Class Bond

All Implemented Interfaces:
Serializable, Cloneable, IBond, ICDKObject, IChemObject, IElectronContainer
Direct Known Subclasses:
DebugBond, PharmacophoreAngleBond, PharmacophoreBond, PharmacophoreQueryAngleBond, PharmacophoreQueryBond

public class Bond extends ElectronContainer implements IBond, Serializable, Cloneable
Implements the concept of a covalent bond between two or more atoms. A bond is considered to be a number of electrons connecting two or more of atoms. It should be noted that the majority of applications will consider 2-center bonds, especially since the bond orders currently supported are really only valid for 2-center bonds. However the code does support multi-center bonds, though the orders may not make sense at this point. In general code that assumes bonds are 2-centered can use this class seamlessly, as the semantics are identical to the older versions. Care shoud be exercised when using multi-center bonds using this class as the orders may not make sense.
Author:
steinbeck
See Also:
Source code:
main
Belongs to CDK module:
data
Keywords:
bond, atom, electron
Created on:
2003-10-02
  • Field Details

    • order

      protected IBond.Order order
      The bond order of this bond.
    • atomCount

      protected int atomCount
      Number of atoms contained by this object.
    • atoms

      protected IAtom[] atoms
      A list of atoms participating in this bond.
    • stereo

      protected IBond.Stereo stereo
      A descriptor the stereochemical orientation of this bond.
    • display

      protected IBond.Display display
  • Constructor Details

    • Bond

      public Bond()
      Constructs an empty bond.
    • Bond

      public Bond(IAtom atom1, IAtom atom2)
      Constructs a bond with a single bond order..
      Parameters:
      atom1 - the first Atom in the bond
      atom2 - the second Atom in the bond
    • Bond

      public Bond(IAtom atom1, IAtom atom2, IBond.Order order)
      Constructs a bond with a given order.
      Parameters:
      atom1 - the first Atom in the bond
      atom2 - the second Atom in the bond
      order - the bond order
    • Bond

      public Bond(IAtom[] atoms)
      Constructs a multi-center bond, with undefined order and no stereo information.
      Parameters:
      atoms - An array of IAtom containing the atoms constituting the bond
    • Bond

      public Bond(IAtom[] atoms, IBond.Order order)
      Constructs a multi-center bond, with a specified order and no stereo information.
      Parameters:
      atoms - An array of IAtom containing the atoms constituting the bond
      order - The order of the bond
    • Bond

      public Bond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo)
      Constructs a bond with a given order and stereo orientation from an array of atoms.
      Parameters:
      atom1 - the first Atom in the bond
      atom2 - the second Atom in the bond
      order - the bond order
      stereo - a descriptor the stereochemical orientation of this bond
  • Method Details

    • atoms

      public Iterable<IAtom> atoms()
      Returns the Iterator to atoms making up this bond. Iterator.remove() is not implemented.
      Specified by:
      atoms in interface IBond
      Returns:
      An Iterator to atoms participating in this bond
      See Also:
    • getIndex

      public int getIndex()
      Specified by:
      getIndex in interface IBond
    • getContainer

      public IAtomContainer getContainer()
      Specified by:
      getContainer in interface IBond
    • setAtoms

      public void setAtoms(IAtom[] atoms)
      Sets the array of atoms making up this bond.
      Specified by:
      setAtoms in interface IBond
      Parameters:
      atoms - An array of atoms that forms this bond
      See Also:
    • getAtomCount

      public int getAtomCount()
      Returns the number of Atoms in this Bond.
      Specified by:
      getAtomCount in interface IBond
      Returns:
      The number of Atoms in this Bond
    • getAtom

      public IAtom getAtom(int position)
      Returns an Atom from this bond.
      Specified by:
      getAtom in interface IBond
      Parameters:
      position - The position in this bond where the atom is
      Returns:
      The atom at the specified position, null if there are no atoms in the bond
      See Also:
    • getBegin

      public IAtom getBegin()
      Access the begin (or first) atom of the bond.
      Specified by:
      getBegin in interface IBond
      Returns:
      the begin atom
    • getEnd

      public IAtom getEnd()
      Access the end (or second) atom of the bond.
      Specified by:
      getEnd in interface IBond
      Returns:
      the end atom
    • getOther

      public IAtom getOther(IAtom atom)
      Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

      
       IAtom beg = bond.getBegin();
       IAtom end = bond.getEnd();
       // bond.getOther(beg) == end
       // bond.getOther(end) == beg
       
      Specified by:
      getOther in interface IBond
      Parameters:
      atom - The atom the bond partner is searched of
      Returns:
      the connected atom or null if the given atom is not part of the bond
    • getConnectedAtom

      public IAtom getConnectedAtom(IAtom atom)
      Returns the other atom in the bond, the atom is connected to the given atom. This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

      
       IAtom beg = bond.getBegin();
       IAtom end = bond.getEnd();
       // bond.getConnectedAtom(beg) == end
       // bond.getConnectedAtom(end) == beg
       
