PIP.Core
Class Atom

java.lang.Object
  PIP.Core.Atom

All Implemented Interfaces:

java.io.Serializable, MSDID, Spatial

public class Atom
extends java.lang.Object
implements Spatial, java.io.Serializable, MSDID

See Also:

Serialized Form

Constructor Summary

Atom(int id)

Method Summary

char	getAlternative()
java.lang.String	getAtomName()
float[]	getCoordinates()
Element	getElement()
int	getMSDID()
Residue	getResidue()
void	setAlternative(char alternative)
void	setAtomName(java.lang.String atomName)
void	setElementSymbol(Element e)
void	setMSDID(int id)
void	setResidue(Residue residue)
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Atom

public Atom(int id)

Method Detail

getMSDID

public int getMSDID()

Specified by:

getMSDID in interface MSDID

Returns:

the msdid serial of the chain (CHAIN_ID in MSD)

setMSDID

public void setMSDID(int id)

Specified by:

setMSDID in interface MSDID

Parameters:

id - - the msdid serial of the chain (CHAIN_ID in MSD)

getAtomName

public java.lang.String getAtomName()

Returns:

The standard PDB name of the atom in the molecule that correspond with the definition of the ligand in the chemical dictionary. This might be different from the name in the PDB entry either due to inconsistent naming, or because this is a totally different ligand.

setAtomName

public void setAtomName(java.lang.String atomName)

Parameters:

atomName - - The standard PDB name of the atom in the molecule that correspond with the definition of the ligand in the chemical dictionary. This might be different from the name in the PDB entry either due to inconsistent naming, or because this is a totally different ligand.

getElement

public Element getElement()

Returns:

The standard one or two character symbol of the chemical element of the atom

setElementSymbol

public void setElementSymbol(Element e)

Parameters:

e - - The standard one or two character symbol of the chemical element of the atom

getAlternative

public char getAlternative()

Returns:

The ALT code of the atom as defined in the PDB

setAlternative

public void setAlternative(char alternative)

Parameters:

alternative - - The ALT code of the atom as defined in the PDB

getResidue

public Residue getResidue()

Returns:

A link back to the residue that the atom belongs to

setResidue

public void setResidue(Residue residue)

Parameters:

residue - - A link back to the residue that the atom belongs to

getCoordinates

public float[] getCoordinates()

Specified by:

getCoordinates in interface Spatial

Returns:

Atom co-ordinates X,Y,Z

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

Atom: ID=msdid