Related Experiment Video
Updated: Jun 5, 2026

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro
Published on: September 26, 2025
momapy: a Python library to work with molecular maps
Adrien Rougny1, Marek Ostaszewski1, Venkata Sagatopam1
1Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
Motivation:
Molecular maps are graphical representations of the molecular mechanisms underlying biological systems. They are a valuable tool for curating, exchanging, and understanding biological knowledge, and may serve as a backbone for data analysis and modelling. Molecular maps are supported by a rich software ecosystem. However, there are currently no tools that support advanced programmatic analysis and processing of maps, in particular the extraction of the biological concepts they represent or their comparison.
Results:
We introduce momapy, a generic Python library to work with molecular maps programmatically. At its core, momapy allows users to extract and separate the data model of a map from its graphical representation, and perform a variety of base operations on them, including their manipulation and comparison. momapy currently supports the SBGN and CellDesigner formats, two of the main standards to represent molecular maps graphically, and can be easily extended to support additional formats and functionalities.
Availability:
momapy is implemented in Python (RRID:SCR_008394) under a GPLv3 license. The code can be downloaded freely from https://github.com/adrienrougny/momapy and is archived on Zenodo (https://doi.org/10.5281/zenodo.19088611). Complete documentation and a user manual are available at https://adrienrougny.github.io/momapy.
Related Concept Videos
Molecular Models
Molecular Geometry and Dipole Moments
Predicting Molecular Geometry
Molecules with Multiple Chiral Centers
Molecular Orbital Theory I
Molecular Shapes

