The FractalDNA package
Geometries for use in molecularDNA can be generated yourself, or with the help of the FractalDNA package in Python.
The FractalDNA package (see the documentation here) provides Python methods for building DNA segments that can be joined together by the molecularDNA application, as well as assembling geometries.
FractalDNA can be installed from PyPI:
pip install fractaldna