astex
Class Bond

java.lang.Object
  astex.generic.Generic
      astex.Bond

All Implemented Interfaces:

GenericInterface

public class Bond
extends Generic

Field Summary

static int	AmideBond Constant that defines an aromatic bond.
static int	AnyBond Constant that defines any bond.
static int	AromaticBond Constant that defines an aromatic bond.
int	attributes The integer that stores the attributes.
static java.lang.String	BondOrder
static double	bondScale
static int	DoubleBond Constant that defines a single bond.
static int	DoubleOrAromaticBond Constant that defines a double or aromatic bond.
static int	ExplicitBond Did the bond come from a CONECT record.
static int	ringBond Is the bond in a ring of any description.
static int	SingleBond Constant that defines a single bond.
static int	SingleOrAromaticBond Constant that defines a single or aromatic bond.
static int	SingleOrDoubleBond Constant that defines a single or double bond.
static int	TripleBond Constant that defines a single bond.
static int	wideBond Is the bond to be drawn wide.

Fields inherited from class astex.generic.Generic

ClassName

Fields inherited from interface astex.generic.GenericInterface

Name

Method Summary

static Bond	create() A method that will create a new Bond.
void	delete() Delete this bond.
java.lang.Object	get(java.lang.Object key, java.lang.Object def) Get Object representing key.
Atom	getAtom(int index) Get the specified atom.
int	getBondColor() Get the value of bondColor.
double	getBondLength() Get the actual bond length.
int	getBondOrder() Get the bond order.
java.lang.String	getBondSymbol() Return a smiles style symbol for the bond.
int	getBondWidth() Get the value of bondWidth.
java.lang.Object	getClassname() Get our class description.
double	getCylinderWidth() Get the value of cylinderWidth.
Atom	getFirstAtom() Return the first atom in a bond.
double	getIdealBondLength() Get the ideal bond length.
Atom	getOtherAtom(Atom knownAtom) Given one atom in a bond return the other atom from the bond.
java.util.Enumeration	getProperties() Return an enumeration of our properties.
Atom	getSecondAtom() Return the second atom in a bond.
double	getStickWidth() Get the value of stickWidth.
Point3d	getUnitVector() Get unit vector.
boolean	isExplicitBond() Is bond an explicit bond.
boolean	isNonRotatable() Is this bond non rotatable.
boolean	isQueryBond() Is the bond a query bond.
boolean	isRingBond() Is the bond in a ring.
boolean	isTerminalBond() Is this a terminal bond.
boolean	isWideBond() Is the bond wide.
java.lang.Object	set(java.lang.Object key, java.lang.Object property) Set an object value.
void	setBondColor(int v) Set the value of bondColor.
void	setBondOrder(int order) Set the bond order.
void	setBondWidth(int v) Set the value of bondWidth.
void	setCylinderWidth(double v) Set the value of cylinderWidth.
void	setExplicitBond(boolean e) Set whehter this bond was an explicit bond.
void	setFirstAtom(Atom newFirstAtom) Set the first atom in the bond.
void	setIdealBondLength(double d) Set the ideal bond length.
void	setRingBond(boolean ring) Set the bond ring status.
void	setSecondAtom(Atom newSecondAtom) Set the second atom in the bond.
void	setStickWidth(double v) Set the value of stickWidth.
void	setWideBond(boolean wide) Set the bond to be wide or not.
java.lang.String	toString() String representation of the bond.

Methods inherited from class astex.generic.Generic

addChild, addListener, addParent, getBoolean, getChildren, getDouble, getInteger, getParents, getString, main, removeChild, removeListener, removeParent, setBoolean, setClassname, setDouble, setInteger, setString

Methods inherited from class java.lang.Object

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

Field Detail

BondOrder

public static final java.lang.String BondOrder

See Also:

Constant Field Values

SingleBond

public static final int SingleBond

Constant that defines a single bond.

See Also:

Constant Field Values

DoubleBond

public static final int DoubleBond

Constant that defines a single bond.

See Also:

Constant Field Values

TripleBond

public static final int TripleBond

Constant that defines a single bond.

See Also:

Constant Field Values

AromaticBond

public static final int AromaticBond

Constant that defines an aromatic bond.

See Also:

Constant Field Values

AmideBond

public static final int AmideBond

Constant that defines an aromatic bond.

See Also:

Constant Field Values

SingleOrDoubleBond

public static final int SingleOrDoubleBond

Constant that defines a single or double bond.

See Also:

Constant Field Values

SingleOrAromaticBond

public static final int SingleOrAromaticBond

Constant that defines a single or aromatic bond.

