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

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