Package org.biojava.nbio.structure

Interface Bond

All Superinterfaces:
Serializable
All Known Implementing Classes:
BondImpl
public interface Bond extends Serializable
A simple bond -- it stores information about two atoms as well as information about its bond order.
Author:
Jules Jacobsen jacobsen@ebi.ac.uk, Ulysse Carion

  • Method Summary

    Modifier and Type
    Method
    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 Details

    • 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

      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:

    • 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.