org.biojava.nbio.structure

Class Bond

java.lang.Object

org.biojava.nbio.structure.Bond

All Implemented Interfaces:

Serializable

public class Bond
extends Object
implements Serializable

A simple bond -- it stores information about two atoms as well as information about its bond order.

Author:

Jules Jacobsen , Ulysse Carion

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Bond(Atom atomA, Atom atomB, int bondOrder) Constructs a new bond from a pair of atoms and the bond order of the bond between them.
Bond(Atom atomA, Atom atomB, int bondOrder, boolean addSelfToAtoms) Constructs a new bond from a pair of atoms and the bond order of the bond between them.

Method Summary

Methods

Modifier and Type	Method and Description
void	addSelfToAtoms() Adds this Bond to its atoms bond lists.
Atom	getAtomA() Gets atom 'A' of this bond.
Atom	getAtomB() Gets atom 'B' of this bond.
int	getBondOrder() Gets the bond order of this bond.
double	getLength() Gets the distance between the two atoms of this bond.
Atom	getOther(Atom exclude) A utility method to get the other atom in a bond, given one of its atoms.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Bond

public Bond(Atom atomA,
    Atom atomB,
    int bondOrder)

Constructs a new bond from a pair of atoms and the bond order of the bond between them.

Note that by forming a bond between atoms 'A' and 'B' with this constructor, atoms 'A' and 'B' will be updated to have this bond in their list of bonds. If you do not want this automatic updating, instead use Bond(Atom, Atom, int, boolean) with the addSelfToAtoms flag set to false.

Parameters:

atomA - one of the atoms in this bond

atomB - the other atom in this bond

bondOrder - the bond order of this bond

Bond

public Bond(Atom atomA,
    Atom atomB,
    int bondOrder,
    boolean addSelfToAtoms)

Constructs a new bond from a pair of atoms and the bond order of the bond between them.

Parameters:

atomA - one of the atoms in this bond

atomB - the other atom in this bond

bondOrder - the bond order of this bond

addSelfToAtoms - if set to true, this bond, once created, will automatically add itself to atomA and atomB's bond lists. (If this argument is set to false, the list returned from Atom.getBonds() will not contain this bond.)

Method Detail

addSelfToAtoms

public void addSelfToAtoms()

Adds this Bond to its atoms bond lists. If this method is not called, then the list returned from calling Atom.getBonds() will not include this bond.

If you created your Bond with the constructor Bond(Atom, Atom, int), this method has already been called for you and should not be called again.

getAtomA

public Atom getAtomA()

Gets atom 'A' of this bond. There is no meaning to which atom is 'A' and which is 'B'; the atoms are labeled 'A' or 'B' based on the order in which they are passed to this class's constructor.

Returns:

one of the two atoms in this bond

See Also:

getAtomB()

getAtomB

public Atom getAtomB()

Gets atom 'B' of this bond. There is no meaning to which atom is 'A' and which is 'B'; the atoms are labeled 'A' or 'B' based on the order in which they are passed to this class's constructor.

Returns:

one of the two atoms in this bond

See Also:

getAtomA()

getOther

public Atom getOther(Atom exclude)

A utility method to get the other atom in a bond, given one of its atoms. If the atom passed is one of the atoms in this bond, then this method is essentially equivalent to saying atom == bond.getAtomA() ? bond.getAtomB() : bond.getAtomA().

Note: Comparison of atoms in this method is done with ==, not equals.

Parameters:

exclude - the atom of the bond to not return

Returns:

the atom in this bond that was not passed as an argument

Throws:

IllegalArgumentException - if the passed atom is not in this bond

getBondOrder

public int getBondOrder()

Gets the bond order of this bond. A return value of '1' corresponds to a single bond, '2' to a double bond, etc.

Returns:

this bond's bond order

getLength

public double getLength()

Gets the distance between the two atoms of this bond.

This distance is calculated by Calc.getDistance(Atom, Atom), but this method will suppress the empty threat of a StructureException that method makes.

Returns:

the distance between the two atoms of this bond.

toString

public String toString()

Overrides:

toString in class Object