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

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

All Implemented Interfaces:

PropAttributesInter

public class Atom
extends java.lang.Object
implements PropAttributesInter

Tripos base Atom class

Field Summary

static java.util.Hashtable	atomColor Atom color map
protected int	charge Atomic charge
protected java.awt.Color	color Current atom color
static java.awt.Color	colorDefault Default color
protected boolean	display Flag indicating if atom label should be displayed
protected boolean	highlight Flag indicating if atom is highlighted
protected int	id Atom id
protected java.lang.String	name Elemental name
PropAttributes	prop Property list at the end of the atom string
protected boolean	select Flag indicating if atom is selcted
protected float	tx Transformed atom coordinates
protected float	ty Transformed atom coordinates
protected java.lang.String	type SYBYL force field atom type
protected float	tz Transformed atom coordinates
protected float	x Atom coordinates
protected float	y Atom coordinates
protected float	z Atom coordinates

Constructor Summary

Atom()
Default constructor

Atom(Atom a)
Copy constructor

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

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

Atom(int id, java.lang.String name, float x, float y, float z, float tx, float ty, float tz, int charge)
constructor, no prop

Atom(int id, java.lang.String name, float x, float y, float z, float tx, float ty, float tz, int charge, java.util.Properties prop)
Full constructor

Method Summary

boolean	equals(Atom a) Compares this atom with another
java.util.Properties	getAttributes() Return the property containing attributes
int	getCharge() Returns the atomic charge
java.awt.Color	getColor() Returns the color with which the atom is to be drawn when displayed
java.awt.Color	getColorFromType() Returns color according to the atom type
int	getId() Returns id of the atom
java.lang.String	getName() Returns the elemental name
PropAttributes	getPropAttributes() Get the encapsluation of the properties object which holds the attributes
float	getTx() Returns the transformed x coordinate of the atom
float	getTy() Returns the transformed y coordinate of the atom
java.lang.String	getType() Returns SYBYL force field atom type
float	getTz() Returns the transformed z coordinate of the atom
float	getX() Returns the x coordinate of the atom
float	getY() Returns the y coordinate of the atom
float	getZ() Returns the z coordinate of the atom
boolean	isCarbon() Return true if the atom is a carbon atom
boolean	isHighlighted() Returns true if the atom is highlighted by user
boolean	isHydrogen() Return true if the atom is a hydrogen atom
boolean	isSelected() Returns true if the atom is selected by user
boolean	needDisplay() Return true if the atom need to be display
void	setAttributes(java.util.Properties p) Set the attributes for the atom
void	setCharge(int c) Set the atomic charge
void	setColor(java.awt.Color color) Set the color with which the atom is drawn
void	setDisplay(boolean displayOrNot) Set the state to indicate whether the atom is to be formally displayed
void	setHighlight(boolean highlightOrNot) Set the state to indicate whether the atom is hightlighted
void	setId(int id) Set the atom id
void	setName(java.lang.String s) Set the name
void	setPropAttributes(PropAttributes p) Set the attributes for the atom
void	setSelect(boolean selectOrNot) Set the state to indicate whether the atom is selected
void	setTx(float tx) Set the transformed x coordinate of the atom
void	setTy(float ty) Set the transformed y coordinate of the atom
void	setType(java.lang.String s) Set the SYBYL force field type
void	setTz(float tz) Set the transformed z coordinate of the atom
void	setX(float x) Set the x coordinate of the atom
void	setY(float y) Set the y coordinate of the atom
void	setZ(float z) Set the z coordinate of the atom
java.lang.String	toString() Returns String representation of Atom

Methods inherited from class java.lang.Object

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

Field Detail

atomColor

public static java.util.Hashtable atomColor

Atom color map

colorDefault

public static final java.awt.Color colorDefault

Default color

id

protected int id

Atom id

name

protected java.lang.String name

Elemental name

type

protected java.lang.String type

SYBYL force field atom type

x

protected float x

Atom coordinates

y

protected float y

Atom coordinates

z

protected float z

Atom coordinates

tx

protected float tx

Transformed atom coordinates

ty

protected float ty

Transformed atom coordinates

tz

protected float tz

Transformed atom coordinates

charge

protected int charge

Atomic charge

select

protected boolean select

Flag indicating if atom is selcted

highlight

protected boolean highlight

Flag indicating if atom is highlighted

display

protected boolean display

Flag indicating if atom label should be displayed

prop

public PropAttributes prop

Property list at the end of the atom string

color

protected java.awt.Color color

Current atom color

Constructor Detail

Atom

public Atom(int id,
            java.lang.String name,
            float x,
            float y,
            float z,
            float tx,
            float ty,
            float tz,
            int charge,
            java.util.Properties prop)

Full constructor

Parameters:

id - atom id

name - elemental name of atom

x - x coordinate of atom

y - y coordinate of atom

z - z coordinate of atom

tx - tx transformed coordinate of atom

ty - ty transformed coordinate of atom

tz - tz transformed coordinate of atom

charge - atom charge

prop - atom attributes strings

Atom

public Atom(int id,
            java.lang.String name,
            float x,
            float y,
            float z,
            float tx,
            float ty,
            float tz,
            int charge)

constructor, no prop

Parameters:

id - atom id

name - elemental name of atom

x - x coordinate of atom

y - y coordinate of atom

z - z coordinate of atom

tx - tx transformed coordinate of atom

ty - ty transformed coordinate of atom

tz - tz transformed coordinate of atom

charge - atom charge

Atom

public Atom()

