momapy 0.1.0

A library for working with molecular maps

momapy

MomaPy is a new Python library for working with molecular maps such as SBGN maps. Its key feature is its definition of a map, that is now 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 layout/render extensions, that allow users to add a layout to an SBML model. MomaPy aims at extending this definition to all types of molecular maps, and in particular to SBGN maps.

MomaPy offers the following features:

• support for SBGN PD and AF maps (read/write SBGN-ML with annotations, rendering information, and notes)
• decomposition of a map object into:
  • a model object;
  • a layout object;
  • a mapping between the model and layout objects' subelements.
• 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 subelements

MomaPy is still in its initial development phase. As such, it is not yet released nor documented, and may change at any time.

However, the features of MomaPy are demonstrated in a jupyter notebook that can be found here.