Package org.openscience.cdk.interfaces

Interface IBond

All Superinterfaces:
Cloneable, ICDKObject, IChemObject, IElectronContainer
All Known Subinterfaces:
IQueryBond
All Known Implementing Classes:
AnyOrderQueryBond, AromaticOrSingleQueryBond, AromaticQueryBond, Bond, Bond, BondRef, CTFileQueryBond, DebugBond, LogicalOperatorBond, OrderQueryBond, OrderQueryBond, OrderQueryBondOrderOnly, PharmacophoreAngleBond, PharmacophoreBond, PharmacophoreQueryAngleBond, PharmacophoreQueryBond, QueryBond, RingBond, SMARTSBond, StereoBond
public interface IBond extends IElectronContainer
Implements the concept of a covalent bond between two or more atoms. A bond is considered to be a number of electrons connecting two ore more atoms. type filter text
Author:
egonw
Keywords:
bond, atom, electron
Created on:
2005-08-24

  • Method Details

    • atoms

      Iterable<IAtom> atoms()
      Returns the Iterable to atoms making up this bond.
      Returns:
      An Iterable to atoms participating in this bond
      See Also:

    • setAtoms

      void setAtoms(IAtom[] atoms)
      Sets the array of atoms making up this bond.
      Parameters:
      atoms - An array of atoms that forms this bond
      See Also:

    • getBegin

      IAtom getBegin()
      Access the begin (or first) atom of the bond.
      Returns:
      the begin atom

    • getEnd

      IAtom getEnd()
      Access the end (or second) atom of the bond.
      Returns:
      the end atom

    • getIndex

      int getIndex()

    • getContainer

      IAtomContainer getContainer()

    • getAtomCount

      int getAtomCount()
      Returns the number of Atoms in this Bond.
      Returns:
      The number of Atoms in this Bond

    • getAtom

      IAtom getAtom(int position)
      Returns an Atom from this bond.
      Parameters:
      position - The position in this bond where the atom is
      Returns:
      The atom at the specified position
      See Also:

    • getConnectedAtom

      @Deprecated IAtom getConnectedAtom(IAtom atom)
      Deprecated.
      use the method getOther(IAtom)
      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 getConnectedAtoms(IAtom) should be used. 

      
 IAtom beg = bond.getBegin();
 IAtom end = bond.getEnd();
 // bond.getConnectedAtom(beg) == end
 // bond.getConnectedAtom(end) == beg
      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

    • getOther

      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 getConnectedAtoms(IAtom) should be used. 

      
 IAtom beg = bond.getBegin();
 IAtom end = bond.getEnd();
 // bond.getOther(beg) == end
 // bond.getOther(end) == beg
      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

      IAtom[] getConnectedAtoms(IAtom atom)
      Returns all the atoms in the bond connected to the given atom.
      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

      default boolean contains(IAtom atom)
      Returns true if the given atom participates in this bond.
      Parameters:
      atom - The atom to be tested if it participates in this bond
      Returns:
      true if the atom participates in this bond

    • getConnectedAtom

      default IAtom getConnectedAtom(IBond other)
      Get the connected atom between two bonds.
      Parameters:
      other - the other bond (not nullable)
      Returns:
      the common atom or null if none in common

    • setAtom

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

    • getOrder

      IBond.Order getOrder()
      Returns the bond order of this bond.
      Returns:
      The bond order of this bond
      See Also:

    • setOrder

      void setOrder(IBond.Order order)
      Sets the bond order of this bond.
      Parameters:
      order - The bond order to be assigned to this bond
      See Also:

    • getStereo

      IBond.Stereo getStereo()
      Deprecated.
      use getDisplay()
      Returns the stereo descriptor for this bond.
      Returns:
      The stereo descriptor for this bond
      See Also:

    • setStereo

      void setStereo(IBond.Stereo stereo)
      Deprecated.
      use setDisplay(org.openscience.cdk.interfaces.IBond.Display)
      Sets the stereo descriptor for this bond. Note this function will also modify the bond display style.
      Parameters:
      stereo - The stereo descriptor to be assigned to this bond.
      See Also:

    • getDisplay

      IBond.Display getDisplay()
      Access the bond display style.
      Returns:
      the bond display

    • setDisplay

      void setDisplay(IBond.Display display)
      Set the bond display style.
      Parameters:
      display - the display

    • get2DCenter

      javax.vecmath.Point2d get2DCenter()
      Returns the geometric 2D center of the bond.
      Returns:
      The geometric 2D center of the bond

    • get3DCenter

      javax.vecmath.Point3d get3DCenter()
      Returns the geometric 3D center of the bond.
      Returns:
      The geometric 3D center of the bond

    • compare

      boolean compare(Object object)
      Compares a bond with this bond.
      Parameters:
      object - Object of type Bond
      Returns:
      Return true, if the bond is equal to this bond

    • isConnectedTo

      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.
      Parameters:
      bond - The bond which is checked to be connect with this one
      Returns:
      True, if the bonds share an atom, otherwise false

    • isAromatic

      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.
      Returns:
      aromatic status
      See Also:

    • setIsAromatic

      void setIsAromatic(boolean arom)
      Mark this bond as being aromatic.
      Parameters:
      arom - aromatic status
      See Also:

    • isInRing

      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.
      Returns:
      ring status
      See Also:

    • setIsInRing

      void setIsInRing(boolean ring)
      Mark this bond as being in a ring.
      Parameters:
      ring - ring status
      See Also:

    • clone

      IBond clone() throws CloneNotSupportedException
      Returns a deep clone of this IChemObject.
      Specified by:
      clone in interface IChemObject
      Returns:
      Object the clone of this IChemObject.
      Throws:
      CloneNotSupportedException - if the IChemObject cannot be cloned