Compartment

The Compartment class represents a spatial or logical container within the SBMLNetwork model. It groups related biological species and reactions within a defined boundary—just as compartments do in SBML itself.

After loading a model you can:

• Get just the IDs (strings) with get_compartment_ids().

• Retrieve one compartment by ID with get_compartment().

• Get the full list of compartment objects via get_compartments_list().

Example:

import sbmlnetwork as sn

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

 # Get compartment ids
 compartment_ids = net.get_compartment_ids()

 # Single compartment
 compartment = net.get_compartment(compartment_ids[0])
 print(compartment.get_compartment_id())

 # All compartments
 for comp in net.get_compartments_list():
    print(comp.get_compartment_id())

In the visualization context, each Compartment includes its own Shapes and Labels, which define how the compartment is drawn and annotated in the rendered network diagram. The diagram below shows how a Compartment connects to its Shape and Label elements:

Core Methods

Identification

get_id()

Return the unique identifier of the drawing glyph for this compartment (the CompartmentGlyph element), as defined in the SBML Layout package.

Return type:

str

get_compartment_id()

Return the SBML object identifier of the underlying compartment in the model.

Return type:

str

Contents

get_species_list()

Return a list‑like wrapper over all species that reside in this compartment.

Return type:

SpeciesList

get_species(id)

Fetch a single species (of type Species) by its SBML identifier.

Parameters:

id (str) – The SBML id of the desired species

Returns:

The matching Species object

get_reactions_list()

Return a list‑like wrapper over all reactions whose products or reactants appear in this compartment.

Return type:

ReactionList

get_reactions(id_list=None)

Fetch one or many reactions scoped to the compartment.

Parameters:

id_list (str | Iterable[str] | None) – None for all reactions, a single id, or an iterable of ids

Returns:

A single Reaction object or a sub‑list depending on id_list

Geometry & Positioning

get_position()

Get the current (x, y) position—upper‑left corner by convention—of the compartment on the canvas.

Returns:

(x, y) tuple in canvas units (typically pixels)

set_position(x, y)

Move the compartment to a new position on the canvas.

Parameters:

• x (float) – X‑coordinate of the upper‑left corner

• y (float) – Y‑coordinate of the upper‑left corner

get_size()

Get the current width and height of the compartment in canvas units.

Returns:

(width, height)

set_size(size)

Resize the compartment.

Parameters:

size (tuple) – (width, height)

Appearance

add_shape(shape_type='rectangle', **options)

Add a new geometric shape that defines the compartment boundary.

Parameters:

• shape_type (str) – 'rectangle', 'ellipse', etc.

• options – Shape‑specific keyword arguments (border thickness, corner radius, …)

get_shape()

Return the primary Shape object that outlines the compartment.

set_shape(shape)

Replace the existing shape with shape.

get_border_color()

Get the current border color (hex string '#rrggbb').

set_border_color(color)

Set the border color.

Parameters:

color (str) – Hex or named color string

get_fill_color()

Get the interior fill color.

set_fill_color(color)

Change the fill color.

Labels

add_label(text, **options)

Attach a textual label to the compartment.

Parameters:

• text (str) – Label text

• options – Keyword arguments forwarded to the underlying Label constructor

get_labels_list()

Return a list of all labels attached to the compartment.

Return type:

LabelList

Visibility

show()

Make the compartment (and all nested shapes & labels) visible on the canvas.

hide()

Hide the compartment without deleting it from the model.

Information

property info

Human-readable summary of glyph state for debugging.

Return type:

str

get_info()

Generate the info string.

Example workflow

import sbmlnetwork as sn

 # Load the network from an SBML file
 net = sn.load('my_model.xml')

 # Get the default compartment
 compartment = net.get_compartment()

 # Move and resize
 compartment.set_position((50, 80))
 compartment.set_size((800, 600))

 # Change shape to ellipse
 compartment.set_shape('ellipse')

 # Style tweaks
 compartment.set_border_color('#3366cc')
 compartment.set_fill_color('#f0f4ff')

 # Add a label
 compartment.add_label('Cytosol', (0, -20))

 # Inspect species
 for s in compartment.get_species_list():
    print(s.get_id(), s.get_position())

 # Finally, draw the full network
 net.draw('my_network.png')