Package org.openscience.cdk.stereo

Class StereoElementFactory

java.lang.Object

org.openscience.cdk.stereo.StereoElementFactory

public abstract class StereoElementFactory
extends Object

Create stereo elements for a structure with 2D and 3D coordinates. The factory does not verify whether atoms can or cannot support stereochemistry - for this functionality use Stereocenters. The factory will not create stereo elements if there is missing information (wedge/hatch bonds, undefined coordinates) or the layout indicates unspecified configuration. Stereocenters specified with inverse down (hatch) bond style are created if the configuration is unambiguous and the bond does not connect to another stereocenter.

 IAtomContainer       container = ...;
 StereoElementFactory stereo    = StereoElementFactory.using2DCoordinates()
                                                      .interpretProjections(Projection.Haworth);

 // set the elements replacing any existing elements
 container.setStereoElements(stereo.createAll());

 // adding elements individually is also possible but existing elements are
 // are not removed
 for (IStereoElement element : stereo.createAll())
     container.addStereoElement(element); // bad, there may already be elements

 

Author:

John May

See Also:

Stereocenters

Source code:

main

Belongs to CDK module:

standard

Field Summary

Fields

Modifier and Type	Field	Description
protected GraphUtil.EdgeToBondMap	bondMap	A bond map for fast access to bond labels between two atom indices.
protected boolean	check	Verify if created stereochemistry are actually stereo-centres.
protected IAtomContainer	container	Native CDK structure representation.
protected int[][]	graph	Adjacency list graph representation.
protected ILoggingTool	logger
protected Set<Projection>	projections
protected boolean	strict

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	StereoElementFactory(IAtomContainer container, int[][] graph, GraphUtil.EdgeToBondMap bondMap)	Internal constructor.

Method Summary

Modifier and Type	Method	Description
StereoElementFactory	checkSymmetry(boolean check)
List<IStereoElement>	createAll()	Creates all stereo elements found by Stereocenters using the or 2D/3D coordinates to specify the configuration (clockwise/anticlockwise).
StereoElementFactory	interpretProjections(Projection... projections)	Indicate that stereochemistry drawn as a certain projection should be interpreted.
static StereoElementFactory	using2DCoordinates(IAtomContainer container)	Create a stereo element factory for creating stereo elements using 2D coordinates and depiction labels (up/down, wedge/hatch).
static StereoElementFactory	using3DCoordinates(IAtomContainer container)	Create a stereo element factory for creating stereo elements using 3D coordinates and depiction labels (up/down, wedge/hatch).
StereoElementFactory	withStrictMode()	Enables stricter stereochemistry checking, specifically tetrahedral centres may not be created from inverse down wedges (i.e.

Methods inherited from class java.lang.Object

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

Field Detail

container

protected final IAtomContainer container

Native CDK structure representation.

graph

protected final int[][] graph

Adjacency list graph representation.

bondMap

protected final GraphUtil.EdgeToBondMap bondMap

A bond map for fast access to bond labels between two atom indices.

projections

protected final Set<Projection> projections

strict

protected boolean strict

logger

protected final ILoggingTool logger

check

protected boolean check

Verify if created stereochemistry are actually stereo-centres.

Constructor Detail

StereoElementFactory

protected StereoElementFactory(IAtomContainer container,
                               int[][] graph,
                               GraphUtil.EdgeToBondMap bondMap)

Internal constructor.

Parameters:

container - an atom container

graph - adjacency list representation

bondMap - lookup bonds by atom index

Method Detail

createAll

public List<IStereoElement> createAll()

Creates all stereo elements found by Stereocenters using the or 2D/3D coordinates to specify the configuration (clockwise/anticlockwise). Currently only ITetrahedralChirality and IDoubleBondStereochemistry elements are created..

Returns:

a list of stereo elements

interpretProjections

public StereoElementFactory interpretProjections(Projection... projections)

Indicate that stereochemistry drawn as a certain projection should be interpreted.

 StereoElementFactory factory =
   StereoElementFactory.using2DCoordinates(container)
                       .interpretProjections(Projection.Fischer, Projection.Haworth);
 

Parameters:

projections - types of projection

Returns:

self

See Also:

Projection

checkSymmetry

public StereoElementFactory checkSymmetry(boolean check)

withStrictMode

public StereoElementFactory withStrictMode()

Enables stricter stereochemistry checking, specifically tetrahedral centres may not be created from inverse down wedges (i.e. Daylight style depictions). This also sets that all stereocentres are tested for asymmetry.

Returns:

stereo element factory.

using2DCoordinates

public static StereoElementFactory using2DCoordinates(IAtomContainer container)

Create a stereo element factory for creating stereo elements using 2D coordinates and depiction labels (up/down, wedge/hatch).

Parameters:

container - the structure to create the factory for

Returns:

the factory instance

using3DCoordinates

public static StereoElementFactory using3DCoordinates(IAtomContainer container)

Create a stereo element factory for creating stereo elements using 3D coordinates and depiction labels (up/down, wedge/hatch).

Parameters:

container - the structure to create the factory for

Returns:

the factory instance