Species

The Species class represents individual biological entities within the SBMLNetwork model — for example, molecules, proteins, or genes. Each Species corresponds to a node in the network diagram and visually communicates its presence and role in the system.

After loading a model you can:

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

• Retrieve one species by ID with get_species().

• Get the full list of species objects via get_species_list().

Example:

import sbmlnetwork as sn

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

# Get Species ids
species_ids = net.get_species_ids()

# Single species
species = net.get_species(species_ids[0])
print(species.get_species_id())

# All species
for sp in net.get_species_list():
   print(sp.get_species_id())

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

Core Methods

Identification

get_id()

Return the unique glyph identifier (the SpeciesGlyph element) as defined in the SBML Layout package.

Return type:

str

get_species_id()

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

Return type:

str

get_compartment_id()

Return the SBML compartment identifier in which this species resides.

Return type:

str

Model Connections

get_reaction_ids()

Return a set of SBML reaction identifiers connected to this species.

Return type:

Set[str]

get_reactions_list()

Return a list-like wrapper over all Reaction objects connected to this species.

Return type:

ReactionList

get_reactions(id_list=None)

Fetch one or many connected reactions.

Parameters:

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

Returns:

A single Reaction or a sub-list

Visual Connections

get_curves_list(reaction=None)

Return all connecting curve glyphs (from substrate/product mapping) optionally scoped to a reaction.

Parameters:

reaction (Reaction | str | None) – an optional Reaction or SBML ID

Return type:

CurveList

get_curves(reaction=None)

Synonym for get_curves_list().

Return type:

CurveList

create_alias(reaction)

Clone this species glyph for a given reaction, producing an alias glyph when species participate in multiple reactions.

Parameters:

reaction – Reaction object or SBML reaction ID

Returns:

A new Species alias or None

Geometry & Positioning

get_position()

Get the current (x, y) position of the glyph’s center on the canvas.

Returns:

(x, y) in canvas units

set_position(position)

Move the glyph to a new canvas position.

Parameters:

position (tuple) – (x, y) coordinates

get_size()

Get the glyph’s width and height.

Returns:

(width, height)

set_size(size)

Resize the glyph.

Parameters:

size (tuple) – (width, height)

move_to(position, move_connected_curves=True)

Move glyph and optionally reposition connected curves.

move_by(delta, move_connected_curves=True)

Translate glyph by a delta vector.

Appearance

add_shape(shape_type, **options)

Attach a geometric shape (rectangle, ellipse, etc.) as the glyph’s outline.

Parameters:

shape_type (str) – one of the SBML geometric shape names

set_shape(shape_type)

Change the existing shape type.

get_shape()

Return the primary shape glyph.

get_shapes_list()

Return all shape glyphs.

get_border_color()

Get outline color.

set_border_color(color)

Set outline color.

get_fill_color()

Get interior fill color.

set_fill_color(color)

Set interior fill color.

Labels

add_label(text, **options)

Attach a text label relative to the glyph.

Parameters:

text (str) – Label text

get_labels_list()

Return all attached label glyphs.

get_text()

Return the label text (single or list).

Geometry Utilities

set_font_size(font_size, adjust_size=False)

Uniformly adjust font size of all labels.

Parameters:

font_size (float) – New font size

Visibility

show()

Make the glyph (and nested elements) visible.

hide()

Hide the glyph.

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

net = sn.load("my_model.xml")
species = net.get_species(net.get_species_ids()[0])

# Inspect identifiers
print(species.get_id(), species.get_species_id(), species.get_compartment_id())

# List connected reactions
for rid in species.get_reaction_ids():
   print(rid)

# Move and style the glyph
species.move_to((200, 150))
species.set_fill_color("#ffeecc")
species.set_border_color("#cc6633")

# Add a custom text label
species.add_label("ATP Molecule", relative_position=(10, 10))

# Highlight its connecting curves which are of type product
for curve in species.get_curves_list():
   if species.get_role(curve.get_reaction()) == "product":
       curve.set_border_color("#3366cc")

# Finally, render the network diagram
net.draw("species_demo.png")