org.openscience.cdk.renderer.generators.standard

Class StandardGenerator

java.lang.Object

org.openscience.cdk.renderer.generators.standard.StandardGenerator

All Implemented Interfaces:

IGenerator<IAtomContainer>

public final class StandardGenerator
extends Object
implements IGenerator<IAtomContainer>

The standard generator creates IRenderingElements for the atoms and bonds of a structure diagram. These are generated together allowing the bonds to drawn cleanly without overlap. The generate is heavily based on ideas documented in (Jonathan Brecher. Pure Appl. Chem. 2008. 80) and (Clark A.. Molecular Informatics. 2013. 32). Atom symbols are provided as GeneralPath outlines. This allows the depiction to be independent of the system used to view the diagram (primarily important for vector graphic depictions). The font used to generate the diagram must be provided to the constructor. Atoms and bonds can be highlighted by setting the HIGHLIGHT_COLOR. The style of highlight is set with the StandardGenerator.Highlighting parameter. The Standard Generator - CDK Wiki page provides extended details of using and configuring this generator.

Author:

John May

See Also:

Standard Generator - CDK Wiki

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StandardGenerator.AnnotationColor The color of the atom numbers.
static class	StandardGenerator.AnnotationDistance The distance of atom numbers from their parent atom as a percentage of bond length, default value is 0.25 (25%)
static class	StandardGenerator.AnnotationFontScale Annotation font size relative to element symbols, default = 0.4 (40%).
static class	StandardGenerator.AtomColor Defines the color of unselected atoms (and bonds).
static class	StandardGenerator.BondSeparation Defines the ratio of the separation between lines in double bonds as a percentage of length (BasicSceneGenerator.BondLength).
static class	StandardGenerator.DashSection The number of sections to render in a dashed 'unknown' bond, default = 4;
static class	StandardGenerator.DelocalisedDonutsBondDisplay Render small delocalised rings as bonds/life buoys? This can sometimes be misleading for fused rings but is commonly used.
static class	StandardGenerator.DeuteriumSymbol Display deuterium [2H] as 'D'.
static class	StandardGenerator.FancyBoldWedges Modify bold wedges to be flush with adjacent bonds, default = true.
static class	StandardGenerator.FancyHashedWedges Modify hashed wedges to be flush when there is a single adjacent bond, default = true.
static class	StandardGenerator.ForceDelocalisedBondDisplay Indicate delocalised/aromatic bonds should always be rendered, even when there is a valid Kekule structure.
static class	StandardGenerator.HashSpacing The preferred spacing between lines in hashed bonds.
static class	StandardGenerator.Highlighting Parameter defines the style of highlight used to emphasis atoms and bonds.
static class	StandardGenerator.HighlightStyle Enumeration of highlight style.
static class	StandardGenerator.OmitMajorIsotopes Whether Major Isotopes e.g.
static class	StandardGenerator.OuterGlowWidth The width of outer glow as a percentage of stroke width.
static class	StandardGenerator.PseudoFontStyle The default font style for pseudo-atoms, is Bold and Italic.
static class	StandardGenerator.SgroupBracketDepth How "deep" are brackets drawn.
static class	StandardGenerator.SgroupFontScale Scale Sgroup annotations relative to the normal font size (atom symbol).
static class	StandardGenerator.StrokeRatio Defines the ratio of the stroke to the width of the stroke of the font used to depict atom symbols.
static class	StandardGenerator.SymbolMarginRatio Defines the margin between an atom symbol and a connected bond based on the stroke width.
static class	StandardGenerator.Visibility Defines which atoms have their symbol displayed.
static class	StandardGenerator.WaveSpacing The spacing of waves (semi circles) drawn in wavy bonds with.
static class	StandardGenerator.WedgeRatio Ratio of the wide end of wedge compared to the narrow end (stroke width).

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANNOTATION_LABEL Defines the annotation label(s) of a chem object in a depiction.
static String	HIDDEN Marks atoms and bonds as being hidden from the actual depiction.
static String	HIDDEN_FULLY
static String	HIGHLIGHT_COLOR Defines that a chem object should be highlighted in a depiction.
static String	ITALIC_DISPLAY_PREFIX A special markup for annotation labels that hints the generator to renderer the annotation label in italic.

Constructor Summary

Constructors

Constructor and Description
StandardGenerator(Font font) Create a new standard generator that utilises the specified font to display atom symbols.

Method Summary

Modifier and Type	Method and Description
static IRenderingElement	embedText(Font font, String text, Color color, double scale) Make an embedded text label for display in a CDK renderer.
IRenderingElement	generate(IAtomContainer container, RendererModel parameters) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
List<IGeneratorParameter<?>>	getParameters() Returns the list of IGeneratorParameter for this particular generator.

Methods inherited from class java.lang.Object

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

Field Detail

HIGHLIGHT_COLOR

public static final String HIGHLIGHT_COLOR

Defines that a chem object should be highlighted in a depiction. Only atom symbols that are displayed are highlighted, the visibility of symbols can be modified with SymbolVisibility.

 atom.setProperty(StandardGenerator.HIGHLIGHT_COLOR, Color.RED);
 

See Also:

Constant Field Values

ANNOTATION_LABEL

public static final String ANNOTATION_LABEL

Defines the annotation label(s) of a chem object in a depiction. The annotation must be a string.

 String number = Integer.toString(1 + container.indexOf(atom));
 atom.setProperty(CDKConstants.ANNOTATION_LABEL, number);
 

See Also:

Constant Field Values

ITALIC_DISPLAY_PREFIX

public static final String ITALIC_DISPLAY_PREFIX

A special markup for annotation labels that hints the generator to renderer the annotation label in italic. The primary use case is for Cahn-Ingold-Prelog descriptors.

 String cipLabel = "R";
 atom.setProperty(CDKConstants.ANNOTATION_LABEL,
                  StandardGenerator.ITALIC_DISPLAY_PREFIX + cipLabel);
 

See Also:

Constant Field Values

HIDDEN

public static final String HIDDEN

Marks atoms and bonds as being hidden from the actual depiction. Set this property to non-null to indicate this.

See Also:

Constant Field Values

HIDDEN_FULLY

public static final String HIDDEN_FULLY

See Also:

Constant Field Values

Constructor Detail

StandardGenerator

public StandardGenerator(Font font)

Create a new standard generator that utilises the specified font to display atom symbols.

Parameters:

font - the font family, size, and style

Method Detail

generate

public IRenderingElement generate(IAtomContainer container,
                                  RendererModel parameters)

Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.

Specified by:

generate in interface IGenerator<IAtomContainer>

Parameters:

container - the chemical entity to be depicted

parameters - the rendering parameters

Returns:

a drawable chemical depiction component

embedText

public static IRenderingElement embedText(Font font,
                                          String text,
                                          Color color,
                                          double scale)

Make an embedded text label for display in a CDK renderer. If a piece of text contains newlines they are centred aligned below each other with a line height of 1.4.

Parameters:

font - the font to embedded

text - the text label

color - the color

scale - the resize, should include the model scale

Returns:

pre-rendered element

getParameters

public List<IGeneratorParameter<?>> getParameters()

Returns the list of IGeneratorParameter for this particular generator.

Specified by:

getParameters in interface IGenerator<IAtomContainer>

Returns:

a List of IGeneratorParameters