Render

The libSBML “render” extension implements support for the SBML Level 3 Graphical Rendering ("render") package. It can be used in SBML Level 3 Version 1 and Version 2 documents.

Introduction

The graphical depiction of a reaction network diagram should be described as graphical representations of species and reactions, and not as arbitrary drawing or graph. While it may seem unnecessary to invent a new language when an existing one like SVG could in principle be used to describe the layout of a reaction network, there are good reasons to have a language tailored specifically for the layout of SBML models. For example, most programs that will use this SBML extension are primarily programs dealing with biochemical models. Internally, they will have data structures for species and reactions, so it will also be natural for them to depict the reaction network in terms of species and reactions (and not in terms of, e.g., polygons or splines).

The Graphical Rendering ("render") package for SBML Level 3 is a companion to the Graphical Layout ("layout") package. Together, they provide a complete format for describing the layout of a diagram and the visual rendition of the entities within it.

Authors

The primary authors of the SBML Level 3 Render specification are Frank T. Bergmann, Sarah M. Keating, Ralph Gauges, Sven Sahle and Katja Wengler.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 “render” package. If you are developing software that uses “render”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any).

Specification for SBML Level 3 Render, current at the time of this libSBML release (5.18.0). Note: an Internet connection is required to access these documents.

Specification (in PDF format)	Known issues
Render package, Version 1 Release 1	Errata page

More...

Classes
class	libsbml.ColorDefinition
	render Definition of an identifier for an RGBA color value. More...
class	libsbml.DefaultValues
	render Encoding of default values. More...
class	libsbml.Ellipse
	render Graphical representation of an ellipse. More...
class	libsbml.GlobalRenderInformation
	render Render information stored in a ListOfLayouts. More...
class	libsbml.GlobalStyle
	render A style that can be associated with a layout. More...
class	libsbml.GradientBase
	render Abstract base class for linear and radial gradients. More...
class	libsbml.GradientStop
	render A color at a certain location in a color gradient. More...
class	libsbml.GraphicalPrimitive1D
	render Base class for graphical primitives implementing 1D attributes. More...
class	libsbml.GraphicalPrimitive2D
	render Base class for graphical primitives implementing 2D attributes. More...
class	libsbml.Image
	render Representation of images. More...
class	libsbml.LinearGradient
	render Representation of a linear gradient. More...
class	libsbml.LineEnding
	render Decoration element for the start and/or end of curves. More...
class	libsbml.ListOfColorDefinitions
	render A list of ColorDefinition objects. More...
class	libsbml.ListOfCurveElements
	render A list of curve elements. More...
class	libsbml.ListOfDrawables
	render A list of Transformation2D objects. More...
class	libsbml.ListOfGlobalRenderInformation
	render A list of GlobalRenderInformation objects. More...
class	libsbml.ListOfGlobalStyles
	render A list of GlobalStyle objects. More...
class	libsbml.ListOfGradientDefinitions
	render A list of GradientBase objects. More...
class	libsbml.ListOfGradientStops
	render A list of one or more GradientStop objects. More...
class	libsbml.ListOfLineEndings
	render A list of LineEnding objects. More...
class	libsbml.ListOfLocalRenderInformation
	render A list of LocalRenderInformation objects. More...
class	libsbml.ListOfLocalStyles
	render A list of LocalStyle objects. More...
class	libsbml.LocalRenderInformation
	render Rendering information stored in Layouts. More...
class	libsbml.LocalStyle
	render Style information object used in LocalRenderInformation. More...
class	libsbml.Polygon
	render Representation of a Polygon More...
class	libsbml.RadialGradient
	render Representation of a radial gradient. More...
class	libsbml.Rectangle
	render Representation of a rectangle. More...
class	libsbml.RelAbsVector
	render Vectors with an absolute value and a relative value. More...
class	libsbml.RenderCubicBezier
	render Representation of cubic Bezier curves. More...
class	libsbml.RenderCurve
	render Representation of curves. More...
class	libsbml.RenderExtension
	render Base extension class for the package. More...
class	libsbml.RenderGraphicalObjectPlugin
	render The Render extension of the layout GraphicalObject class. More...
class	libsbml.RenderGroup
	render A group of graphical primitives creating a composite. More...
class	libsbml.RenderInformationBase
	render Abstract base class for local and global rendering information. More...
class	libsbml.RenderLayoutPlugin
	render LibSBML implementation for the extension to the Layout class by the Render extension. More...
class	libsbml.RenderListOfLayoutsPlugin
	render A list of layout objects used by the 'render' extension. More...
class	libsbml.RenderPoint
	render A point with both absolute and relative values More...
class	libsbml.Style
	render Abstract base class for local and global styles. More...
class	libsbml.Text
	render Representation of text elements. More...
class	libsbml.Transformation
	render Implementation of a 3D transformation matrix. More...
class	libsbml.Transformation2D
	render Implementation of a 2D transformation matrix. More...

Functions
def	libsbml.Style.__init__ (self, orig)

Detailed Description

The libSBML “render” extension implements support for the SBML Level 3 Graphical Rendering ("render") package. It can be used in SBML Level 3 Version 1 and Version 2 documents.

Introduction

The graphical depiction of a reaction network diagram should be described as graphical representations of species and reactions, and not as arbitrary drawing or graph. While it may seem unnecessary to invent a new language when an existing one like SVG could in principle be used to describe the layout of a reaction network, there are good reasons to have a language tailored specifically for the layout of SBML models. For example, most programs that will use this SBML extension are primarily programs dealing with biochemical models. Internally, they will have data structures for species and reactions, so it will also be natural for them to depict the reaction network in terms of species and reactions (and not in terms of, e.g., polygons or splines).

The Graphical Rendering ("render") package for SBML Level 3 is a companion to the Graphical Layout ("layout") package. Together, they provide a complete format for describing the layout of a diagram and the visual rendition of the entities within it.

Authors

The primary authors of the SBML Level 3 Render specification are Frank T. Bergmann, Sarah M. Keating, Ralph Gauges, Sven Sahle and Katja Wengler.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 “render” package. If you are developing software that uses “render”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any).

Specification for SBML Level 3 Render, current at the time of this libSBML release (5.18.0). Note: an Internet connection is required to access these documents.

Specification (in PDF format)	Known issues
Render package, Version 1 Release 1	Errata page

Function Documentation

def libsbml.Style.__init__	(		self,
			orig
	)

__init__(Style orig)   Style

render Abstract base class for local and global styles.

Local and global styles in the SBML Level 3 Render package have many attributes and methods in common. These have been implemented in the abstract base class Style.

A style is a graphical representation for certain layout objects. The assignment of styles to individual layout objects can either be done through layout object ids (local styles only), layout object types (SPECIES, COMPARTMENT, etc.) or layout object roles.