()

getName

java.lang.String getName()

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

Returns:

a String representing the name value

See Also:

setName(java.lang.String)

setFullName

void setFullName(java.lang.String s)

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

Parameters:

s - a String specifying the full name value

See Also:

getFullName()

getFullName

java.lang.String getFullName()

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

Returns:

a String representing the full name value

See Also:

setFullName(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.bio.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:

an array of doubles representing the coords value

See Also:

setCoords(double[])

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(java.lang.Character c)

get set alternate Location.

Parameters:

c - a Character object specifying the alt loc value

See Also:

getAltLoc()

getAltLoc

java.lang.Character getAltLoc()

get set alternate Location.

Returns:

a Character object representing the alt loc value

See Also:

setAltLoc(java.lang.Character)

setPDBline

void setPDBline(java.lang.String s)

Deprecated. replaced by PDBRecord.toPDB()

store the whole line.

Parameters:

s - a String specifying the PDBline value

See Also:

getPDBline()

getPDBline

java.lang.String getPDBline()

Deprecated. @deprecated replaced by PDBRecord.toPDB()

store the whole line.

Returns:

a String representing the PDBline value

See Also:

setPDBline(java.lang.String)

setOccupancy

void setOccupancy(double occupancy)

set occupancy.

Parameters:

occupancy - a double specifying the occupancy value

See Also:

getOccupancy()

getOccupancy

double getOccupancy()

get occupancy.

Returns:

a double representing the occupancy value

See Also:

setOccupancy(double)

setTempFactor

void setTempFactor(double temp)

get set temp factor .

Parameters:

temp - a double specifying the temp factor value

See Also:

getTempFactor()

getTempFactor

double getTempFactor()

get set temp factor.

Returns:

a double representing the temp factor value

See Also:

setTempFactor(double)

clone

java.lang.Object clone()

returns and identical copy of this object .

Returns:

and identical copy of this object

setParent

void setParent(Group parent)

Deprecated. replaced by setGroup(Group)

Sets the back-reference to its parent Group.

Parameters:

parent - the parent Group

See Also:

getParent()

setGroup

void setGroup(Group parent)

Sets the back-reference to its parent Group.

Parameters:

parent - the parent Group

See Also:

getGroup()

getParent

Group getParent()

Deprecated. replaced by getGroup()

Returns 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:

setParent(Group)

getGroup

Group getGroup()

Returns 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:

setParent(Group)

addBond

void addBond(Bond bond)

Adds a bond

Parameters:

bond - to be added

See Also:

getBonds()

getBonds

java.util.List<Bond> getBonds()

Gets all Bonds this atom is part of.

Returns:

a list of Bonds.