org.biojava.bio.structure
Interface Atom

All Superinterfaces:
Cloneable, PDBRecord
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
 Object clone()
          returns and identical copy of this object .
 Character getAltLoc()
          get set alternate Location.
 double[] getCoords()
          get the coordinates.
 Element getElement()
          get element of the atom, e.g.
 String getFullName()
          get full name of atom e.g.
 Group getGroup()
          Returns the parent Group of the Atom.
 String getName()
          get trimmed version of atom name, e.g.
 double getOccupancy()
          get occupancy.
 Group getParent()
          Deprecated. replaced by getGroup()
 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(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(String s)
          set full name of atom e.g.
 void setGroup(Group parent)
          Sets the back-reference to its parent Group.
 void setName(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(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(String s)
set trimmed version of atom name, e.g. "CA".

Parameters:
s - a String specifying the name value
See Also:
getName()

getName

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(String s)
set full name of atom e.g. " CA ".

Parameters:
s - a String specifying the full name value
See Also:
getFullName()

getFullName

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(Character c)
get set alternate Location.

Parameters:
c - a Character object specifying the alt loc value
See Also:
getAltLoc()

getAltLoc

Character getAltLoc()
get set alternate Location.

Returns:
a Character object representing the alt loc value
See Also:
setAltLoc(java.lang.Character)

setPDBline

void setPDBline(String s)
Deprecated. replaced by PDBRecord.toPDB()

store the whole line.

Parameters:
s - a String specifying the PDBline value
See Also:
getPDBline()

getPDBline

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

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)