org.openscience.cdk.renderer.generators

Class BasicAtomGenerator

java.lang.Object

org.openscience.cdk.renderer.generators.BasicAtomGenerator

All Implemented Interfaces:

IGenerator<IAtomContainer>

Direct Known Subclasses:

AtomMassGenerator, ExtendedAtomGenerator

public class BasicAtomGenerator
extends Object
implements IGenerator<IAtomContainer>

Generates basic IRenderingElements for atoms in an atom container.

Source code:

master

Belongs to CDK module:

renderbasic

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BasicAtomGenerator.AtomColor Class to hold the color by which atom labels are drawn.
static class	BasicAtomGenerator.AtomColorer IAtomColorer used to draw elements.
static class	BasicAtomGenerator.AtomRadius Magic number with unknown units that defines the radius around an atom, e.g.
static class	BasicAtomGenerator.ColorByType Boolean property that triggers atoms to be colored by type when set to true.
static class	BasicAtomGenerator.CompactAtom Boolean parameters that will cause atoms to be drawn as filled shapes when set to true.
static class	BasicAtomGenerator.CompactShape Shape to be used when drawing atoms in compact mode, as defined by the BasicAtomGenerator.CompactAtom parameter.
static class	BasicAtomGenerator.KekuleStructure Determines whether structures should be drawn as Kekule structures, thus giving each carbon element explicitly, instead of not displaying the element symbol.
static class	BasicAtomGenerator.Shape When atoms are selected or in compact mode, they will be covered by a shape determined by this enumeration.
static class	BasicAtomGenerator.ShowEndCarbons Boolean parameters that will show carbons with only one (non-hydrogen) neighbor to be drawn with an element symbol.
static class	BasicAtomGenerator.ShowExplicitHydrogens Boolean property that triggers explicit hydrogens to be drawn if set to true.

Constructor Summary

Constructors

Constructor and Description
BasicAtomGenerator() An empty constructor necessary for reflection.

Method Summary

Modifier and Type	Method and Description
protected boolean	canDraw(IAtom atom, IAtomContainer container, RendererModel model) Checks an atom to see if it should be drawn.
IRenderingElement	generate(IAtomContainer atomContainer, IAtom atom, RendererModel model) Generate the rendering element(s) for a particular atom.
IRenderingElement	generate(IAtomContainer container, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
IRenderingElement	generateCompactElement(IAtom atom, RendererModel model) Generate a compact element for an atom, such as a circle or a square, rather than text element.
AtomSymbolElement	generateElement(IAtom atom, int alignment, RendererModel model) Generate an atom symbol element.
protected Color	getAtomColor(IAtom atom, RendererModel model) Returns the drawing color of the given atom.
List<IGeneratorParameter<?>>	getParameters() Returns the list of IGeneratorParameter for this particular generator.
protected boolean	hasCoordinates(IAtom atom) Checks an atom to see if it has 2D coordinates.
protected boolean	invisibleCarbon(IAtom atom, IAtomContainer atomContainer, RendererModel model) Checks an atom to see if it is an 'invisible carbon' - that is, it is: a) a carbon atom and b) this carbon should not be shown.
protected boolean	invisibleHydrogen(IAtom atom, RendererModel model) Checks an atom to see if it is an 'invisible hydrogen' - that is, it is a) an (explicit) hydrogen, and b) explicit hydrogens are set to off.
protected boolean	isHydrogen(IAtom atom) Determines if the atom is a hydrogen.
protected boolean	showCarbon(IAtom carbonAtom, IAtomContainer container, RendererModel model) Checks a carbon atom to see if it should be shown.

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicAtomGenerator

public BasicAtomGenerator()

An empty constructor necessary for reflection.

Method Detail

generate

public IRenderingElement generate(IAtomContainer container,
                                  RendererModel model)

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

model - the rendering parameters

Returns:

a drawable chemical depiction component

hasCoordinates

protected boolean hasCoordinates(IAtom atom)

Checks an atom to see if it has 2D coordinates.

Parameters:

atom - the atom to check

Returns:

true if the atom is not null, and it has non-null coordinates

isHydrogen

protected boolean isHydrogen(IAtom atom)

Determines if the atom is a hydrogen.

Parameters:

atom - IAtom to be tested

Returns:

true, if the atom is a hydrogen, and false, otherwise.

invisibleHydrogen

protected boolean invisibleHydrogen(IAtom atom,
                                    RendererModel model)

Checks an atom to see if it is an 'invisible hydrogen' - that is, it is a) an (explicit) hydrogen, and b) explicit hydrogens are set to off.

Parameters:

atom - the atom to check

model - the renderer model

Returns:

true if this atom should not be shown

invisibleCarbon

protected boolean invisibleCarbon(IAtom atom,
                                  IAtomContainer atomContainer,
                                  RendererModel model)

Checks an atom to see if it is an 'invisible carbon' - that is, it is: a) a carbon atom and b) this carbon should not be shown.

Parameters:

atom - the atom to check

atomContainer - the atom container the atom is part of

model - the renderer model

Returns:

true if this atom should not be shown

canDraw

protected boolean canDraw(IAtom atom,
                          IAtomContainer container,
                          RendererModel model)

Checks an atom to see if it should be drawn. There are three reasons not to draw an atom - a) no coordinates, b) an invisible hydrogen or c) an invisible carbon.

Parameters:

atom - the atom to check

container - the atom container the atom is part of

model - the renderer model

Returns:

true if the atom should be drawn

generate

public IRenderingElement generate(IAtomContainer atomContainer,
                                  IAtom atom,
                                  RendererModel model)

Generate the rendering element(s) for a particular atom.

Parameters:

atomContainer - the atom container that the atom is from

atom - the atom to generate the rendering element for

model - the renderer model

Returns:

a rendering element, or group of elements

generateCompactElement

public IRenderingElement generateCompactElement(IAtom atom,
                                                RendererModel model)

Generate a compact element for an atom, such as a circle or a square, rather than text element.

Parameters:

atom - the atom to generate the compact element for

model - the renderer model

Returns:

a compact rendering element

generateElement

public AtomSymbolElement generateElement(IAtom atom,
                                         int alignment,
                                         RendererModel model)

Generate an atom symbol element.

Parameters:

atom - the atom to use

alignment - the alignment of the atom's label

model - the renderer model

Returns:

an atom symbol element

showCarbon

protected boolean showCarbon(IAtom carbonAtom,
                             IAtomContainer container,
                             RendererModel model)

Checks a carbon atom to see if it should be shown.

Parameters:

carbonAtom - the carbon atom to check

container - the atom container

model - the renderer model

Returns:

true if the carbon should be shown

getAtomColor

protected Color getAtomColor(IAtom atom,
                             RendererModel model)

Returns the drawing color of the given atom. An atom is colored as highlighted if highlighted. The atom is color marked if in a substructure. If not, the color from the CDK2DAtomColor is used (if selected). Otherwise, the atom is colored black.

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