org.jscience.chemistry.gui.extended.molecule
Class Ring

java.lang.Object
  org.jscience.chemistry.gui.extended.molecule.Ring

public class Ring
extends java.lang.Object

Tripos base Ring class

Field Summary

protected int[]	atoms Ids of the atoms in the ring *
protected int	id Ring id
protected int	numAtoms Number of atoms in ring *
protected float	tx Transformed ring centroid *
protected float	ty Transformed ring centroid *
protected float	tz Transformed ring centroid *
protected float	x Ring centroid *
protected float	y Ring centroid *
protected float	z Ring centroid *

Constructor Summary

Ring()
Default constructor

Ring(float x, float y, float z)
Real coordinates constructor

Ring(float x, float y, float z, float tx, float ty, float tz)
Real and transformed coordinates constructor

Ring(int id, float x, float y, float z, float tx, float ty, float tz, int numAtoms, int[] atoms)
Full constructor

Ring(Ring ring)
Copy constructor

Method Summary

boolean	contains(Atom a) Return true if an atom is in this ring
int	getId() Return ring id
int	getNumAtoms() Return number of atoms in the ring
float	getTx() Return transformed ring centroid X coordinate
float	getTy() Return transformed ring centroid Y coordinate
float	getTz() Return transformed ring centroid Z coordinate
float	getX() Return ring centroid X coordinate
float	getY() Return ring centroid Y coordinate
float	getZ() Return ring centroid Z coordinate
protected void	setCentroid(float x, float y, float z) Set the centroid of the ring
void	setId(int id) Set ring id
void	setTx(float x) Set transformed ring centroid X coordinate
void	setTy(float y) Set transformed ring centroid Y coordinate
void	setTz(float z) Set transformed ring centroid Z coordinate
void	setX(float x) Set ring centroid X coordinate
void	setY(float y) Set ring centroid Y coordinate
void	setZ(float z) Set ring centroid Z coordinate
protected void	transform(Matrix3D m) Transforms center point coordinates

Methods inherited from class java.lang.Object

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

Field Detail

id

protected int id

Ring id

x

protected float x

Ring centroid *

y

protected float y

Ring centroid *

z

protected float z

Ring centroid *

tx

protected float tx

Transformed ring centroid *

ty

protected float ty

Transformed ring centroid *

tz

protected float tz

Transformed ring centroid *

numAtoms

protected int numAtoms

Number of atoms in ring *

atoms

protected int[] atoms

Ids of the atoms in the ring *

Constructor Detail

Ring

public Ring(int id,
            float x,
            float y,
            float z,
            float tx,
            float ty,
            float tz,
            int numAtoms,
            int[] atoms)

Full constructor

Parameters:

id - ring id (1 based)

x - x coord of centroid

y - y coord of centroid

z - z coord of centroid

tx - tx coord of centroid

ty - ty coord of centroid

tz - tz coord of centroid

numAtoms - number of atoms in the ring

atoms - ids of the atoms in the ring

Ring

public Ring()

Default constructor

Ring

public Ring(float x,
            float y,
            float z)

Real coordinates constructor

Parameters:

x - x coord of centroid

y - y coord of centroid

z - z coord of centroid

Ring

public Ring(float x,
            float y,
            float z,
            float tx,
            float ty,
            float tz)

Real and transformed coordinates constructor

Parameters:

x - x coord of centroid

y - y coord of centroid

z - z coord of centroid

tx - tx coord of centroid

ty - ty coord of centroid

tz - tz coord of centroid

Ring

public Ring(Ring ring)

Copy constructor

Parameters:

ring - ring to be copied

Method Detail

setCentroid

protected void setCentroid(float x,
                           float y,
                           float z)

Set the centroid of the ring

Parameters:

x - x coordinate of the centroid

y - y coordinate of the centroid

z - z coordinate of the centroid

transform

protected void transform(Matrix3D m)

Transforms center point coordinates

Parameters:

m - the trnasformation matrix to be applied

getId

public int getId()

Return ring id

getNumAtoms

public int getNumAtoms()

Return number of atoms in the ring

getX

public float getX()

Return ring centroid X coordinate

getY

public float getY()

Return ring centroid Y coordinate

getZ

public float getZ()

Return ring centroid Z coordinate

getTx

public float getTx()

Return transformed ring centroid X coordinate

getTy

public float getTy()

Return transformed ring centroid Y coordinate

getTz

public float getTz()

Return transformed ring centroid Z coordinate

contains

public boolean contains(Atom a)

Return true if an atom is in this ring

Parameters:

atom - the atom

setId

public void setId(int id)

Set ring id

setX

public void setX(float x)

Set ring centroid X coordinate

setY

public void setY(float y)

Set ring centroid Y coordinate

setZ

public void setZ(float z)

Set ring centroid Z coordinate

setTx

public void setTx(float x)

Set transformed ring centroid X coordinate

setTy

public void setTy(float y)

Set transformed ring centroid Y coordinate

setTz

public void setTz(float z)

Set transformed ring centroid Z coordinate