org.openscience.cdk.isomorphism.matchers

Class QueryBond

java.lang.Object

org.openscience.cdk.isomorphism.matchers.QueryChemObject

org.openscience.cdk.isomorphism.matchers.QueryBond

All Implemented Interfaces:

Cloneable, IBond, ICDKObject, IChemObject, IElectronContainer, IQueryBond

Direct Known Subclasses:

CTFileQueryBond, OrderQueryBond, OrderQueryBondOrderOnly, SMARTSBond

public abstract class QueryBond
extends QueryChemObject
implements IQueryBond

Implements the concept of a "query bond" between two or more atoms. Query bonds can be used to capture types such as "Single or Double" or "Any".

Source code:

master

Belongs to CDK module:

isomorphism

Created on:

2010-12-16

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IBond

IBond.Order, IBond.Stereo

Field Summary

Fields

Modifier and Type	Field and Description
protected int	atomCount Number of atoms contained by this object.
protected IAtom[]	atoms A list of atoms participating in this query bond.
protected Integer	electronCount Number of electrons in the ElectronContainer.
protected IBond.Order	order The bond order of this query bond.
protected IBond.Stereo	stereo A descriptor the stereochemical orientation of this query bond.

Constructor Summary

Constructors

Constructor and Description
QueryBond(IAtom[] atoms, IBond.Order order, IChemObjectBuilder builder) Constructs a multi-center query bond, with a specified order and no stereo information.
QueryBond(IAtom[] atoms, IChemObjectBuilder builder) Constructs a multi-center query bond, with undefined order and no stereo information.
QueryBond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo, IChemObjectBuilder builder) Constructs a query bond with a given order and stereo orientation from an array of atoms.
QueryBond(IAtom atom1, IAtom atom2, IBond.Order order, IChemObjectBuilder builder) Constructs a query bond with a given order.
QueryBond(IAtom atom1, IAtom atom2, IChemObjectBuilder builder) Constructs a query bond with a single query bond order..
QueryBond(IChemObjectBuilder builder) Constructs an empty query bond.

Method Summary

Methods

Modifier and Type	Method and Description
Iterable<IAtom>	atoms() Returns the Iterator to atoms making up this query bond.
IQueryBond	clone() Clones this query bond object, including clones of the atoms between which the query bond is defined.
boolean	compare(Object object) Compares a query bond with this query bond.
boolean	contains(IAtom atom) Returns true if the given atom participates in this query bond.
javax.vecmath.Point2d	get2DCenter() Returns the geometric 2D center of the query bond.
javax.vecmath.Point3d	get3DCenter() Returns the geometric 3D center of the query bond.
IAtom	getAtom(int position) Returns an Atom from this query 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.
Integer	getElectronCount() Returns the number of electrons in this bond
IAtom	getEnd() Access the end (or second) atom of the bond.
IBond.Order	getOrder() Returns the query bond order of this query 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 correct IBond.getConnectedAtoms(IAtom) should be used.
IBond.Stereo	getStereo() Returns the stereo descriptor for this query bond.
boolean	isAromatic() Access whether this bond has been marked as aromatic.
boolean	isConnectedTo(IBond bond) Checks whether a query 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 query bond.
void	setAtoms(IAtom[] atoms) Sets the array of atoms making up this query bond.
void	setElectronCount(Integer electronCount) Sets the number of electrons in this bond
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 query bond.
void	setStereo(IBond.Stereo stereo) Sets the stereo descriptor for this query bond.
String	toString() Returns a one line string representation of this query bond.

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject

addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, matches, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.isomorphism.matchers.IQueryBond

matches

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Field Detail

order

protected IBond.Order order

The bond order of this query bond.

atomCount

protected int atomCount

Number of atoms contained by this object.

atoms

protected IAtom[] atoms

A list of atoms participating in this query bond.

stereo

protected IBond.Stereo stereo

A descriptor the stereochemical orientation of this query bond.

electronCount

protected Integer electronCount

Number of electrons in the ElectronContainer.

Constructor Detail

QueryBond

public QueryBond(IChemObjectBuilder builder)

Constructs an empty query bond.

QueryBond

public QueryBond(IAtom atom1,
         IAtom atom2,
         IChemObjectBuilder builder)

Constructs a query bond with a single query bond order..

Parameters:

atom1 - the first Atom in the query bond

atom2 - the second Atom in the query bond

QueryBond

public QueryBond(IAtom atom1,
         IAtom atom2,
         IBond.Order order,
         IChemObjectBuilder builder)

Constructs a query bond with a given order.

Parameters:

atom1 - the first Atom in the query bond

atom2 - the second Atom in the query bond

order - the query bond order

QueryBond

public QueryBond(IAtom[] atoms,
         IChemObjectBuilder builder)

Constructs a multi-center query bond, with undefined order and no stereo information.

Parameters:

atoms - An array of IAtom containing the atoms constituting the query bond

QueryBond

public QueryBond(IAtom[] atoms,
         IBond.Order order,
         IChemObjectBuilder builder)

Constructs a multi-center query bond, with a specified order and no stereo information.