See Also:

Constant Field Values

DoubleOrAromaticBond

public static final int DoubleOrAromaticBond

Constant that defines a double or aromatic bond.

See Also:

Constant Field Values

AnyBond

public static final int AnyBond

Constant that defines any bond.

See Also:

Constant Field Values

bondScale

public static final double bondScale

See Also:

Constant Field Values

attributes

public int attributes

The integer that stores the attributes.

wideBond

public static int wideBond

Is the bond to be drawn wide.

ringBond

public static int ringBond

Is the bond in a ring of any description.

ExplicitBond

public static int ExplicitBond

Did the bond come from a CONECT record.

Method Detail

getClassname

public java.lang.Object getClassname()

Description copied from interface: GenericInterface

Get our class description.

Specified by:

getClassname in interface GenericInterface

Overrides:

getClassname in class Generic

set

public java.lang.Object set(java.lang.Object key,
                            java.lang.Object property)

Description copied from interface: GenericInterface

Set an object value.

Specified by:

set in interface GenericInterface

Overrides:

set in class Generic

get

public java.lang.Object get(java.lang.Object key,
                            java.lang.Object def)

Description copied from interface: GenericInterface

Get Object representing key.

Specified by:

get in interface GenericInterface

Overrides:

get in class Generic

getProperties

public java.util.Enumeration getProperties()

Description copied from interface: GenericInterface

Return an enumeration of our properties.

Specified by:

getProperties in interface GenericInterface

Overrides:

getProperties in class Generic

isExplicitBond

public boolean isExplicitBond()

Is bond an explicit bond.

setExplicitBond

public void setExplicitBond(boolean e)

Set whehter this bond was an explicit bond.

getBondWidth

public int getBondWidth()

Get the value of bondWidth.

Returns:

value of bondWidth.

setBondWidth

public void setBondWidth(int v)

Set the value of bondWidth.

Parameters:

v - Value to assign to bondWidth.

getStickWidth

public double getStickWidth()

Get the value of stickWidth.

Returns:

value of stickWidth.

setStickWidth

public void setStickWidth(double v)

Set the value of stickWidth.

Parameters:

v - Value to assign to stickWidth.

getCylinderWidth

public double getCylinderWidth()

Get the value of cylinderWidth.

Returns:

value of cylinderWidth.

setCylinderWidth

public void setCylinderWidth(double v)

Set the value of cylinderWidth.

Parameters:

v - Value to assign to cylinderWidth.

getBondColor

public int getBondColor()

Get the value of bondColor.

Returns:

value of bondColor.

setBondColor

public void setBondColor(int v)

Set the value of bondColor.

Parameters:

v - Value to assign to bondColor.

setWideBond

public void setWideBond(boolean wide)

Set the bond to be wide or not.

setRingBond

public void setRingBond(boolean ring)

Set the bond ring status.

isWideBond

public boolean isWideBond()

Is the bond wide.

isRingBond

public boolean isRingBond()

Is the bond in a ring.

setBondOrder

public void setBondOrder(int order)

Set the bond order.

getBondOrder

public int getBondOrder()

Get the bond order.

isQueryBond

public boolean isQueryBond()

Is the bond a query bond.

create

public static Bond create()

A method that will create a new Bond. This may in the future reuse bonds from a list of those that are no longer in use.

setFirstAtom

public void setFirstAtom(Atom newFirstAtom)

Set the first atom in the bond.

setSecondAtom

public void setSecondAtom(Atom newSecondAtom)

Set the second atom in the bond.

getFirstAtom

public Atom getFirstAtom()

Return the first atom in a bond.

getSecondAtom

public Atom getSecondAtom()

Return the second atom in a bond.

getAtom

public Atom getAtom(int index)

Get the specified atom.

getOtherAtom

public Atom getOtherAtom(Atom knownAtom)

Given one atom in a bond return the other atom from the bond. If the atom isn't in the bond return null.

getBondSymbol

public java.lang.String getBondSymbol()

Return a smiles style symbol for the bond.

isTerminalBond

public boolean isTerminalBond()

Is this a terminal bond.

isNonRotatable

public boolean isNonRotatable()

Is this bond non rotatable.

setIdealBondLength

public void setIdealBondLength(double d)

Set the ideal bond length.

getIdealBondLength

public double getIdealBondLength()

Get the ideal bond length.

getBondLength

public double getBondLength()

Get the actual bond length.

toString

public java.lang.String toString()

String representation of the bond.

Overrides:

toString in class java.lang.Object

getUnitVector

public Point3d getUnitVector()

Get unit vector.

delete

public void delete()

Delete this bond.