sbgn2bcsl

The sbgn2bcsl tool is a CLI tool written in python 3 that converts CellDesigner models into BioChemical Space Language rules conforming to the eBCSgen definition of the "rule" term.

Usage Instructions

$python sbgn2bcsl --help
usage: sbgn2bcsl path out_path [options]

Tool for converting CellDesigner 4.4.2 diagrams to BCSL

positional arguments:
  path                  The path to the CellDesigner 4.4.2 diagram SBML file
  out_path              The path to the file where the BCSL result will be
                        saved

optional arguments:
  -h, --help            show this help message and exit
  -q, --quiet           Disable the generation of warning messages.
  -c, --unpack-complexes
                        Enable the unpacking of top-level complexes.
  -C, --unpack-nested-complexes
                        Enable the unpacking of nested complexes.
  -i, --include-positive-influences
                        Include positive influences on both sides of the rule.
  -w, --replace-non-word-chars
                        Replace whitespaces in names with an underscore.
  -r, --rates           Include artificial rates to the output rules.