Default constructor

Atom

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

Real coordinates constructor

Parameters:

x - x coordinate of atom

y - y coordinate of atom

z - z coordinate of atom

Atom

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

Real and transformed coordinates constructor

Parameters:

x - x coordinate of atom

y - y coordinate of atom

z - z coordinate of atom

tx - tx transformed coordinate of atom

ty - ty transformed coordinate of atom

tz - tz transformed coordinate of atom

Atom

public Atom(Atom a)

Copy constructor

Parameters:

a - atom to be copied

Method Detail

setName

public void setName(java.lang.String s)

Set the name

Parameters:

s - elemental name of atom

See Also:

getName()

setType

public void setType(java.lang.String s)

Set the SYBYL force field type

See Also:

getType()

setCharge

public void setCharge(int c)

Set the atomic charge

Parameters:

c - charge

See Also:

getCharge()

getName

public java.lang.String getName()

Returns the elemental name

See Also:

setName(java.lang.String)

getType

public java.lang.String getType()

Returns SYBYL force field atom type

See Also:

setType(java.lang.String)

getCharge

public int getCharge()

Returns the atomic charge

See Also:

setCharge(int)

equals

public boolean equals(Atom a)

Compares this atom with another

Parameters:

a - atom to compare with

Returns:

true if atoms are equal, else false

toString

public java.lang.String toString()

Returns String representation of Atom

Overrides:

toString in class java.lang.Object

getAttributes

public java.util.Properties getAttributes()

Return the property containing attributes

Specified by:

getAttributes in interface PropAttributesInter

Returns:

DOCUMENT ME!

getPropAttributes

public PropAttributes getPropAttributes()

Get the encapsluation of the properties object which holds the attributes

Specified by:

getPropAttributes in interface PropAttributesInter

Returns:

DOCUMENT ME!

setAttributes

public void setAttributes(java.util.Properties p)

Set the attributes for the atom

Specified by:

setAttributes in interface PropAttributesInter

Parameters:

p - Property for the atom

setPropAttributes

public void setPropAttributes(PropAttributes p)

Set the attributes for the atom

Specified by:

setPropAttributes in interface PropAttributesInter

Parameters:

p - Property for the atom

getId

public int getId()

Returns id of the atom

getX

public float getX()

Returns the x coordinate of the atom

getY

public float getY()

Returns the y coordinate of the atom

getZ

public float getZ()

Returns the z coordinate of the atom

getTx

public float getTx()

Returns the transformed x coordinate of the atom

getTy

public float getTy()

Returns the transformed y coordinate of the atom

getTz

public float getTz()

Returns the transformed z coordinate of the atom

getColor

public java.awt.Color getColor()

Returns the color with which the atom is to be drawn when displayed

getColorFromType

public java.awt.Color getColorFromType()

Returns color according to the atom type

isSelected

public boolean isSelected()

Returns true if the atom is selected by user

isHighlighted

public boolean isHighlighted()

Returns true if the atom is highlighted by user

needDisplay

public boolean needDisplay()

Return true if the atom need to be display

isCarbon

public boolean isCarbon()

Return true if the atom is a carbon atom

isHydrogen

public boolean isHydrogen()

Return true if the atom is a hydrogen atom

setId

public void setId(int id)

Set the atom id

Parameters:

id - id

See Also:

getId()

setX

public void setX(float x)

Set the x coordinate of the atom

Parameters:

x - X-coordinate of the atom

See Also:

getX()

setY

public void setY(float y)

Set the y coordinate of the atom

Parameters:

y - Y-coordinate of the atom

See Also:

getY()

setZ

public void setZ(float z)

Set the z coordinate of the atom

Parameters:

z - Z-coordinate of the atom

See Also:

getZ()

setTx

public void setTx(float tx)

Set the transformed x coordinate of the atom

Parameters:

tx - transformed X-coordinate of the atom

See Also:

getTx()

setTy

public void setTy(float ty)

Set the transformed y coordinate of the atom

Parameters:

ty - transformed Y-coordinate of the atom

See Also:

getTy()

setTz

public void setTz(float tz)

Set the transformed z coordinate of the atom

Parameters:

tz - transformed Z-coordinate of the atom

See Also:

getTz()

setSelect

public void setSelect(boolean selectOrNot)

Set the state to indicate whether the atom is selected

Parameters:

selectOrNot - select state of the atom

See Also:

isSelected()

setHighlight

public void setHighlight(boolean highlightOrNot)

Set the state to indicate whether the atom is hightlighted

Parameters:

highlightOrNot - highlight state of the atom

See Also:

isHighlighted()

setDisplay

public void setDisplay(boolean displayOrNot)

Set the state to indicate whether the atom is to be formally displayed

Parameters:

displayOrNot - highlight state of the atom

See Also:

needDisplay()

setColor

public void setColor(java.awt.Color color)

Set the color with which the atom is drawn

Parameters:

color - color for the atom

See Also:

getColor()