ProGAL.proteins.structure
Class Atom

java.lang.Object
  ProGAL.geomNd.Point
      ProGAL.geom3d.Point
          ProGAL.proteins.structure.Atom

All Implemented Interfaces:

java.io.Serializable, Shape, Simplex

public class Atom
extends Point

A class to represent the following properties of an atom:

• Position
• Van der waals radius
• covalent bonds
• name
• an id unique to this atom among all the atoms within the same amino acid
• a pointer to the residue that the atom belongs to

The position is maintained in the super-class Point. The preferred way to change the position of an atom is therefore not to replace it, but to call either the set(Point p) method or setCoord(int d, double v). This changes the coordinates but not the Atom-pointer.

Author:

R.Fonseca

See Also:

Serialized Form

Constructor Summary

Atom(java.lang.String name)

Atom(java.lang.String name, char element, double radius)

Method Summary

AminoAcid	aminoAcid()
Atom	clone() Return a new object that equals this object.
CBond[]	covalentBonds()
char	element()
int	index()
boolean	isBB()
java.lang.String	name()
double	radius()
void	setCovalentBonds(CBond[] bonds)
java.lang.String	toString() Returns a string-representation of this point formatted with two decimals precision.

Methods inherited from class ProGAL.geom3d.Point

add, addThis, addThis, collinear, coplanar, distance, distanceSquared, dominates, dominates, dot, dot, equals, equals, getAngle, getBisector, getCenter, getCircumCenter, getCosDihedralAngle, getDihedralAngle, getDimension, getEquilateralPoint, getMidpoint, getPoint, getSteinerPoint, inSphere, main, orientation, orientation, polarAngleCosZ, polarAngleSinZ, reflectThroughOrigoThis, rotation, rotation, scaleThis, setX, setY, setZ, subtract, subtractThis, subtractThis, toConsole, toConsole, toScene, toString, toVector, translateThis, vectorTo, x, y, z

Methods inherited from class ProGAL.geomNd.Point

addThis, distance, distance, distanceSquared, distanceSquared, distanceSquaredXY, distanceXY, dot, get, getCoord, getCoords, getDimensions, multiplyThis, polarAngleCosXY, polarAngleSinXY, polarAngleXY, set, set, setCoord, setCoord, vectorTo

Methods inherited from class java.lang.Object

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

Constructor Detail

Atom

public Atom(java.lang.String name)

Atom

public Atom(java.lang.String name,
            char element,
            double radius)

Method Detail

setCovalentBonds

public void setCovalentBonds(CBond[] bonds)

radius

public double radius()

element

public char element()

name

public java.lang.String name()

aminoAcid

public AminoAcid aminoAcid()

index

public int index()

covalentBonds

public CBond[] covalentBonds()

isBB

public boolean isBB()

toString

public java.lang.String toString()

Description copied from class: Point

Returns a string-representation of this point formatted with two decimals precision.

Overrides:

toString in class Point

clone

public Atom clone()

Description copied from class: Point

Return a new object that equals this object.

Overrides:

clone in class Point