Package org.openscience.cdk
Class Bond
- java.lang.Object
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- org.openscience.cdk.ChemObject
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- org.openscience.cdk.ElectronContainer
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- org.openscience.cdk.Bond
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- 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:
- Serialized Form
- Source code:
- main
- Belongs to CDK module:
- data
- Keywords:
- bond, atom, electron
- Created on:
- 2003-10-02
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IBond
IBond.Display, IBond.Order, IBond.Stereo
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Field Summary
Fields Modifier and Type Field Description protected int
atomCount
Number of atoms contained by this object.protected IAtom[]
atoms
A list of atoms participating in this bond.protected IBond.Display
display
protected IBond.Order
order
The bond order of this bond.protected IBond.Stereo
stereo
A descriptor the stereochemical orientation of this bond.-
Fields inherited from class org.openscience.cdk.ElectronContainer
electronCount
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Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
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Constructor Summary
Constructors Constructor Description Bond()
Constructs an empty bond.Bond(IAtom[] atoms)
Constructs a multi-center bond, with undefined order and no stereo information.Bond(IAtom[] atoms, IBond.Order order)
Constructs a multi-center bond, with a specified order and no stereo information.Bond(IAtom atom1, IAtom atom2)
Constructs a bond with a single bond order..Bond(IAtom atom1, IAtom atom2, IBond.Order order)
Constructs a bond with a given order.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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Iterable<IAtom>
atoms()
Returns the Iterator to atoms making up this bond.IBond
clone()
Clones this bond object, including clones of the atoms between which the bond is defined.boolean
compare(Object object)
Compares a bond with this bond.boolean
contains(IAtom atom)
Returns true if the given atom participates in this bond.boolean
equals(Object obj)
javax.vecmath.Point2d
get2DCenter()
Returns the geometric 2D center of the bond.javax.vecmath.Point3d
get3DCenter()
Returns the geometric 3D center of the bond.IAtom
getAtom(int position)
Returns an Atom from this bond.int
getAtomCount()
Returns the number of Atoms in this Bond.IAtom
getBegin()
Access the begin (or first) atom of the bond.IAtom
getConnectedAtom(IAtom atom)
Returns the other atom in the bond, the atom is connected to the given atom.IAtom[]
getConnectedAtoms(IAtom atom)
Returns all the atoms in the bond connected to the given atom.IAtomContainer
getContainer()
IBond.Display
getDisplay()
Access the bond display style.IAtom
getEnd()
Access the end (or second) atom of the bond.int
getIndex()
IBond.Order
getOrder()
Returns the bond order of this bond.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 correctIBond.getConnectedAtoms(IAtom)
should be used.IBond.Stereo
getStereo()
Returns the stereo descriptor for this bond.int
hashCode()
boolean
isAromatic()
Access whether this bond has been marked as aromatic.boolean
isConnectedTo(IBond bond)
Checks whether a bond is connected to another one.boolean
isInRing()
Access whether this bond has been flagged as in a ring.void
setAtom(IAtom atom, int position)
Sets an Atom in this bond.void
setAtoms(IAtom[] atoms)
Sets the array of atoms making up this bond.void
setDisplay(IBond.Display display)
Set the bond display style.void
setIsAromatic(boolean arom)
Mark this bond as being aromatic.void
setIsInRing(boolean ring)
Mark this bond as being in a ring.void
setOrder(IBond.Order order)
Sets the bond order of this bond.void
setStereo(IBond.Stereo stereo)
Sets the stereo descriptor for this bond.String
toString()
Returns a one line string representation of this Container.-
Methods inherited from class org.openscience.cdk.ElectronContainer
getElectronCount, setElectronCount
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Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, clear, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
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Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IBond
getConnectedAtom
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty
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Methods inherited from interface org.openscience.cdk.interfaces.IElectronContainer
getElectronCount, setElectronCount
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Field Detail
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order
protected IBond.Order order
The bond order of this bond.
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atomCount
protected int atomCount
Number of atoms contained by this object.
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atoms
protected IAtom[] atoms
A list of atoms participating in this bond.
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stereo
protected IBond.Stereo stereo
A descriptor the stereochemical orientation of this bond.
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display
protected IBond.Display display
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Constructor Detail
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Bond
public Bond()
Constructs an empty bond.
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Bond
public Bond(IAtom atom1, IAtom atom2)
Constructs a bond with a single bond order..- Parameters:
atom1
- the first Atom in the bondatom2
- the second Atom in the bond
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Bond
public Bond(IAtom atom1, IAtom atom2, IBond.Order order)
Constructs a bond with a given order.- Parameters:
atom1
- the first Atom in the bondatom2
- the second Atom in the bondorder
- the bond order
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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
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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 bondorder
- The order of the bond
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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 bondatom2
- the second Atom in the bondorder
- the bond orderstereo
- a descriptor the stereochemical orientation of this bond
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Method Detail
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atoms
public Iterable<IAtom> atoms()
Returns the Iterator to atoms making up this bond. Iterator.remove() is not implemented.- Specified by:
atoms
in interfaceIBond
- Returns:
- An Iterator to atoms participating in this bond
- See Also:
setAtoms(org.openscience.cdk.interfaces.IAtom[])
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getContainer
public IAtomContainer getContainer()
- Specified by:
getContainer
in interfaceIBond
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setAtoms
public void setAtoms(IAtom[] atoms)
Sets the array of atoms making up this bond.
