org.openscience.cdk.stereo

Class DoubleBondStereochemistry

java.lang.Object

org.openscience.cdk.stereo.DoubleBondStereochemistry

All Implemented Interfaces:

Cloneable, ICDKObject, IDoubleBondStereochemistry, IStereoElement

public class DoubleBondStereochemistry
extends Object
implements IDoubleBondStereochemistry

Stereochemistry specification for double bonds. See IDoubleBondStereochemistry for further details.

See Also:

IDoubleBondStereochemistry

Source code:

master

Belongs to CDK module:

core

Nested Class Summary

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

IDoubleBondStereochemistry.Conformation

Constructor Summary

Constructors

Constructor and Description
DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, IDoubleBondStereochemistry.Conformation stereo) Creates a new double bond stereo chemistry.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	contains(IAtom atom) Does the stereo element contain the provided atom.
IBond[]	getBonds() Returns an array of ligand bonds around the double bond.
IChemObjectBuilder	getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IDoubleBondStereochemistry.Conformation	getStereo() Defines the stereochemistry around the double bond.
IBond	getStereoBond() IBond that is the stereo center.
IDoubleBondStereochemistry	map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds) Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
void	setBuilder(IChemObjectBuilder builder) Sets a new IChemObjectBuilder.

Methods inherited from class java.lang.Object

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

Constructor Detail

DoubleBondStereochemistry

public DoubleBondStereochemistry(IBond stereoBond,
                         IBond[] ligandBonds,
                         IDoubleBondStereochemistry.Conformation stereo)

Creates a new double bond stereo chemistry. The path of length three is defined by ligandBonds[0], stereoBonds, and ligandBonds[1].

Method Detail

setBuilder

public void setBuilder(IChemObjectBuilder builder)

Sets a new IChemObjectBuilder.

Parameters:

builder - the new IChemObjectBuilder to be returned

See Also:

getBuilder()

getBuilder

public IChemObjectBuilder getBuilder()

Returns a IChemObjectBuilder for the data classes that extend this class.

Specified by:

getBuilder in interface ICDKObject

Returns:

The IChemObjectBuilder matching this ICDKObject

getBonds

public IBond[] getBonds()

Returns an array of ligand bonds around the double bond.

Specified by:

getBonds in interface IDoubleBondStereochemistry

Returns:

an array of two IBonds.

getStereoBond

public IBond getStereoBond()

IBond that is the stereo center.

Specified by:

getStereoBond in interface IDoubleBondStereochemistry

Returns:

the double IBond.

getStereo

public IDoubleBondStereochemistry.Conformation getStereo()

Defines the stereochemistry around the double bond.

Specified by:

getStereo in interface IDoubleBondStereochemistry

Returns:

the IDoubleBondStereochemistry.Conformation for this stereo element.

contains

public boolean contains(IAtom atom)

Does the stereo element contain the provided atom.

Specified by:

contains in interface IStereoElement

Parameters:

atom - an atom to test membership

Returns:

whether the atom is present

map

public IDoubleBondStereochemistry map(Map<IAtom,IAtom> atoms,
                             Map<IBond,IBond> bonds)

Description copied from interface: IDoubleBondStereochemistry

Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. This allows the stereo element to be transferred between a cloned or aligned (i.e. isomorphic) chemical graph. If no mapping is found for a given atom or bond it is replaced with a null reference. However the provided atom and bonds maps must not be null.

Specified by:

map in interface IDoubleBondStereochemistry

Specified by:

map in interface IStereoElement

Parameters:

atoms - non-null atom mapping, used to convert the original atoms to their mapped counterparts

bonds - non-null bond mapping, used to convert the original bonds to their mapped counterparts

Returns:

a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.