org.biojava.bio.structure
Class AtomImpl

java.lang.Object
  extended by org.biojava.bio.structure.AtomImpl
All Implemented Interfaces:
Serializable, Cloneable, Atom, PDBRecord

public class AtomImpl
extends Object
implements Atom, Serializable, PDBRecord

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

Constructor Summary
AtomImpl()
           
 
Method Summary
 Object clone()
          returns and identical copy of this object .
 Character getAltLoc()
          get alternate Location.
 double[] getCoords()
          get the coordinates as a double[3] array .
 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.
 long getId()
          Get the Hibernate database ID.
 String getName()
          Gets this object's name.
 double getOccupancy()
          get occupancy.
 Group getParent()
          Returns the parent Group of the Atom.
 String getPDBline()
          Deprecated.  
 int getPDBserial()
          get PDB atom number.
 double getTempFactor()
          get set temp factor.
 double getX()
          Get the X coordinate.
 double getY()
          Get the Y coordinate.
 double getZ()
          Get the Z coordinate.
 void setAltLoc(Character c)
          set alternate Location.
 void setCoords(double[] c)
          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 setId(long id)
          Set the Hibernate database ID.
 void setName(String s)
          trimmed version of atom name, e.g.
 void setOccupancy(double occu)
          set occupancy.
 void setParent(Group parent)
          Sets the back-reference to its parent Group.
 void setPDBline(String s)
          Deprecated.  
 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.
 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()
          string representation.
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

AtomImpl

public AtomImpl()
Method Detail

getId

public long getId()
Get the Hibernate database ID.

Returns:
the id
See Also:
setId(long)

setId

public void setId(long id)
Set the Hibernate database ID.

Parameters:
id - the hibernate id
See Also:
getId()

setName

public void setName(String s)
trimmed version of atom name, e.g. "CA"

Specified by:
setName in interface Atom
Parameters:
s - a String specifying the name value
See Also:
getName()

getName

public String getName()
Gets this object's name.

Specified by:
getName in interface Atom
Returns:
a String representing the name value
See Also:
setName(java.lang.String)

setFullName

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

Specified by:
setFullName in interface Atom
Parameters:
s - a String specifying the full name value
See Also:
getFullName()

getFullName

public String getFullName()
get full name of atom e.g. " CA ".

Specified by:
getFullName in interface Atom
Returns:
a String representing the full name value
See Also:
setFullName(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:
getPDBserial()

getPDBserial

public int getPDBserial()
get PDB atom number.

Specified by:
getPDBserial in interface Atom
Returns:
an int representing the PDBserial value
See Also:
setPDBserial(int)

setCoords

public void setCoords(double[] c)
the coordinates.

Specified by:
setCoords in interface Atom
Parameters:
c - an array of doubles specifying the coords value
See Also:
getCoords()

getCoords

public double[] getCoords()
get the coordinates as a double[3] array .

Specified by:
getCoords in interface Atom
Returns:
an array of doubles representing the coords value
See Also:
setCoords(double[])

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 the X coordinate.

Specified by:
getX in interface Atom
Returns:
a double
See Also:
setX(double)

getY

public double getY()
Get the Y coordinate.

Specified by:
getY in interface Atom
Returns:
a double
See Also:
setY(double)

getZ

public double getZ()
Get the Z coordinate.

Specified by:
getZ in interface Atom
Returns:
a double
See Also:
setZ(double)

setAltLoc

public void setAltLoc(Character c)
set alternate Location.

Specified by:
setAltLoc in interface Atom
Parameters:
c - a Character object specifying the alt loc value
See Also:
getAltLoc()

getAltLoc

public Character getAltLoc()
get alternate Location.

Specified by:
getAltLoc in interface Atom
Returns:
a Character object representing the alt loc value
See Also:
setAltLoc(java.lang.Character)

setPDBline

public void setPDBline(String s)
Deprecated. 

store the whole line.

Specified by:
setPDBline in interface Atom
Parameters:
s - a String specifying the PDBline value
See Also:
getPDBline()

getPDBline

public String getPDBline()
Deprecated. 

get the whole line .

Specified by:
getPDBline in interface Atom
Returns:
a String representing the PDBline value
See Also:
setPDBline(java.lang.String)

toString

public String toString()
string representation.

Overrides:
toString in class Object

setOccupancy

public void setOccupancy(double occu)
Description copied from interface: Atom
set occupancy.

Specified by:
setOccupancy in interface Atom
Parameters:
occu - a double specifying the occupancy value
See Also:
Atom.getOccupancy()

getOccupancy

public double getOccupancy()
Description copied from interface: Atom
get occupancy.

Specified by:
getOccupancy in interface Atom
Returns:
a double representing the occupancy value
See Also:
Atom.setOccupancy(double)

setTempFactor

public void setTempFactor(double temp)
Description copied from interface: Atom
get set temp factor .

Specified by:
setTempFactor in interface Atom
Parameters:
temp - a double specifying the temp factor value
See Also:
Atom.getTempFactor()

getTempFactor

public double getTempFactor()
Description copied from interface: Atom
get set temp factor.

Specified by:
getTempFactor in interface Atom
Returns:
a double representing the temp factor value
See Also:
Atom.setTempFactor(double)

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

setParent

public void setParent(Group parent)
Description copied from interface: Atom
Sets the back-reference to its parent Group.

Specified by:
setParent in interface Atom
Parameters:
parent - the parent Group
See Also:
Atom.getParent()

getParent

public Group getParent()
Description copied from interface: Atom
Returns the parent Group of the Atom. returns null if the referenced object is not Group

Specified by:
getParent in interface Atom
Returns:
Group the parent Group of the Atom, or null
See Also:
Atom.setParent(Group)

setGroup

public void setGroup(Group parent)
Description copied from interface: Atom
Sets 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()
Description copied from interface: Atom
Returns 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.setParent(Group)

getElement

public Element getElement()
Description copied from interface: Atom
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.bio.structure.Element)

setElement

public void setElement(Element e)
Description copied from interface: Atom
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