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getAtomCount
public int getAtomCount()
Returns the number of Atoms in this Bond.- Specified by:
getAtomCount
in interfaceIBond
- Returns:
- The number of Atoms in this Bond
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getAtom
public IAtom getAtom(int position)
Returns an Atom from this bond.- Specified by:
getAtom
in interfaceIBond
- 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:
setAtom(org.openscience.cdk.interfaces.IAtom, int)
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getBegin
public IAtom getBegin()
Access the begin (or first) atom of the bond.
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getEnd
public IAtom getEnd()
Access the end (or second) atom of the bond.
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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 correctIBond.getConnectedAtoms(IAtom)
should be used.IAtom beg = bond.getBegin(); IAtom end = bond.getEnd(); // bond.getOther(beg) == end // bond.getOther(end) == beg
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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 correctIBond.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 interfaceIBond
- 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
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getConnectedAtoms
public IAtom[] getConnectedAtoms(IAtom atom)
Returns all the atoms in the bond connected to the given atom.- Specified by:
getConnectedAtoms
in interfaceIBond
- 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
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contains
public boolean contains(IAtom atom)
Returns true if the given atom participates in this bond.
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setAtom
public void setAtom(IAtom atom, int position)
Sets an Atom in this bond.- Specified by:
setAtom
in interfaceIBond
- Parameters:
atom
- The atom to be setposition
- The position in this bond where the atom is to be inserted- See Also:
getAtom(int)
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getOrder
public IBond.Order getOrder()
Returns the bond order of this bond.- Specified by:
getOrder
in interfaceIBond
- Returns:
- The bond order of this bond
- See Also:
org.openscience.cdk.CDKConstants for predefined values.
,setOrder(org.openscience.cdk.interfaces.IBond.Order)
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setOrder
public void setOrder(IBond.Order order)
Sets the bond order of this bond.- Specified by:
setOrder
in interfaceIBond
- Parameters:
order
- The bond order to be assigned to this bond- See Also:
org.openscience.cdk.CDKConstants for predefined values.
,getOrder()
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getStereo
public IBond.Stereo getStereo()
Returns the stereo descriptor for this bond.- Specified by:
getStereo
in interfaceIBond
- Returns:
- The stereo descriptor for this bond
- See Also:
setStereo(org.openscience.cdk.interfaces.IBond.Stereo)
,for predefined values.
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setStereo
public void setStereo(IBond.Stereo stereo)
Sets the stereo descriptor for this bond.- Specified by:
setStereo
in interfaceIBond
- Parameters:
stereo
- The stereo descriptor to be assigned to this bond.- See Also:
getStereo()
,for predefined values.
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getDisplay
public IBond.Display getDisplay()
Access the bond display style.- Specified by:
getDisplay
in interfaceIBond
- Returns:
- the bond display
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setDisplay
public void setDisplay(IBond.Display display)
Set the bond display style.- Specified by:
setDisplay
in interfaceIBond
- Parameters:
display
- the display
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get2DCenter
public javax.vecmath.Point2d get2DCenter()
Returns the geometric 2D center of the bond.- Specified by:
get2DCenter
in interfaceIBond
- Returns:
- The geometric 2D center of the bond
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get3DCenter
public javax.vecmath.Point3d get3DCenter()
Returns the geometric 3D center of the bond.- Specified by:
get3DCenter
in interfaceIBond
- Returns:
- The geometric 3D center of the bond
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compare
public boolean compare(Object object)
Compares a bond with this bond.- Specified by:
compare
in interfaceIBond
- Overrides:
compare
in classChemObject
- Parameters:
object
- Object of type Bond- Returns:
- true if the bond is equal to this bond
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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 interfaceIBond
- Parameters:
bond
- The bond which is checked to be connect with this one- Returns:
- true if the bonds share an atom, otherwise false
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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 interfaceIBond
- Returns:
- aromatic status
- See Also:
IChemObject.getFlag(int)
,Aromaticity
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setIsAromatic
public void setIsAromatic(boolean arom)
Mark this bond as being aromatic.- Specified by:
setIsAromatic
in interfaceIBond
- Parameters:
arom
- aromatic status- See Also:
IChemObject.setFlag(int, boolean)
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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 interfaceIBond
- Returns:
- ring status
- See Also:
IChemObject.getFlag(int)
,RingSearch
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setIsInRing
public void setIsInRing(boolean ring)
Mark this bond as being in a ring.- Specified by:
setIsInRing
in interfaceIBond
- Parameters:
ring
- ring status- See Also:
IChemObject.setFlag(int, boolean)
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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 interfaceIBond
- Specified by:
clone
in interfaceIChemObject
- Overrides:
clone
in classElectronContainer
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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toString
public String toString()
Returns a one line string representation of this Container. This method is conform RFC #9.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classElectronContainer
- Returns:
- The string representation of this Container
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