Shape

The Shape class captures the geometric appearance of any network element (Compartment, Species, or Reaction). A Shape contains the type of geometry (e.g., rectangle, ellipse, polygon), its position and dimensions in the diagram, and styling info such as border or fill colour. Every visual object that appears on the canvas can have mutliple Shapes associated with it.

After loading a model and retreiving a model element, you can

• Retrieve the first associated Shape with get_shape().

• Retrieve all the Shape objects associated with the network element get_shapes_list() helper.

Example:

import sbmlnetwork as sn

net = sn.load("my_model.xml")

# Get species ids
species_ids = net.get_species_ids()

# Shape for a specific species
species_shape = net.get_species(species_ids[0]).get_shape()
print(species_shape.get_type())

# Add a new shape to the species
net.get_species(species_ids[0]).add_shape("ellipse")

# All shapes for a species
for sh in net.get_species(species_ids[0]).get_shapes_list():
    print(sh.get_type())

A Shape records the styling and geometry details needed to draw a network element. The diagram below shows the inheritance structure: the abstract base Shape class is extended by concrete shapes like Rectangle, Ellipse, and Polygon.

Core Methods

Identificaiton

get_type()

Return the geometry type – "rectangle", "ellipse", "polygon", "curve", etc.

Return type:

str

get_element_id()

Return the SBML identifier of the parent network element this Shape belongs to.

Return type:

str

Styling

get_border_color()

Current border colour of the Shape as a CSS hex string ("#rrggbb") or a colour name supported by the renderer.

Return type:

str

set_border_color(border_color)

Set the border colour. Accepts a CSS hex string or a RGB tuple / list with values in the range 0‑255, e.g. (255, 0, 0) for red.

Parameters:

border_color (str | tuple[int, int, int] | list[int]) – New colour.

get_border_thickness()

Border line width in pixels.

Return type:

float

set_border_thickness(thickness)

Set the border line width.

Parameters:

thickness (float) – New width in pixels.

get_fill_color()

Current interior (fill) colour.

Return type:

str

set_fill_color(fill_color)

Set the interior colour. Accepts the same value formats as set_border_color().

Parameters:

fill_color (str | tuple[int, int, int] | list[int]) – New fill colour.

Information

property info

Human-readable summary of glyph state for debugging.

Return type:

str

get_info()

Generate the info string.

Example workflow

The short script below demonstrates how to discover Shapes, change their appearance, and render the diagram.

import sbmlnetwork as sn

# Load the SBML file
net = sn.load("my_model.xml")

# Grab a Species glyph and its first Shape
species = net.get_species_list()[0]
shape = species.get_shapes_list()[0]

# Inspect its current state
print("Type :", shape.get_type())
print("Border:", shape.get_border_color())
print("Fill  :", shape.get_fill_color())

# Make it visually stand‑out
shape.set_fill_color("#cc6633")
shape.set_border_color("#cc6633")
shape.set_border_thickness(10)

# Render the whole network to a PNG image
net.draw("shape_demo.png")

# Print a summary for the shapes info
print(shape.get_info())