edu.sdsc.mbt
Class Bond

java.lang.Object
  edu.sdsc.mbt.StructureComponent
      edu.sdsc.mbt.Bond

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable

public class Bond

extends StructureComponent

implements java.lang.Cloneable

Implements a StructureComponent container for bond information. This may be a covalent or a hydrogen bond.

Author:

John L. Moreland

See Also:

StructureComponent, Atom, Serialized Form

Field Summary

float	order
short	quality
short	render
static java.lang.String	TYPE_COVALENT Type for a covalent bond (bonding interaction due to electron sharing).
static java.lang.String	TYPE_HYDROGEN Type for a hydrogen bond (bonding interaction due to partial charges).
static java.lang.String	TYPE_IONIC Type for an ionic bond (bonding interaction due to electrostatic attraction between cations and anions).
boolean	visible

Fields inherited from class edu.sdsc.mbt.StructureComponent

structure

Constructor Summary

Bond(Atom atom0, Atom atom1)
Constructor variant used when there will likely be no atom list (eg: when only sequence data is loaded).

Method Summary

java.lang.Object	clone() Clone this object.
void	copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
boolean	equals(java.lang.Object o) One Bond is equal to another Bond if they hashCode values are equal.
Atom	getAtom(int index) Get the specified Atom record that forms this Bond.
static java.lang.String	getClassName() This method returns the fully qualified name of this class.
double	getDistance() Get the distance for the bond.
static double	getDistance(Atom atom0, Atom atom1)
Atom	getReferenceAtom()
java.lang.String	getStructureComponentType() This method returns the fully qualified name of this class.
boolean	isVisible()
void	setOrder(float order) Set the bond order (the number of covalently shared electron pairs).
void	setOrderOnly(float order) This method sets order without editing atoms' hybridization states it is used in the loading of data with predefined bonding to avoid overwriting of hybridization data in subsequent passes over atoms that participate in bonds of different orders
void	setReferenceAtom(Atom atom)
void	setReferenceAtom(int index)

Methods inherited from class edu.sdsc.mbt.StructureComponent

getStructure, setStructure

Methods inherited from class java.lang.Object

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

Field Detail

TYPE_COVALENT

public static final java.lang.String TYPE_COVALENT

Type for a covalent bond (bonding interaction due to electron sharing).

See Also:

Constant Field Values

TYPE_HYDROGEN

public static final java.lang.String TYPE_HYDROGEN

Type for a hydrogen bond (bonding interaction due to partial charges).

See Also:

Constant Field Values

TYPE_IONIC

public static final java.lang.String TYPE_IONIC

Type for an ionic bond (bonding interaction due to electrostatic attraction between cations and anions).

See Also:

Constant Field Values

order

public float order

render

public short render

quality

public short quality

visible

public boolean visible

Constructor Detail

Bond

public Bond(Atom atom0,
            Atom atom1)

Constructor variant used when there will likely be no atom list (eg: when only sequence data is loaded).

Method Detail

copy

public void copy(StructureComponent structureComponent)

Copy all of the field values from the parameter object into "this".

Specified by:

copy in class StructureComponent

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Clone this object.

Overrides:

clone in class StructureComponent

Throws:

java.lang.CloneNotSupportedException

equals

public boolean equals(java.lang.Object o)

One Bond is equal to another Bond if they hashCode values are equal. That is if they contain (in either order) the same two Atom objects.

getClassName

public static java.lang.String getClassName()

This method returns the fully qualified name of this class.

This name is used by the StructureComponentRegistry class to enable dynamic registration and discovery of new StructureComponent sub-classes/types. The name is also used to create a unique integer indentifier for each type in order to make run-time type comparisons fast.

getStructureComponentType

public java.lang.String getStructureComponentType()

This method returns the fully qualified name of this class.

Specified by:

getStructureComponentType in class StructureComponent

setOrder

public void setOrder(float order)

Set the bond order (the number of covalently shared electron pairs). Generally this is a value from 1.0 to 6.0 but may be 1.5 for aromatic (benzene ring bonds) or 0.0 for unspecified order (the default).

See Also:

#getOrder( )

setOrderOnly

public void setOrderOnly(float order)

This method sets order without editing atoms' hybridization states it is used in the loading of data with predefined bonding to avoid overwriting of hybridization data in subsequent passes over atoms that participate in bonds of different orders

Parameters:

order -

getDistance

public double getDistance()

Get the distance for the bond.

getDistance

public static final double getDistance(Atom atom0,
                                       Atom atom1)

getAtom

public Atom getAtom(int index)

Get the specified Atom record that forms this Bond.

setReferenceAtom

public void setReferenceAtom(int index)

setReferenceAtom

public void setReferenceAtom(Atom atom)

getReferenceAtom

public Atom getReferenceAtom()

isVisible

public boolean isVisible()

Specified by:

isVisible in class StructureComponent