pd2af

A library and CLI to transform process-description (PD) maps into activity-flow (AF) maps.

Features

• CellDesigner and SBGN-PD input: a CellDesigner map gives a CellDesigner map, an SBGN-PD map gives an SBGN-AF map
• Three transformation modes: normal, no-complex and keep-reactions, with the --keep-species and --drop-compartments options
• Three layout modes: dot (Graphviz auto-layout), plain (reuse of the original positions) and overlay (the original layout, with the elements that have no match dimmed)
• Annotations and notes carried over: from the input elements to the elements they produce

Installation

pd2af is available as a Python package and can be installed with pip as follows (Python >=3.12):

pip install pd2af

The dot layout mode requires Graphviz's dot binary on your PATH.

Quick example

import momapy.io
import pd2af

pd_map = momapy.io.read("my_map.xml").obj
af_map = pd2af.transform(
    pd_map,
    mode="no-complex",
    layout_mode="dot",
    keep_species=True,
    drop_compartments=True,
).obj
momapy.io.write(af_map, "my_map_af.xml", writer="celldesigner")

pd2af transform my_map.xml -m no-complex -l dot --keep-species --drop-compartments -o my_map_af.xml
pd2af list-modes

Documentation

The documentation for pd2af is available here.