Parameters:

atoms - An array of IAtom containing the atoms constituting the query bond

order - The order of the query bond

QueryBond

public QueryBond(IAtom atom1,
         IAtom atom2,
         IBond.Order order,
         IBond.Stereo stereo,
         IChemObjectBuilder builder)

Constructs a query bond with a given order and stereo orientation from an array of atoms.

Parameters:

atom1 - the first Atom in the query bond

atom2 - the second Atom in the query bond

order - the query bond order

stereo - a descriptor the stereochemical orientation of this query bond

Method Detail

atoms

public Iterable<IAtom> atoms()

Returns the Iterator to atoms making up this query bond. Iterator.remove() is not implemented.

Specified by:

atoms in interface IBond

Returns:

An Iterator to atoms participating in this query bond

See Also:

setAtoms(org.openscience.cdk.interfaces.IAtom[])

setAtoms

public void setAtoms(IAtom[] atoms)

Sets the array of atoms making up this query bond.

Specified by:

setAtoms in interface IBond

Parameters:

atoms - An array of atoms that forms this query bond

See Also:

atoms

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 query bond.

Specified by:

getAtom in interface IBond

Parameters:

position - The position in this query bond where the atom is

Returns:

The atom at the specified position, null if there are no atoms in the query bond

See Also:

setAtom(org.openscience.cdk.interfaces.IAtom, int)

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 query bond.

Specified by:

contains in interface IBond

Parameters:

atom - The atom to be tested if it participates in this query bond

Returns:

true if the atom participates in this query bond

setAtom

public void setAtom(IAtom atom,
           int position)

Sets an atom in this query bond.

Specified by:

setAtom in interface IBond

Parameters:

atom - The atom to be set

position - The position in this query bond where the atom is to be inserted

See Also:

getAtom(int)

getOrder

public IBond.Order getOrder()

Returns the query bond order of this query bond.

Specified by:

getOrder in interface IBond

Returns:

The query bond order of this query bond

See Also:

org.openscience.cdk.CDKConstants for predefined values., setOrder(org.openscience.cdk.interfaces.IBond.Order)

setOrder

public void setOrder(IBond.Order order)

Sets the bond order of this query bond.

Specified by:

setOrder in interface IBond

Parameters:

order - The query bond order to be assigned to this query bond

See Also:

org.openscience.cdk.CDKConstants for predefined values., getOrder()

getStereo

public IBond.Stereo getStereo()

Returns the stereo descriptor for this query bond.

Specified by:

getStereo in interface IBond

Returns:

The stereo descriptor for this query bond

See Also:

setStereo(org.openscience.cdk.interfaces.IBond.Stereo), for predefined values.

setStereo

public void setStereo(IBond.Stereo stereo)

Sets the stereo descriptor for this query bond.

Specified by:

setStereo in interface IBond

Parameters:

stereo - The stereo descriptor to be assigned to this query bond.

See Also:

getStereo(), for predefined values.

get2DCenter

public javax.vecmath.Point2d get2DCenter()

Returns the geometric 2D center of the query bond.

Specified by:

get2DCenter in interface IBond

Returns:

The geometric 2D center of the query bond

get3DCenter

public javax.vecmath.Point3d get3DCenter()

Returns the geometric 3D center of the query bond.

Specified by:

get3DCenter in interface IBond

Returns:

The geometric 3D center of the query bond

compare

public boolean compare(Object object)

Compares a query bond with this query bond.

Specified by:

compare in interface IBond

Parameters:

object - Object of type Bond

Returns:

true if the query bond is equal to this query bond

isConnectedTo

public boolean isConnectedTo(IBond bond)

Checks whether a query bond is connected to another one. This can only be true if the query bonds have an Atom in common.

Specified by:

isConnectedTo in interface IBond

Parameters:

bond - bond The query bond which is checked to be connect with this one

Returns:

true if the query bonds share an atom, otherwise false

clone

public IQueryBond clone()
                 throws CloneNotSupportedException

Clones this query bond object, including clones of the atoms between which the query bond is defined.

Specified by:

clone in interface IBond

Specified by:

clone in interface IChemObject

Overrides:

clone in class QueryChemObject

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

toString

public String toString()

Returns a one line string representation of this query bond.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

Returns:

The string representation of this query bond

getElectronCount

public Integer getElectronCount()

Returns the number of electrons in this bond

Specified by:

getElectronCount in interface IElectronContainer

Returns:

The number of electrons in this electron container.

See Also:

setElectronCount(java.lang.Integer)

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:

IChemObject.getFlag(int), Aromaticity

setIsAromatic

public void setIsAromatic(boolean arom)

Mark this bond as being aromatic.

Specified by:

setIsAromatic in interface IBond

Parameters:

arom - aromatic status

See Also:

IChemObject.setFlag(int, boolean)

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:

IChemObject.getFlag(int), RingSearch

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:

IChemObject.setFlag(int, boolean)

setElectronCount

public void setElectronCount(Integer electronCount)

Sets the number of electrons in this bond

Specified by:

setElectronCount in interface IElectronContainer

Parameters:

electronCount - The number of electrons in this electron container.

See Also:

getElectronCount()