      Specified by:
      getConnectedAtom in interface IBond
      Parameters:
      atom - The atom the bond partner is searched of
      Returns:
      the connected atom or null if the given atom is not part of the bond
    • getConnectedAtoms

      public IAtom[] getConnectedAtoms(IAtom atom)
      Returns all the atoms in the bond connected to the given atom.
      Specified by:
      getConnectedAtoms in interface IBond
      Parameters:
      atom - The atoms the bond partner is searched of
      Returns:
      the connected atoms or null if the given atom is not part of the bond
    • contains

      public boolean contains(IAtom atom)
      Returns true if the given atom participates in this bond.
      Specified by:
      contains in interface IBond
      Parameters:
      atom - The atom to be tested if it participates in this bond
      Returns:
      true if the atom participates in this bond
    • setAtom

      public void setAtom(IAtom atom, int position)
      Sets an Atom in this bond.
      Specified by:
      setAtom in interface IBond
      Parameters:
      atom - The atom to be set
      position - The position in this bond where the atom is to be inserted
      See Also:
    • getOrder

      public IBond.Order getOrder()
      Returns the bond order of this bond.
      Specified by:
      getOrder in interface IBond
      Returns:
      The bond order of this bond
      See Also:
    • setOrder

      public void setOrder(IBond.Order order)
      Sets the bond order of this bond.
      Specified by:
      setOrder in interface IBond
      Parameters:
      order - The bond order to be assigned to this bond
      See Also:
    • getStereo

      public IBond.Stereo getStereo()
      Returns the stereo descriptor for this bond.
      Specified by:
      getStereo in interface IBond
      Returns:
      The stereo descriptor for this bond
      See Also:
    • setStereo

      public void setStereo(IBond.Stereo stereo)
      Sets the stereo descriptor for this bond.
      Specified by:
      setStereo in interface IBond
      Parameters:
      stereo - The stereo descriptor to be assigned to this bond.
      See Also:
    • getDisplay

      public IBond.Display getDisplay()
      Access the bond display style.
      Specified by:
      getDisplay in interface IBond
      Returns:
      the bond display
    • setDisplay

      public void setDisplay(IBond.Display display)
      Set the bond display style.
      Specified by:
      setDisplay in interface IBond
      Parameters:
      display - the display
    • get2DCenter

      public javax.vecmath.Point2d get2DCenter()
      Returns the geometric 2D center of the bond.
      Specified by:
      get2DCenter in interface IBond
      Returns:
      The geometric 2D center of the bond
    • get3DCenter

      public javax.vecmath.Point3d get3DCenter()
      Returns the geometric 3D center of the bond.
      Specified by:
      get3DCenter in interface IBond
      Returns:
      The geometric 3D center of the bond
    • compare

      public boolean compare(Object object)
      Compares a bond with this bond.
      Specified by:
      compare in interface IBond
      Overrides:
      compare in class ChemObject
      Parameters:
      object - Object of type Bond
      Returns:
      true if the bond is equal to this bond
    • isConnectedTo

      public boolean isConnectedTo(IBond bond)
      Checks whether a bond is connected to another one. This can only be true if the bonds have an Atom in common.
      Specified by:
      isConnectedTo in interface IBond
      Parameters:
      bond - The bond which is checked to be connect with this one
      Returns:
      true if the bonds share an atom, otherwise false
    • isAromatic

      public boolean isAromatic()
      Access whether this bond has been marked as aromatic. The default value is false and you must explicitly perceive aromaticity with one of the available models.
      Specified by:
      isAromatic in interface IBond
      Returns:
      aromatic status
      See Also:
    • setIsAromatic

      public void setIsAromatic(boolean arom)
      Mark this bond as being aromatic.
      Specified by:
      setIsAromatic in interface IBond
      Parameters:
      arom - aromatic status
      See Also:
    • isInRing

      public boolean isInRing()
      Access whether this bond has been flagged as in a ring. The default value is false and you must explicitly find rings first.
      Specified by:
      isInRing in interface IBond
      Returns:
      ring status
      See Also:
    • setIsInRing

      public void setIsInRing(boolean ring)
      Mark this bond as being in a ring.
      Specified by:
      setIsInRing in interface IBond
      Parameters:
      ring - ring status
      See Also:
    • clone

      public IBond clone() throws CloneNotSupportedException
      Clones this bond object, including clones of the atoms between which the bond is defined.
      Specified by:
      clone in interface IBond
      Specified by:
      clone in interface IChemObject
      Overrides:
      clone in class ElectronContainer
      Returns:
      The cloned object
      Throws:
      CloneNotSupportedException - if the IChemObject cannot be cloned
    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object
    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object
    • toString

      public String toString()
      Returns a one line string representation of this Container. This method is conform RFC #9.
      Specified by:
      toString in interface IChemObject
      Overrides:
      toString in class ElectronContainer
      Returns:
      The string representation of this Container