org.simtk.molecularstructure.atom
Class AtomClass

java.lang.Object
  org.simtk.molecularstructure.atom.AtomClass

All Implemented Interfaces:

MassBody, Atom, ChemicalElement, Chemical

public class AtomClass
extends java.lang.Object
implements Atom

Author:

Christopher Bruns \brief A chemical atom including members found in Protein Data Bank flat structure files.

Constructor Summary

AtomClass(java.lang.String pdbLine)

Method Summary

void	addPosition(AtomPosition pos)
java.util.Set<Atom>	bonds()
double	distance(Atom atom2)
java.lang.String	getAtomName()
Vector3D	getCenterOfMass()
Vector3D	getCoordinates()
double	getCovalentRadius()
java.lang.String	getElementName()
java.lang.String	getElementSymbol()
double	getMass()
double	getOccupancy()
Residue	getResidue()
double	getTemperatureFactor()
double	getVanDerWaalsRadius()
void	readPdbLine(java.lang.String pdbLine)
void	setAtomName(java.lang.String atomName)
void	setCoordinates(Vector3D v)
protected void	setElement(ChemicalElement element)
void	setResidue(Residue r)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AtomClass

public AtomClass(java.lang.String pdbLine)
          throws java.text.ParseException

Throws:

java.text.ParseException

Method Detail

addPosition

public void addPosition(AtomPosition pos)

Specified by:

addPosition in interface Atom

getCenterOfMass

public Vector3D getCenterOfMass()

Specified by:

getCenterOfMass in interface MassBody

getCoordinates

public Vector3D getCoordinates()

Specified by:

getCoordinates in interface Atom

setCoordinates

public void setCoordinates(Vector3D v)

Specified by:

setCoordinates in interface Atom

distance

public double distance(Atom atom2)

Specified by:

distance in interface Atom

getResidue

public Residue getResidue()

Specified by:

getResidue in interface Atom

setResidue

public void setResidue(Residue r)

bonds

public java.util.Set<Atom> bonds()

Specified by:

bonds in interface Atom

setElement

protected void setElement(ChemicalElement element)

getCovalentRadius

public double getCovalentRadius()

Specified by:

getCovalentRadius in interface ChemicalElement

getElementSymbol

public java.lang.String getElementSymbol()

Specified by:

getElementSymbol in interface ChemicalElement

getElementName

public java.lang.String getElementName()

Specified by:

getElementName in interface ChemicalElement

getMass

public double getMass()

Specified by:

getMass in interface MassBody

Specified by:

getMass in interface ChemicalElement

getVanDerWaalsRadius

public double getVanDerWaalsRadius()

Specified by:

getVanDerWaalsRadius in interface ChemicalElement

getAtomName

public java.lang.String getAtomName()

Specified by:

getAtomName in interface Atom

getOccupancy

public double getOccupancy()

Specified by:

getOccupancy in interface Atom

getTemperatureFactor

public double getTemperatureFactor()

Specified by:

getTemperatureFactor in interface Atom

setAtomName

public void setAtomName(java.lang.String atomName)

Specified by:

setAtomName in interface Atom

readPdbLine

public void readPdbLine(java.lang.String pdbLine)
                 throws java.text.ParseException

Throws:

java.text.ParseException