momapy 0.3.0

A library to work with molecular maps

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 only, with annotations)
• 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,<=3.12):

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.core import read

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

Or rendering its layout:

from momapy.rendering.core import render_map

render_map(map_, "my_file.svg")

Demo

Online (no installation required)

Local

To run the demo locally:

git clone https://github.com/adrienrougny/momapy.git
cd momapy
pip install . jupyter
jupyter notebook demo/demo.ipynb

The demo includes additional files (utils.py, example data) in the demo/ directory that are only available in the repository.

Documentation

The documentation for momapy is available here.