momapy 0.2.0

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

Some python packages depend on system packages that might require installation:

• pygobject (https://pygobject.gnome.org/guide/sysdeps.html):
  • glib
  • libffi
• skia-python (https://github.com/kyamagu/skia-python):
  • opengl
  • libegl
  • fontconfig

Usage

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

import momapy.sbgn.io.sbgnml
from momapy.io import read

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

Or rendering its layout:

import momapy.rendering.skia
from momapy.rendering.core import render_map

render_map(map_, "my_file.pdf", format_="pdf", renderer="skia")

Documentation

The documentation for momapy can be found here.