sbmlmath — a Python library for handling SBML MathML

sbmlmath is a Python library for interconverting SymPy expressions and SBML-MathML. SBML uses a subset of MathML that this library aims to support. This is not (intended to be) a general MathML parser.

Main functionality:

• sympy -> SBML MathML
• SBML MathML -> sympy
  • in particular for cases where sympy.sympify(libsbml.formulaToL3String(...)) won't do the job (mind, e.g., the differences in operator precedence between sympy/Python and libsbml L3 formulas!)
  • retaining unit annotations and other <ci> attributes

NOTE: This is under development and the API is to be considered unstable

Python support policy: sbmlmath follows NEP 29.

Usage

from sbmlmath import SBMLMathMLPrinter, SBMLMathMLParser
import sympy as sp

sympy_expr = sp.sympify("A ** B + exp(C) * D")
mathml = SBMLMathMLPrinter().doprint(sympy_expr)
print(mathml)

cycled_sympy = SBMLMathMLParser().parse_str(mathml)
print(cycled_sympy)
assert sympy_expr == cycled_sympy

Documentation

Under construction at sbmlmath.readthedocs.io.

Installation

Releases from PyPI:

pip install sbmlmath

The latest development version from GitHub:

pip install git+https://github.com/dweindl/sbmlmath.git#egg=sbmlmath