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.

Constructor Summary

AtomImpl()

Method Summary

double[]	getCoords() get the coordinates as a double[3] array
String	getFullName() get full name of atom e.g.
String	getName()
double	getOccupancy() get occupancy
String	getPDBline() get the whole line
int	getPDBserial() get PDB atom number
double	getTempFactor()
double	getX() get the X coordinate
double	getY() get the Y coordinate
double	getZ() get the Z coordinate
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	setPDBline(String s) store the whole line
void	setPDBserial(int i) set PDB atom number
void	setTempFactor(double temp)
String	toString() string representation

Methods inherited from class java.lang.Object

clone, 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

getName

public String getName()

Specified by:

getName in interface Atom

setFullName

public void setFullName(String s)

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

Specified by:

setFullName in interface Atom

getFullName

public String getFullName()

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

Specified by:

getFullName in interface Atom

setPDBserial

public void setPDBserial(int i)

set PDB atom number

Specified by:

setPDBserial in interface Atom

getPDBserial

public int getPDBserial()

get PDB atom number

Specified by:

getPDBserial in interface Atom

setCoords

public void setCoords(double[] c)

the coordinates

Specified by:

setCoords in interface Atom

getCoords

public double[] getCoords()

get the coordinates as a double[3] array

Specified by:

getCoords in interface Atom

getX

public double getX()

get the X coordinate

Specified by:

getX in interface Atom

getY

public double getY()

get the Y coordinate

Specified by:

getY in interface Atom

getZ

public double getZ()

get the Z coordinate

Specified by:

getZ in interface Atom

setPDBline

public void setPDBline(String s)

store the whole line

Specified by:

setPDBline in interface Atom

getPDBline

public String getPDBline()

get the whole line

Specified by:

getPDBline in interface Atom

toString

public String toString()

string representation

setOccupancy

public void setOccupancy(double occu)

Description copied from interface: Atom

set occupancy

Specified by:

setOccupancy in interface Atom

getOccupancy

public double getOccupancy()

Description copied from interface: Atom

get occupancy

Specified by:

getOccupancy in interface Atom

setTempFactor

public void setTempFactor(double temp)

Specified by:

setTempFactor in interface Atom

getTempFactor

public double getTempFactor()

Specified by:

getTempFactor in interface Atom