Package org.biojava.nbio.structure

Class BondImpl

java.lang.Object
org.biojava.nbio.structure.BondImpl
All Implemented Interfaces:
Serializable, Bond
public class BondImpl extends Object implements Serializable, Bond
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
See Also:

  • Constructor Summary

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

    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.
    String
    toString()
     

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • BondImpl

      public BondImpl(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

    • BondImpl

      public BondImpl(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 Details

    • 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.
      Specified by:
      getAtomA in interface Bond
      Returns:
      one of the two atoms in this bond
      See Also:

    • 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.
      Specified by:
      getAtomB in interface Bond
      Returns:
      one of the two atoms in this bond
      See Also:

    • 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.

      Specified by:
      getOther in interface Bond
      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.
      Specified by:
      getBondOrder in interface Bond
      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.

      Specified by:
      getLength in interface Bond
      Returns:
      the distance between the two atoms of this bond.

    • toString

      public String toString()
      Overrides:
      toString in class Object