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momapy

momapy is a library for working with molecular maps. It currently supports SBGN and CellDesigner maps. Its key feature is its definition of a map, that is formed of two entities: a model, that describes what concepts are represented, and a layout, that describes how these concepts are represented. This definition is borrowed from SBML and its extensions layout+render, that allow users to add a layout to an SBML model. momapy aims at extending this definition to SBGN and CellDesigner maps.

Features of momapy include the following:

  • support for SBGN PD and AF maps (read/write SBGN-ML with annotations, rendering information, and notes) and CellDesigner (read/write, with annotations and notes)
  • decomposition of a map object into:
    • a model object;
    • a layout object;
    • a mapping from layout element objects to model element objects.
  • map, model, layout and mapping objects comparison; fast object in set checking
  • rendering of maps to images (SVG, PDF, JPEG, PNG, WebP) and other surfaces (e.g. GLFW window)
  • support for styling and CSS-like stylesheets (including effects such as shadows)
  • automatic geometry and anchors (for arcs, shape borders)
  • local positioning (e.g. right of shape, fit set of shapes)
  • easy extension with new model and layout element types

Installation

momapy is available as a Python package and can be installed with pip as follows (Python >=3.10,<=3.14):

pip install momapy

Optional dependencies

momapy includes several optional dependencies for rendering maps with the skia or cairo backends:

skia

pip install momapy[skia]

This extra depends on skia-python (https://github.com/kyamagu/skia-python), which itself depends on the following system packages:

  • opengl
  • libegl
  • fontconfig

cairo

pip install momapy[cairo]

This extra depends on pygobject (https://pygobject.gnome.org/guide/sysdeps.html), which itself depends on the following system packages:

  • glib
  • libffi

all

All optional dependencies can also be installed together:

pip install momapy[all]

Usage

Typical usage of momapy includes reading a map and exploring its model:

from momapy.io import read

map_ = read("my_map.sbgn").obj
for process in map_.model.processes:
    print(process)

Or rendering its layout:

from momapy.rendering import render_map

render_map(map_, "my_file.svg")

momapy also provides a command-line interface:

momapy render my_map.sbgn -o output.pdf
momapy export my_map.sbgn -o output.sbgn

See CLI reference for details.

You can also customize the appearance using CSS-like stylesheets:

from momapy.styling import StyleSheet, apply_style_sheet

style_sheet = StyleSheet.from_file("my_style.css")
apply_style_sheet(map_.layout, style_sheet)

User manual

A user manual showcasing the main feature of momapy is available here: User manual.

Documentation

A complete documentaton for momapy's API is available here: API reference.