org.biojava.nbio.structure

Interface Bond

All Known Implementing Classes:

BondImpl

public interface Bond

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

Author:

Jules Jacobsen , Ulysse Carion

Method Summary

Methods

Modifier and Type	Method and Description
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.

Method Detail

getAtomA

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

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

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

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

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.