org.openscience.cdk.stereo

Class TetrahedralChirality

java.lang.Object

org.openscience.cdk.stereo.TetrahedralChirality

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement, ITetrahedralChirality

public class TetrahedralChirality
extends Object
implements ITetrahedralChirality

Stereochemistry specification for quadrivalent atoms. See ITetrahedralChirality for further details.

See Also:

ITetrahedralChirality

Source code:

master

Belongs to CDK module:

core

Nested Class Summary

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

ITetrahedralChirality.Stereo

Constructor Summary

Constructors

Constructor and Description
TetrahedralChirality(IAtom chiralAtom, IAtom[] ligandAtoms, ITetrahedralChirality.Stereo chirality) Constructor to create a new ITetrahedralChirality implementation instance.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	contains(IAtom atom) Does the stereo element contain the provided atom.
IChemObjectBuilder	getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IAtom	getChiralAtom() Atom that is the chirality center.
IAtom[]	getLigands() Returns an array of ligand atoms around the chiral atom.
ITetrahedralChirality.Stereo	getStereo() Defines the stereochemistry around the chiral atom.
ITetrahedralChirality	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.
void	setStereo(ITetrahedralChirality.Stereo stereo) Set the stereochemistry of this tetrahedral centre.
String	toString() Returns a String representation of this chiral element.

Methods inherited from class java.lang.Object

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

Constructor Detail

TetrahedralChirality

public TetrahedralChirality(IAtom chiralAtom,
                    IAtom[] ligandAtoms,
                    ITetrahedralChirality.Stereo chirality)

Constructor to create a new ITetrahedralChirality implementation instance.

Parameters:

chiralAtom - The chiral IAtom.

ligandAtoms - The ligand atoms around the chiral atom.

chirality - The ITetrahedralChirality.Stereo chirality.

Method Detail

getLigands

public IAtom[] getLigands()

Returns an array of ligand atoms around the chiral atom.

Specified by:

getLigands in interface ITetrahedralChirality

Returns:

an array of four IAtoms.

getChiralAtom

public IAtom getChiralAtom()

Atom that is the chirality center.

Specified by:

getChiralAtom in interface ITetrahedralChirality

Returns:

the chiral IAtom.

getStereo

public ITetrahedralChirality.Stereo getStereo()

Defines the stereochemistry around the chiral atom. The value depends on the order of ligand atoms.

Specified by:

getStereo in interface ITetrahedralChirality

Returns:

the ITetrahedralChirality.Stereo for this stereo element.

setStereo

public void setStereo(ITetrahedralChirality.Stereo stereo)

Set the stereochemistry of this tetrahedral centre.

Specified by:

setStereo in interface ITetrahedralChirality

Parameters:

stereo - the new stereo assignment

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

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 ITetrahedralChirality 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. 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 IStereoElement

Specified by:

map in interface ITetrahedralChirality

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.

toString

public String toString()

Returns a String representation of this chiral element.

Overrides:

toString in class Object

Returns:

the String representation